From 58bc0282455204dd3eeda4fd338d2a37aed7b48e Mon Sep 17 00:00:00 2001
From: xieshu95 <xieshu95@gmail.com>
Date: Mon, 9 May 2022 16:00:29 +0200
Subject: [PATCH 01/73] delete tests in main functions

---
 R/DAISIE_rates.R                  | 67 ++++++++++++++-----------------
 R/DAISIE_sample_event_trait_dep.R |  6 +--
 R/DAISIE_sim_core_trait_dep.R     | 62 ++++++----------------------
 3 files changed, 45 insertions(+), 90 deletions(-)

diff --git a/R/DAISIE_rates.R b/R/DAISIE_rates.R
index 45a235de..a0c9ba55 100644
--- a/R/DAISIE_rates.R
+++ b/R/DAISIE_rates.R
@@ -153,7 +153,7 @@ update_rates_trait <- function(timeval,
     trait_pars = trait_pars,
     island_spec = island_spec
   )
-  testit::assert(is.list(immig_rate))
+
   ext_rate <- get_ext_rate(
     mu = mu,
     hyper_pars = hyper_pars,
@@ -163,14 +163,13 @@ update_rates_trait <- function(timeval,
     trait_pars = trait_pars,
     island_spec = island_spec
   )
-  testit::assert(is.list(ext_rate))
+
   ana_rate <- get_ana_rate(
     laa = laa,
     num_immigrants = num_immigrants,
     trait_pars = trait_pars,
     island_spec = island_spec
   )
-  testit::assert(is.list(ana_rate))
   clado_rate <- get_clado_rate(
     lac = lac,
     hyper_pars = hyper_pars,
@@ -180,19 +179,13 @@ update_rates_trait <- function(timeval,
     trait_pars = trait_pars,
     island_spec = island_spec
   )
-  testit::assert(is.list(clado_rate))
 
-  testit::assert(!is.null(trait_pars))
+
+
   trans_rate <- get_trans_rate(trait_pars = trait_pars,
                                island_spec = island_spec)
-  testit::assert(is.list(trans_rate))
-  # trait_pars <- create_trait_pars(trans_rate = trans_rate$trans_rate1,
-  #                                    immig_rate2 = immig_rate$immig_rate2,
-  #                                    ext_rate2 = ext_rate$ext_rate2,
-  #                                    ana_rate2 = ana_rate$ana_rate2,
-  #                                    clado_rate2 = clado_rate$clado_rate2,
-  #                                    trans_rate2 = trans_rate$trans_rate2,
-  #                                    M2 = trait_pars$M2)
+
+
   rates <- list(
     immig_rate = immig_rate$immig_rate1,
     ext_rate = ext_rate$ext_rate1,
@@ -345,7 +338,7 @@ get_ana_rate <- function(laa,
     ana_rate1 = laa * length(intersect(which(island_spec[,4] == "I"),
                                        which(island_spec[,8] == "1")))
     ana_rate2 = trait_pars$ana_rate2 * length(intersect(which(island_spec[,4] == "I"),
-                                                   which(island_spec[,8] == "2")))
+                                                        which(island_spec[,8] == "2")))
     # testit::assert(is.numeric(ana_rate1))
     # testit::assert(ana_rate1 >= 0)
     # testit::assert(is.numeric(ana_rate2))
@@ -377,12 +370,12 @@ get_clado_rate <- function(lac,
 
   d <- hyper_pars$d
   if (is.null(trait_pars)) {
-  clado_rate <- max(
-    0, lac * num_spec * (A ^ d) * (1 - num_spec / (K * A)), na.rm = TRUE
-  )
-  # testit::assert(clado_rate >= 0)
-  # testit::assert(is.numeric(clado_rate))
-  return(clado_rate)
+    clado_rate <- max(
+      0, lac * num_spec * (A ^ d) * (1 - num_spec / (K * A)), na.rm = TRUE
+    )
+    # testit::assert(clado_rate >= 0)
+    # testit::assert(is.numeric(clado_rate))
+    return(clado_rate)
   }else{
     num_spec_trait1 <- length(which(island_spec[, 8] == "1"))
     num_spec_trait2 <- length(which(island_spec[, 8] == "2"))
@@ -434,9 +427,9 @@ get_immig_rate <- function(gam,
     mainland_n2 <- trait_pars$M2
     gam2 <- trait_pars$immig_rate2
     immig_rate1 <- max(c(mainland_n * gam * (1 - (num_spec / (A * K))),
-                        0), na.rm = TRUE)
+                         0), na.rm = TRUE)
     immig_rate2 <- max(c(mainland_n2 * gam2 * (1 - (num_spec / (A * K))),
-                        0), na.rm = TRUE)
+                         0), na.rm = TRUE)
     # testit::assert(is.numeric(immig_rate1))
     # testit::assert(immig_rate1 >= 0)
     # testit::assert(is.numeric(immig_rate2))
@@ -469,20 +462,20 @@ get_immig_rate <- function(gam,
 get_trans_rate <- function(trait_pars,
                            island_spec){
 
-    # Make function accept island_spec matrix or numeric
-    if (is.matrix(island_spec) || is.null(island_spec)) {
-      num_spec_trait1 <- length(which(island_spec[, 8] == "1"))
-      num_spec_trait2 <- length(which(island_spec[, 8] == "2"))
-    }
-    trans_rate1 <- trait_pars$trans_rate * num_spec_trait1
-    trans_rate2 <- trait_pars$trans_rate2 * num_spec_trait2
-    testit::assert(is.numeric(trans_rate1))
-    testit::assert(trans_rate1 >= 0)
-    testit::assert(is.numeric(trans_rate2))
-    testit::assert(trans_rate2 >= 0)
-    trans_list <- list(trans_rate1 = trans_rate1,
-                       trans_rate2 = trans_rate2)
-    return(trans_list)
+  # Make function accept island_spec matrix or numeric
+  if (is.matrix(island_spec) || is.null(island_spec)) {
+    num_spec_trait1 <- length(which(island_spec[, 8] == "1"))
+    num_spec_trait2 <- length(which(island_spec[, 8] == "2"))
+  }
+  trans_rate1 <- trait_pars$trans_rate * num_spec_trait1
+  trans_rate2 <- trait_pars$trans_rate2 * num_spec_trait2
+  # testit::assert(is.numeric(trans_rate1))
+  # testit::assert(trans_rate1 >= 0)
+  # testit::assert(is.numeric(trans_rate2))
+  # testit::assert(trans_rate2 >= 0)
+  trans_list <- list(trans_rate1 = trans_rate1,
+                     trans_rate2 = trans_rate2)
+  return(trans_list)
 
 }
 
@@ -567,7 +560,7 @@ calc_Abeta <- function(proptime,
   a <- f * peak / (1 + f)
   b <- peak / (1 + f)
   At <- Amax * proptime ^ a *
-           (1 - proptime) ^ b / ((a / (a + b)) ^ a * (b / (a + b)) ^ b)
+    (1 - proptime) ^ b / ((a / (a + b)) ^ a * (b / (a + b)) ^ b)
   return(At)
 }
 
diff --git a/R/DAISIE_sample_event_trait_dep.R b/R/DAISIE_sample_event_trait_dep.R
index e3d381c0..e9c0c200 100644
--- a/R/DAISIE_sample_event_trait_dep.R
+++ b/R/DAISIE_sample_event_trait_dep.R
@@ -19,7 +19,7 @@
 #' @author Shu Xie
 #' @keywords internal
 DAISIE_sample_event_trait_dep <- function(rates) {
-  testit::assert(are_rates(rates))
+  # testit::assert(are_rates(rates))
   possible_event <- sample(x = 1:10,
                            size = 1,
                            replace = FALSE,
@@ -34,8 +34,8 @@ DAISIE_sample_event_trait_dep <- function(rates) {
                                     rates$clado_rate2,
                                     rates$trans_rate2)
   )
-  testit::assert(is.numeric(possible_event))
-  testit::assert(possible_event >= 1)
+  # testit::assert(is.numeric(possible_event))
+  # testit::assert(possible_event >= 1)
   return(possible_event)
 }
 
diff --git a/R/DAISIE_sim_core_trait_dep.R b/R/DAISIE_sim_core_trait_dep.R
index a24b7094..d35e5c87 100644
--- a/R/DAISIE_sim_core_trait_dep.R
+++ b/R/DAISIE_sim_core_trait_dep.R
@@ -3,15 +3,15 @@
 #' @inheritParams default_params_doc
 #' @keywords internal
 DAISIE_sim_core_trait_dep <- function(
-  time,
-  mainland_n,
-  pars,
-  island_ontogeny = 0,
-  sea_level = 0,
-  hyper_pars,
-  area_pars,
-  extcutoff = 1000,
-  trait_pars = NULL
+    time,
+    mainland_n,
+    pars,
+    island_ontogeny = 0,
+    sea_level = 0,
+    hyper_pars,
+    area_pars,
+    extcutoff = 1000,
+    trait_pars = NULL
 ) {
 
   #### Initialization ####
@@ -31,16 +31,13 @@ DAISIE_sim_core_trait_dep <- function(
     colonisation is zero. Island cannot be colonised.")
   }
 
-
-  ####  what is the useage of maxspecID and how to set M1 and M2??####
-
   mainland_n2 <- trait_pars$M2
   mainland_ntotal <- mainland_n + mainland_n2
   testit::assert(mainland_ntotal > 0)
   if(mainland_n != 0){
     mainland_spec <- seq(1, mainland_n, 1)
   }else{
-    mainland_spec = c()
+    mainland_spec <- c()
   }
   maxspecID <- mainland_ntotal
 
@@ -48,14 +45,6 @@ DAISIE_sim_core_trait_dep <- function(
   stt_table <- matrix(ncol = 7)
   colnames(stt_table) <- c("Time","nI","nA","nC","nI2","nA2","nC2")
   stt_table[1,] <- c(total_time,0,0,0,0,0,0)
-  # spec_tables <- list(stt_table = stt_table,
-  #                     init_nonend_spec = init_nonend_spec,
-  #                     init_end_spec = init_end_spec,
-  #                     mainland_spec = mainland_spec,
-  #                     island_spec = island_spec)
-  # stt_table <- spec_tables$stt_table
-  # mainland_spec <- spec_tables$mainland_spec
-  # island_spec <- spec_tables$island_spec
   lac <- pars[1]
   mu <- pars[2]
   K <- pars[3]
@@ -63,13 +52,7 @@ DAISIE_sim_core_trait_dep <- function(
   laa <- pars[5]
 
   num_spec <- length(island_spec[, 1])
-  num_spec_trait1 <- length(which(island_spec[,8] == "1"))
-  num_spec_trait2 <- length(which(island_spec[,8] == "2"))
   num_immigrants <- length(which(island_spec[, 4] == "I"))
-  num_immigrants_trait1 <- length(intersect(which(island_spec[, 4] == "I"),
-                                            which(island_spec[, 8] == "1")))
-  num_immigrants_trait2 <- length(intersect(which(island_spec[, 4] == "I"),
-                                            which(island_spec[, 8] == "2")))
 
   #### Start Monte Carlo iterations ####
   while (timeval < total_time) {
@@ -92,7 +75,6 @@ DAISIE_sim_core_trait_dep <- function(
       island_spec = island_spec,
       trait_pars = trait_pars
     )
-    testit::assert(are_rates(rates))
     timeval_and_dt <- calc_next_timeval(
       max_rates = rates,
       timeval = timeval
@@ -100,26 +82,6 @@ DAISIE_sim_core_trait_dep <- function(
     timeval <- timeval_and_dt$timeval
 
     if (timeval < total_time) {
-      rates <- update_rates(
-        timeval = timeval,
-        total_time = total_time,
-        gam = gam,
-        laa = laa,
-        lac = lac,
-        mu = mu,
-        hyper_pars = hyper_pars,
-        area_pars = area_pars,
-        K = K,
-        num_spec = num_spec,
-        num_immigrants = num_immigrants,
-        mainland_n = mainland_n,
-        extcutoff = NULL,
-        island_ontogeny = 0,
-        sea_level = 0,
-        island_spec = island_spec,
-        trait_pars = trait_pars
-      )
-      testit::assert(are_rates(rates))
       possible_event <- DAISIE_sample_event_trait_dep(
         rates = rates
       )
@@ -161,7 +123,7 @@ DAISIE_sim_core_trait_dep <- function(
     island_spec = island_spec,
     mainland_n = mainland_n,
     trait_pars = trait_pars)
-  ordered_stt_times <- sort(island$stt_table[, 1], decreasing = TRUE)
-  testit::assert(all(ordered_stt_times == island$stt_table[, 1]))
+  # ordered_stt_times <- sort(island$stt_table[, 1], decreasing = TRUE)
+  # testit::assert(all(ordered_stt_times == island$stt_table[, 1]))
   return(island)
 }

From 9914b2f384729d46bc460a252b9d054654e5514e Mon Sep 17 00:00:00 2001
From: xieshu95 <xieshu95@gmail.com>
Date: Mon, 9 May 2022 16:01:04 +0200
Subject: [PATCH 02/73] clean

---
 R/DAISIE_sim_trait_dep.R | 92 ++++------------------------------------
 1 file changed, 9 insertions(+), 83 deletions(-)

diff --git a/R/DAISIE_sim_trait_dep.R b/R/DAISIE_sim_trait_dep.R
index 3a217615..0af0077b 100644
--- a/R/DAISIE_sim_trait_dep.R
+++ b/R/DAISIE_sim_trait_dep.R
@@ -64,7 +64,6 @@ DAISIE_sim_trait_dep <- function(
   pars,
   replicates,
   divdepmodel = "CS",
-  num_guilds = NULL,
   sample_freq = 25,
   plot_sims = TRUE,
   island_ontogeny = "const",
@@ -84,20 +83,6 @@ DAISIE_sim_trait_dep <- function(
   trait_pars = NULL,
   ...
 ) {
-  testit::assert(
-    "island_ontogeny is not valid input. Specify 'const',\n
-    or  'beta'", is_island_ontogeny_input(island_ontogeny)
-  )
-  testit::assert(
-    "sea_level is not valid input. Specify 'const, \n or 'sine'",
-    is_sea_level_input(sea_level)
-  )
-
-  testit::assert(
-    "length(pars) is not five",
-    length(pars) == 5
-  )
-
   total_time <- time
   island_replicates <- list()
   island_ontogeny <- translate_island_ontogeny(island_ontogeny)
@@ -141,10 +126,11 @@ DAISIE_sim_trait_dep <- function(
         number_present <- 0
       }
       while (number_present < cond) {
-        if(M == 0){
-          if(is.null(trait_pars)){
-            stop("There is no species on mainland.")
-          }else{   ## only have state2 species on mainland
+        if(M == 0 || is.null(trait_pars)){
+          stop("One state exist on mainland, should use constant rate DAISIE.")
+        }else{
+          for (m_spec in 1:M) {
+            ### M1 = 1, M2 = 0
             trait_pars_onecolonize <- create_trait_pars(
               trans_rate = trait_pars$trans_rate,
               immig_rate2 = trait_pars$immig_rate2,
@@ -152,31 +138,7 @@ DAISIE_sim_trait_dep <- function(
               ana_rate2 = trait_pars$ana_rate2,
               clado_rate2 = trait_pars$clado_rate2,
               trans_rate2 = trait_pars$trans_rate2,
-              M2 = 1)
-            for (m_spec in 1:trait_pars$M2) {
-              full_list[[m_spec]] <- DAISIE_sim_core_trait_dep(
-                time = total_time,
-                mainland_n = 0,
-                pars = pars,
-                island_ontogeny = island_ontogeny,
-                sea_level = sea_level,
-                hyper_pars = hyper_pars,
-                area_pars = area_pars,
-                extcutoff = extcutoff,
-                trait_pars = trait_pars_onecolonize
-              )
-            }
-          }
-        }else{
-          trait_pars_addcol <- create_trait_pars(
-            trans_rate = trait_pars$trans_rate,
-            immig_rate2 = trait_pars$immig_rate2,
-            ext_rate2 = trait_pars$ext_rate2,
-            ana_rate2 = trait_pars$ana_rate2,
-            clado_rate2 = trait_pars$clado_rate2,
-            trans_rate2 = trait_pars$trans_rate2,
-            M2 = 0)
-          for (m_spec in 1:M) {
+              M2 = 0)
             full_list[[m_spec]] <- DAISIE_sim_core_trait_dep(
               time = total_time,
               mainland_n = 1,
@@ -186,11 +148,11 @@ DAISIE_sim_trait_dep <- function(
               hyper_pars = hyper_pars,
               area_pars = area_pars,
               extcutoff = extcutoff,
-              trait_pars = trait_pars_addcol
+              trait_pars = trait_pars_onecolonize
             )
           }
-          for(m_spec in (M + 1):(M + trait_pars$M2))
-          {
+          for(m_spec in (M + 1):(M + trait_pars$M2)) {
+            ### M1 = 0, M2 = 1
             trait_pars_onecolonize <- create_trait_pars(
               trans_rate = trait_pars$trans_rate,
               immig_rate2 = trait_pars$immig_rate2,
@@ -231,42 +193,6 @@ DAISIE_sim_trait_dep <- function(
     )
   }
 
-  #### GW ####
-  if (divdepmodel == "GW") {
-    if (!is.numeric(num_guilds)) {
-      stop("num_guilds must be numeric")
-    }
-    guild_size <- M / num_guilds
-    testit::assert(num_guilds < M)
-    testit::assert(M %% num_guilds == 0)
-    for (rep in 1:replicates) {
-      island_replicates[[rep]] <- list()
-      full_list <- list()
-      for (m_spec in 1:num_guilds) {
-        full_list[[m_spec]]  <- DAISIE_sim_core_trait_dep(
-          time = total_time,
-          mainland_n = guild_size,
-          pars = pars,
-          island_ontogeny = island_ontogeny,
-          sea_level = sea_level,
-          hyper_pars = hyper_pars,
-          area_pars = area_pars,
-          extcutoff = extcutoff
-        )
-      }
-      island_replicates[[rep]] <- full_list
-      if (verbose == TRUE) {
-        print(paste("Island replicate ", rep, sep = ""))
-      }
-    }
-    island_replicates <- DAISIE_format_GW(island_replicates = island_replicates,
-                                          time = total_time,
-                                          M = M,
-                                          sample_freq = sample_freq,
-                                          num_guilds = num_guilds,
-                                          verbose = verbose)
-  }
-
   if (plot_sims == TRUE) {
     DAISIE_plot_sims(
       island_replicates = island_replicates,

From 4f364857e694833ed5442d10a393defb74e14bc3 Mon Sep 17 00:00:00 2001
From: xieshu95 <xieshu95@gmail.com>
Date: Tue, 7 Jun 2022 11:06:30 +0200
Subject: [PATCH 03/73] don't run tests to be faster

---
 R/DAISIE_sim_update_state_trait_dep.R | 91 +--------------------------
 R/create_pars.R                       | 28 ++++-----
 2 files changed, 15 insertions(+), 104 deletions(-)

diff --git a/R/DAISIE_sim_update_state_trait_dep.R b/R/DAISIE_sim_update_state_trait_dep.R
index 6b6cf889..9ae62d23 100644
--- a/R/DAISIE_sim_update_state_trait_dep.R
+++ b/R/DAISIE_sim_update_state_trait_dep.R
@@ -416,93 +416,4 @@ DAISIE_sim_update_state_trait_dep <- function(timeval,
   return(updated_state)
 }
 
-# !POTENTIALLY WRONG DUPLICATE FUNCTION! ---------------------------------------
-# DAISIE_ONEcolonist <- function(time,island_spec,stt_table)
-# {
-#   total_time <- time
-#   ### number of independent colonisations
-#   uniquecolonisation <- as.numeric(unique(island_spec[,"Colonisation time (BP)"]))
-#   number_colonisations <- length(uniquecolonisation)
-#
-#   ### if there is only one independent colonisation - anagenetic and cladogenetic
-#   #species are classed as stac=2; immigrant classed as stac=4:
-#   if(number_colonisations == 1)
-#   {
-#     if(island_spec[1,"Species type"] == "I")
-#     {
-#       descendants <- list(stt_table = stt_table,
-#                           branching_times = c(total_time,as.numeric(island_spec[1,"Colonisation time (BP)"])),
-#                           stac = 4,
-#                           missing_species = 0)
-#     }
-#     if(island_spec[1,"Species type"] == "A")
-#     {
-#       descendants <- list(stt_table = stt_table,
-#                           branching_times = c(total_time,as.numeric(island_spec[1,"Colonisation time (BP)"])),
-#                           stac = 2,
-#                           missing_species = 0)
-#     }
-#     if(island_spec[1,"Species type"] == "C")
-#     {
-#       descendants <- list(stt_table = stt_table,
-#                           branching_times = c(total_time,rev(sort(as.numeric(island_spec[,"branching time (BP)"])))),
-#                           stac = 2,
-#                           missing_species = 0)
-#     }
-#   }
-#
-#   ### if there are two or more independent colonisations, all species are classed as stac=3 and put within same list item:
-#   else if(number_colonisations > 1)
-#   {
-#     descendants <- list(stt_table = stt_table,
-#                         branching_times = NA,stac = 2,missing_species = 0,
-#                         other_clades_same_ancestor = list())
-#     ### create table with information on other clades with same ancestor, but this information is not used in DAISIE_ML
-#     oldest <- which(as.numeric(island_spec[,"Colonisation time (BP)"]) == max(as.numeric(island_spec[,"Colonisation time (BP)"])))
-#
-#     oldest_table <- island_spec[oldest,]
-#     if(class(oldest_table) == 'character')
-#     {
-#       oldest_table <- t(as.matrix(oldest_table))
-#     }
-#     if(oldest_table[1,'Species type'] == 'A')
-#     {
-#       descendants$branching_times <- c(total_time, as.numeric(oldest_table[1,"Colonisation time (BP)"]))
-#     } else if(oldest_table[1,'Species type'] == 'C')
-#     {
-#       descendants$branching_times <- c(total_time, rev(sort(as.numeric(oldest_table[,'branching time (BP)']))))
-#     }
-#
-#     youngest_table = island_spec[-oldest,]
-#     if(class(youngest_table) == 'character')
-#     {
-#       youngest_table <- t(as.matrix(youngest_table))
-#     }
-#
-#     uniquecol <- as.numeric(unique(youngest_table[,"Colonisation time (BP)"]))
-#
-#     descendants$missing_species <- length(which(youngest_table[,"Species type"]!='I'))
-#     for(colonisation in 1:length(uniquecol))
-#     {
-#       descendants$other_clades_same_ancestor[[colonisation]] <- list(brts_miss = NA,species_type = NA)
-#
-#       samecolonisation <- which(as.numeric(youngest_table[,"Colonisation time (BP)"]) == uniquecol[colonisation])
-#
-#       if(youngest_table[samecolonisation[1],"Species type"] == "I")
-#       {
-#         descendants$stac <- 3
-#         descendants$other_clades_same_ancestor[[colonisation]]$brts_miss <- as.numeric(youngest_table[samecolonisation,"Colonisation time (BP)"])
-#         descendants$other_clades_same_ancestor[[colonisation]]$species_type <- "I"
-#       } else if(youngest_table[samecolonisation[1],"Species type"] == "A")
-#       {
-#         descendants$other_clades_same_ancestor[[colonisation]]$brts_miss <- as.numeric(youngest_table[samecolonisation,"Colonisation time (BP)"])
-#         descendants$other_clades_same_ancestor[[colonisation]]$species_type <- "A"
-#       } else if (youngest_table[samecolonisation[1],"Species type"] == "C")
-#       {
-#         descendants$other_clades_same_ancestor[[colonisation]]$brts_miss <- rev(sort(as.numeric(youngest_table[samecolonisation,"branching time (BP)"])))
-#         descendants$other_clades_same_ancestor[[colonisation]]$species_type <- "C"
-#       }
-#     }
-#   }
-#   descendants
-# }
+
diff --git a/R/create_pars.R b/R/create_pars.R
index b2576576..a5549a6c 100644
--- a/R/create_pars.R
+++ b/R/create_pars.R
@@ -121,20 +121,20 @@ create_trait_pars <- function(trans_rate,
                               clado_rate2,
                               trans_rate2,
                               M2) {
-  testit::assert(is.numeric(trans_rate))
-  testit::assert(is.numeric(immig_rate2))
-  testit::assert(is.numeric(ext_rate2))
-  testit::assert(is.numeric(ana_rate2))
-  testit::assert(is.numeric(clado_rate2))
-  testit::assert(is.numeric(trans_rate2))
-  testit::assert(floor(M2) == M2)
-  testit::assert(trans_rate >= 0.0)
-  testit::assert(immig_rate2 >= 0.0)
-  testit::assert(ext_rate2 >= 0.0)
-  testit::assert(ana_rate2 >= 0.0)
-  testit::assert(clado_rate2 >= 0.0)
-  testit::assert(trans_rate2 >=0.0)
-  testit::assert(M2 >=0)
+  # testit::assert(is.numeric(trans_rate))
+  # testit::assert(is.numeric(immig_rate2))
+  # testit::assert(is.numeric(ext_rate2))
+  # testit::assert(is.numeric(ana_rate2))
+  # testit::assert(is.numeric(clado_rate2))
+  # testit::assert(is.numeric(trans_rate2))
+  # testit::assert(floor(M2) == M2)
+  # testit::assert(trans_rate >= 0.0)
+  # testit::assert(immig_rate2 >= 0.0)
+  # testit::assert(ext_rate2 >= 0.0)
+  # testit::assert(ana_rate2 >= 0.0)
+  # testit::assert(clado_rate2 >= 0.0)
+  # testit::assert(trans_rate2 >=0.0)
+  # testit::assert(M2 >=0)
   list(trans_rate = trans_rate,
        immig_rate2 = immig_rate2,
        ext_rate2 = ext_rate2,

From 0c80f78136ece8787c4ab8f8fd647161f986c6ef Mon Sep 17 00:00:00 2001
From: xieshu95 <xieshu95@gmail.com>
Date: Wed, 22 Jun 2022 10:06:57 +0200
Subject: [PATCH 04/73] allow to use two Ks IN traisie simulations

---
 R/DAISIE_rates.R            |  54 +++++++---
 R/DAISIE_sim_trait_dep_2K.R | 206 ++++++++++++++++++++++++++++++++++++
 R/create_pars.R             |  35 ++++++
 3 files changed, 282 insertions(+), 13 deletions(-)
 create mode 100644 R/DAISIE_sim_trait_dep_2K.R

diff --git a/R/DAISIE_rates.R b/R/DAISIE_rates.R
index a0c9ba55..adce87e2 100644
--- a/R/DAISIE_rates.R
+++ b/R/DAISIE_rates.R
@@ -379,13 +379,23 @@ get_clado_rate <- function(lac,
   }else{
     num_spec_trait1 <- length(which(island_spec[, 8] == "1"))
     num_spec_trait2 <- length(which(island_spec[, 8] == "2"))
-    clado_rate1 <- max(
-      0, lac * num_spec_trait1 * (1 - num_spec / K),
-      na.rm = TRUE)
-    clado_rate2 <- max(
-      0, trait_pars$clado_rate2 * num_spec_trait2 * (1 - num_spec / K),
-      na.rm = TRUE
-    )
+
+    if ("K2" %in% names(trait_pars)) {
+      clado_rate1 <- max(
+        0, lac * num_spec_trait1 * (1 - num_spec_trait1 / K),
+        na.rm = TRUE)
+      clado_rate2 <- max(
+        0, trait_pars$clado_rate2 * num_spec_trait2 * (1 - num_spec_trait2 / trait_pars$K2),
+        na.rm = TRUE)
+    } else {
+      clado_rate1 <- max(
+        0, lac * num_spec_trait1 * (1 - num_spec / K),
+        na.rm = TRUE)
+      clado_rate2 <- max(
+        0, trait_pars$clado_rate2 * num_spec_trait2 * (1 - num_spec / K),
+        na.rm = TRUE)
+    }
+
     # testit::assert(clado_rate1 >= 0)
     # testit::assert(clado_rate2 >= 0)
     # testit::assert(is.numeric(clado_rate1))
@@ -426,10 +436,20 @@ get_immig_rate <- function(gam,
   } else {
     mainland_n2 <- trait_pars$M2
     gam2 <- trait_pars$immig_rate2
-    immig_rate1 <- max(c(mainland_n * gam * (1 - (num_spec / (A * K))),
-                         0), na.rm = TRUE)
-    immig_rate2 <- max(c(mainland_n2 * gam2 * (1 - (num_spec / (A * K))),
-                         0), na.rm = TRUE)
+    num_spec_trait1 <- length(which(island_spec[, 8] == "1"))
+    num_spec_trait2 <- length(which(island_spec[, 8] == "2"))
+    if ("K2" %in% names(trait_pars)) {
+      immig_rate1 <- max(c(mainland_n * gam * (1 - (num_spec_trait1 / K)),
+                           0), na.rm = TRUE)
+      immig_rate2 <- max(c(mainland_n2 * gam2 * (1 - (num_spec_trait2 / trait_pars$K2)),
+                           0), na.rm = TRUE)
+    } else {
+      immig_rate1 <- max(c(mainland_n * gam * (1 - (num_spec / K)),
+                           0), na.rm = TRUE)
+      immig_rate2 <- max(c(mainland_n2 * gam2 * (1 - (num_spec / K)),
+                           0), na.rm = TRUE)
+    }
+
     # testit::assert(is.numeric(immig_rate1))
     # testit::assert(immig_rate1 >= 0)
     # testit::assert(is.numeric(immig_rate2))
@@ -467,8 +487,16 @@ get_trans_rate <- function(trait_pars,
     num_spec_trait1 <- length(which(island_spec[, 8] == "1"))
     num_spec_trait2 <- length(which(island_spec[, 8] == "2"))
   }
-  trans_rate1 <- trait_pars$trans_rate * num_spec_trait1
-  trans_rate2 <- trait_pars$trans_rate2 * num_spec_trait2
+  if ("K2" %in% names(trait_pars)) {
+    trans_rate1 <- trait_pars$trans_rate * num_spec_trait1 *
+      (1 - (num_spec_trait2 / trait_pars$K2))
+    trans_rate2 <- trait_pars$trans_rate2 * num_spec_trait2 *
+      (1 - (num_spec_trait1 / trait_pars$K))
+  } else {
+    trans_rate1 <- trait_pars$trans_rate * num_spec_trait1
+    trans_rate2 <- trait_pars$trans_rate2 * num_spec_trait2
+  }
+
   # testit::assert(is.numeric(trans_rate1))
   # testit::assert(trans_rate1 >= 0)
   # testit::assert(is.numeric(trans_rate2))
diff --git a/R/DAISIE_sim_trait_dep_2K.R b/R/DAISIE_sim_trait_dep_2K.R
new file mode 100644
index 00000000..021cd32e
--- /dev/null
+++ b/R/DAISIE_sim_trait_dep_2K.R
@@ -0,0 +1,206 @@
+#' @title Simulate islands with given parameters.
+#' @description This function simulates islands with given cladogenesis,
+#' extinction, Kprime, immigration and anagenesis parameters. If a single
+#' parameter set is provided (5 parameters) it simulates islands where all
+#' species have the same macro-evolutionary process. If two paramater sets
+#' (10 parameters) are provided, it simulates islands where two different
+#' macro-evolutionary processes operate, one applying to type 1 species and
+#' other to type 2 species. If two parameter sets and a time shift (11
+#' parameters) are provided, it simulates islands where at the given time
+#' a shift between the parameter sets will occur.
+#'
+#' Returns R list object that contains the simulated islands
+#'
+#' @inheritParams default_params_doc
+#'
+#' @return Each simulated dataset is an element of the list, which can be
+#' called using [[x]]. For example if the object is called island_replicates,
+#' the last replicates is a list in itself. The first (e.g.
+#' \code{island_replicates[[x]][[1]]}) element of that list has the following
+#' components: \cr \code{$island_age} - the island age \cr Then, depending on
+#' whether a distinction between types is made, we have:\cr \code{$not_present}
+#' - the number of mainland lineages that are not present on the island \cr
+#' or:\cr \code{$not_present_type1} - the number of mainland lineages of type 1
+#' that are not present on the island \cr \code{$not_present_type2} - the
+#' number of mainland lineages of type 2 that are not present on the island \cr
+#' \code{$stt_all} - STT table for all species on the island (nI - number of
+#' non-endemic species; nA - number of anagenetic species, nC - number of
+#' cladogenetic species, present - number of independent colonisations present
+#' )\cr \code{$stt_stt_type1} - STT table for type 1 species on the island -
+#' only if 2 types of species were simulated (nI - number of non-endemic
+#' species; nA - number of anagenetic species, nC - number of cladogenetic
+#' species, present - number of independent colonisations present )\cr
+#' \code{$stt_stt_type2} - STT table for type 2 species on the island - only if
+#' 2 types of species were simulated (nI - number of non-endemic species; nA -
+#' number of anagenetic species, nC - number of cladogenetic species, present -
+#' number of independent colonisations present )\cr \code{$brts_table} - Only
+#' for simulations under 'IW'. Table containing information on order of events
+#' in the data, for use in maximum likelihood optimization.)\cr
+#'
+#' The subsequent elements of the list each contain information on a single
+#' colonist lineage on the island and has 4 components:\cr
+#' \code{$branching_times} - island age and stem age of the population/species
+#' in the case of Non-endemic, Non-endemic_MaxAge and Endemic anagenetic
+#' species. For cladogenetic species these should be island age and branching
+#' times of the radiation including the stem age of the radiation.\cr
+#' \code{$stac} - the status of the colonist \cr * Non_endemic_MaxAge: 1 \cr *
+#' ndemic: 2 \cr * Endemic&Non_Endemic: 3 \cr * Non_endemic: 4 \cr
+#' \code{$missing_species} - number of island species that were not sampled for
+#' particular clade (only applicable for endemic clades) \cr \code{$type_1or2}
+#' - whether the colonist belongs to type 1 or type 2 \cr
+#' @author Luis Valente and Albert Phillimore
+#' @seealso \code{\link{DAISIE_format_CS}} \code{\link{DAISIE_plot_sims}}
+#' @references Valente, L.M., A.B. Phillimore and R.S. Etienne (2015).
+#' Equilibrium and non-equilibrium dynamics simultaneously operate in the
+#' Galapagos islands. Ecology Letters 18: 844-852.
+#' Hauffe, T., D. Delicado, R.S. Etienne and L. Valente (submitted).
+#' Lake expansion increases equilibrium diversity via the target effect of
+#' island biogeography.
+#' @keywords models
+#' @export
+DAISIE_sim_trait_dep_2K <- function(
+    time,
+    M,
+    pars,
+    replicates,
+    divdepmodel = "CS",
+    sample_freq = 25,
+    plot_sims = TRUE,
+    island_ontogeny = "const",
+    sea_level = "const",
+    hyper_pars = create_hyper_pars(d = 0, x = 0),
+    area_pars = DAISIE::create_area_pars(
+      max_area = 1,
+      current_area = 1,
+      proportional_peak_t = 0,
+      total_island_age = 0,
+      sea_level_amplitude = 0,
+      sea_level_frequency = 0,
+      island_gradient_angle = 0),
+    extcutoff = 1000,
+    cond = 0,
+    verbose = TRUE,
+    trait_pars = NULL,
+    ...
+) {
+  total_time <- time
+  island_replicates <- list()
+  island_ontogeny <- translate_island_ontogeny(island_ontogeny)
+  sea_level <- translate_sea_level(sea_level)
+
+  #### IW ####
+  if (divdepmodel == "IW") {
+    for (rep in 1:replicates) {
+      island_replicates[[rep]] <- DAISIE_sim_core_trait_dep(
+        time = total_time,
+        mainland_n = M,
+        pars = pars,
+        island_ontogeny = island_ontogeny,
+        sea_level = sea_level,
+        hyper_pars = hyper_pars,
+        area_pars = area_pars,
+        extcutoff = extcutoff,
+        trait_pars = trait_pars
+      )
+      if (verbose == TRUE) {
+        print(paste("Island replicate ", rep, sep = ""))
+      }
+    }
+    island_replicates <- DAISIE_format_IW(
+      island_replicates = island_replicates,
+      time = total_time,
+      M = M,
+      sample_freq = sample_freq,
+      verbose = verbose,
+      trait_pars = trait_pars)
+  }
+
+  #### CS ####
+  if (divdepmodel == "CS") {
+    for (rep in 1:replicates) {
+      island_replicates[[rep]] <- list()
+      full_list <- list()
+      if (cond == 0) {
+        number_present <- -1
+      } else {
+        number_present <- 0
+      }
+      while (number_present < cond) {
+        if(M == 0 || is.null(trait_pars)){
+          stop("One state exist on mainland, should use constant rate DAISIE.")
+        }else{
+          for (m_spec in 1:M) {
+            ### M1 = 1, M2 = 0
+            trait_pars_onecolonize <- create_trait_pars_2K(
+              trans_rate = trait_pars$trans_rate,
+              immig_rate2 = trait_pars$immig_rate2,
+              ext_rate2 = trait_pars$ext_rate2,
+              ana_rate2 = trait_pars$ana_rate2,
+              clado_rate2 = trait_pars$clado_rate2,
+              trans_rate2 = trait_pars$trans_rate2,
+              M2 = 0,
+              K2 = trait_pars$K2)
+            full_list[[m_spec]] <- DAISIE_sim_core_trait_dep(
+              time = total_time,
+              mainland_n = 1,
+              pars = pars,
+              island_ontogeny = island_ontogeny,
+              sea_level = sea_level,
+              hyper_pars = hyper_pars,
+              area_pars = area_pars,
+              extcutoff = extcutoff,
+              trait_pars = trait_pars_onecolonize
+            )
+          }
+          for(m_spec in (M + 1):(M + trait_pars$M2)) {
+            ### M1 = 0, M2 = 1
+            trait_pars_onecolonize <- create_trait_pars_2K(
+              trans_rate = trait_pars$trans_rate,
+              immig_rate2 = trait_pars$immig_rate2,
+              ext_rate2 = trait_pars$ext_rate2,
+              ana_rate2 = trait_pars$ana_rate2,
+              clado_rate2 = trait_pars$clado_rate2,
+              trans_rate2 = trait_pars$trans_rate2,
+              M2 = 1,
+              K2 = trait_pars$K2)
+            full_list[[m_spec]] <- DAISIE_sim_core_trait_dep(
+              time = total_time,
+              mainland_n = 0,
+              pars = pars,
+              island_ontogeny = island_ontogeny,
+              sea_level = sea_level,
+              hyper_pars = hyper_pars,
+              area_pars = area_pars,
+              extcutoff = extcutoff,
+              trait_pars = trait_pars_onecolonize
+            )
+          }
+        }
+        stac_vec <- unlist(full_list)[which(names(unlist(full_list)) == "stac")]
+        present <- which(stac_vec != 0)
+        number_present <- length(present)
+      }
+      island_replicates[[rep]] <- full_list
+      if (verbose == TRUE) {
+        print(paste("Island replicate ", rep, sep = ""))
+      }
+    }
+    island_replicates <- DAISIE_format_CS(
+      island_replicates = island_replicates,
+      time = total_time,
+      M = M,
+      sample_freq = sample_freq,
+      verbose = verbose,
+      trait_pars = trait_pars
+    )
+  }
+
+  if (plot_sims == TRUE) {
+    DAISIE_plot_sims(
+      island_replicates = island_replicates,
+      sample_freq = sample_freq,
+      trait_pars = trait_pars
+    )
+  }
+  return(island_replicates)
+}
diff --git a/R/create_pars.R b/R/create_pars.R
index a5549a6c..0fd3fbb6 100644
--- a/R/create_pars.R
+++ b/R/create_pars.R
@@ -144,6 +144,41 @@ create_trait_pars <- function(trans_rate,
        M2 = M2)
 }
 
+
+
+#' Create named list of trait state parameters
+#'
+#' @param trans_rate   A numeric with the per capita transition rate with state1
+#' @param immig_rate2  A numeric with the per capita immigration rate with state2
+#' @param ext_rate2    A numeric with the per capita extinction rate with state2
+#' @param ana_rate2    A numeric with the per capita anagenesis rate with state2
+#' @param clado_rate2  A numeric with the per capita cladogenesis rate with state2
+#' @param trans_rate2  A numeric with the per capita transition rate with state2
+#' @param M2           A numeric with the number of species with trait state 2 on mainland
+#' @param K2           A numeric with the carrying capacity for state 2
+#'
+#' @return list of numerical values containing trait state parameters
+#' @export
+#'
+create_trait_pars_2K <- function(trans_rate,
+                                 immig_rate2,
+                                 ext_rate2,
+                                 ana_rate2,
+                                 clado_rate2,
+                                 trans_rate2,
+                                 M2,
+                                 K2) {
+  list(trans_rate = trans_rate,
+       immig_rate2 = immig_rate2,
+       ext_rate2 = ext_rate2,
+       ana_rate2 = ana_rate2,
+       clado_rate2 = clado_rate2,
+       trans_rate2 = trans_rate2,
+       M2 = M2,
+       K2 = K2)
+}
+
+
 #' Creates the list object for CS_version argument in DAISIE_ML_CS
 #'
 #' @param model the CS model to run, options are \code{1} for single rate

From a64e2bfbfbb2d5d468de8c53135cee72061608a2 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Wed, 29 Jun 2022 13:58:11 +0200
Subject: [PATCH 05/73] Properly comapring res with number of missing species

---
 R/DAISIE_ML1.R | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/R/DAISIE_ML1.R b/R/DAISIE_ML1.R
index 9eacd329..26d898b4 100644
--- a/R/DAISIE_ML1.R
+++ b/R/DAISIE_ML1.R
@@ -240,13 +240,19 @@ DAISIE_ML1 <- function(
   idpars <- sort(c(idparsopt, idparsfix, idparsnoshift, idparseq))
 
   missnumspec <- unlist(lapply(datalist, function(list) {list$missing_species})) # nolint
-  if (sum(missnumspec) > (res - 1)) {
+  if (max(missnumspec) > (res - 1)) {
     cat(
       "The number of missing species is too large relative to the
         resolution of the ODE.\n")
     return(out2err)
   }
 
+  if (max(missnumspec) > res/10) {
+    warning(
+      "The number of missing species is quite low relative to the
+        resolution of the ODE.\n")
+  }
+
   if ((length(idpars) != max(idpars))) {
     cat("The parameters to be optimized and/or fixed are incoherent.\n")
     return(out2err)

From 7a6bf9f5376b9a0b9ac38434b88fee8b16655a2d Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 14 Jul 2022 09:13:05 +0200
Subject: [PATCH 06/73] Output loglikelihood = -Inf if
 probability_of_initial_presence becomes larger than 1.

---
 R/DAISIE_ML1.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/R/DAISIE_ML1.R b/R/DAISIE_ML1.R
index 26d898b4..0f51918e 100644
--- a/R/DAISIE_ML1.R
+++ b/R/DAISIE_ML1.R
@@ -12,11 +12,13 @@ DAISIE_loglik_all_choosepar <- function(trparsopt,
                                         abstolint = 1E-16,
                                         reltolint = 1E-10) {
   all_no_shift <- 6:10
+  non_oceanic_option <- FALSE
   if (max(idparsopt,-Inf) <= 6 &&
       max(idparsfix,-Inf) <= 6 &&
       (6 %in% idparsopt || 6 %in% idparsfix)) {
     idparsnoshift <- 7:11
     all_no_shift <- 7:11
+    non_oceanic_option <- TRUE
   }
   if (sum(idparsnoshift %in% (all_no_shift)) != 5) {
     trpars1 <- rep(0, 11)
@@ -45,7 +47,7 @@ DAISIE_loglik_all_choosepar <- function(trparsopt,
         pars1[idparsnoshift] <- pars1[idparsnoshift - 5]
       }
     }
-    if (min(pars1) < 0) {
+    if (min(pars1) < 0 | (pars1[6] > 1 && non_oceanic_option == TRUE)) {
       loglik <- -Inf
     } else {
       loglik <- DAISIE_loglik_all(

From 621270971f57d1ff7fc4ab9450dd3341b13ed07d Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 21 Jul 2022 11:17:37 +0200
Subject: [PATCH 07/73] Add par_upper_bound to create_CS_version

---
 R/create_pars.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/create_pars.R b/R/create_pars.R
index b2576576..0e7e2ce6 100644
--- a/R/create_pars.R
+++ b/R/create_pars.R
@@ -163,7 +163,8 @@ create_trait_pars <- function(trans_rate,
 #' }
 #' @export
 create_CS_version <- function(model = 1,
-                              relaxed_par = NULL) {
+                              relaxed_par = NULL,
+                              par_upper_bound = Inf) {
 
   if (model != 1 && model != 2 && model != 3) {
     stop("model must be either 1, 2 or 3")
@@ -172,7 +173,8 @@ create_CS_version <- function(model = 1,
     stop("relaxed_par required for multi-rate model")
   }
   CS_version <- list(model = model,
-                     relaxed_par = relaxed_par)
+                     relaxed_par = relaxed_par,
+                     par_upper_bound = par_upper_bound)
   return(CS_version)
 }
 

From 7d1181fd54c6d20cd5759e6b48de022a81670110 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 21 Jul 2022 11:18:07 +0200
Subject: [PATCH 08/73] In simulation example rename sd to par_sd to be
 consistent with naming

---
 R/DAISIE_sim_relaxed_rate.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/DAISIE_sim_relaxed_rate.R b/R/DAISIE_sim_relaxed_rate.R
index 92cc9ddd..1c2271df 100644
--- a/R/DAISIE_sim_relaxed_rate.R
+++ b/R/DAISIE_sim_relaxed_rate.R
@@ -76,8 +76,8 @@
 #' carr_cap <- Inf
 #' immig_rate <- 0.005
 #' ana_rate <- 1
-#' sd <- 1
-#' sim_pars <- c(clado_rate, ext_rate, carr_cap, immig_rate, ana_rate, sd)
+#' par_sd <- 1
+#' sim_pars <- c(clado_rate, ext_rate, carr_cap, immig_rate, ana_rate, par_sd)
 #' set.seed(1)
 #' island_replicates <- DAISIE_sim_relaxed_rate(
 #'   time = 1,

From eaaf59156782401b15239353693bbeac0c39d6b1 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 21 Jul 2022 11:18:53 +0200
Subject: [PATCH 09/73] In loglik_integrate, rename sd to par_sd and add
 par_upper_bound

---
 R/DAISIE_loglik_integrate.R | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/R/DAISIE_loglik_integrate.R b/R/DAISIE_loglik_integrate.R
index 6e7cedaf..2d7f187a 100644
--- a/R/DAISIE_loglik_integrate.R
+++ b/R/DAISIE_loglik_integrate.R
@@ -19,7 +19,8 @@ DAISIE_loglik_integrate <- function(
   verbose) {
 
   testit::assert(is.list(CS_version))
-  par_sd <- CS_version$sd
+  par_sd <- CS_version$par_sd
+  par_upper_bound <- CS_version$par_upper_bound
   pick <- which(c("cladogenesis",
                   "extinction",
                   "carrying_capacity",
@@ -44,7 +45,8 @@ DAISIE_loglik_integrate <- function(
     verbose = verbose,
     pick = pick,
     par_mean = par_mean,
-    par_sd = par_sd)
+    par_sd = par_sd,
+    par_upper_bound = par_upper_bound)
   return(integrated_loglik)
 }
 
@@ -146,7 +148,8 @@ integral_peak <- function(logfun,
                           verbose,
                           pick,
                           par_mean,
-                          par_sd) {
+                          par_sd,
+                          par_upper_bound) {
   fun <- function(x) {
     exp(logfun(x,
                pars1,
@@ -240,7 +243,7 @@ integral_peak <- function(logfun,
                          abs.tol = 1e-10)
   Q2 <- stats::integrate(f = fun,
                          lower = exp(xmax),
-                         upper = Inf,
+                         upper = par_upper_bound,
                          subdivisions = 1000,
                          rel.tol = 1e-10,
                          abs.tol = 1e-10)

From 09325d9bc29414958d886a2ea569533857dcfee8 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 21 Jul 2022 11:23:02 +0200
Subject: [PATCH 10/73] Rename sd to par_sd and add par_upper_bound

---
 R/DAISIE_ML4.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/DAISIE_ML4.R b/R/DAISIE_ML4.R
index a08cbbe1..ce6d50fd 100644
--- a/R/DAISIE_ML4.R
+++ b/R/DAISIE_ML4.R
@@ -18,7 +18,7 @@ DAISIE_loglik_all_choosepar4 <- function(trparsopt,
     loglik <- -Inf
   } else {
     pars1 <- trpars1 / (1 - trpars1)
-    CS_version$sd <- pars1[6]
+    CS_version$par_sd <- pars1[6]
     pars1 <- pars1[-6]
     if (min(pars1) < 0) {
       loglik <- -Inf
@@ -82,7 +82,9 @@ DAISIE_ML4 <- function(
   methode = "lsodes",
   optimmethod = "subplex",
   CS_version = create_CS_version(model = 2,
-                                 relaxed_par = "cladogenesis"),
+                                 relaxed_par = "cladogenesis",
+                                 par_sd = 0,
+                                 par_upper_bound = Inf),
   verbose = 0,
   tolint = c(1E-16, 1E-10),
   island_ontogeny = NA,

From a62ad34aa6c7e3ebcaafff28673e4b0017bcccab Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 21 Jul 2022 11:23:20 +0200
Subject: [PATCH 11/73] Add par_sd in create_CS_version

---
 R/create_pars.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/create_pars.R b/R/create_pars.R
index 0e7e2ce6..9e676d15 100644
--- a/R/create_pars.R
+++ b/R/create_pars.R
@@ -164,6 +164,7 @@ create_trait_pars <- function(trans_rate,
 #' @export
 create_CS_version <- function(model = 1,
                               relaxed_par = NULL,
+                              par_sd = 0,
                               par_upper_bound = Inf) {
 
   if (model != 1 && model != 2 && model != 3) {
@@ -174,6 +175,7 @@ create_CS_version <- function(model = 1,
   }
   CS_version <- list(model = model,
                      relaxed_par = relaxed_par,
+                     par_sd = par_sd,
                      par_upper_bound = par_upper_bound)
   return(CS_version)
 }

From 52db6942ee59d33af7c53ab910ba9c217f012540 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 21 Jul 2022 13:55:35 +0200
Subject: [PATCH 12/73] update tests

---
 tests/testthat/test-DAISIE_loglik_integrate.R |  6 ++++--
 tests/testthat/test-DAISIE_utils.R            | 12 +++++++++---
 2 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/tests/testthat/test-DAISIE_loglik_integrate.R b/tests/testthat/test-DAISIE_loglik_integrate.R
index 7b7cdf18..1aad41c9 100644
--- a/tests/testthat/test-DAISIE_loglik_integrate.R
+++ b/tests/testthat/test-DAISIE_loglik_integrate.R
@@ -8,7 +8,8 @@ test_that("DAISIE_loglik_integrate produces correct ouput on single lineage", {
   methode <- "lsodes"
   CS_version <- list(model = 2,
                      relaxed_par = 'carrying_capacity',
-                     sd = 2)
+                     par_sd = 2,
+                     par_upper_bound = Inf)
   abstolint <- 1e-16
   reltolint <- 1e-10
   verbose <- FALSE
@@ -38,7 +39,8 @@ test_that("DAISIE_loglik_integrate produces correct ouput on radiation", {
   methode <- "lsodes"
   CS_version <- list(model = 2,
                      relaxed_par = 'carrying_capacity',
-                     sd = 10)
+                     par_sd = 10,
+                     par_upper_bound = Inf)
   abstolint <- 1e-16
   reltolint <- 1e-10
   verbose <- FALSE
diff --git a/tests/testthat/test-DAISIE_utils.R b/tests/testthat/test-DAISIE_utils.R
index f954bdb7..d38b2a0d 100644
--- a/tests/testthat/test-DAISIE_utils.R
+++ b/tests/testthat/test-DAISIE_utils.R
@@ -234,13 +234,19 @@ test_that("create_CS_version produces correct output", {
   expect_equal(CS_version, list(model = 1,
                                 relaxed_par = NULL))
   CS_version <- create_CS_version(model = 2,
-                                  relaxed_par = "cladogenesis")
+                                  relaxed_par = "cladogenesis",
+                                  par_sd = 10,
+                                  par_upper_bound = Inf)
   expect_equal(CS_version, list(model = 2,
-                                relaxed_par = "cladogenesis"))
+                                relaxed_par = "cladogenesis",
+                                par_sd = 10,
+                                par_upper_bound = Inf))
   CS_version <- create_CS_version(model = 3,
                                   relaxed_par = NULL)
   expect_equal(CS_version, list(model = 3,
-                                relaxed_par = NULL))
+                                relaxed_par = NULL,
+                                par_sd = 0,
+                                par_upper_bound = Inf))
 
 })
 

From 0b5fbbc5de79c7ec964685ec446b46aafb5b177d Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 21 Jul 2022 14:04:56 +0200
Subject: [PATCH 13/73] cumulative gamma function

---
 R/DAISIE_loglik_integrate.R | 28 +++++++++++++++++++++++++++-
 1 file changed, 27 insertions(+), 1 deletion(-)

diff --git a/R/DAISIE_loglik_integrate.R b/R/DAISIE_loglik_integrate.R
index 2d7f187a..c7cf4f02 100644
--- a/R/DAISIE_loglik_integrate.R
+++ b/R/DAISIE_loglik_integrate.R
@@ -46,7 +46,12 @@ DAISIE_loglik_integrate <- function(
     pick = pick,
     par_mean = par_mean,
     par_sd = par_sd,
-    par_upper_bound = par_upper_bound)
+    par_upper_bound = par_upper_bound) -
+    cum_rho(DAISIE_par = DAISIE_par,
+            DAISIE_dist_pars = list(par_mean = par_mean,
+                                    par_sd = par_sd),
+            par_upper_bound = par_upper_bound
+    )
   return(integrated_loglik)
 }
 
@@ -111,6 +116,27 @@ rho <- function(DAISIE_par, DAISIE_dist_pars) {
   return(gamma_den)
 }
 
+#' Cumulative Gamma distribution parameterised with mean and standard deviation
+#'
+#' @inheritParams default_params_doc
+#'
+#' @return Numeric
+#' @keywords internal
+cum_rho <- function(DAISIE_par, DAISIE_dist_pars, par_upper_bound) {
+
+  gamma_pars <- transform_gamma_pars(
+    par_mean = DAISIE_dist_pars$par_mean,
+    par_sd = DAISIE_dist_pars$par_sd)
+
+  gamma_cum_prob <- stats::pgamma(
+    q = par_upper_bound,
+    shape = gamma_pars$shape,
+    scale = gamma_pars$scale,
+    log.p = TRUE)
+
+  return(gamma_cum_prob)
+}
+
 #' @title Computes integral of a very peaked function, modified from the
 #' SADISA package
 #' @description computes the logarithm of the integral of exp(logfun) from 0

From 82030564a948e1001f99348fdbfd3d6ce6fca565 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 21 Jul 2022 14:06:37 +0200
Subject: [PATCH 14/73] update cum_rho

---
 R/DAISIE_loglik_integrate.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/DAISIE_loglik_integrate.R b/R/DAISIE_loglik_integrate.R
index c7cf4f02..04e0e16a 100644
--- a/R/DAISIE_loglik_integrate.R
+++ b/R/DAISIE_loglik_integrate.R
@@ -122,7 +122,7 @@ rho <- function(DAISIE_par, DAISIE_dist_pars) {
 #'
 #' @return Numeric
 #' @keywords internal
-cum_rho <- function(DAISIE_par, DAISIE_dist_pars, par_upper_bound) {
+cum_rho <- function(par_upper_bound, DAISIE_dist_pars) {
 
   gamma_pars <- transform_gamma_pars(
     par_mean = DAISIE_dist_pars$par_mean,

From bd95e851b446c26cd61bd011803c290d0f3f707c Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 21 Jul 2022 14:47:03 +0200
Subject: [PATCH 15/73] bug fix cum_rho

---
 R/DAISIE_loglik_integrate.R        | 5 ++---
 tests/testthat/test-DAISIE_utils.R | 4 +++-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/R/DAISIE_loglik_integrate.R b/R/DAISIE_loglik_integrate.R
index 04e0e16a..7bf7c847 100644
--- a/R/DAISIE_loglik_integrate.R
+++ b/R/DAISIE_loglik_integrate.R
@@ -47,10 +47,9 @@ DAISIE_loglik_integrate <- function(
     par_mean = par_mean,
     par_sd = par_sd,
     par_upper_bound = par_upper_bound) -
-    cum_rho(DAISIE_par = DAISIE_par,
+    cum_rho(par_upper_bound = par_upper_bound,
             DAISIE_dist_pars = list(par_mean = par_mean,
-                                    par_sd = par_sd),
-            par_upper_bound = par_upper_bound
+                                    par_sd = par_sd)
     )
   return(integrated_loglik)
 }
diff --git a/tests/testthat/test-DAISIE_utils.R b/tests/testthat/test-DAISIE_utils.R
index d38b2a0d..f3d90d6d 100644
--- a/tests/testthat/test-DAISIE_utils.R
+++ b/tests/testthat/test-DAISIE_utils.R
@@ -232,7 +232,9 @@ test_that("create_CS_version produces correct output", {
   CS_version <- create_CS_version(model = 1,
                                   relaxed_par = NULL)
   expect_equal(CS_version, list(model = 1,
-                                relaxed_par = NULL))
+                                relaxed_par = NULL,
+                                par_sd = 0,
+                                par_upper_bound = Inf))
   CS_version <- create_CS_version(model = 2,
                                   relaxed_par = "cladogenesis",
                                   par_sd = 10,

From 2ab727332b5282d4ca8806dc80cca739e0ca89d7 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 21 Jul 2022 18:10:24 +0200
Subject: [PATCH 16/73] Make sure upper bound is larger than xmax

---
 R/DAISIE_loglik_integrate.R | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/R/DAISIE_loglik_integrate.R b/R/DAISIE_loglik_integrate.R
index 7bf7c847..6d424a88 100644
--- a/R/DAISIE_loglik_integrate.R
+++ b/R/DAISIE_loglik_integrate.R
@@ -268,14 +268,11 @@ integral_peak <- function(logfun,
                          abs.tol = 1e-10)
   Q2 <- stats::integrate(f = fun,
                          lower = exp(xmax),
-                         upper = par_upper_bound,
+                         upper = max(1 + exp(xmax),par_upper_bound),
                          subdivisions = 1000,
                          rel.tol = 1e-10,
                          abs.tol = 1e-10)
-  Q1 <- Q1$value
-  Q2 <- Q2$value
-  logQ <- log(Q0 + Q1 + Q2)
-
+  logQ <- log(Q0 + Q1$value + Q2$value)
   return(logQ)
 }
 

From 38a08cf8c3fe890dacd3456d9fe456aff713fdf8 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 21 Jul 2022 18:11:08 +0200
Subject: [PATCH 17/73] Make complete CS_version in tests

---
 tests/testthat/test-DAISIE_ML4.R       | 11 ++++++++---
 tests/testthat/test-DAISIE_loglik_CS.R |  3 ++-
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-DAISIE_ML4.R b/tests/testthat/test-DAISIE_ML4.R
index b6642552..4f81aa9c 100644
--- a/tests/testthat/test-DAISIE_ML4.R
+++ b/tests/testthat/test-DAISIE_ML4.R
@@ -3,12 +3,15 @@ test_that("DAISIE_ML4 is silent and produces correct output", {
   utils::data(Galapagos_datalist)
   loglik <- DAISIE_ML4(
     datalist = Galapagos_datalist,
-    initparsopt = c(2.5, 2.7, 20, 0.009, 1.01, 2),
+    initparsopt = c(2.5, 0.2, 20, 0.009, 1.01, 2),
     idparsopt = 1:6,
     parsfix = NULL,
     idparsfix = NULL,
+    methode = 'lsodes',
     CS_version = create_CS_version(model = 2,
-                                   relaxed_par = "cladogenesis"))
+                                   relaxed_par = "cladogenesis",
+                                   par_sd = 2,
+                                   par_upper_bound = 2))
   expect_equal(2, 2)
 })
 
@@ -27,7 +30,9 @@ test_that("DAISIE_loglik_all_choosepar4 is silent and produces correct output",
       datalist = Galapagos_datalist,
       methode = "lsodes",
       CS_version = list(model = 2,
-                        relaxed_par = "cladogenesis"),
+                        relaxed_par = "cladogenesis",
+                        par_sd = 1,
+                        par_upper_bound = Inf),
       abstolint = 1e-16,
       reltolint = 1e-10
     ))))
diff --git a/tests/testthat/test-DAISIE_loglik_CS.R b/tests/testthat/test-DAISIE_loglik_CS.R
index 071c5036..7c43451a 100644
--- a/tests/testthat/test-DAISIE_loglik_CS.R
+++ b/tests/testthat/test-DAISIE_loglik_CS.R
@@ -30,7 +30,8 @@ test_that("DAISIE_loglik_CS_choice produces correct output for relaxed-rate
   missnumspec <- 0
   CS_version <- list(model = 2,
                      relaxed_par = "cladogenesis",
-                     sd = 1)
+                     sd = 1,
+                     par_upper_bound = Inf)
 
   invisible(capture.output(loglik <- DAISIE_loglik_CS_choice(pars1 = pars1,
                                                              pars2 = pars2,

From 415209c29dede3fa928dda8707b81a2d2e89e471 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 21 Jul 2022 20:33:43 +0200
Subject: [PATCH 18/73] update documentation

---
 man/DAISIE_ML4.Rd                |  3 ++-
 man/DAISIE_sim_relaxed_rate.Rd   |  4 ++--
 man/create_CS_version.Rd         |  7 ++++++-
 man/cum_rho.Rd                   | 19 +++++++++++++++++++
 man/integral_peak.Rd             |  3 ++-
 tests/testthat/test-DAISIE_ML4.R |  4 ++--
 6 files changed, 33 insertions(+), 7 deletions(-)
 create mode 100644 man/cum_rho.Rd

diff --git a/man/DAISIE_ML4.Rd b/man/DAISIE_ML4.Rd
index 78c068d8..b30ae271 100644
--- a/man/DAISIE_ML4.Rd
+++ b/man/DAISIE_ML4.Rd
@@ -18,7 +18,8 @@ DAISIE_ML4(
   maxiter = 1000 * round((1.25)^length(idparsopt)),
   methode = "lsodes",
   optimmethod = "subplex",
-  CS_version = create_CS_version(model = 2, relaxed_par = "cladogenesis"),
+  CS_version = create_CS_version(model = 2, relaxed_par = "cladogenesis", par_sd = 0,
+    par_upper_bound = Inf),
   verbose = 0,
   tolint = c(1e-16, 1e-10),
   island_ontogeny = NA,
diff --git a/man/DAISIE_sim_relaxed_rate.Rd b/man/DAISIE_sim_relaxed_rate.Rd
index 6158fd41..fc62a68b 100644
--- a/man/DAISIE_sim_relaxed_rate.Rd
+++ b/man/DAISIE_sim_relaxed_rate.Rd
@@ -183,8 +183,8 @@ ext_rate <- 0.2
 carr_cap <- Inf
 immig_rate <- 0.005
 ana_rate <- 1
-sd <- 1
-sim_pars <- c(clado_rate, ext_rate, carr_cap, immig_rate, ana_rate, sd)
+par_sd <- 1
+sim_pars <- c(clado_rate, ext_rate, carr_cap, immig_rate, ana_rate, par_sd)
 set.seed(1)
 island_replicates <- DAISIE_sim_relaxed_rate(
   time = 1,
diff --git a/man/create_CS_version.Rd b/man/create_CS_version.Rd
index df1864ff..e86b380e 100644
--- a/man/create_CS_version.Rd
+++ b/man/create_CS_version.Rd
@@ -4,7 +4,12 @@
 \alias{create_CS_version}
 \title{Creates the list object for CS_version argument in DAISIE_ML_CS}
 \usage{
-create_CS_version(model = 1, relaxed_par = NULL)
+create_CS_version(
+  model = 1,
+  relaxed_par = NULL,
+  par_sd = 0,
+  par_upper_bound = Inf
+)
 }
 \arguments{
 \item{model}{the CS model to run, options are \code{1} for single rate
diff --git a/man/cum_rho.Rd b/man/cum_rho.Rd
new file mode 100644
index 00000000..10257ffc
--- /dev/null
+++ b/man/cum_rho.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/DAISIE_loglik_integrate.R
+\name{cum_rho}
+\alias{cum_rho}
+\title{Cumulative Gamma distribution parameterised with mean and standard deviation}
+\usage{
+cum_rho(par_upper_bound, DAISIE_dist_pars)
+}
+\arguments{
+\item{DAISIE_dist_pars}{A numeric vector of two elements, first is the mean
+and second the standard deviation of the distribution.}
+}
+\value{
+Numeric
+}
+\description{
+Cumulative Gamma distribution parameterised with mean and standard deviation
+}
+\keyword{internal}
diff --git a/man/integral_peak.Rd b/man/integral_peak.Rd
index 86f33bcb..0a837384 100644
--- a/man/integral_peak.Rd
+++ b/man/integral_peak.Rd
@@ -21,7 +21,8 @@ integral_peak(
   verbose,
   pick,
   par_mean,
-  par_sd
+  par_sd,
+  par_upper_bound
 )
 }
 \arguments{
diff --git a/tests/testthat/test-DAISIE_ML4.R b/tests/testthat/test-DAISIE_ML4.R
index 4f81aa9c..7219812d 100644
--- a/tests/testthat/test-DAISIE_ML4.R
+++ b/tests/testthat/test-DAISIE_ML4.R
@@ -3,7 +3,7 @@ test_that("DAISIE_ML4 is silent and produces correct output", {
   utils::data(Galapagos_datalist)
   loglik <- DAISIE_ML4(
     datalist = Galapagos_datalist,
-    initparsopt = c(2.5, 0.2, 20, 0.009, 1.01, 2),
+    initparsopt = c(2.5, 0.2, 20, 0.009, 1.01, 0.001),
     idparsopt = 1:6,
     parsfix = NULL,
     idparsfix = NULL,
@@ -11,7 +11,7 @@ test_that("DAISIE_ML4 is silent and produces correct output", {
     CS_version = create_CS_version(model = 2,
                                    relaxed_par = "cladogenesis",
                                    par_sd = 2,
-                                   par_upper_bound = 2))
+                                   par_upper_bound = Inf))
   expect_equal(2, 2)
 })
 

From fc047b35879d441b9a25b3daa5ef764b82589a0a Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 21 Jul 2022 20:43:03 +0200
Subject: [PATCH 19/73] Date update

---
 DESCRIPTION | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index b1773b26..93bc93b2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: DAISIE
 Type: Package
 Title: Dynamical Assembly of Islands by Speciation, Immigration and Extinction
-Version: 4.2.1
-Date: 2022-06-08
+Version: 4.2.2
+Date: 2022-07-21
 Depends: R (>= 3.5.0)
 biocViews:
 SystemRequirements: C++14
@@ -115,4 +115,4 @@ Encoding: UTF-8
 VignetteBuilder: knitr
 URL: https://github.com/rsetienne/DAISIE
 BugReports: https://github.com/rsetienne/DAISIE/issues
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.1

From 65541a1d3aeb5ba18c830aab24aa228550c451a2 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 21 Jul 2022 20:43:14 +0200
Subject: [PATCH 20/73] rename sd to par_sd

---
 tests/testthat/test-DAISIE_loglik_CS.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-DAISIE_loglik_CS.R b/tests/testthat/test-DAISIE_loglik_CS.R
index 7c43451a..1de5544d 100644
--- a/tests/testthat/test-DAISIE_loglik_CS.R
+++ b/tests/testthat/test-DAISIE_loglik_CS.R
@@ -30,7 +30,7 @@ test_that("DAISIE_loglik_CS_choice produces correct output for relaxed-rate
   missnumspec <- 0
   CS_version <- list(model = 2,
                      relaxed_par = "cladogenesis",
-                     sd = 1,
+                     par_sd = 1,
                      par_upper_bound = Inf)
 
   invisible(capture.output(loglik <- DAISIE_loglik_CS_choice(pars1 = pars1,
@@ -86,7 +86,8 @@ test_that("DAISIE_loglik_all produces correct output for relaxed-rate model", {
       methode = "lsodes",
       CS_version = list(model = 2,
                         relaxed_par = "cladogenesis",
-                        sd = 1),
+                        par_sd = 1,
+                        par_upper_bound = Inf),
       abstolint = 1e-16,
       reltolint = 1e-10
     )

From 43d709737026db53c078792b7eee5679c9fee028 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 21 Jul 2022 21:49:12 +0200
Subject: [PATCH 21/73] Better handling when exp(xmax) > par_upper_bound

---
 R/DAISIE_loglik_integrate.R | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/R/DAISIE_loglik_integrate.R b/R/DAISIE_loglik_integrate.R
index 6d424a88..17c1f3d3 100644
--- a/R/DAISIE_loglik_integrate.R
+++ b/R/DAISIE_loglik_integrate.R
@@ -266,12 +266,16 @@ integral_peak <- function(logfun,
                          subdivisions = 1000,
                          rel.tol = 1e-10,
                          abs.tol = 1e-10)
-  Q2 <- stats::integrate(f = fun,
-                         lower = exp(xmax),
-                         upper = max(1 + exp(xmax),par_upper_bound),
-                         subdivisions = 1000,
-                         rel.tol = 1e-10,
-                         abs.tol = 1e-10)
+  if(exp(xmax) < par_upper_bound) {
+    Q2 <- stats::integrate(f = fun,
+                           lower = exp(xmax),
+                           upper = par_upper_bound,
+                           subdivisions = 1000,
+                           rel.tol = 1e-10,
+                           abs.tol = 1e-10)
+  } else {
+    Q2 <- 0
+  }
   logQ <- log(Q0 + Q1$value + Q2$value)
   return(logQ)
 }

From dc20126499cf60ead09f560bbe9fdb182ee8e86e Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 21 Jul 2022 21:51:21 +0200
Subject: [PATCH 22/73] Documentation create_CS_version

---
 R/create_pars.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/create_pars.R b/R/create_pars.R
index 9e676d15..0a032c1b 100644
--- a/R/create_pars.R
+++ b/R/create_pars.R
@@ -152,6 +152,8 @@ create_trait_pars <- function(trans_rate,
 #' @param relaxed_par the parameter to relax (integrate over). Options are
 #' \code{"cladogenesis"}, \code{"extinction"}, \code{"carrying_capacity"},
 #' \code{"immigration"}, or \code{"anagenesis"}
+#' @param par_sd standard deviation of the parameter to relax
+#' @param par_upper_bound upper bound of the parameter to relax
 #' @return A list of two elements
 #' \itemize{
 #'   \item{model: the CS model to run, options are \code{1} for single rate

From bda01137b6fa0d54d9f801f7ef8b192e4459640c Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 21 Jul 2022 21:53:01 +0200
Subject: [PATCH 23/73] Update documentation

---
 man/create_CS_version.Rd | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/man/create_CS_version.Rd b/man/create_CS_version.Rd
index e86b380e..0409316d 100644
--- a/man/create_CS_version.Rd
+++ b/man/create_CS_version.Rd
@@ -19,6 +19,10 @@ model}
 \item{relaxed_par}{the parameter to relax (integrate over). Options are
 \code{"cladogenesis"}, \code{"extinction"}, \code{"carrying_capacity"},
 \code{"immigration"}, or \code{"anagenesis"}}
+
+\item{par_sd}{standard deviation of the parameter to relax}
+
+\item{par_upper_bound}{upper bound of the parameter to relax}
 }
 \value{
 A list of two elements

From 33912b6dfb93fe967929d161fbdf7b39ebbc97c7 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 21 Jul 2022 23:47:42 +0200
Subject: [PATCH 24/73] Different value of par_sd in test

---
 tests/testthat/test-DAISIE_ML4.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-DAISIE_ML4.R b/tests/testthat/test-DAISIE_ML4.R
index 7219812d..bbf9bf30 100644
--- a/tests/testthat/test-DAISIE_ML4.R
+++ b/tests/testthat/test-DAISIE_ML4.R
@@ -10,7 +10,7 @@ test_that("DAISIE_ML4 is silent and produces correct output", {
     methode = 'lsodes',
     CS_version = create_CS_version(model = 2,
                                    relaxed_par = "cladogenesis",
-                                   par_sd = 2,
+                                   par_sd = 0.001,
                                    par_upper_bound = Inf))
   expect_equal(2, 2)
 })

From 67050f11b1ddb399ef735c8f9578aedea146a569 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Fri, 22 Jul 2022 16:09:02 +0200
Subject: [PATCH 25/73] optimization cannot yield a higher value than the upper
 bound; loglik will then be -Inf

---
 R/DAISIE_ML4.R | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/R/DAISIE_ML4.R b/R/DAISIE_ML4.R
index ce6d50fd..4b75f572 100644
--- a/R/DAISIE_ML4.R
+++ b/R/DAISIE_ML4.R
@@ -20,7 +20,12 @@ DAISIE_loglik_all_choosepar4 <- function(trparsopt,
     pars1 <- trpars1 / (1 - trpars1)
     CS_version$par_sd <- pars1[6]
     pars1 <- pars1[-6]
-    if (min(pars1) < 0) {
+    pick <- which(c("cladogenesis",
+                    "extinction",
+                    "carrying_capacity",
+                    "immigration",
+                    "anagenesis") == CS_version$relaxed_par)
+    if (min(pars1) < 0 | pars1[pick] > CS_version$par_upper_bound) {
       loglik <- -Inf
     } else {
       loglik <- DAISIE::DAISIE_loglik_all(

From 367dd89867ffa5310c3a14896e8598489a523f54 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Fri, 22 Jul 2022 16:09:37 +0200
Subject: [PATCH 26/73] pars1 should only be changed for Q0

---
 R/DAISIE_loglik_integrate.R | 20 ++++++++++++++------
 1 file changed, 14 insertions(+), 6 deletions(-)

diff --git a/R/DAISIE_loglik_integrate.R b/R/DAISIE_loglik_integrate.R
index 17c1f3d3..32def81a 100644
--- a/R/DAISIE_loglik_integrate.R
+++ b/R/DAISIE_loglik_integrate.R
@@ -27,7 +27,6 @@ DAISIE_loglik_integrate <- function(
                   "immigration",
                   "anagenesis") == CS_version$relaxed_par)
   par_mean <- pars1[pick]
-
   integrated_loglik <- integral_peak(
     logfun = Vectorize(DAISIE_loglik_integrand,
                        vectorize.args = "DAISIE_par"),
@@ -243,9 +242,10 @@ integral_peak <- function(logfun,
     par_sd = par_sd)
   if (gamma_pars$shape < 1) {
     lower <- min(exp(xmax), 1E-3)
-    pars1[pick] <- lower / 2
+    pars1f <- pars1
+    pars1f[pick] <- lower / 2
     Q0 <- exp(DAISIE_loglik(
-      pars1 = pars1,
+      pars1 = pars1f,
       pars2 = pars2,
       brts = brts,
       stac = stac,
@@ -265,18 +265,26 @@ integral_peak <- function(logfun,
                          upper = exp(xmax),
                          subdivisions = 1000,
                          rel.tol = 1e-10,
-                         abs.tol = 1e-10)
+                         abs.tol = 1e-10)$value
   if(exp(xmax) < par_upper_bound) {
     Q2 <- stats::integrate(f = fun,
                            lower = exp(xmax),
                            upper = par_upper_bound,
                            subdivisions = 1000,
                            rel.tol = 1e-10,
-                           abs.tol = 1e-10)
+                           abs.tol = 1e-10)$value
   } else {
     Q2 <- 0
   }
-  logQ <- log(Q0 + Q1$value + Q2$value)
+  logQ <- log(Q0 + Q1 + Q2)
+  print(pars1)
+  print(brts)
+  print(Q0)
+  print(Q1)
+  print(Q2)
+  print(exp(xmax))
+  print(par_upper_bound)
+  print(logQ)
   return(logQ)
 }
 

From c1721252eb9c29c75eabd8848cda0718d9548b65 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Fri, 22 Jul 2022 16:10:13 +0200
Subject: [PATCH 27/73] Update test so that it runs better, but still slow and
 DLSODES warnings. These results from the finch data.

---
 tests/testthat/test-DAISIE_ML4.R | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-DAISIE_ML4.R b/tests/testthat/test-DAISIE_ML4.R
index bbf9bf30..9449ba2a 100644
--- a/tests/testthat/test-DAISIE_ML4.R
+++ b/tests/testthat/test-DAISIE_ML4.R
@@ -3,15 +3,16 @@ test_that("DAISIE_ML4 is silent and produces correct output", {
   utils::data(Galapagos_datalist)
   loglik <- DAISIE_ML4(
     datalist = Galapagos_datalist,
-    initparsopt = c(2.5, 0.2, 20, 0.009, 1.01, 0.001),
+    initparsopt = c(1.05, 0.36, 26.6, 0.0029, 0.73, 0.1),
     idparsopt = 1:6,
     parsfix = NULL,
     idparsfix = NULL,
     methode = 'lsodes',
+    optimmethod = 'simplex',
     CS_version = create_CS_version(model = 2,
-                                   relaxed_par = "cladogenesis",
-                                   par_sd = 0.001,
-                                   par_upper_bound = Inf))
+                                   relaxed_par = "extinction",
+                                   par_sd = 0.1,
+                                   par_upper_bound = 1))
   expect_equal(2, 2)
 })
 

From 34b30edcabd3ac2c04817c00b66b8431d084ebe5 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <j.w.l.lambert@rug.nl>
Date: Thu, 28 Jul 2022 12:20:35 +0200
Subject: [PATCH 28/73] removed prints from relaxed rate

---
 R/DAISIE_loglik_integrate.R | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/R/DAISIE_loglik_integrate.R b/R/DAISIE_loglik_integrate.R
index 32def81a..d8eb6baf 100644
--- a/R/DAISIE_loglik_integrate.R
+++ b/R/DAISIE_loglik_integrate.R
@@ -277,14 +277,6 @@ integral_peak <- function(logfun,
     Q2 <- 0
   }
   logQ <- log(Q0 + Q1 + Q2)
-  print(pars1)
-  print(brts)
-  print(Q0)
-  print(Q1)
-  print(Q2)
-  print(exp(xmax))
-  print(par_upper_bound)
-  print(logQ)
   return(logQ)
 }
 

From ced9b742ba996997b887df3a88e6634d30ed0bad Mon Sep 17 00:00:00 2001
From: Luis Valente <luis.valente@naturalis.nl>
Date: Fri, 19 Aug 2022 14:47:49 +0200
Subject: [PATCH 29/73] Removed assignation of new levels when DAISIE
 endemicity status is being changed (for example from Endemic to
 Endemic_Maxage if the colonisation time is older than the island age). This
 was causing problems because when endemicity status had to be changed more
 than once, it would give an error saying that the new level had already been
 created. I have tested this code with different datasets and it works well,
 and the data generated is compatible with the downstream ML and plotting
 functions.

---
 R/DAISIE_dataprep.R | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/R/DAISIE_dataprep.R b/R/DAISIE_dataprep.R
index fd5823d9..95a36060 100644
--- a/R/DAISIE_dataprep.R
+++ b/R/DAISIE_dataprep.R
@@ -186,13 +186,11 @@ DAISIE_dataprep = function(datatable,
     if(is.na(the_brts[1])){
       the_brts<-island_age
       if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
-        levels(datatable$Status) = append(levels(datatable$Status),"Endemic_MaxAge")
         datatable[i,"Status"] <-"Endemic_MaxAge"}
       if(datatable[i,"Status"] == "Non_endemic" | datatable[i,"Status"] == "Non_Endemic"
          | datatable[i,"Status"] == "NonEndemic" | datatable[i,"Status"] == "Nonendemic" |
          datatable[i,"Status"] == "nonendemic" | datatable[i,"Status"] == "non_endemic")
       {
-        levels(datatable$Status) = append(levels(datatable$Status),"Non_endemic_MaxAge")
         datatable[i,"Status"] <-"Non_endemic_MaxAge"}
     }
 
@@ -205,13 +203,11 @@ DAISIE_dataprep = function(datatable,
                     " is older than island age", sep = ""))
       }
       if(datatable[i,"Status"] == "Endemic" | datatable[i,"Status"] == "endemic" ){
-        levels(datatable$Status) = append(levels(datatable$Status),"Endemic_MaxAge")
         datatable[i,"Status"] <-"Endemic_MaxAge"}
       if(datatable[i,"Status"] == "Non_endemic" | datatable[i,"Status"] == "Non_Endemic"
          | datatable[i,"Status"] == "NonEndemic" | datatable[i,"Status"] == "Nonendemic" |
          datatable[i,"Status"] == "nonendemic" | datatable[i,"Status"] == "non_endemic"
       ) {
-        levels(datatable$Status) = append(levels(datatable$Status),"Non_endemic_MaxAge")
         datatable[i,"Status"] <-"Non_endemic_MaxAge"}
     }
 

From 9f800b175154178efb410704e42d7d2280f3d181 Mon Sep 17 00:00:00 2001
From: luislvalente <luislvalente@gmail.com>
Date: Tue, 23 Aug 2022 18:01:57 +0200
Subject: [PATCH 30/73] New function and documentation to count numbers of
 species and clade sizes.

---
 NAMESPACE                   |  1 +
 R/DAISIE_count_species.R    | 93 +++++++++++++++++++++++++++++++++++++
 R/default_params_doc.R      |  6 +++
 man/DAISIE_count_species.Rd | 57 +++++++++++++++++++++++
 man/default_params_doc.Rd   |  8 ++++
 5 files changed, 165 insertions(+)
 create mode 100644 R/DAISIE_count_species.R
 create mode 100644 man/DAISIE_count_species.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 49285890..3892ea8a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -14,6 +14,7 @@ export(DAISIE_SR_loglik_CS)
 export(DAISIE_SR_loglik_all)
 export(DAISIE_abm_factor)
 export(DAISIE_convertprobdist)
+export(DAISIE_count_species)
 export(DAISIE_dataprep)
 export(DAISIE_loglik_CS)
 export(DAISIE_loglik_IW)
diff --git a/R/DAISIE_count_species.R b/R/DAISIE_count_species.R
new file mode 100644
index 00000000..d1e923c9
--- /dev/null
+++ b/R/DAISIE_count_species.R
@@ -0,0 +1,93 @@
+#' @title Count number of species in DAISIE datalist or simulated data.
+#'
+#' @description Calculates various island diversity metrics from island datasets.
+#'
+#' @inheritParams default_params_doc
+#' @author Luis Valente
+#' @seealso \code{\link{DAISIE_dataprep}},
+#' \code{\link{DAISIE_plot_island}}
+#'
+#' @return The output is a list containing the following items:
+#' \item{clade_sizes_sorted}{ List showing the total number of species in each
+#' island clade (including missing species). Each item [[i]] on the list
+#' gives the sizes of all clades for a single island. If option
+#' sort_clade_sizes = T,
+#' the clade sizes for are
+#' sorted by increasing number of species. If option sort_clade_sizes = F
+#' the clade sizes are given in the same order as in the input datalist.}
+#' \item{size_largest_clade}{ The total number of species in the largest
+#' island clade
+#' for each island.}
+#' \item{mean_clade_size}{ Mean clade size (average of all island clades)}
+#' \item{number_colonisations}{ The total number of colonisations (clades) on
+#' each island.}
+#' \item{total_number_species}{ The total number of species on each island. These
+#' are the extant species at present, including missing species; in case of
+#' simulations, this is the number of species present on the island at the
+#' end of the
+#' simulation.}
+#' @examples
+#' # Run function with clade sizes in ascending order
+#' data("NewZealand_birds_datalist")
+#' DAISIE_count_species(NewZealand_birds_datalist)
+#'
+#' # Run function with clade sizes in the order they appear in the input data
+#' DAISIE_count_species(NewZealand_birds_datalist,
+#'                        clade_sizes_sorted=T)
+#' @export
+DAISIE_count_species<- function(islands,sort_clade_sizes=T){
+
+if(length(grep("not_present",islands))==1) {islands<-list(islands)}
+
+replicates<-length(islands)
+time<-islands[[1]][[1]]$island_age
+
+
+###### Calculate overall species richness and
+## colonization statistics across all islands
+number_colonists<-c()
+number_species<-c()
+size_largest_clade<-c()
+mean_clade_size<-c()
+clade_sizes<-c()
+
+for(i in 1:replicates){
+  the_island<-islands[[i]]
+  ncols<-length(the_island)-1
+  number_colonists<-append(number_colonists,ncols)
+
+  if(ncols==0){
+    number_species<-append(number_species,0)
+    size_largest_clade<-append(size_largest_clade,0)
+    mean_clade_size<-append(mean_clade_size,0)
+    clade_sizes<-append(clade_sizes,0)
+     }
+
+  if(ncols>0){
+    btimes<-c()
+    miss_specs<-c()
+
+    for(o in 2:length(the_island)){
+      btimes<-append(btimes,length(the_island[[o]]$branching_times)-1)
+      miss_specs<-append(miss_specs,the_island[[o]]$missing_species)
+    }
+    number_species<-append(number_species,sum(btimes,miss_specs))}
+    clade_sizes_dist<-btimes+miss_specs
+    size_largest_clade<-append(size_largest_clade,max(clade_sizes_dist))
+    mean_clade_size<-append(mean_clade_size,round(mean(clade_sizes_dist),2))
+    if(sort_clade_sizes==T) {clade_sizes[i]<-list(sort(clade_sizes_dist))} else{
+    clade_sizes[i]<-list(clade_sizes_dist)}
+
+}
+
+overall_results<-list(clade_sizes_sorted=clade_sizes,
+                      size_largest_clade=size_largest_clade,
+                      mean_clade_size=mean_clade_size,
+                      number_colonisations=number_colonists,
+                      total_number_species=number_species
+                      )
+
+if(sort_clade_sizes==F) {names(overall_results)[1]<-"clade_sizes"}
+
+return(overall_results)
+}
diff --git a/R/default_params_doc.R b/R/default_params_doc.R
index f8381be2..e205477a 100644
--- a/R/default_params_doc.R
+++ b/R/default_params_doc.R
@@ -469,6 +469,12 @@
 #' @param carr_cap Numeric carrying capacity
 #' @param immig_rate Numeric rate of immigration
 #' @param ana_rate Numeric rate of anagenesis
+#' @param islands Island datalist or simulated data in DAISIE datalist format.
+#' Can be a single island (empirical data) generated with DAISIE_dataprep or
+#' DAISIEprep. Can also be simulated data generated with DAISIE_sim function.
+#' @param sort_clade_sizes Default sort_clade_sizes=T outputs clade sizes
+#' sorted in ascending order of number of species. sort_clade_sizes=F outputs
+#' clade sizes in the same order as they appear in the input datalist.
 #'
 #'
 #' @return Nothing
diff --git a/man/DAISIE_count_species.Rd b/man/DAISIE_count_species.Rd
new file mode 100644
index 00000000..c3cde9bc
--- /dev/null
+++ b/man/DAISIE_count_species.Rd
@@ -0,0 +1,57 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/DAISIE_count_species.R
+\name{DAISIE_count_species}
+\alias{DAISIE_count_species}
+\title{Count number of species in DAISIE datalist or simulated data.}
+\usage{
+DAISIE_count_species(islands, sort_clade_sizes = T)
+}
+\arguments{
+\item{islands}{Island datalist or simulated data in DAISIE datalist format.
+Can be a single island (empirical data) generated with DAISIE_dataprep or
+DAISIEprep. Can also be simulated data generated with DAISIE_sim function.}
+
+\item{sort_clade_sizes}{Default sort_clade_sizes=T outputs clade sizes
+sorted in ascending order of number of species. sort_clade_sizes=F outputs
+clade sizes in the same order as they appear in the input datalist.}
+}
+\value{
+The output is a list containing the following items:
+\item{clade_sizes_sorted}{ List showing the total number of species in each
+island clade (including missing species). Each item [[i]] on the list
+gives the sizes of all clades for a single island. If option
+sort_clade_sizes = T,
+the clade sizes for are
+sorted by increasing number of species. If option sort_clade_sizes = F
+the clade sizes are given in the same order as in the input datalist.}
+\item{size_largest_clade}{ The total number of species in the largest
+island clade
+for each island.}
+\item{mean_clade_size}{ Mean clade size (average of all island clades)}
+\item{number_colonisations}{ The total number of colonisations (clades) on
+each island.}
+\item{total_number_species}{ The total number of species on each island. These
+are the extant species at present, including missing species; in case of
+simulations, this is the number of species present on the island at the
+end of the
+simulation.}
+}
+\description{
+Calculates various island diversity metrics from island datasets.
+}
+\examples{
+# Run function with clade sizes in ascending order
+data("NewZealand_birds_datalist")
+DAISIE_count_species(NewZealand_birds_datalist)
+
+# Run function with clade sizes in the order they appear in the input data
+DAISIE_count_species(NewZealand_birds_datalist,
+                       clade_sizes_sorted=T)
+}
+\seealso{
+\code{\link{DAISIE_dataprep}},
+\code{\link{DAISIE_plot_island}}
+}
+\author{
+Luis Valente
+}
diff --git a/man/default_params_doc.Rd b/man/default_params_doc.Rd
index 1cd4d25c..3c74d4a7 100644
--- a/man/default_params_doc.Rd
+++ b/man/default_params_doc.Rd
@@ -726,6 +726,14 @@ relaxed-rate model}
 \item{immig_rate}{Numeric rate of immigration}
 
 \item{ana_rate}{Numeric rate of anagenesis}
+
+\item{islands}{Island datalist or simulated data in DAISIE datalist format.
+Can be a single island (empirical data) generated with DAISIE_dataprep or
+DAISIEprep. Can also be simulated data generated with DAISIE_sim function.}
+
+\item{sort_clade_sizes}{Default sort_clade_sizes=T outputs clade sizes
+sorted in ascending order of number of species. sort_clade_sizes=F outputs
+clade sizes in the same order as they appear in the input datalist.}
 }
 \value{
 Nothing

From 19c36739168b0fddc9a378e68e23e0337c39d8c9 Mon Sep 17 00:00:00 2001
From: Yangshen0325 <89144088+Yangshen0325@users.noreply.github.com>
Date: Mon, 12 Sep 2022 17:15:19 +0200
Subject: [PATCH 31/73] Fix https://github.com/rsetienne/DAISIE/issues/147

Fixes https://github.com/rsetienne/DAISIE/issues/147
Correctly compute number of species at present in IW simulations
---
 R/DAISIE_sim_cr_iw.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/DAISIE_sim_cr_iw.R b/R/DAISIE_sim_cr_iw.R
index 8090f2f8..d2db9bad 100644
--- a/R/DAISIE_sim_cr_iw.R
+++ b/R/DAISIE_sim_cr_iw.R
@@ -30,7 +30,8 @@ DAISIE_sim_cr_iw <- function(total_time,
         hyper_pars = hyper_pars,
         area_pars = area_pars
       )
-      stac_vec <- unlist(island_replicates)[which(names(unlist(island_replicates)) == "taxon_list.stac")]
+      temp_island_replicates <- island_replicates[[rep]]
+      stac_vec <- unlist(temp_island_replicates)[which(names(unlist(temp_island_replicates)) == "taxon_list.stac")]
       present <- which(stac_vec != 0)
       number_present <- length(present)
     }

From dbd0a9eff780e235021af7c43307b7cedb0f4487 Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Tue, 13 Sep 2022 13:22:07 +0200
Subject: [PATCH 32/73] Fix example, style

---
 R/DAISIE_count_species.R    | 108 +++++++++++++++++++-----------------
 man/DAISIE_count_species.Rd |  14 +++--
 2 files changed, 66 insertions(+), 56 deletions(-)

diff --git a/R/DAISIE_count_species.R b/R/DAISIE_count_species.R
index d1e923c9..b81c9e0a 100644
--- a/R/DAISIE_count_species.R
+++ b/R/DAISIE_count_species.R
@@ -27,67 +27,75 @@
 #' end of the
 #' simulation.}
 #' @examples
-#' # Run function with clade sizes in ascending order
+#' # Run function with clade sizes in the order they appear in the input data
 #' data("NewZealand_birds_datalist")
-#' DAISIE_count_species(NewZealand_birds_datalist)
+#' species_count <- DAISIE_count_species(NewZealand_birds_datalist)
 #'
-#' # Run function with clade sizes in the order they appear in the input data
-#' DAISIE_count_species(NewZealand_birds_datalist,
-#'                        clade_sizes_sorted=T)
+#' # Run function with clade sizes in ascending order
+#' species_count_sorted <- DAISIE_count_species(
+#'   NewZealand_birds_datalist,
+#'   sort_clade_sizes = TRUE
+#' )
 #' @export
-DAISIE_count_species<- function(islands,sort_clade_sizes=T){
-
-if(length(grep("not_present",islands))==1) {islands<-list(islands)}
+DAISIE_count_species <- function(islands, sort_clade_sizes = TRUE) {
+  if (length(grep("not_present", islands)) == 1) {
+    islands <- list(islands)
+  }
 
-replicates<-length(islands)
-time<-islands[[1]][[1]]$island_age
+  replicates <- length(islands)
+  time <- islands[[1]][[1]]$island_age
 
+  ###### Calculate overall species richness and
+  ## colonization statistics across all islands
+  number_colonists <- c()
+  number_species <- c()
+  size_largest_clade <- c()
+  mean_clade_size <- c()
+  clade_sizes <- c()
 
-###### Calculate overall species richness and
-## colonization statistics across all islands
-number_colonists<-c()
-number_species<-c()
-size_largest_clade<-c()
-mean_clade_size<-c()
-clade_sizes<-c()
+  for (i in 1:replicates) {
+    the_island <- islands[[i]]
+    ncols <- length(the_island) - 1
+    number_colonists <- append(number_colonists, ncols)
 
-for(i in 1:replicates){
-  the_island<-islands[[i]]
-  ncols<-length(the_island)-1
-  number_colonists<-append(number_colonists,ncols)
-
-  if(ncols==0){
-    number_species<-append(number_species,0)
-    size_largest_clade<-append(size_largest_clade,0)
-    mean_clade_size<-append(mean_clade_size,0)
-    clade_sizes<-append(clade_sizes,0)
-     }
+    if (ncols == 0) {
+      number_species <- append(number_species, 0)
+      size_largest_clade <- append(size_largest_clade, 0)
+      mean_clade_size <- append(mean_clade_size, 0)
+      clade_sizes <- append(clade_sizes, 0)
+    }
 
-  if(ncols>0){
-    btimes<-c()
-    miss_specs<-c()
+    if (ncols > 0) {
+      btimes <- c()
+      miss_specs <- c()
 
-    for(o in 2:length(the_island)){
-      btimes<-append(btimes,length(the_island[[o]]$branching_times)-1)
-      miss_specs<-append(miss_specs,the_island[[o]]$missing_species)
+      for (o in 2:length(the_island)) {
+        btimes <- append(btimes, length(the_island[[o]]$branching_times) - 1)
+        miss_specs <- append(miss_specs, the_island[[o]]$missing_species)
+      }
+      number_species <- append(number_species, sum(btimes, miss_specs))
     }
-    number_species<-append(number_species,sum(btimes,miss_specs))}
-    clade_sizes_dist<-btimes+miss_specs
-    size_largest_clade<-append(size_largest_clade,max(clade_sizes_dist))
-    mean_clade_size<-append(mean_clade_size,round(mean(clade_sizes_dist),2))
-    if(sort_clade_sizes==T) {clade_sizes[i]<-list(sort(clade_sizes_dist))} else{
-    clade_sizes[i]<-list(clade_sizes_dist)}
-
-}
+    clade_sizes_dist <- btimes + miss_specs
+    size_largest_clade <- append(size_largest_clade, max(clade_sizes_dist))
+    mean_clade_size <- append(mean_clade_size, round(mean(clade_sizes_dist), 2))
+    if (isTRUE(sort_clade_sizes)) {
+      clade_sizes[i] <- list(sort(clade_sizes_dist))
+    } else {
+      clade_sizes[i] <- list(clade_sizes_dist)
+    }
+  }
 
-overall_results<-list(clade_sizes_sorted=clade_sizes,
-                      size_largest_clade=size_largest_clade,
-                      mean_clade_size=mean_clade_size,
-                      number_colonisations=number_colonists,
-                      total_number_species=number_species
-                      )
+  overall_results <- list(
+    clade_sizes_sorted = clade_sizes,
+    size_largest_clade = size_largest_clade,
+    mean_clade_size = mean_clade_size,
+    number_colonisations = number_colonists,
+    total_number_species = number_species
+  )
 
-if(sort_clade_sizes==F) {names(overall_results)[1]<-"clade_sizes"}
+  if (sort_clade_sizes == F) {
+    names(overall_results)[1] <- "clade_sizes"
+  }
 
-return(overall_results)
+  return(overall_results)
 }
diff --git a/man/DAISIE_count_species.Rd b/man/DAISIE_count_species.Rd
index c3cde9bc..c522d1eb 100644
--- a/man/DAISIE_count_species.Rd
+++ b/man/DAISIE_count_species.Rd
@@ -4,7 +4,7 @@
 \alias{DAISIE_count_species}
 \title{Count number of species in DAISIE datalist or simulated data.}
 \usage{
-DAISIE_count_species(islands, sort_clade_sizes = T)
+DAISIE_count_species(islands, sort_clade_sizes = TRUE)
 }
 \arguments{
 \item{islands}{Island datalist or simulated data in DAISIE datalist format.
@@ -40,13 +40,15 @@ simulation.}
 Calculates various island diversity metrics from island datasets.
 }
 \examples{
-# Run function with clade sizes in ascending order
+# Run function with clade sizes in the order they appear in the input data
 data("NewZealand_birds_datalist")
-DAISIE_count_species(NewZealand_birds_datalist)
+species_count <- DAISIE_count_species(NewZealand_birds_datalist)
 
-# Run function with clade sizes in the order they appear in the input data
-DAISIE_count_species(NewZealand_birds_datalist,
-                       clade_sizes_sorted=T)
+# Run function with clade sizes in ascending order
+species_count_sorted <- DAISIE_count_species(
+  NewZealand_birds_datalist,
+  sort_clade_sizes = TRUE
+)
 }
 \seealso{
 \code{\link{DAISIE_dataprep}},

From b19445877bdcd6e7ee02a682938085ae761541ec Mon Sep 17 00:00:00 2001
From: xieshu95 <xieshu95@gmail.com>
Date: Wed, 30 Nov 2022 09:39:01 +0100
Subject: [PATCH 33/73] fix test

---
 tests/testthat/test-DAISIE_format_IW.R | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/tests/testthat/test-DAISIE_format_IW.R b/tests/testthat/test-DAISIE_format_IW.R
index b2506e96..246d0622 100644
--- a/tests/testthat/test-DAISIE_format_IW.R
+++ b/tests/testthat/test-DAISIE_format_IW.R
@@ -540,24 +540,24 @@ test_that("silent when species with two trait states with
             brts_table <- matrix(ncol = 5, nrow = 4)
             colnames(brts_table) <- c("brt", "clade", "event", "endemic", "col")
             brts_table[1, ] <- c(5.00000000000000, 0, 0, NA, NA)
-            brts_table[2, ] <- c(3.10634202528338, 1, 1, 1, NA)
-            brts_table[3, ] <- c(1.52330128016821, 2, 1, 1, NA)
-            brts_table[4, ] <- c(1.28012784155125, 2, 2, 1, NA)
+            brts_table[2, ] <- c(3.10261367452990, 1, 1, 1, NA)
+            brts_table[3, ] <- c(1.50562999775257, 2, 1, 1, NA)
+            brts_table[4, ] <- c(1.26245655913561, 2, 2, 1, NA)
             expected_IW_format[[1]][[1]] <- list(island_age = 5,
                                                  not_present = 13,
                                                  stt_all = stt_all,
                                                  brts_table = brts_table)
 
             expected_IW_format[[1]][[2]] <- list(
-              branching_times = c(5.00000000000000,
-                                  3.10634202528338),
+              branching_times = c(5.0000000000000,
+                                  3.1026136745299),
               stac = 2,
               missing_species = 0
             )
             expected_IW_format[[1]][[3]] <- list(
               branching_times = c(5.00000000000000,
-                                  1.52330128016821,
-                                  1.28012784155125),
+                                  1.50562999775257,
+                                  1.26245655913561),
               stac = 2,
               missing_species = 0
             )

From da0d4c168afa8d11db79b223b5de9197be2964e0 Mon Sep 17 00:00:00 2001
From: xieshu95 <xieshu95@gmail.com>
Date: Wed, 30 Nov 2022 23:12:54 +0100
Subject: [PATCH 34/73] fix trait documents

---
 NAMESPACE                      |   2 +
 R/DAISIE_sim_trait_dep.R       |  76 +++++-------
 R/DAISIE_sim_trait_dep_2K.R    |  77 ++++++-------
 man/DAISIE_sim_trait_dep.Rd    |  80 +++++--------
 man/DAISIE_sim_trait_dep_2K.Rd | 205 +++++++++++++++++++++++++++++++++
 man/create_trait_pars_2K.Rd    |  40 +++++++
 6 files changed, 343 insertions(+), 137 deletions(-)
 create mode 100644 man/DAISIE_sim_trait_dep_2K.Rd
 create mode 100644 man/create_trait_pars_2K.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 3892ea8a..3cf5beee 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -33,12 +33,14 @@ export(DAISIE_sim_cr_shift)
 export(DAISIE_sim_relaxed_rate)
 export(DAISIE_sim_time_dep)
 export(DAISIE_sim_trait_dep)
+export(DAISIE_sim_trait_dep_2K)
 export(are_area_pars)
 export(create_CS_version)
 export(create_area_pars)
 export(create_hyper_pars)
 export(create_pars)
 export(create_trait_pars)
+export(create_trait_pars_2K)
 export(daisie_odeint_cs)
 export(daisie_odeint_iw)
 import(Rcpp)
diff --git a/R/DAISIE_sim_trait_dep.R b/R/DAISIE_sim_trait_dep.R
index 0af0077b..4beeb503 100644
--- a/R/DAISIE_sim_trait_dep.R
+++ b/R/DAISIE_sim_trait_dep.R
@@ -1,53 +1,41 @@
-#' @title Simulate islands with given parameters.
+#' @title Simulate islands with given trait-dependent parameters.
 #' @description This function simulates islands with given cladogenesis,
-#' extinction, Kprime, immigration and anagenesis parameters. If a single
-#' parameter set is provided (5 parameters) it simulates islands where all
-#' species have the same macro-evolutionary process. If two paramater sets
-#' (10 parameters) are provided, it simulates islands where two different
-#' macro-evolutionary processes operate, one applying to type 1 species and
-#' other to type 2 species. If two parameter sets and a time shift (11
-#' parameters) are provided, it simulates islands where at the given time
-#' a shift between the parameter sets will occur.
+#' extinction, K, immigration and anagenesis parameters for binary states.
 #'
 #' Returns R list object that contains the simulated islands
 #'
 #' @inheritParams default_params_doc
 #'
-#' @return Each simulated dataset is an element of the list, which can be
-#' called using [[x]]. For example if the object is called island_replicates,
-#' the last replicates is a list in itself. The first (e.g.
-#' \code{island_replicates[[x]][[1]]}) element of that list has the following
-#' components: \cr \code{$island_age} - the island age \cr Then, depending on
-#' whether a distinction between types is made, we have:\cr \code{$not_present}
-#' - the number of mainland lineages that are not present on the island \cr
-#' or:\cr \code{$not_present_type1} - the number of mainland lineages of type 1
-#' that are not present on the island \cr \code{$not_present_type2} - the
-#' number of mainland lineages of type 2 that are not present on the island \cr
-#' \code{$stt_all} - STT table for all species on the island (nI - number of
-#' non-endemic species; nA - number of anagenetic species, nC - number of
-#' cladogenetic species, present - number of independent colonisations present
-#' )\cr \code{$stt_stt_type1} - STT table for type 1 species on the island -
-#' only if 2 types of species were simulated (nI - number of non-endemic
-#' species; nA - number of anagenetic species, nC - number of cladogenetic
-#' species, present - number of independent colonisations present )\cr
-#' \code{$stt_stt_type2} - STT table for type 2 species on the island - only if
-#' 2 types of species were simulated (nI - number of non-endemic species; nA -
-#' number of anagenetic species, nC - number of cladogenetic species, present -
-#' number of independent colonisations present )\cr \code{$brts_table} - Only
-#' for simulations under 'IW'. Table containing information on order of events
-#' in the data, for use in maximum likelihood optimization.)\cr
-#'
-#' The subsequent elements of the list each contain information on a single
-#' colonist lineage on the island and has 4 components:\cr
-#' \code{$branching_times} - island age and stem age of the population/species
-#' in the case of Non-endemic, Non-endemic_MaxAge and Endemic anagenetic
-#' species. For cladogenetic species these should be island age and branching
-#' times of the radiation including the stem age of the radiation.\cr
-#' \code{$stac} - the status of the colonist \cr * Non_endemic_MaxAge: 1 \cr *
-#' ndemic: 2 \cr * Endemic&Non_Endemic: 3 \cr * Non_endemic: 4 \cr
-#' \code{$missing_species} - number of island species that were not sampled for
-#' particular clade (only applicable for endemic clades) \cr \code{$type_1or2}
-#' - whether the colonist belongs to type 1 or type 2 \cr
+#' @return
+#' A list. The highest level of the least corresponds to each individual
+#' replciate. The first element of each replicate is composed of island
+#' information containing:
+#' \itemize{
+#'   \item{\code{$island_age}: A numeric with the island age.}
+#'   \item{\code{$not_present}: A numeric with the number of mainland lineages
+#'   that are not present on the island.}
+#'   \item{\code{$stt_all}: STT table for all species on the island
+#'     (nI - number of non-endemic species; nA - number of anagenetic species,
+#'     nC - number of cladogenetic species, present - number of independent
+#'     colonisations present)}
+#'   \item{\code{$brts_table}: Only for simulations under \code{"IW"}. Table
+#' containing information on order of events in the data, for use in maximum
+#' likelihood optimization.).}
+#' }
+#' The subsequent elements of the list pertaining to each replcate contain
+#' information on a single colonist lineage on the island and have 4 components:
+#' \itemize{
+#'   \item{\code{$branching_times}: island age and stem age of the
+#'     population/species in the case of Non-endemic, Non-endemic_MaxAge and
+#'     Endemic anagenetic species. For cladogenetic species these should
+#'     be island age and branching times of the radiation including the
+#'     stem age of the radiation.}
+#'   \item{\code{$stac}: An integer ranging from 1 to 4
+#'   indicating the status of the colonist:}
+#' \item{\code{$missing_species}: number of island species that were
+#' not sampled for particular clade (only applicable for endemic clades)}
+#' \item{\code{$type_1or2}: whether the colonist belongs to type 1 or type 2}
+#' }
 #' @author Luis Valente and Albert Phillimore
 #' @seealso \code{\link{DAISIE_format_CS}} \code{\link{DAISIE_plot_sims}}
 #' @references Valente, L.M., A.B. Phillimore and R.S. Etienne (2015).
diff --git a/R/DAISIE_sim_trait_dep_2K.R b/R/DAISIE_sim_trait_dep_2K.R
index 021cd32e..5496884e 100644
--- a/R/DAISIE_sim_trait_dep_2K.R
+++ b/R/DAISIE_sim_trait_dep_2K.R
@@ -1,53 +1,42 @@
-#' @title Simulate islands with given parameters.
+#' @title Simulate islands with given trait-dependent parameters.
 #' @description This function simulates islands with given cladogenesis,
-#' extinction, Kprime, immigration and anagenesis parameters. If a single
-#' parameter set is provided (5 parameters) it simulates islands where all
-#' species have the same macro-evolutionary process. If two paramater sets
-#' (10 parameters) are provided, it simulates islands where two different
-#' macro-evolutionary processes operate, one applying to type 1 species and
-#' other to type 2 species. If two parameter sets and a time shift (11
-#' parameters) are provided, it simulates islands where at the given time
-#' a shift between the parameter sets will occur.
+#' extinction, K, immigration and anagenesis parameters. In this version,
+#' rates and K are both trait-dependent.
 #'
 #' Returns R list object that contains the simulated islands
 #'
 #' @inheritParams default_params_doc
 #'
-#' @return Each simulated dataset is an element of the list, which can be
-#' called using [[x]]. For example if the object is called island_replicates,
-#' the last replicates is a list in itself. The first (e.g.
-#' \code{island_replicates[[x]][[1]]}) element of that list has the following
-#' components: \cr \code{$island_age} - the island age \cr Then, depending on
-#' whether a distinction between types is made, we have:\cr \code{$not_present}
-#' - the number of mainland lineages that are not present on the island \cr
-#' or:\cr \code{$not_present_type1} - the number of mainland lineages of type 1
-#' that are not present on the island \cr \code{$not_present_type2} - the
-#' number of mainland lineages of type 2 that are not present on the island \cr
-#' \code{$stt_all} - STT table for all species on the island (nI - number of
-#' non-endemic species; nA - number of anagenetic species, nC - number of
-#' cladogenetic species, present - number of independent colonisations present
-#' )\cr \code{$stt_stt_type1} - STT table for type 1 species on the island -
-#' only if 2 types of species were simulated (nI - number of non-endemic
-#' species; nA - number of anagenetic species, nC - number of cladogenetic
-#' species, present - number of independent colonisations present )\cr
-#' \code{$stt_stt_type2} - STT table for type 2 species on the island - only if
-#' 2 types of species were simulated (nI - number of non-endemic species; nA -
-#' number of anagenetic species, nC - number of cladogenetic species, present -
-#' number of independent colonisations present )\cr \code{$brts_table} - Only
-#' for simulations under 'IW'. Table containing information on order of events
-#' in the data, for use in maximum likelihood optimization.)\cr
-#'
-#' The subsequent elements of the list each contain information on a single
-#' colonist lineage on the island and has 4 components:\cr
-#' \code{$branching_times} - island age and stem age of the population/species
-#' in the case of Non-endemic, Non-endemic_MaxAge and Endemic anagenetic
-#' species. For cladogenetic species these should be island age and branching
-#' times of the radiation including the stem age of the radiation.\cr
-#' \code{$stac} - the status of the colonist \cr * Non_endemic_MaxAge: 1 \cr *
-#' ndemic: 2 \cr * Endemic&Non_Endemic: 3 \cr * Non_endemic: 4 \cr
-#' \code{$missing_species} - number of island species that were not sampled for
-#' particular clade (only applicable for endemic clades) \cr \code{$type_1or2}
-#' - whether the colonist belongs to type 1 or type 2 \cr
+#' @return
+#' A list. The highest level of the least corresponds to each individual
+#' replciate. The first element of each replicate is composed of island
+#' information containing:
+#' \itemize{
+#'   \item{\code{$island_age}: A numeric with the island age.}
+#'   \item{\code{$not_present}: A numeric with the number of mainland lineages
+#'   that are not present on the island.}
+#'   \item{\code{$stt_all}: STT table for all species on the island
+#'     (nI - number of non-endemic species; nA - number of anagenetic species,
+#'     nC - number of cladogenetic species, present - number of independent
+#'     colonisations present)}
+#'   \item{\code{$brts_table}: Only for simulations under \code{"IW"}. Table
+#' containing information on order of events in the data, for use in maximum
+#' likelihood optimization.).}
+#' }
+#' The subsequent elements of the list pertaining to each replcate contain
+#' information on a single colonist lineage on the island and have 4 components:
+#' \itemize{
+#'   \item{\code{$branching_times}: island age and stem age of the
+#'     population/species in the case of Non-endemic, Non-endemic_MaxAge and
+#'     Endemic anagenetic species. For cladogenetic species these should
+#'     be island age and branching times of the radiation including the
+#'     stem age of the radiation.}
+#'   \item{\code{$stac}: An integer ranging from 1 to 4
+#'   indicating the status of the colonist:}
+#' \item{\code{$missing_species}: number of island species that were
+#' not sampled for particular clade (only applicable for endemic clades)}
+#' \item{\code{$type_1or2}: whether the colonist belongs to type 1 or type 2}
+#' }
 #' @author Luis Valente and Albert Phillimore
 #' @seealso \code{\link{DAISIE_format_CS}} \code{\link{DAISIE_plot_sims}}
 #' @references Valente, L.M., A.B. Phillimore and R.S. Etienne (2015).
diff --git a/man/DAISIE_sim_trait_dep.Rd b/man/DAISIE_sim_trait_dep.Rd
index fada74dc..6e082fe5 100644
--- a/man/DAISIE_sim_trait_dep.Rd
+++ b/man/DAISIE_sim_trait_dep.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/DAISIE_sim_trait_dep.R
 \name{DAISIE_sim_trait_dep}
 \alias{DAISIE_sim_trait_dep}
-\title{Simulate islands with given parameters.}
+\title{Simulate islands with given trait-dependent parameters.}
 \usage{
 DAISIE_sim_trait_dep(
   time,
@@ -10,7 +10,6 @@ DAISIE_sim_trait_dep(
   pars,
   replicates,
   divdepmodel = "CS",
-  num_guilds = NULL,
   sample_freq = 25,
   plot_sims = TRUE,
   island_ontogeny = "const",
@@ -71,10 +70,6 @@ carrying capacity, where diversity-dependence operates within and among
 clades. Option divdepmodel = 'GW' runs a model with diversity-dependence
 operates within a guild.}
 
-\item{num_guilds}{The number of guilds on the mainland. The number of
-mainland species is divided by the number of guilds when
-\code{divdepmodel = "GW"}}
-
 \item{sample_freq}{Numeric specifing the number of units times should be
 divided by for plotting purposes. Larger values will lead to plots with
 higher resolution, but will also run slower.}
@@ -156,52 +151,39 @@ means also intermediate progress during loglikelihood computation is shown.}
 \item{...}{Any arguments to pass on to plotting functions.}
 }
 \value{
-Each simulated dataset is an element of the list, which can be
-called using [[x]]. For example if the object is called island_replicates,
-the last replicates is a list in itself. The first (e.g.
-\code{island_replicates[[x]][[1]]}) element of that list has the following
-components: \cr \code{$island_age} - the island age \cr Then, depending on
-whether a distinction between types is made, we have:\cr \code{$not_present}
-- the number of mainland lineages that are not present on the island \cr
-or:\cr \code{$not_present_type1} - the number of mainland lineages of type 1
-that are not present on the island \cr \code{$not_present_type2} - the
-number of mainland lineages of type 2 that are not present on the island \cr
-\code{$stt_all} - STT table for all species on the island (nI - number of
-non-endemic species; nA - number of anagenetic species, nC - number of
-cladogenetic species, present - number of independent colonisations present
-)\cr \code{$stt_stt_type1} - STT table for type 1 species on the island -
-only if 2 types of species were simulated (nI - number of non-endemic
-species; nA - number of anagenetic species, nC - number of cladogenetic
-species, present - number of independent colonisations present )\cr
-\code{$stt_stt_type2} - STT table for type 2 species on the island - only if
-2 types of species were simulated (nI - number of non-endemic species; nA -
-number of anagenetic species, nC - number of cladogenetic species, present -
-number of independent colonisations present )\cr \code{$brts_table} - Only
-for simulations under 'IW'. Table containing information on order of events
-in the data, for use in maximum likelihood optimization.)\cr
-
-The subsequent elements of the list each contain information on a single
-colonist lineage on the island and has 4 components:\cr
-\code{$branching_times} - island age and stem age of the population/species
-in the case of Non-endemic, Non-endemic_MaxAge and Endemic anagenetic
-species. For cladogenetic species these should be island age and branching
-times of the radiation including the stem age of the radiation.\cr
-\code{$stac} - the status of the colonist \cr * Non_endemic_MaxAge: 1 \cr *
-ndemic: 2 \cr * Endemic&Non_Endemic: 3 \cr * Non_endemic: 4 \cr
-\code{$missing_species} - number of island species that were not sampled for
-particular clade (only applicable for endemic clades) \cr \code{$type_1or2}
-- whether the colonist belongs to type 1 or type 2 \cr
+A list. The highest level of the least corresponds to each individual
+replciate. The first element of each replicate is composed of island
+information containing:
+\itemize{
+  \item{\code{$island_age}: A numeric with the island age.}
+  \item{\code{$not_present}: A numeric with the number of mainland lineages
+  that are not present on the island.}
+  \item{\code{$stt_all}: STT table for all species on the island
+    (nI - number of non-endemic species; nA - number of anagenetic species,
+    nC - number of cladogenetic species, present - number of independent
+    colonisations present)}
+  \item{\code{$brts_table}: Only for simulations under \code{"IW"}. Table
+containing information on order of events in the data, for use in maximum
+likelihood optimization.).}
+}
+The subsequent elements of the list pertaining to each replcate contain
+information on a single colonist lineage on the island and have 4 components:
+\itemize{
+  \item{\code{$branching_times}: island age and stem age of the
+    population/species in the case of Non-endemic, Non-endemic_MaxAge and
+    Endemic anagenetic species. For cladogenetic species these should
+    be island age and branching times of the radiation including the
+    stem age of the radiation.}
+  \item{\code{$stac}: An integer ranging from 1 to 4
+  indicating the status of the colonist:}
+\item{\code{$missing_species}: number of island species that were
+not sampled for particular clade (only applicable for endemic clades)}
+\item{\code{$type_1or2}: whether the colonist belongs to type 1 or type 2}
+}
 }
 \description{
 This function simulates islands with given cladogenesis,
-extinction, Kprime, immigration and anagenesis parameters. If a single
-parameter set is provided (5 parameters) it simulates islands where all
-species have the same macro-evolutionary process. If two paramater sets
-(10 parameters) are provided, it simulates islands where two different
-macro-evolutionary processes operate, one applying to type 1 species and
-other to type 2 species. If two parameter sets and a time shift (11
-parameters) are provided, it simulates islands where at the given time
-a shift between the parameter sets will occur.
+extinction, K, immigration and anagenesis parameters for binary states.
 
 Returns R list object that contains the simulated islands
 }
diff --git a/man/DAISIE_sim_trait_dep_2K.Rd b/man/DAISIE_sim_trait_dep_2K.Rd
new file mode 100644
index 00000000..414661a5
--- /dev/null
+++ b/man/DAISIE_sim_trait_dep_2K.Rd
@@ -0,0 +1,205 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/DAISIE_sim_trait_dep_2K.R
+\name{DAISIE_sim_trait_dep_2K}
+\alias{DAISIE_sim_trait_dep_2K}
+\title{Simulate islands with given trait-dependent parameters.}
+\usage{
+DAISIE_sim_trait_dep_2K(
+  time,
+  M,
+  pars,
+  replicates,
+  divdepmodel = "CS",
+  sample_freq = 25,
+  plot_sims = TRUE,
+  island_ontogeny = "const",
+  sea_level = "const",
+  hyper_pars = create_hyper_pars(d = 0, x = 0),
+  area_pars = DAISIE::create_area_pars(max_area = 1, current_area = 1,
+    proportional_peak_t = 0, total_island_age = 0, sea_level_amplitude = 0,
+    sea_level_frequency = 0, island_gradient_angle = 0),
+  extcutoff = 1000,
+  cond = 0,
+  verbose = TRUE,
+  trait_pars = NULL,
+  ...
+)
+}
+\arguments{
+\item{time}{Numeric defining the length of the simulation in time units.
+For example, if an island is known to be 4 million years old, setting
+time = 4 will simulate the entire life span of the island; setting time = 2
+will stop the simulation at the mid-life of the island.}
+
+\item{M}{Numeric defining the size of mainland pool, i.e. the number of
+species that can potentially colonize the island.}
+
+\item{pars}{A numeric vector containing the model parameters:
+\itemize{
+  \item{\code{pars[1]}: lambda^c (cladogenesis rate)}
+  \item{\code{pars[2]}: mu (extinction rate)}
+  \item{\code{pars[3]}: K (carrying capacity), set K=Inf for diversity
+  independence.}
+  \item{\code{pars[4]}: gamma (immigration rate)}
+  \item{\code{pars[5]}: lambda^a (anagenesis rate)}
+  \item{\code{pars[6]}: lambda^c (cladogenesis rate) for either type 2 species
+  or rate set 2 in rate shift model}
+  \item{\code{pars[7]}: mu (extinction rate) for either type 2 species or rate
+  set 2 in rate shift model}
+  \item{\code{pars[8]}: K (carrying capacity) for either type 2 species or rate
+  set 2 in rate shift model, set K=Inf for diversity independence.}
+  \item{\code{pars[9]}: gamma (immigration rate) for either type 2 species
+  or rate set 2 in rate shift model}
+  \item{\code{pars[10]}: lambda^a (anagenesis rate) for either type 2
+  species or rate set 2 in rate shift model}
+}
+Elements 6:10 are required only when type 2 species are included
+or in the rate shift model. For \code{\link{DAISIE_sim_relaxed_rate}()}
+\code{pars[6]} is the standard deviation of the gamma distribution for the
+relaxed parameter and the parameter chosen by the \code{relaxed_par}
+argument is the mean of the gamma distribution for the relaxed parameter.}
+
+\item{replicates}{Integer specifying number of island replicates to be
+simulated.}
+
+\item{divdepmodel}{Option divdepmodel = 'CS' runs a model with clade-specific
+carrying capacity, where diversity-dependence operates only within single
+clades, i.e. only among species originating from the same mainland
+colonist. Option divdepmodel = 'IW' runs a model with island-wide
+carrying capacity, where diversity-dependence operates within and among
+clades. Option divdepmodel = 'GW' runs a model with diversity-dependence
+operates within a guild.}
+
+\item{sample_freq}{Numeric specifing the number of units times should be
+divided by for plotting purposes. Larger values will lead to plots with
+higher resolution, but will also run slower.}
+
+\item{plot_sims}{\code{Default = TRUE} plots species-through-time (STT)
+plots. It detects how many types of species are present. If only one type
+of species is present, STT is plotted for all species. If two types are
+present, three plots are produced: STT for all, STT for type 1 and STT for
+type 2.}
+
+\item{island_ontogeny}{In \code{\link{DAISIE_sim_time_dep}()},
+\code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
+island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
+describing area through time. String checked by
+\code{\link{is_island_ontogeny_input}()}. \cr In all other functions a
+numeric describing the type of island ontogeny. Can be \code{0} for
+constant, \code{1} for a beta function describing area through time. In ML
+functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
+dependent estimation is not yet available as development is still ongoing.
+Will return an error if called in that case.}
+
+\item{sea_level}{In \code{\link{DAISIE_sim_time_dep}()} and plotting a
+string describing the type of sea level. Can be \code{"const"} or
+\code{"sine"} for a sine function describing area through time. String
+checked by \code{\link{is_sea_level_input}()}.
+\cr In all other functions a numeric describing the type of sea level. Can
+be \code{0} for constant, \code{1} for a sine function describing area
+through time.}
+
+\item{hyper_pars}{A named list of numeric hyperparameters for the rate
+calculations as returned by \code{\link{create_hyper_pars}()}:
+\itemize{
+  \item{[1]: is d the scaling parameter for exponent for calculating
+  cladogenesis rate}
+  \item{[2]: is x the exponent for calculating extinction rate}
+}}
+
+\item{area_pars}{A named list containing area and sea level parameters as
+created by \code{\link{create_area_pars}()}:
+\itemize{
+  \item{[1]: maximum area}
+  \item{[2]: current area}
+  \item{[3]: value from 0 to 1 indicating where in the island's history the
+  peak area is achieved}
+  \item{[4]: total island age}
+  \item{[5]: amplitude of area fluctuation from sea level}
+  \item{[6]: frequency of sine wave of area change from sea level}
+  \item{[7]: angle of the slope of the island}
+}}
+
+\item{extcutoff}{A numeric with the cutoff for the the maximum extinction
+rate preventing it from being too large and slowing down simulation.}
+
+\item{cond}{cond = 0 : conditioning on island age \cr cond = 1 :
+conditioning on island age and non-extinction of the island biota \cr.
+cond > 1 : conditioning on island age and having at least cond colonizations
+on the island. This last option is not yet available for the IW model \cr}
+
+\item{verbose}{In simulation and dataprep functions a logical,
+\code{Default = TRUE} gives intermediate output should be printed.
+For ML functions a numeric determining if intermediate output should be
+printed, \code{Default = 0} does not print, \code{verbose = 1} prints
+intermediate output of the parameters and loglikelihood, \code{verbose = 2}
+means also intermediate progress during loglikelihood computation is shown.}
+
+\item{trait_pars}{A named list containing diversification rates considering
+  two trait states created by \code{\link{create_trait_pars}}:
+\itemize{
+  \item{[1]:A numeric with the per capita transition rate with state1}
+  \item{[2]:A numeric with the per capita immigration rate with state2}
+  \item{[3]:A numeric with the per capita extinction rate with state2}
+  \item{[4]:A numeric with the per capita anagenesis rate with state2}
+  \item{[5]:A numeric with the per capita cladogenesis rate with state2}
+  \item{[6]:A numeric with the per capita transition rate with state2}
+  \item{[7]:A numeric with the number of species with trait state 2 on
+   mainland}
+}}
+
+\item{...}{Any arguments to pass on to plotting functions.}
+}
+\value{
+A list. The highest level of the least corresponds to each individual
+replciate. The first element of each replicate is composed of island
+information containing:
+\itemize{
+  \item{\code{$island_age}: A numeric with the island age.}
+  \item{\code{$not_present}: A numeric with the number of mainland lineages
+  that are not present on the island.}
+  \item{\code{$stt_all}: STT table for all species on the island
+    (nI - number of non-endemic species; nA - number of anagenetic species,
+    nC - number of cladogenetic species, present - number of independent
+    colonisations present)}
+  \item{\code{$brts_table}: Only for simulations under \code{"IW"}. Table
+containing information on order of events in the data, for use in maximum
+likelihood optimization.).}
+}
+The subsequent elements of the list pertaining to each replcate contain
+information on a single colonist lineage on the island and have 4 components:
+\itemize{
+  \item{\code{$branching_times}: island age and stem age of the
+    population/species in the case of Non-endemic, Non-endemic_MaxAge and
+    Endemic anagenetic species. For cladogenetic species these should
+    be island age and branching times of the radiation including the
+    stem age of the radiation.}
+  \item{\code{$stac}: An integer ranging from 1 to 4
+  indicating the status of the colonist:}
+\item{\code{$missing_species}: number of island species that were
+not sampled for particular clade (only applicable for endemic clades)}
+\item{\code{$type_1or2}: whether the colonist belongs to type 1 or type 2}
+}
+}
+\description{
+This function simulates islands with given cladogenesis,
+extinction, K, immigration and anagenesis parameters. In this version,
+rates and K are both trait-dependent.
+
+Returns R list object that contains the simulated islands
+}
+\references{
+Valente, L.M., A.B. Phillimore and R.S. Etienne (2015).
+Equilibrium and non-equilibrium dynamics simultaneously operate in the
+Galapagos islands. Ecology Letters 18: 844-852.
+Hauffe, T., D. Delicado, R.S. Etienne and L. Valente (submitted).
+Lake expansion increases equilibrium diversity via the target effect of
+island biogeography.
+}
+\seealso{
+\code{\link{DAISIE_format_CS}} \code{\link{DAISIE_plot_sims}}
+}
+\author{
+Luis Valente and Albert Phillimore
+}
+\keyword{models}
diff --git a/man/create_trait_pars_2K.Rd b/man/create_trait_pars_2K.Rd
new file mode 100644
index 00000000..da15473f
--- /dev/null
+++ b/man/create_trait_pars_2K.Rd
@@ -0,0 +1,40 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/create_pars.R
+\name{create_trait_pars_2K}
+\alias{create_trait_pars_2K}
+\title{Create named list of trait state parameters}
+\usage{
+create_trait_pars_2K(
+  trans_rate,
+  immig_rate2,
+  ext_rate2,
+  ana_rate2,
+  clado_rate2,
+  trans_rate2,
+  M2,
+  K2
+)
+}
+\arguments{
+\item{trans_rate}{A numeric with the per capita transition rate with state1}
+
+\item{immig_rate2}{A numeric with the per capita immigration rate with state2}
+
+\item{ext_rate2}{A numeric with the per capita extinction rate with state2}
+
+\item{ana_rate2}{A numeric with the per capita anagenesis rate with state2}
+
+\item{clado_rate2}{A numeric with the per capita cladogenesis rate with state2}
+
+\item{trans_rate2}{A numeric with the per capita transition rate with state2}
+
+\item{M2}{A numeric with the number of species with trait state 2 on mainland}
+
+\item{K2}{A numeric with the carrying capacity for state 2}
+}
+\value{
+list of numerical values containing trait state parameters
+}
+\description{
+Create named list of trait state parameters
+}

From defdcea71fd39fa356a4a95f6dd99f6f4c69e8c9 Mon Sep 17 00:00:00 2001
From: hanno <hanno@DESKTOP-R4>
Date: Wed, 7 Dec 2022 20:08:54 +0100
Subject: [PATCH 35/73] rosenbrock4

---
 src/DAISIE_odeint.h | 157 ++++++++++++++++++--------------------------
 src/DAISIE_types.h  |   2 +
 src/ublas_types.h   | 116 ++++++++++++++++++++++++++++++++
 3 files changed, 181 insertions(+), 94 deletions(-)
 create mode 100644 src/DAISIE_types.h
 create mode 100644 src/ublas_types.h

diff --git a/src/DAISIE_odeint.h b/src/DAISIE_odeint.h
index 4bea02d3..78f98b96 100644
--- a/src/DAISIE_odeint.h
+++ b/src/DAISIE_odeint.h
@@ -1,124 +1,85 @@
+#pragma once
 #ifndef DAISIE_ODEINT_H_INCLUDED
 #define DAISIE_ODEINT_H_INCLUDED
 
 
-// boiler-plate code calling into boost::odeint
-
-
-#define STRICT_R_HEADERS
-#include <RcppCommon.h>
-
-// [[Rcpp::plugins(cpp14)]]
-// [[Rcpp::depends(BH)]]
-
-#include <boost/numeric/ublas/vector.hpp>
-
-// Provide Forward Declarations
-namespace Rcpp {
-
-  namespace traits{
-
-    // Setup non-intrusive extension via template specialization for
-    // 'ublas' class boost::numeric::ublas
-
-    // Support for wrap
-    template <typename T> SEXP wrap(const boost::numeric::ublas::vector<T> & obj);
-
-    // Support for as<T>
-    template <typename T> class Exporter< boost::numeric::ublas::vector<T> >;
-
-  }
-}
-
-
-#include <Rcpp.h>
+#include "ublas_types.h"
 #include <boost/numeric/odeint.hpp>
-#include <vector>
 #include <algorithm>
 #include <stdexcept>
 
 
-// boost::numeric::ublas wrapping from:
-// https://gallery.rcpp.org/articles/custom-templated-wrap-and-as-for-seamingless-interfaces/
-namespace Rcpp {
-
-  namespace traits{
-
-    // Defined wrap case
-    template <typename T> SEXP wrap(const boost::numeric::ublas::vector<T> & obj){
-      const int RTYPE = Rcpp::traits::r_sexptype_traits<T>::rtype ;
-
-      return Rcpp::Vector< RTYPE >(obj.begin(), obj.end());
-    };
-
-
-    // Defined as< > case
-    template<typename T> class Exporter< boost::numeric::ublas::vector<T> > {
-      typedef typename boost::numeric::ublas::vector<T> OUT ;
-
-      // Convert the type to a valid rtype.
-      const static int RTYPE = Rcpp::traits::r_sexptype_traits< T >::rtype ;
-      Rcpp::Vector<RTYPE> vec;
-
-    public:
-      Exporter(SEXP x) : vec(x) {
-        if (TYPEOF(x) != RTYPE)
-          throw std::invalid_argument("Wrong R type for mapped 1D array");
-      }
-      OUT get() {
-        // Need to figure out a way to perhaps do a pointer pass?
-        OUT x(vec.size());
-        std::copy(vec.begin(), vec.end(), x.begin()); // have to copy data
-        return x;
-      }
-    };
-
-  }
-
-}
-
-
 using namespace Rcpp;
 using namespace boost::numeric::odeint;
 
 
 // type of the ode state
-using state_type = boost::numeric::ublas::vector<double>;
+using state_type = vector_t<double>;
 
 
 
 namespace daisie_odeint {
 
 
-extern double abm_factor;
+  extern double abm_factor;
 
 
-template <typename Stepper, typename Rhs>
-inline void do_integrate(double atol, double rtol, Rhs rhs, state_type& y, double t0, double t1)
-{
-  integrate_adaptive(make_controlled<Stepper>(atol, rtol), rhs, y, t0, t1, 0.1 * (t1 - t0));
-}
+  template <typename Stepper, typename Rhs>
+  inline void do_integrate(double atol, double rtol, Rhs rhs, state_type& y, double t0, double t1)
+  {
+    integrate_adaptive(make_controlled<Stepper>(atol, rtol), rhs, y, t0, t1, 0.1 * (t1 - t0));
+  }
 
 
-template <size_t Steps, typename Rhs>
-inline void abm(Rhs rhs, state_type& y, double t0, double t1)
-{
-  auto abm = adams_bashforth_moulton<Steps, state_type>{};
-  abm.initialize(rhs, y, t0, abm_factor * (t1 - t0));
-  integrate_const(abm, rhs, y, t0, t1, abm_factor * (t1 - t0));
-}
+  template <size_t Steps, typename Rhs>
+  inline void abm(Rhs rhs, state_type& y, double t0, double t1)
+  {
+    auto abm = adams_bashforth_moulton<Steps, state_type>{};
+    abm.initialize(rhs, y, t0, abm_factor * (t1 - t0));
+    integrate_const(abm, rhs, y, t0, t1, abm_factor * (t1 - t0));
+  }
 
 
-template <size_t Steps, typename Rhs>
-inline void ab(Rhs rhs, state_type& y, double t0, double t1)
-{
-  auto ab = adams_bashforth<Steps, state_type>{};
-  ab.initialize(rhs, y, t0, abm_factor * (t1 - t0));
-  integrate_const(ab, rhs, y, t0, t1, abm_factor * (t1 - t0));
-}
+  template <size_t Steps, typename Rhs>
+  inline void ab(Rhs rhs, state_type& y, double t0, double t1)
+  {
+    auto ab = adams_bashforth<Steps, state_type>{};
+    ab.initialize(rhs, y, t0, abm_factor * (t1 - t0));
+    integrate_const(ab, rhs, y, t0, t1, abm_factor * (t1 - t0));
+  }
+
+
+  template <typename RHS>
+  struct const_jacobian_from_rhs
+  {
+    const_jacobian_from_rhs(RHS& rhs) : rhs_(rhs)
+    {
+    }
 
+    void operator()(const vector_t<double>& x, matrix_t<double>& J, double t, vector_t<double>& /*dfdt*/)
+    {
+      if (!J_) {
+        J_ = std::make_unique<matrix_t<double>>(J.size1(), J.size2());
+        auto single = vector_t<double>(x.size(), 0);
+        auto dxdt = vector_t<double>(x.size());
+        for (size_t i = 0; i < J.size1(); ++i) {
+          single[i] = 1.0;
+          auto col = ublas::matrix_column<matrix_t<double>>(*J_, i);
+          std::copy(col.begin(), col.end(), dxdt.begin());
+          rhs_(single, dxdt, 0);
+          std::copy(dxdt.begin(), dxdt.end(), col.begin());
+          single[i] = 0.0;
+        }
+      }
+      J = *J_;
+    }
+
+    RHS& rhs_;
+    std::unique_ptr<matrix_t<double>> J_;
+  };
 
-// wrapper around odeint::integrate
+
+  // wrapper around odeint::integrate
   // maps runtime stepper name -> compiletime odeint::stepper type
   template <typename Rhs>
   inline void integrate(
@@ -155,7 +116,7 @@ inline void ab(Rhs rhs, state_type& y, double t0, double t1)
       case '6': ab<6>(rhs, y, t0, t1); break;
       case '7': ab<7>(rhs, y, t0, t1); break;
       case '8': ab<8>(rhs, y, t0, t1); break;
-      default: throw std::runtime_error("DAISIE_odeint_helper::integrate: unsupported steps for admam_bashforth_moulton");
+      default: throw std::runtime_error("DAISIE_odeint_helper::integrate: unsupported steps for admam_bashforth");
       }
     }
     else if (0 == stepper.compare(0, stepper.size() - 2, "odeint::adams_bashforth_moulton")) {
@@ -172,6 +133,14 @@ inline void ab(Rhs rhs, state_type& y, double t0, double t1)
       default: throw std::runtime_error("DAISIE_odeint_helper::integrate: unsupported steps for admam_bashforth_moulton");
       }
     }
+    else if ("odeint::rosenbrock4" == stepper) {
+      // another outlier in calling convention
+      using stepper_t = rosenbrock4<double>;
+      using controlled_stepper_t = rosenbrock4_controller<stepper_t>;
+      auto jac = const_jacobian_from_rhs<Rhs>{rhs};
+      auto sys = std::make_pair(std::ref(rhs), std::ref(jac));
+      integrate_adaptive(controlled_stepper_t(atol, rtol), sys, y, t0, t1, 0.1 * (t1 - t0));
+    }
     else {
       throw std::runtime_error("DAISIE_odeint_helper::integrate: unknown stepper");
     }
diff --git a/src/DAISIE_types.h b/src/DAISIE_types.h
new file mode 100644
index 00000000..1f21d261
--- /dev/null
+++ b/src/DAISIE_types.h
@@ -0,0 +1,2 @@
+#pragma once
+#include "odeint_types.h"
diff --git a/src/ublas_types.h b/src/ublas_types.h
new file mode 100644
index 00000000..125cc936
--- /dev/null
+++ b/src/ublas_types.h
@@ -0,0 +1,116 @@
+#pragma once
+#ifndef UBLAS_TYPES_H_INCLUDED
+#define UBLAS_TYPES_H_INCLUDED
+
+#include <RcppCommon.h>
+#include <boost/numeric/ublas/vector.hpp>
+#include <boost/numeric/ublas/matrix.hpp>
+
+
+namespace ublas = boost::numeric::ublas;
+
+
+template <typename T> using vector_t = ublas::vector<T>;
+template <typename T> using matrix_t = ublas::matrix<T>;
+
+
+// forward declarations Rcpp <-> boost::numeric::ublas
+namespace Rcpp {
+
+  namespace traits {
+
+    template <typename T> SEXP wrap(const vector_t<T>&);
+    template <typename T> SEXP wrap(const matrix_t<T>&);
+
+    template <typename T> vector_t<T> as(SEXP);
+    template <typename T> matrix_t<T> as(SEXP);
+
+    template <typename T> class Exporter<vector_t<T>>;
+    template <typename T> class Exporter<matrix_t<T>>;
+
+  }
+
+}
+
+
+#include <Rcpp.h>
+
+
+namespace Rcpp {
+
+  namespace traits {
+
+    template <typename T> inline SEXP wrap(const vector_t<T>& obj) {
+      const int RTYPE = Rcpp::traits::r_sexptype_traits<T>::rtype;
+      return Rcpp::Vector<RTYPE>(obj.begin(), obj.end());
+    }
+
+
+    template <typename T> inline SEXP wrap(const matrix_t<T>& obj) {
+      const size_t nr = static_cast<size_t>(obj.size1());
+      const size_t nc = static_cast<size_t>(obj.size2());
+      const int RTYPE = Rcpp::traits::r_sexptype_traits<T>::rtype;
+      Rcpp::Matrix<RTYPE> rmat(nr, nc);
+      for (size_t i = 0; i < nr; ++i) {
+        for (size_t j = 0; j < nc; ++j) {
+          rmat(i, j) = obj(i, j);
+        }
+      }
+      return rmat;
+    }
+
+
+    template<typename T>
+    class Exporter<vector_t<T>>
+    {
+    private:
+      static constexpr int RTYPE = Rcpp::traits::r_sexptype_traits<T>::rtype;
+      Rcpp::Vector<RTYPE> rvec;
+
+    public:
+      Exporter(SEXP x) : rvec(x) {
+        if (TYPEOF(x) != RTYPE) {
+          throw std::invalid_argument("Wrong R type for mapped 1D array");
+        }
+      }
+
+      vector_t<T> get() {
+        vector_t<T> x(rvec.size());
+        std::copy(rvec.begin(), rvec.end(), x.begin());
+        return x;
+      }
+    };
+
+
+    template<typename T>
+    class Exporter<matrix_t<T>>
+    {
+    private:
+      static constexpr int RTYPE = Rcpp::traits::r_sexptype_traits<T>::rtype;
+      Rcpp::Matrix<RTYPE> rmat;
+
+    public:
+      Exporter(SEXP x) : rmat(x) {
+        if (TYPEOF(x) != RTYPE) {
+          throw std::invalid_argument("Wrong R type for mapped 2D array");
+        }
+      }
+
+      matrix_t<T> get() {
+        const size_t nr = static_cast<size_t>(rmat.rows());
+        const size_t nc = static_cast<size_t>(rmat.cols());
+        matrix_t<T> x(nr, nc);
+        for (size_t i = 0; i < nr; ++i) {
+          for (size_t j = 0; j < nc; ++j) {
+            x(i, j) = rmat(i, j);
+          }
+        }
+        return x;
+      }
+    };
+
+  }
+
+}
+
+#endif

From 95650b91c16003e2e118c7c399d9c4a22dc50c6c Mon Sep 17 00:00:00 2001
From: hanno <hanno@DESKTOP-R4>
Date: Thu, 8 Dec 2022 11:47:42 +0100
Subject: [PATCH 36/73] nop

---
 src/DAISIE_odeint.h | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/DAISIE_odeint.h b/src/DAISIE_odeint.h
index 78f98b96..c24a1d32 100644
--- a/src/DAISIE_odeint.h
+++ b/src/DAISIE_odeint.h
@@ -49,16 +49,19 @@ namespace daisie_odeint {
   }
 
 
+  // Evaluator of the Jacobian for linear, time independent systems 
+  // dxdt = Ax => Jacobian = t(A)
   template <typename RHS>
-  struct const_jacobian_from_rhs
+  struct const_jacobian_from_linear_rhs
   {
-    const_jacobian_from_rhs(RHS& rhs) : rhs_(rhs)
+    explicit const_jacobian_from_linear_rhs(RHS& rhs) : rhs_(rhs)
     {
     }
 
     void operator()(const vector_t<double>& x, matrix_t<double>& J, double t, vector_t<double>& /*dfdt*/)
     {
       if (!J_) {
+        // once-only, generic evaluation
         J_ = std::make_unique<matrix_t<double>>(J.size1(), J.size2());
         auto single = vector_t<double>(x.size(), 0);
         auto dxdt = vector_t<double>(x.size());
@@ -137,7 +140,7 @@ namespace daisie_odeint {
       // another outlier in calling convention
       using stepper_t = rosenbrock4<double>;
       using controlled_stepper_t = rosenbrock4_controller<stepper_t>;
-      auto jac = const_jacobian_from_rhs<Rhs>{rhs};
+      auto jac = const_jacobian_from_linear_rhs<Rhs>{rhs};
       auto sys = std::make_pair(std::ref(rhs), std::ref(jac));
       integrate_adaptive(controlled_stepper_t(atol, rtol), sys, y, t0, t1, 0.1 * (t1 - t0));
     }

From 3449da86c01ac07f502ac6f2e0f1c568a6b65031 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Wed, 14 Dec 2022 13:37:58 +0100
Subject: [PATCH 37/73] Correcting index for laavec in C++ code. Removing
 FORTRAN and R code from C++ code.

---
 src/DAISIE_CS.cpp | 171 ++--------------------------------------------
 1 file changed, 7 insertions(+), 164 deletions(-)

diff --git a/src/DAISIE_CS.cpp b/src/DAISIE_CS.cpp
index 902ffdeb..efb35ba0 100644
--- a/src/DAISIE_CS.cpp
+++ b/src/DAISIE_CS.cpp
@@ -72,21 +72,11 @@ namespace {
     {
       if (++p_.steps > max_cs_steps) throw std::runtime_error("cpp_daisie_cs_runmod: too many steps");
 
-      // xx1 = c(0,0,x[1:lx],0)
-      // xx2 = c(0,0,x[(lx + 1):(2 * lx)],0)
-      // xx3 = x[2 * lx + 1]
       // using padded views instead of vectors:
       const auto xx1 = padded_vector_view(2, x.data().begin(), p_.lx);
       const auto xx2 = padded_vector_view(2, x.data().begin() + p_.lx, p_.lx);
       const auto xx3 = x[2 * p_.lx];
 
-      // DO I = 1, N + 4 + 2 * kk
-      //   laavec(I) = P(I)
-      //   lacvec(I) = P(I + N + 4 + 2 * kk)
-      //   muvec(I)  = P(I + 2 * (N + 4 + 2 * kk))
-      //   gamvec(I) = P(I + 3 * (N + 4 + 2 * kk))
-      //   nn(I)     = P(I + 4 * (N + 4 + 2 * kk))
-      // ENDDO
       // using views instead of vectors:
       const auto chunk = p_.lx + 4 + 2 * p_.kk;
       const auto laavec = p_.P.data().begin();
@@ -95,17 +85,6 @@ namespace {
       const auto gamvec = p_.P.data().begin() + 3 * chunk;
       const auto nn = p_.P.data().begin() + 4 * chunk;
 
-      // DO I = 3, N + 2
-      //   il1(I - 2) = I + kk - 1
-      //   il2(I - 2) = I + kk + 1
-      //   il3in3(I - 2) = I + kk
-      //   il4(I - 2) = I + kk - 2
-      //   in1(I - 2) = I + 2 * kk - 1
-      //   in2ix2(I - 2) = I + 1
-      //   ix1(I - 2) = I - 1
-      //   ix3(I - 2) = I
-      //   ix4(I - 2) = I - 2
-      // ENDDO
       // using offsets into our views instead of vectors:
       const int il1 = 2 + p_.kk - 1;
       const int il2 = 2 + p_.kk + 1;
@@ -117,24 +96,6 @@ namespace {
       const int ix3 = 2;
       const int ix4 = 2 - 2;
 
-      // DO I = 1, N
-      //   FF1 = laavec(il1(I) + 1) * xx2(ix1(I))
-      //   FF1 = FF1 + lacvec(il4(I) + 1) * xx2(ix4(I))
-      //   FF1 = FF1 + muvec(il2(I) + 1) * xx2(ix3(I))
-      //   FF1 = FF1 + lacvec(il1(I)) * nn(in1(I)) * xx1(ix1(I))
-      //   FF1 = FF1 + muvec(il2(I)) * nn(in2ix2(I)) * xx1(in2ix2(I))
-      //   FFF = (muvec(il3in3(I)) + lacvec(il3in3(I)))
-      //   FF1 = FF1 - FFF * nn(il3in3(I)) * xx1(ix3(I))
-      //   FF1 = FF1 - gamvec(il3in3(I)) * xx1(ix3(I))
-      //   dConc(I) = FF1
-      //   FF1 = gamvec(il3in3(I)) * xx1(ix3(I))
-      //   FF1 = FF1 + lacvec(il1(I) + 1) * nn(in1(I)) * xx2(ix1(I))
-      //   FF1 = FF1 + muvec(il2(I)+1) * nn(in2ix2(I)) * xx2(in2ix2(I))
-      //   FFF = muvec(il3in3(I) + 1) + lacvec(il3in3(I) + 1)
-      //   FF1 = FF1 - FFF * nn(il3in3(I) + 1) * xx2(ix3(I))
-      //   FF1 = FF1 - laavec(il3in3(I) + 1) * xx2(ix3(I))
-      //   dConc(N + I) = FF1
-      // ENDDO
       // using views into output vector:
       auto dx1 = dx.data().begin();
       auto dx2 = dx1 + p_.lx;
@@ -149,24 +110,12 @@ namespace {
         dx2[i] = gamvec[il3in3 + i] * xx1[ix3 + i]
                + lacvec[il1 + i + 1] * nn[in1 + i] * xx2[ix1 + i]
                + muvec[il2 + i + 1] * nn[in2ix2 + i] * xx2[in2ix2 + i]
-               - (muvec[il3in3 + 1 + i] + lacvec[il3in3 + 1 + i]) * nn[il3in3 + i + 1] * xx2[ix3 + i]
-               - laavec[il3in3 + i] * xx2[ix3 + i];
+               - (muvec[il3in3 + i + 1] + lacvec[il3in3 + i + 1]) * nn[il3in3 + i + 1] * xx2[ix3 + i]
+               - laavec[il3in3 + i + 1] * xx2[ix3 + i];
       }
 
-      // IF(kk .EQ. 1) THEN
-      //   dConc(1) = dConc(1) + laavec(il3in3(1)) * xx3
-      //   dConc(2) = dConc(2) + 2 * lacvec(il3in3(1)) * xx3
-      // ENDIF
-      // if (1 == p_.kk) {
-      //  dx1[0] += laavec[il3in3] * xx3;
-      //  dx2[1] += 2.0 * lacvec[il3in3] * xx3;
-      //}
-
-      // FFF = laavec(il3in3(1)) + lacvec(il3in3(1))
-      // FFF = FFF + gamvec(il3in3(1)) + muvec(il3in3(1))
-      // dConc(2 * N + 1) = -1 * FFF * xx3
       auto dx3 = dx2 + p_.lx;
-      dx3[0] = -(laavec[il3in3] + lacvec[il3in3] + gamvec[il3in3] + muvec[il3in3]) * xx3;
+      dx3[0] = 0;
     }
 
   private:
@@ -186,23 +135,12 @@ namespace {
     {
       if (++p_.steps > max_cs_steps) throw std::runtime_error("cpp_daisie_cs_runmod_1: too many steps");
 
-      // xx1 = c(0,0,x[1:lx],0)
-      // xx2 = c(0,0,x[(lx + 1):(2 * lx)],0)
-      // xx3 = c(0,0,x[(2 * lx + 1):(3 * lx)],0)
-      // xx4 <- c(0,0,x[(3 * lx + 1):(4 * lx)],0)
       // using padded views instead of vectors:
       const auto xx1 = padded_vector_view(2, x.data().begin(), p_.lx);
       const auto xx2 = padded_vector_view(2, x.data().begin() + p_.lx, p_.lx);
       const auto xx3 = padded_vector_view(2, x.data().begin() + 2 * p_.lx, p_.lx);
       const auto xx4 = padded_vector_view(2, x.data().begin() + 3 * p_.lx, p_.lx);
 
-      // DO I = 1, N + 4 + 2 * kk
-      //   laavec(I) = P(I)
-      //   lacvec(I) = P(I + N + 4 + 2 * kk)
-      //   muvec(I)  = P(I + 2 * (N + 4 + 2 * kk))
-      //   gamvec(I) = P(I + 3 * (N + 4 + 2 * kk))
-      //   nn(I)     = P(I + 4 * (N + 4 + 2 * kk))
-      // ENDDO
       // using views instead of vectors:
       const auto chunk = p_.lx + 4 + 2 * p_.kk;
       const auto laavec = p_.P.data().begin();
@@ -211,17 +149,6 @@ namespace {
       const auto gamvec = p_.P.data().begin() + 3 * chunk;
       const auto nn = p_.P.data().begin() + 4 * chunk;
 
-      // DO I = 3, N + 2
-      //   il1(I - 2) = I + kk - 1
-      //   il2(I - 2) = I + kk + 1
-      //   il3in3(I - 2) = I + kk
-      //   il4(I - 2) = I + kk - 2
-      //   in1(I - 2) = I + 2 * kk - 1
-      //   in2ix2(I - 2) = I + 1
-      //   in4ix1(I - 2) = I - 1
-      //   ix3(I - 2) = I
-      //   ix4(I - 2) = I - 2
-      // ENDDO
       // using offsets into our views instead of vectors:
       const int il1 = 2 + p_.kk - 1;
       const int il2 = 2 + p_.kk + 1;
@@ -233,40 +160,6 @@ namespace {
       const int ix3 = 2;
       const int ix4 = 2 - 2;
 
-      //DO I = 1, N
-      //  FF1 = lacvec(il1(I)) * xx1(in4ix1(I))
-      //  FF1 = FF1 + laavec(il1(I) + 1) * xx2(in4ix1(I))
-      //  FF1 = FF1 + lacvec(il4(I) + 1) * xx2(ix4(I))
-      //  FF1 = FF1 + muvec(il2(I)) * nn(in2ix2(I)) * xx1(in2ix2(I))
-      //  FF1 = FF1 + muvec(il3in3(I) + 1) * xx2(ix3(I))
-      //  FFF = muvec(il3in3(I)) + lacvec(il3in3(I))
-      //  FF1 = FF1 - FFF * nn(il3in3(I)) * xx1(ix3(I))
-      //  dConc(I) = FF1 - gamvec(il3in3(I)) * xx1(ix3(I))
-      //  FF1 = gamvec(il3in3(I)) * xx1(ix3(I))
-      //  FF1 = FF1 + gamvec(il3in3(I)) * xx3(ix3(I))
-      //  FF1 = FF1 + gamvec(il3in3(I) + 1) * xx4(ix3(I))
-      //  FF1 = FF1 + lacvec(il1(I) + 1) * nn(in1(I)) * xx2(in4ix1(I))
-      //  FF1 = FF1 + muvec(il2(I) + 1) * nn(in2ix2(I)) * xx2(in2ix2(I))
-      //  FFF = muvec(il3in3(I) + 1) + lacvec(il3in3(I) + 1)
-      //  FF1 = FF1 - FFF * nn(il3in3(I) + 1) * xx2(ix3(I))
-      //  FF1 = FF1 - laavec(il3in3(I) + 1) * xx2(ix3(I))
-      //  dConc(N + I) = FF1
-      //  FF1 = lacvec(il1(I)) * nn(in1(I)) * xx3(in4ix1(I))
-      //  FF1 = FF1 + laavec(il1(I) + 1) * xx4(in4ix1(I))
-      //  FF1 = FF1 + lacvec(il4(I) + 1) * xx4(ix4(I))
-      //  FF1 = FF1 + muvec(il2(I)) * nn(in2ix2(I)) * xx3(in2ix2(I))
-      //  FF1 = FF1 + muvec(il3in3(I) + 1) * xx4(ix3(I))
-      //  FFF = lacvec(il3in3(I)) + muvec(il3in3(I))
-      //  FF1 = FF1 - FFF * nn(il3in3(I)) * xx3(ix3(I))
-      //  FF1 = FF1 - gamvec(il3in3(I)) * xx3(ix3(I))
-      //  dConc(2 * N + I) = FF1
-      //  FF1 = lacvec(il1(I) + 1) * nn(in1(I)) * xx4(in4ix1(I))
-      //  FF1 = FF1 + muvec(il2(I) + 1) * nn(in2ix2(I)) * xx4(in2ix2(I))
-      //  FFF = lacvec(il3in3(I) + 1) + muvec(il3in3(I) + 1)
-      //  FF1 = FF1 - FFF * nn(il3in3(I) + 1) * xx4(ix3(I))
-      //  FF1 = FF1 - gamvec(il3in3(I) + 1) * xx4(ix3(I))
-      //  dConc(3 * N + I) = FF1
-      //ENDDO
       // using views into output vector:
       auto dx1 = dx.data().begin();
       auto dx2 = dx1 + p_.lx;
@@ -285,8 +178,8 @@ namespace {
         + gamvec[il3in3 + i + 1] * xx4[ix3 + i]
         + lacvec[il1 + i + 1] * nn[in1 + i] * xx2[in4ix1 + i]
         + muvec[il2 + i + 1] * nn[in2ix2 + i] * xx2[in2ix2 + i]
-        - (muvec[il3in3 + 1 + i] + lacvec[il3in3 + 1 + i]) * nn[il3in3 + i + 1] * xx2[ix3 + i]
-        - laavec[il3in3 + i] * xx2[ix3 + i];
+        - (muvec[il3in3 + i + 1] + lacvec[il3in3 + i + 1]) * nn[il3in3 + i + 1] * xx2[ix3 + i]
+        - laavec[il3in3 + i + 1] * xx2[ix3 + i];
         dx3[i] = lacvec[il1 + i] * nn[in1 + i] * xx3[in4ix1 + i]
         + laavec[il1 + i + 1] * xx4[in4ix1 + i]
         + lacvec[il4 + i + 1] * xx4[ix4 + i]
@@ -319,21 +212,11 @@ namespace {
     {
       if (++p_.steps > max_cs_steps) throw std::runtime_error("cpp_daisie_cs_runmod_2: too many steps");
 
-      // xx1 = c(0,0,x[1:lx],0)
-      // xx2 = c(0,0,x[(lx + 1):(2 * lx)],0)
-      // xx3 = c(0,0,x[(2 * lx + 1):(3 * lx)],0)
       // using padded views instead of vectors:
       const auto xx1 = padded_vector_view(2, x.data().begin(), p_.lx);
       const auto xx2 = padded_vector_view(2, x.data().begin() + p_.lx, p_.lx);
       const auto xx3 = padded_vector_view(2, x.data().begin() + 2 * p_.lx, p_.lx);
 
-      // DO I = 1, N + 4 + 2 * kk
-      //   laavec(I) = P(I)
-      //   lacvec(I) = P(I + N + 4 + 2 * kk)
-      //   muvec(I)  = P(I + 2 * (N + 4 + 2 * kk))
-      //   gamvec(I) = P(I + 3 * (N + 4 + 2 * kk))
-      //   nn(I)     = P(I + 4 * (N + 4 + 2 * kk))
-      // ENDDO
       // using views instead of vectors:
       const auto chunk = p_.lx + 4 + 2 * p_.kk;
       const auto laavec = p_.P.data().begin();
@@ -342,17 +225,6 @@ namespace {
       const auto gamvec = p_.P.data().begin() + 3 * chunk;
       const auto nn = p_.P.data().begin() + 4 * chunk;
 
-      // DO I = 3, N + 2
-      //   il1(I - 2) = I + kk - 1
-      //   il2(I - 2) = I + kk + 1
-      //   il3in3(I - 2) = I + kk
-      //   il4(I - 2) = I + kk - 2
-      //   in1(I - 2) = I + 2 * kk - 1
-      //   in2ix2(I - 2) = I + 1
-      //   in4ix1(I - 2) = I - 1
-      //   ix3(I - 2) = I
-      //   ix4(I - 2) = I - 2
-      // ENDDO
       // using offsets into our views instead of vectors:
       const int il1 = 2 + p_.kk - 1;
       const int il2 = 2 + p_.kk + 1;
@@ -364,35 +236,6 @@ namespace {
       const int ix3 = 2;
       const int ix4 = 2 - 2;
 
-      // DO I = 1, N
-      //   FF1 = laavec(il1(I) + 1) * xx2(in4ix1(I))
-      //   FF1 = FF1 + lacvec(il4(I) + 1) * xx2(ix4(I))
-      //   FF1 = FF1 + muvec(il2(I) + 1) * xx2(ix3(I))
-      //   FF1 = FF1 + lacvec(il1(I)) * nn(in1(I)) * xx1(in4ix1(I))
-      //   FF1 = FF1 + muvec(il2(I)) * nn(in2ix2(I)) * xx1(in2ix2(I))
-      //   FFF = muvec(il3in3(I)) + lacvec(il3in3(I))
-      //   FF1 = FF1 - FFF * nn(il3in3(I)) * xx1(ix3(I))
-      //   FF1 = FF1 - gamvec(il3in3(I)) * xx1(ix3(I))
-      //   FFF = 0
-      //   IF(kk .EQ. 1) THEN
-      //     FFF = laavec(il3in3(I)) * xx3(ix3(I))
-      //     FFF = FFF + 2 * lacvec(il1(I)) * xx3(in4ix1(I))
-      //   ENDIF
-      //   dConc(I) = FF1 + FFF
-      //   FF1 = gamvec(il3in3(I)) * xx1(ix3(I))
-      //   FF1 = FF1 + lacvec(il1(I) + 1) * nn(in1(I)) * xx2(in4ix1(I))
-      //   FF1 = FF1 + muvec(il2(I)+1) * nn(in2ix2(I)) * xx2(in2ix2(I))
-      //   FFF = muvec(il3in3(I) + 1) + lacvec(il3in3(I) + 1)
-      //   FF1 = FF1 - FFF * nn(il3in3(I) + 1) * xx2(ix3(I))
-      //   FF1 = FF1 - laavec(il3in3(I) + 1) * xx2(ix3(I))
-      //   dConc(N + I) = FF1
-      //   FF1 = lacvec(il1(I)) * nn(in4ix1(I)) * xx3(in4ix1(I))
-      //   FF1 = FF1 + muvec(il2(I)) * nn(in2ix2(I)) * xx3(in2ix2(I))
-      //   FFF = lacvec(il3in3(I)) + muvec(il3in3(I))
-      //   FF1 = FF1 - FFF * nn(il3in3(I)) * xx3(ix3(I))
-      //   FF1 = FF1-(laavec(il3in3(I))+gamvec(il3in3(I)))*xx3(ix3(I))
-      //   dConc(2 * N + I) = FF1
-      // ENDDO
       // using views into output vector:
       auto dx1 = dx.data().begin();
       auto dx2 = dx1 + p_.lx;
@@ -411,8 +254,8 @@ namespace {
         dx2[i] = gamvec[il3in3 + i] * xx1[ix3 + i]
                + lacvec[il1 + i + 1] * nn[in1 + i] * xx2[in4ix1 + i]
                + muvec[il2 + i + 1] * nn[in2ix2 + i] * xx2[in2ix2 + i]
-               - (muvec[il3in3 + 1 + i] + lacvec[il3in3 + 1 + i]) * nn[il3in3 + i + 1] * xx2[ix3 + i]
-               - laavec[il3in3 + i] * xx2[ix3 + i];
+               - (muvec[il3in3 + i + 1] + lacvec[il3in3 + i + 1]) * nn[il3in3 + i + 1] * xx2[ix3 + i]
+               - laavec[il3in3 + i + 1] * xx2[ix3 + i];
         dx3[i] = lacvec[il1 + i] * nn[in4ix1 + i] * xx3[in4ix1 + i]
                + muvec[il2 + i] * nn[in2ix2 + i] * xx3[in2ix2 + i]
                - (lacvec[il3in3 + i] + muvec[il3in3 + i]) * nn[il3in3 + i] * xx3[ix3 + i]

From 5cc799fc5aae8ffdebfe7ddefb0af2c2cad09a73 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 15 Dec 2022 15:37:07 +0100
Subject: [PATCH 38/73] Version and date change

---
 DESCRIPTION | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 93bc93b2..b39c710a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: DAISIE
 Type: Package
 Title: Dynamical Assembly of Islands by Speciation, Immigration and Extinction
-Version: 4.2.2
-Date: 2022-07-21
+Version: 4.2.3
+Date: 2022-12-16
 Depends: R (>= 3.5.0)
 biocViews:
 SystemRequirements: C++14

From 649de7442a020c5bc3a8bfd93d427672a43fd4c6 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Fri, 16 Dec 2022 15:41:44 +0100
Subject: [PATCH 39/73] Proper handling of infinite lambda case

---
 R/DAISIE_loglik_CS.R | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/R/DAISIE_loglik_CS.R b/R/DAISIE_loglik_CS.R
index a108688a..d605c311 100644
--- a/R/DAISIE_loglik_CS.R
+++ b/R/DAISIE_loglik_CS.R
@@ -495,11 +495,10 @@ DAISIE_loglik_CS_M1 <- DAISIE_loglik <- function(pars1,
     loglik <- -Inf
     return(loglik)
   }
-  N <- length(brts) - 1
-  # exception for N = 1 in high lambda case
   lac <- pars1[1]
-  if(lac == Inf & missnumspec == 0 & length(pars1) == 5 & N > 1) {
-    loglik <- DAISIE_loglik_high_lambda(pars1, -brts, stac)
+  if(lac == Inf & missnumspec == 0 & length(pars1) == 5) {
+      if(verbose) warning('Infinite lambda detected')
+      loglik <- DAISIE_loglik_high_lambda(pars1, -brts, stac)
   } else {
     if (ddep == 1 | ddep == 11) {
       lx <- min(

From 4d1cc7f66d69c10520f6f7ef8b3fea46bdc8b6bd Mon Sep 17 00:00:00 2001
From: xieshu95 <xieshu95@gmail.com>
Date: Wed, 21 Dec 2022 16:59:01 +0100
Subject: [PATCH 40/73] Increment version number to 4.3.0

---
 DESCRIPTION | 4 ++--
 NEWS.md     | 5 +++++
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index b39c710a..bc7fb01e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: DAISIE
 Type: Package
 Title: Dynamical Assembly of Islands by Speciation, Immigration and Extinction
-Version: 4.2.3
-Date: 2022-12-16
+Version: 4.3.0
+Date: 2022-12-21
 Depends: R (>= 3.5.0)
 biocViews:
 SystemRequirements: C++14
diff --git a/NEWS.md b/NEWS.md
index 85b744f9..7a3a6fcf 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,8 @@
+# DAISIE 4.3.0
+* Add code for the trait-dependent simulations considering two carrying capacities for each trait state.
+* Bug fix in 'DAISIE_sim_cr_iw()', which wrongly computed number of species at present
+* Improve the likelihood calculation.
+
 # DAISIE 4.2.1
 
 * Bug fixes in `DAISIE_loglik_CS()`on the likelihood code for the continental sampling (probability of initial presence on the island).

From 79f2b1b12d3f2d0335cd502926547cf7a552bd7a Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 22 Dec 2022 12:26:23 +0100
Subject: [PATCH 41/73] Replacing sprintf by format

---
 R/DAISIE_ML1.R          |  60 +++++++--------
 R/DAISIE_ML2.R          |  11 ++-
 R/DAISIE_ML4.R          |  21 +++---
 R/DAISIE_ML_IW.R        |  11 ++-
 R/DAISIE_MW_ML.R        | 162 ++++++++++++++++++++--------------------
 R/DAISIE_SR_ML_CS.R     |  17 ++++-
 R/DAISIE_SR_loglik_CS.R |   8 +-
 R/DAISIE_loglik_CS.R    |  34 ++++-----
 8 files changed, 171 insertions(+), 153 deletions(-)

diff --git a/R/DAISIE_ML1.R b/R/DAISIE_ML1.R
index 0f51918e..945013b6 100644
--- a/R/DAISIE_ML1.R
+++ b/R/DAISIE_ML1.R
@@ -399,20 +399,18 @@ DAISIE_ML1 <- function(
       df = length(initparsopt),
       conv = unlist(out$conv)
     )
-    s1 <- sprintf(
-      "Maximum likelihood parameter estimates:\n lambda_c: %f\n mu: %f\n K: %f\n gamma: %f\n lambda_a: %f\n lambda_c2: %f\n mu2: %f\n K2: %f\n gamma2: %f\n lambda_a2: %f\n prop_type2: %f",
-      MLpars1[1],
-      MLpars1[2],
-      MLpars1[3],
-      MLpars1[4],
-      MLpars1[5],
-      MLpars1[6],
-      MLpars1[7],
-      MLpars1[8],
-      MLpars1[9],
-      MLpars1[10],
-      MLpars1[11]
-    )
+    s1 <- c('Maximum likelihood parameter estimates:',
+            '\n lambda_c:', format(MLpars1[1], format = 'f', digits = 6),
+            '\n mu:', format(MLpars1[2], format = 'f', digits = 6),
+            '\n K:', format(MLpars1[3], format = 'f', digits = 6),
+            '\n gamma:', format(MLpars1[4], format = 'f', digits = 6),
+            '\n lambda_a:', format(MLpars1[5], format = 'f', digits = 6),
+            '\n lambda_c2:', format(MLpars1[6], format = 'f', digits = 6),
+            '\n mu2:', format(MLpars1[7], format = 'f', digits = 6),
+            '\n K2:', format(MLpars1[8], format = 'f', digits = 6),
+            '\n gamma2:', format(MLpars1[9], format = 'f', digits = 6),
+            '\n lambda_a2:', format(MLpars1[10], format = 'f', digits = 6),
+            '\n prop_type2:', format(MLpars1[11], format = 'f', digits = 6))
   } else if (all(all_no_shift == 7:11)) {
     out2 <- data.frame(
       lambda_c = MLpars1[1],
@@ -425,15 +423,13 @@ DAISIE_ML1 <- function(
       df = length(initparsopt),
       conv = unlist(out$conv)
     )
-    s1 <- sprintf(
-      "Maximum likelihood parameter estimates:\n lambda_c: %f\n mu: %f\n K: %f\n gamma: %f\n lambda_a: %f\n prob_init_pres: %f",
-      MLpars1[1],
-      MLpars1[2],
-      MLpars1[3],
-      MLpars1[4],
-      MLpars1[5],
-      MLpars1[6]
-    )
+    s1 <- c('Maximum likelihood parameter estimates:',
+            '\n lambda_c:', format(MLpars1[1], format = 'f', digits = 6),
+            '\n mu:', format(MLpars1[2], format = 'f', digits = 6),
+            '\n K:', format(MLpars1[3], format = 'f', digits = 6),
+            '\n gamma:', format(MLpars1[4], format = 'f', digits = 6),
+            '\n lambda_a:', format(MLpars1[5], format = 'f', digits = 6),
+            '\n prop_init_pres:', format(MLpars1[6], format = 'f', digits = 6))
   } else {
     out2 <- data.frame(
       lambda_c = MLpars1[1],
@@ -445,17 +441,15 @@ DAISIE_ML1 <- function(
       df = length(initparsopt),
       conv = unlist(out$conv)
     )
-    s1 <- sprintf(
-      "Maximum likelihood parameter estimates:\n lambda_c: %f\n mu: %f\n K: %f\n gamma: %f\n lambda_a: %f\n",
-      MLpars1[1],
-      MLpars1[2],
-      MLpars1[3],
-      MLpars1[4],
-      MLpars1[5]
-    )
+    s1 <- c('Maximum likelihood parameter estimates:',
+            '\n lambda_c:', format(MLpars1[1], format = 'f', digits = 6),
+            '\n mu:', format(MLpars1[2], format = 'f', digits = 6),
+            '\n K:', format(MLpars1[3], format = 'f', digits = 6),
+            '\n gamma:', format(MLpars1[4], format = 'f', digits = 6),
+            '\n lambda_a:', format(MLpars1[5], format = 'f', digits = 6))
   }
-  s2 <- sprintf("Maximum loglikelihood: %f", ML)
-  cat("\n", s1, "\n", s2, "\n")
+  s2 <- c('Maximum loglikelihood:', format(ML, format = 'f', digits = 6))
+  cat("\n", s1, "\n", s2, "\n", sep = ' ')
   if (eqmodel > 0) {
     M <- calcMN(datalist, MLpars1)
     ExpEIN <- DAISIE_ExpEIN(datalist[[1]]$island_age, MLpars1, M) # nolint start
diff --git a/R/DAISIE_ML2.R b/R/DAISIE_ML2.R
index 3cff782b..11972681 100644
--- a/R/DAISIE_ML2.R
+++ b/R/DAISIE_ML2.R
@@ -197,8 +197,13 @@ DAISIE_ML2 <- function(
     }
   }
   out2 <- data.frame(lambda_c = MLpars1[, 1], mu = MLpars1[, 2], K = MLpars1[, 3], gamma = MLpars1[, 4], lambda_a = MLpars1[, 5], loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
-  s1 <- sprintf("Maximum likelihood parameter estimates: %f", MLpars1)
-  s2 <- sprintf("Maximum loglikelihood: %f", ML)
-  cat("\n", s1, "\n", s2, "\n")
+  s1 <- c('Maximum likelihood parameter estimates:',
+          '\n lambda_c:', format(MLpars1[1], format = 'f', digits = 6),
+          '\n mu:', format(MLpars1[2], format = 'f', digits = 6),
+          '\n K:', format(MLpars1[3], format = 'f', digits = 6),
+          '\n gamma:', format(MLpars1[4], format = 'f', digits = 6),
+          '\n lambda_a:', format(MLpars1[5], format = 'f', digits = 6))
+  s2 <- c('Maximum loglikelihood:', format(ML, format = 'f', digits = 6))
+  cat("\n", s1, "\n", s2, "\n", sep = ' ')
   return(invisible(out2))
 }
diff --git a/R/DAISIE_ML4.R b/R/DAISIE_ML4.R
index 4b75f572..dc0ecccf 100644
--- a/R/DAISIE_ML4.R
+++ b/R/DAISIE_ML4.R
@@ -236,17 +236,14 @@ DAISIE_ML4 <- function(
     df = length(initparsopt),
     conv = unlist(out$conv)
   )
-  s1 <- sprintf(
-    "Maximum likelihood parameter estimates: lambda_c: %f, mu: %f, K: %f,
-      gamma: %f, lambda_a: %f, sd: %f",
-    MLpars1[1],
-    MLpars1[2],
-    MLpars1[3],
-    MLpars1[4],
-    MLpars1[5],
-    MLpars1[6]
-  )
-  s2 <- sprintf("Maximum loglikelihood: %f", ML)
-  cat("\n", s1, "\n", s2, "\n")
+  s1 <- c('Maximum likelihood parameter estimates:',
+          '\n lambda_c:', format(MLpars1[1], format = 'f', digits = 6),
+          '\n mu:', format(MLpars1[2], format = 'f', digits = 6),
+          '\n K:', format(MLpars1[3], format = 'f', digits = 6),
+          '\n gamma:', format(MLpars1[4], format = 'f', digits = 6),
+          '\n lambda_a:', format(MLpars1[5], format = 'f', digits = 6),
+          '\n sd:', format(MLpars1[6], format = 'f', digits = 6))
+  s2 <- c('Maximum loglikelihood:', format(ML, format = 'f', digits = 6))
+  cat("\n", s1, "\n", s2, "\n", sep = ' ')
   return(invisible(out2))
 }
diff --git a/R/DAISIE_ML_IW.R b/R/DAISIE_ML_IW.R
index c130e12b..e7a6b943 100644
--- a/R/DAISIE_ML_IW.R
+++ b/R/DAISIE_ML_IW.R
@@ -171,8 +171,13 @@ DAISIE_ML_IW <- function(
   if (length(idparsfix) != 0) { MLpars1[idparsfix] <- parsfix }
   if (MLpars1[3] > 10 ^ 7){ MLpars1[3] <- Inf }
   out2 <- data.frame(lambda_c = MLpars1[1], mu = MLpars1[2], K = MLpars1[3], gamma = MLpars1[4], lambda_a = MLpars1[5], loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
-  s1 <- sprintf("Maximum likelihood parameter estimates: lambda_c: %f, mu: %f, K: %f, gamma: %f, lambda_a: %f", MLpars1[1], MLpars1[2], MLpars1[3], MLpars1[4], MLpars1[5])
-  s2 <- sprintf("Maximum loglikelihood: %f", ML)
-  cat("\n", s1, "\n", s2, "\n")
+  s1 <- c('Maximum likelihood parameter estimates:',
+          '\n lambda_c:', format(MLpars1[1], format = 'f', digits = 6),
+          '\n mu:', format(MLpars1[2], format = 'f', digits = 6),
+          '\n K:', format(MLpars1[3], format = 'f', digits = 6),
+          '\n gamma:', format(MLpars1[4], format = 'f', digits = 6),
+          '\n lambda_a:', format(MLpars1[5], format = 'f', digits = 6))
+  s2 <- c('Maximum loglikelihood:', format(ML, format = 'f', digits = 6))
+  cat("\n", s1, "\n", s2, "\n", sep = ' ')
   return(invisible(out2))
 }
diff --git a/R/DAISIE_MW_ML.R b/R/DAISIE_MW_ML.R
index 3b2ae608..60511399 100644
--- a/R/DAISIE_MW_ML.R
+++ b/R/DAISIE_MW_ML.R
@@ -477,85 +477,84 @@ DAISIE_MW_ML = function(
   MLpars1[idparsopt] = MLpars
   if(length(idparsfix) != 0) { MLpars1[idparsfix] = parsfix }
   if(MLpars1[5] > 10^7){ MLpars1[5] = Inf }
-  s1output <- function(MLpars1,distance_dep)
-  {
-    s1 <- switch(distance_dep,
-                 power = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * A^ %f\n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * d^ -%f\n
-               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-                 signoidal_col = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * A^ %f\n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * (1 - (d/%f)^%f / (1 + (d/%f)^%f )\n
-               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[11],MLpars1[8],MLpars1[11],MLpars1[8],MLpars1[9],MLpars1[10]),
-                 sigmoidal_ana = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * A^ %f\n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * d^ -%f\n
-               lambda_a = %f * (d/%f)^%f / (1 + (d/%f)^%f )\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[11],MLpars1[10],MLpars1[11],MLpars1[10]),
-                 sigmoidal_clado = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * (d/%f)^%f / (1 + (d/%f)^%f )\n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * d^ -%f\n
-               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[11],MLpars1[2],MLpars1[11],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-                 sigmoidal_col_ana = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * A^ %f\n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * (1 - (d/%f)^%f / (1 + (d/%f)^%f )\n
-               lambda_a = %f * (d/%f)^%f / (1 + (d/%f)^%f )\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[11],MLpars1[8],MLpars1[11],MLpars1[8],MLpars1[9],MLpars1[12],MLpars1[10],MLpars1[12],MLpars1[10]),
-                 area_additive_clado = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * A^ %f * d^ %f \n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * d^ -%f\n
-               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-                 area_interactive_clado = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * A^ (%f + %f * log(d)) \n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * d^ -%f\n
-               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-                 area_interactive_clado0 = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * A^ (%f + %f * log(d)) \n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * d^ -%f\n
-               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-                 area_interactive_clado1 = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * A^ (%f + d/%f)) \n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * d^ -%f\n
-               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-                 area_interactive_clado2 = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * A^ (%f + d/(d + %f)) \n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * d^ -%f\n
-               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-                 area_interactive_clado3 = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * (A + d/%f)^ %f\n \n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * d^ -%f\n
-               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[11],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-                 area_interactive_clado4 = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * A^ (%f * d/(d + %f)) \n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * d^ -%f\n
-               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10])
-    )
-    return(s1)
-  }
-  s2 = sprintf('Maximum loglikelihood: %f',ML)
+#  s1output <- function(MLpars1,distance_dep)
+#  {
+#    s1 <- switch(distance_dep,
+#                 power = sprintf('Maximum likelihood parameter estimates:\n
+#               lambda_c = %f * A^ %f\n
+#               mu = %f * A^ -%f\n
+#               K = %f * A^ %f\n
+#               M * gamma = %f * d^ -%f\n
+#               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+#                 signoidal_col = sprintf('Maximum likelihood parameter estimates:\n
+#               lambda_c = %f * A^ %f\n
+#               mu = %f * A^ -%f\n
+#               K = %f * A^ %f\n
+#               M * gamma = %f * (1 - (d/%f)^%f / (1 + (d/%f)^%f )\n
+#               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[11],MLpars1[8],MLpars1[11],MLpars1[8],MLpars1[9],MLpars1[10]),
+#                 sigmoidal_ana = sprintf('Maximum likelihood parameter estimates:\n
+#               lambda_c = %f * A^ %f\n
+#               mu = %f * A^ -%f\n
+#               K = %f * A^ %f\n
+#               M * gamma = %f * d^ -%f\n
+#               lambda_a = %f * (d/%f)^%f / (1 + (d/%f)^%f )\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[11],MLpars1[10],MLpars1[11],MLpars1[10]),
+#                 sigmoidal_clado = sprintf('Maximum likelihood parameter estimates:\n
+#               lambda_c = %f * (d/%f)^%f / (1 + (d/%f)^%f )\n
+#               mu = %f * A^ -%f\n
+#               K = %f * A^ %f\n
+#               M * gamma = %f * d^ -%f\n
+#               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[11],MLpars1[2],MLpars1[11],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+#                 sigmoidal_col_ana = sprintf('Maximum likelihood parameter estimates:\n
+#               lambda_c = %f * A^ %f\n
+#               mu = %f * A^ -%f\n
+#               K = %f * A^ %f\n
+#               M * gamma = %f * (1 - (d/%f)^%f / (1 + (d/%f)^%f )\n
+#               lambda_a = %f * (d/%f)^%f / (1 + (d/%f)^%f )\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[11],MLpars1[8],MLpars1[11],MLpars1[8],MLpars1[9],MLpars1[12],MLpars1[10],MLpars1[12],MLpars1[10]),
+#                 area_additive_clado = sprintf('Maximum likelihood parameter estimates:\n
+#               lambda_c = %f * A^ %f * d^ %f \n
+#               mu = %f * A^ -%f\n
+#               K = %f * A^ %f\n
+#               M * gamma = %f * d^ -%f\n
+#               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+#                 area_interactive_clado = sprintf('Maximum likelihood parameter estimates:\n
+#               lambda_c = %f * A^ (%f + %f * log(d)) \n
+#               mu = %f * A^ -%f\n
+#               K = %f * A^ %f\n
+#               M * gamma = %f * d^ -%f\n
+#               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+#                 area_interactive_clado0 = sprintf('Maximum likelihood parameter estimates:\n
+#               lambda_c = %f * A^ (%f + %f * log(d)) \n
+#               mu = %f * A^ -%f\n
+#               K = %f * A^ %f\n
+#               M * gamma = %f * d^ -%f\n
+#               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+#                 area_interactive_clado1 = sprintf('Maximum likelihood parameter estimates:\n
+#               lambda_c = %f * A^ (%f + d/%f)) \n
+#               mu = %f * A^ -%f\n
+#               K = %f * A^ %f\n
+#               M * gamma = %f * d^ -%f\n
+#               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+#                 area_interactive_clado2 = sprintf('Maximum likelihood parameter estimates:\n
+#               lambda_c = %f * A^ (%f + d/(d + %f)) \n
+#               mu = %f * A^ -%f\n
+#               K = %f * A^ %f\n
+#               M * gamma = %f * d^ -%f\n
+#               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+#                 area_interactive_clado3 = sprintf('Maximum likelihood parameter estimates:\n
+#               lambda_c = %f * (A + d/%f)^ %f\n \n
+#               mu = %f * A^ -%f\n
+#               K = %f * A^ %f\n
+#               M * gamma = %f * d^ -%f\n
+#               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[11],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+#                 area_interactive_clado4 = sprintf('Maximum likelihood parameter estimates:\n
+#               lambda_c = %f * A^ (%f * d/(d + %f)) \n
+#               mu = %f * A^ -%f\n
+#               K = %f * A^ %f\n
+#               M * gamma = %f * d^ -%f\n
+#               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10])
+#    )
+#    return(s1)
+# }
   if(is.element(distance_dep,distance_dep_options1))
   {
     out2 = data.frame(lambda_c0 = MLpars1[1], y = MLpars1[2], mu_0 = MLpars1[3], x = MLpars1[4], K_0 = MLpars1[5], z = MLpars1[6], gamma_0 = MLpars1[7], alpha = MLpars1[8], lambda_a0 = MLpars1[9], beta = MLpars1[10], d_0 = MLpars1[11], loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
@@ -567,6 +566,9 @@ DAISIE_MW_ML = function(
     {
       out2 = data.frame(lambda_c0 = MLpars1[1], y = MLpars1[2], mu_0 = MLpars1[3], x = MLpars1[4], K_0 = MLpars1[5], z = MLpars1[6], gamma_0 = MLpars1[7], alpha = MLpars1[8], lambda_a0 = MLpars1[9], beta = MLpars1[10], loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
     }
-  cat("\n",s1output(MLpars1,distance_dep),"\n",s2,"\n")
+  #cat("\n",s1output(MLpars1,distance_dep),"\n",s2,"\n")
+  s1 <- c('Parameters:', format(MLpars1, format = 'f', digits = 6))
+  s2 <- c('Maximum loglikelihood:',format(ML, format = 'f', digits = 6))
+  cat("\n",s1,"\n",s2,"\n", sep = ' ')
   return(invisible(out2))
 }
diff --git a/R/DAISIE_SR_ML_CS.R b/R/DAISIE_SR_ML_CS.R
index 76b0b3fd..83b522ad 100644
--- a/R/DAISIE_SR_ML_CS.R
+++ b/R/DAISIE_SR_ML_CS.R
@@ -427,8 +427,19 @@ DAISIE_SR_ML_CS <- DAISIE_SR_ML <- function(
     MLpars1[8] <- Inf
   }
   out2 <- data.frame(lambda_c = MLpars1[1], mu = MLpars1[2], K = MLpars1[3], gamma = MLpars1[4], lambda_a = MLpars1[5], lambda_c2 = MLpars1[6], mu2 = MLpars1[7], K2 = MLpars1[8], gamma2 = MLpars1[9], lambda_a2 = MLpars1[10], tshift = MLpars1[11], loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
-  s1 <- sprintf("Maximum likelihood parameter estimates: lambda_c: %f, mu: %f, K: %f, gamma: %f, lambda_a: %f, lambda_c2: %f, mu2: %f, K2: %f, gamma2: %f, lambda_a2: %f, time of shift: %f", MLpars1[1], MLpars1[2], MLpars1[3], MLpars1[4], MLpars1[5], MLpars1[6], MLpars1[7], MLpars1[8], MLpars1[9], MLpars1[10], MLpars1[11])
-  s2 <- sprintf("Maximum loglikelihood: %f", ML)
-  cat("\n", s1, "\n", s2, "\n")
+  s1 <- c('Maximum likelihood parameter estimates:',
+          '\n lambda_c:', format(MLpars1[1], format = 'f', digits = 6),
+          '\n mu:', format(MLpars1[2], format = 'f', digits = 6),
+          '\n K:', format(MLpars1[3], format = 'f', digits = 6),
+          '\n gamma:', format(MLpars1[4], format = 'f', digits = 6),
+          '\n lambda_a:', format(MLpars1[5], format = 'f', digits = 6),
+          '\n lambda_c2:', format(MLpars1[6], format = 'f', digits = 6),
+          '\n mu2:', format(MLpars1[7], format = 'f', digits = 6),
+          '\n K2:', format(MLpars1[8], format = 'f', digits = 6),
+          '\n gamma2:', format(MLpars1[9], format = 'f', digits = 6),
+          '\n lambda_a2:', format(MLpars1[10], format = 'f', digits = 6),
+          '\n time of shift:', format(MLpars1[11], format = 'f', digits = 6))
+  s2 <- c('Maximum loglikelihood:', format(ML, format = 'f', digits = 6))
+  cat("\n", s1, "\n", s2, "\n", sep = ' ')
   return(invisible(out2))
 }
diff --git a/R/DAISIE_SR_loglik_CS.R b/R/DAISIE_SR_loglik_CS.R
index adc596c0..e0d04012 100644
--- a/R/DAISIE_SR_loglik_CS.R
+++ b/R/DAISIE_SR_loglik_CS.R
@@ -234,9 +234,13 @@ DAISIE_SR_loglik_CS_M1 <- DAISIE_SR_loglik <- function(
   #print(head(probs,n = 15))
   if (pars2[4] >= 1) {
     # if (length(pars1 > 5)) {
-      s1 <- sprintf("Status of colonist: %d, Parameters: %f %f %f %f %f ", stac, pars1[1], pars1[2], pars1[3], pars1[4], pars1[5])
+    s1 <- c('Status of colonist:',
+              format(stac, format = 'd'),
+              '\n Parameters:',
+              format(pars1[1:5], format = 'f', digits = 6))
     # }
-    s2 <- sprintf(", Loglikelihood: %f", loglik)
+    s2 <- c('\n Loglikelihood:',
+            format(loglik, format = 'f', digits = 6))
     cat(s1, s2, "\n", sep = "")
     utils::flush.console()
   }
diff --git a/R/DAISIE_loglik_CS.R b/R/DAISIE_loglik_CS.R
index a108688a..f69fd266 100644
--- a/R/DAISIE_loglik_CS.R
+++ b/R/DAISIE_loglik_CS.R
@@ -678,20 +678,19 @@ DAISIE_loglik_CS_M1 <- DAISIE_loglik <- function(pars1,
   if(pars2[4] >= 1)
   {
     if (length(pars1) == 11) { # CHANGE
-      s1 <- sprintf('Status of colonist: %d, Parameters: %f %f %f %f %f %f', stac, pars1[5], pars1[6], pars1[7], pars1[8], pars1[9], pars1[10])
+      s1 <- c('Status of colonist:',
+              format(stac, format = 'd'),
+              '\n Parameters:',
+              format(pars1[6:11], format = 'f', digits = 6))
     } else {
-      s1 <- sprintf(
-        "Status of colonist: %d, Parameters: %f %f %f %f %f ",
-        stac,
-        pars1[1],
-        pars1[2],
-        pars1[3],
-        pars1[4],
-        pars1[5]
-      )
+      s1 <- c('Status of colonist:',
+              format(stac, format = 'd'),
+              '\n Parameters:',
+              format(pars1[1:5], format = 'f', digits = 6))
     }
-    s2 <- sprintf(", Loglikelihood: %f", loglik)
-    cat(s1, s2, "\n", sep = "")
+    s2 <- c('\n Loglikelihood:',
+             format(loglik, format = 'f', digits = 6))
+    cat(s1, s2, "\n", sep = " ")
     utils::flush.console()
   }
   if (is.na(loglik)) {
@@ -1044,13 +1043,14 @@ DAISIE_loglik_CS <- DAISIE_loglik_all <- function(
   return(loglik)
 }
 
-print_parameters_and_loglik <- function(pars, loglik, verbose)
+print_parameters_and_loglik <- function(pars, loglik, verbose, dgts = 6)
 {
   if (verbose >= 1) {
-    s1 <- sprintf("Parameters: ")
-    s2 <- sprintf("%f ", pars)
-    s3 <- sprintf(", Loglikelihood: %f", loglik)
-    cat(s1, s2, s3, "\n", sep = "")
+    s1 <- c('Parameters:',
+            format(pars, format = 'f', digits = dgts))
+    s2 <- c('Loglikelihood:',
+            format(loglik, format = 'f', digits = dgts))
+    cat(s1, "\n", s2, "\n", sep = " ")
     utils::flush.console()
   }
 }

From 7097a0c5eec9131867f8abb51111f5c2ccf9ec4c Mon Sep 17 00:00:00 2001
From: Hanno Hildenbrandt <h.hildenbrandt@rug.nl>
Date: Thu, 22 Dec 2022 20:33:29 +0100
Subject: [PATCH 42/73] src/DAISIE_CS.cpp rewritten along R code

Signed-off-by: Hanno Hildenbrandt <h.hildenbrandt@rug.nl>
---
 R/DAISIE_loglik_CS.R |  10 +-
 src/DAISIE_CS.cpp    | 405 +++++++++++++------------------------------
 src/DAISIE_odeint.h  |  22 +++
 3 files changed, 145 insertions(+), 292 deletions(-)

diff --git a/R/DAISIE_loglik_CS.R b/R/DAISIE_loglik_CS.R
index d605c311..14a4800f 100644
--- a/R/DAISIE_loglik_CS.R
+++ b/R/DAISIE_loglik_CS.R
@@ -133,7 +133,6 @@ DAISIE_loglik_rhs <- function(t, x, parsvec) {
     -(muvec[il3 + 1] + lacvec[il3 + 1]) * nn[in3 + 1] * xx2[ix3] +
     -laavec[il3 + 1] * xx2[ix3]
   dx3 <- 0
-
   return(list(c(dx1,dx2,dx3)))
 }
 
@@ -310,8 +309,9 @@ checkprobs2 <- function(lv, loglik, probs, verbose) {
   } else if (sum(probs) <= 0) {
     loglik <- -Inf
   } else {
-    loglik = loglik + log(sum(probs))
-    probs = probs/sum(probs)
+    sp <- sum(sort(probs))
+    loglik = loglik + log(sp)
+    probs = probs/sp
   }
   if (verbose) {
     message("Numerical issues encountered \n")
@@ -680,7 +680,7 @@ DAISIE_loglik_CS_M1 <- DAISIE_loglik <- function(pars1,
       s1 <- sprintf('Status of colonist: %d, Parameters: %f %f %f %f %f %f', stac, pars1[5], pars1[6], pars1[7], pars1[8], pars1[9], pars1[10])
     } else {
       s1 <- sprintf(
-        "Status of colonist: %d, Parameters: %f %f %f %f %f ",
+        "Status of colonist: %d, Parameters: %f %f %f %f %f",
         stac,
         pars1[1],
         pars1[2],
@@ -1193,6 +1193,8 @@ DAISIE_ode_cs <- function(
                       times = tvec,
                       func = rhs_func,
                       parms = parsvec,
+                      atol = atol,
+                      rtol = rtol,
                       method = methode)[,1:(N + 1)]
     probs <- y[-1,-1]
   } else {
diff --git a/src/DAISIE_CS.cpp b/src/DAISIE_CS.cpp
index 902ffdeb..0cb7be55 100644
--- a/src/DAISIE_CS.cpp
+++ b/src/DAISIE_CS.cpp
@@ -21,29 +21,6 @@ namespace {
   static constexpr double default_abm_factor = 0.0001;
   static double abm_factor = default_abm_factor;
 
-  //
-  class padded_vector_view
-  {
-  public:
-    padded_vector_view(int pad, const double* data, int n) :
-    data_(data), pad_(pad), n_(n)
-    {
-    }
-
-    // return 0.0 for indices 'i' outside [pad, pad + n)
-    double operator[](int i) const
-    {
-      const auto ii = i - pad_;
-      return (ii >= 0 && i < n_) ? *(data_ + ii) : 0.0;
-    }
-
-  private:
-    const double* data_ = nullptr;  // this->operator[pad_] == *data_
-    int pad_ = 0;
-    int n_ = 0;
-  };
-
-
   // common parameter
   struct param_t
   {
@@ -68,26 +45,13 @@ namespace {
     }
 
     // odeint interface
-    void operator()(const state_type& x, state_type& dx, double) const
+    void operator()(const state_type& x, state_type& dx, double t) const
     {
       if (++p_.steps > max_cs_steps) throw std::runtime_error("cpp_daisie_cs_runmod: too many steps");
 
-      // xx1 = c(0,0,x[1:lx],0)
-      // xx2 = c(0,0,x[(lx + 1):(2 * lx)],0)
-      // xx3 = x[2 * lx + 1]
-      // using padded views instead of vectors:
-      const auto xx1 = padded_vector_view(2, x.data().begin(), p_.lx);
-      const auto xx2 = padded_vector_view(2, x.data().begin() + p_.lx, p_.lx);
-      const auto xx3 = x[2 * p_.lx];
-
-      // DO I = 1, N + 4 + 2 * kk
-      //   laavec(I) = P(I)
-      //   lacvec(I) = P(I + N + 4 + 2 * kk)
-      //   muvec(I)  = P(I + 2 * (N + 4 + 2 * kk))
-      //   gamvec(I) = P(I + 3 * (N + 4 + 2 * kk))
-      //   nn(I)     = P(I + 4 * (N + 4 + 2 * kk))
-      // ENDDO
-      // using views instead of vectors:
+      const auto xx1 = padded_vector_view<2>(x.data().begin(), p_.lx);
+      const auto xx2 = padded_vector_view<2>(x.data().begin() + p_.lx, p_.lx);
+
       const auto chunk = p_.lx + 4 + 2 * p_.kk;
       const auto laavec = p_.P.data().begin();
       const auto lacvec = p_.P.data().begin() + chunk;
@@ -95,78 +59,41 @@ namespace {
       const auto gamvec = p_.P.data().begin() + 3 * chunk;
       const auto nn = p_.P.data().begin() + 4 * chunk;
 
-      // DO I = 3, N + 2
-      //   il1(I - 2) = I + kk - 1
-      //   il2(I - 2) = I + kk + 1
-      //   il3in3(I - 2) = I + kk
-      //   il4(I - 2) = I + kk - 2
-      //   in1(I - 2) = I + 2 * kk - 1
-      //   in2ix2(I - 2) = I + 1
-      //   ix1(I - 2) = I - 1
-      //   ix3(I - 2) = I
-      //   ix4(I - 2) = I - 2
-      // ENDDO
       // using offsets into our views instead of vectors:
-      const int il1 = 2 + p_.kk - 1;
-      const int il2 = 2 + p_.kk + 1;
-      const int il3in3 = 2 + p_.kk;
-      const int il4 = 2 + p_.kk - 2;
-      const int in1 = 2 + 2 * p_.kk - 1;
-      const int in2ix2 = 2 + 1;
-      const int ix1 = 2 - 1;
-      const int ix3 = 2;
-      const int ix4 = 2 - 2;
-
-      // DO I = 1, N
-      //   FF1 = laavec(il1(I) + 1) * xx2(ix1(I))
-      //   FF1 = FF1 + lacvec(il4(I) + 1) * xx2(ix4(I))
-      //   FF1 = FF1 + muvec(il2(I) + 1) * xx2(ix3(I))
-      //   FF1 = FF1 + lacvec(il1(I)) * nn(in1(I)) * xx1(ix1(I))
-      //   FF1 = FF1 + muvec(il2(I)) * nn(in2ix2(I)) * xx1(in2ix2(I))
-      //   FFF = (muvec(il3in3(I)) + lacvec(il3in3(I)))
-      //   FF1 = FF1 - FFF * nn(il3in3(I)) * xx1(ix3(I))
-      //   FF1 = FF1 - gamvec(il3in3(I)) * xx1(ix3(I))
-      //   dConc(I) = FF1
-      //   FF1 = gamvec(il3in3(I)) * xx1(ix3(I))
-      //   FF1 = FF1 + lacvec(il1(I) + 1) * nn(in1(I)) * xx2(ix1(I))
-      //   FF1 = FF1 + muvec(il2(I)+1) * nn(in2ix2(I)) * xx2(in2ix2(I))
-      //   FFF = muvec(il3in3(I) + 1) + lacvec(il3in3(I) + 1)
-      //   FF1 = FF1 - FFF * nn(il3in3(I) + 1) * xx2(ix3(I))
-      //   FF1 = FF1 - laavec(il3in3(I) + 1) * xx2(ix3(I))
-      //   dConc(N + I) = FF1
-      // ENDDO
-      // using views into output vector:
+      const int nil2lx = 2;
+      const int il1 = nil2lx + p_.kk - 1;
+      const int il2 = nil2lx + p_.kk + 1;
+      const int il3 = nil2lx + p_.kk;
+      const int il4 = nil2lx + p_.kk - 2;
+
+      const int in1 = nil2lx + 2 * p_.kk - 1;
+      const int in2 = nil2lx + 1;
+      const int in3 = nil2lx + p_.kk;
+
+      const int ix1 = nil2lx - 1;
+      const int ix2 = nil2lx + 1;
+      const int ix3 = nil2lx;
+      const int ix4 = nil2lx - 2;
+
       auto dx1 = dx.data().begin();
       auto dx2 = dx1 + p_.lx;
+      auto dx3 = dx2 + p_.lx;
+      // Note: in C++, '+1' is dealt with by the compiler
       for (int i = 0; i < p_.lx; ++i) {
         dx1[i] = laavec[il1 + i + 1] * xx2[ix1 + i]
                + lacvec[il4 + i + 1] * xx2[ix4 + i]
                + muvec[il2 + i + 1] * xx2[ix3 + i]
                + lacvec[il1 + i] * nn[in1 + i] * xx1[ix1 + i]
-               + muvec[il2 + i] * nn[in2ix2 + i] * xx1[in2ix2 + i]
-               - (muvec[il3in3 + i] + lacvec[il3in3 + i]) * nn[il3in3 + i] * xx1[ix3 + i]
-               - gamvec[il3in3 + i] * xx1[ix3 + i];
-        dx2[i] = gamvec[il3in3 + i] * xx1[ix3 + i]
+               + muvec[il2 + i] * nn[in2 + i] * xx1[ix2 + i]
+               - (muvec[il3 + i] + lacvec[il3 + i]) * nn[in3 + i] * xx1[ix3 + i]
+               - gamvec[il3 + i] * xx1[ix3 + i];
+        dx2[i] = gamvec[il3 + i] * xx1[ix3 + i]
                + lacvec[il1 + i + 1] * nn[in1 + i] * xx2[ix1 + i]
-               + muvec[il2 + i + 1] * nn[in2ix2 + i] * xx2[in2ix2 + i]
-               - (muvec[il3in3 + 1 + i] + lacvec[il3in3 + 1 + i]) * nn[il3in3 + i + 1] * xx2[ix3 + i]
-               - laavec[il3in3 + i] * xx2[ix3 + i];
+               + muvec[il2 + i + 1] * nn[in2 + i] * xx2[ix2 + i]
+               - (muvec[il3 + 1 + i] + lacvec[il3 + 1 + i]) * nn[in3 + i + 1] * xx2[ix3 + i]
+               - laavec[il3 + i] * xx2[ix3 + i];
       }
-
-      // IF(kk .EQ. 1) THEN
-      //   dConc(1) = dConc(1) + laavec(il3in3(1)) * xx3
-      //   dConc(2) = dConc(2) + 2 * lacvec(il3in3(1)) * xx3
-      // ENDIF
-      // if (1 == p_.kk) {
-      //  dx1[0] += laavec[il3in3] * xx3;
-      //  dx2[1] += 2.0 * lacvec[il3in3] * xx3;
-      //}
-
-      // FFF = laavec(il3in3(1)) + lacvec(il3in3(1))
-      // FFF = FFF + gamvec(il3in3(1)) + muvec(il3in3(1))
-      // dConc(2 * N + 1) = -1 * FFF * xx3
-      auto dx3 = dx2 + p_.lx;
-      dx3[0] = -(laavec[il3in3] + lacvec[il3in3] + gamvec[il3in3] + muvec[il3in3]) * xx3;
+      dx3[0] = 0.0;
     }
 
   private:
@@ -176,8 +103,8 @@ namespace {
   class cpp_daisie_cs_runmod_1
   {
   public:
-    cpp_daisie_cs_runmod_1(param_t&& p) :
-    p_(p)
+    cpp_daisie_cs_runmod_1(param_t&& par) :
+      p_(std::move(par))
     {
     }
 
@@ -186,24 +113,11 @@ namespace {
     {
       if (++p_.steps > max_cs_steps) throw std::runtime_error("cpp_daisie_cs_runmod_1: too many steps");
 
-      // xx1 = c(0,0,x[1:lx],0)
-      // xx2 = c(0,0,x[(lx + 1):(2 * lx)],0)
-      // xx3 = c(0,0,x[(2 * lx + 1):(3 * lx)],0)
-      // xx4 <- c(0,0,x[(3 * lx + 1):(4 * lx)],0)
-      // using padded views instead of vectors:
-      const auto xx1 = padded_vector_view(2, x.data().begin(), p_.lx);
-      const auto xx2 = padded_vector_view(2, x.data().begin() + p_.lx, p_.lx);
-      const auto xx3 = padded_vector_view(2, x.data().begin() + 2 * p_.lx, p_.lx);
-      const auto xx4 = padded_vector_view(2, x.data().begin() + 3 * p_.lx, p_.lx);
-
-      // DO I = 1, N + 4 + 2 * kk
-      //   laavec(I) = P(I)
-      //   lacvec(I) = P(I + N + 4 + 2 * kk)
-      //   muvec(I)  = P(I + 2 * (N + 4 + 2 * kk))
-      //   gamvec(I) = P(I + 3 * (N + 4 + 2 * kk))
-      //   nn(I)     = P(I + 4 * (N + 4 + 2 * kk))
-      // ENDDO
-      // using views instead of vectors:
+      const auto xx1 = padded_vector_view<2>(x.data().begin(), p_.lx);
+      const auto xx2 = padded_vector_view<2>(x.data().begin() + p_.lx, p_.lx);
+      const auto xx3 = padded_vector_view<2>(x.data().begin() + 2 * p_.lx, p_.lx);
+      const auto xx4 = padded_vector_view<2>(x.data().begin() + 3 * p_.lx, p_.lx);
+
       const auto chunk = p_.lx + 4 + 2 * p_.kk;
       const auto laavec = p_.P.data().begin();
       const auto lacvec = p_.P.data().begin() + chunk;
@@ -211,93 +125,53 @@ namespace {
       const auto gamvec = p_.P.data().begin() + 3 * chunk;
       const auto nn = p_.P.data().begin() + 4 * chunk;
 
-      // DO I = 3, N + 2
-      //   il1(I - 2) = I + kk - 1
-      //   il2(I - 2) = I + kk + 1
-      //   il3in3(I - 2) = I + kk
-      //   il4(I - 2) = I + kk - 2
-      //   in1(I - 2) = I + 2 * kk - 1
-      //   in2ix2(I - 2) = I + 1
-      //   in4ix1(I - 2) = I - 1
-      //   ix3(I - 2) = I
-      //   ix4(I - 2) = I - 2
-      // ENDDO
       // using offsets into our views instead of vectors:
-      const int il1 = 2 + p_.kk - 1;
-      const int il2 = 2 + p_.kk + 1;
-      const int il3in3 = 2 + p_.kk;
-      const int il4 = 2 + p_.kk - 2;
-      const int in1 = 2 + 2 * p_.kk - 1;
-      const int in2ix2 = 2 + 1;   // spilt in in2, ix2 at no cost?
-      const int in4ix1 = 2 - 1;   // split in in4, ix1 at no cost?
-      const int ix3 = 2;
-      const int ix4 = 2 - 2;
-
-      //DO I = 1, N
-      //  FF1 = lacvec(il1(I)) * xx1(in4ix1(I))
-      //  FF1 = FF1 + laavec(il1(I) + 1) * xx2(in4ix1(I))
-      //  FF1 = FF1 + lacvec(il4(I) + 1) * xx2(ix4(I))
-      //  FF1 = FF1 + muvec(il2(I)) * nn(in2ix2(I)) * xx1(in2ix2(I))
-      //  FF1 = FF1 + muvec(il3in3(I) + 1) * xx2(ix3(I))
-      //  FFF = muvec(il3in3(I)) + lacvec(il3in3(I))
-      //  FF1 = FF1 - FFF * nn(il3in3(I)) * xx1(ix3(I))
-      //  dConc(I) = FF1 - gamvec(il3in3(I)) * xx1(ix3(I))
-      //  FF1 = gamvec(il3in3(I)) * xx1(ix3(I))
-      //  FF1 = FF1 + gamvec(il3in3(I)) * xx3(ix3(I))
-      //  FF1 = FF1 + gamvec(il3in3(I) + 1) * xx4(ix3(I))
-      //  FF1 = FF1 + lacvec(il1(I) + 1) * nn(in1(I)) * xx2(in4ix1(I))
-      //  FF1 = FF1 + muvec(il2(I) + 1) * nn(in2ix2(I)) * xx2(in2ix2(I))
-      //  FFF = muvec(il3in3(I) + 1) + lacvec(il3in3(I) + 1)
-      //  FF1 = FF1 - FFF * nn(il3in3(I) + 1) * xx2(ix3(I))
-      //  FF1 = FF1 - laavec(il3in3(I) + 1) * xx2(ix3(I))
-      //  dConc(N + I) = FF1
-      //  FF1 = lacvec(il1(I)) * nn(in1(I)) * xx3(in4ix1(I))
-      //  FF1 = FF1 + laavec(il1(I) + 1) * xx4(in4ix1(I))
-      //  FF1 = FF1 + lacvec(il4(I) + 1) * xx4(ix4(I))
-      //  FF1 = FF1 + muvec(il2(I)) * nn(in2ix2(I)) * xx3(in2ix2(I))
-      //  FF1 = FF1 + muvec(il3in3(I) + 1) * xx4(ix3(I))
-      //  FFF = lacvec(il3in3(I)) + muvec(il3in3(I))
-      //  FF1 = FF1 - FFF * nn(il3in3(I)) * xx3(ix3(I))
-      //  FF1 = FF1 - gamvec(il3in3(I)) * xx3(ix3(I))
-      //  dConc(2 * N + I) = FF1
-      //  FF1 = lacvec(il1(I) + 1) * nn(in1(I)) * xx4(in4ix1(I))
-      //  FF1 = FF1 + muvec(il2(I) + 1) * nn(in2ix2(I)) * xx4(in2ix2(I))
-      //  FFF = lacvec(il3in3(I) + 1) + muvec(il3in3(I) + 1)
-      //  FF1 = FF1 - FFF * nn(il3in3(I) + 1) * xx4(ix3(I))
-      //  FF1 = FF1 - gamvec(il3in3(I) + 1) * xx4(ix3(I))
-      //  dConc(3 * N + I) = FF1
-      //ENDDO
+      const int nil2lx = 2;
+      const int il1 = nil2lx + p_.kk - 1;
+      const int il2 = nil2lx + p_.kk + 1;
+      const int il3 = nil2lx + p_.kk;
+      const int il4 = nil2lx + p_.kk - 2;
+
+      const int in1 = nil2lx + 2 * p_.kk - 1;
+      const int in2 = nil2lx + 1;
+      const int in3 = nil2lx + p_.kk;
+
+      const int ix1 = nil2lx - 1;
+      const int ix2 = nil2lx + 1;
+      const int ix3 = nil2lx;
+      const int ix4 = nil2lx - 2;
+
       // using views into output vector:
       auto dx1 = dx.data().begin();
       auto dx2 = dx1 + p_.lx;
       auto dx3 = dx2 + p_.lx;
       auto dx4 = dx3 + p_.lx;
       for (int i = 0; i < p_.lx; ++i) {
-        dx1[i] = lacvec[il1 + i] * nn[in1 + i] * xx1[in4ix1 + i]
-        + laavec[il1 + i + 1] * xx2[in4ix1 + i]
-        + lacvec[il4 + i + 1] * xx2[ix4 + i]
-        + muvec[il2 + i] * nn[in2ix2 + i] * xx1[in2ix2 + i]
-        + muvec[il3in3 + i + 1] * xx2[ix3 + i]
-        - (muvec[il3in3 + i] + lacvec[il3in3 + i]) * nn[il3in3 + i] * xx1[ix3 + i]
-        - gamvec[il3in3 + i] * xx1[ix3 + i];
-        dx2[i] = gamvec[il3in3 + i] * xx1[ix3 + i]
-        + gamvec[il3in3 + i] * xx3[ix3 + i]
-        + gamvec[il3in3 + i + 1] * xx4[ix3 + i]
-        + lacvec[il1 + i + 1] * nn[in1 + i] * xx2[in4ix1 + i]
-        + muvec[il2 + i + 1] * nn[in2ix2 + i] * xx2[in2ix2 + i]
-        - (muvec[il3in3 + 1 + i] + lacvec[il3in3 + 1 + i]) * nn[il3in3 + i + 1] * xx2[ix3 + i]
-        - laavec[il3in3 + i] * xx2[ix3 + i];
-        dx3[i] = lacvec[il1 + i] * nn[in1 + i] * xx3[in4ix1 + i]
-        + laavec[il1 + i + 1] * xx4[in4ix1 + i]
-        + lacvec[il4 + i + 1] * xx4[ix4 + i]
-        + muvec[il2 + i] * nn[in2ix2 + i] * xx3[in2ix2 + i]
-        + muvec[il3in3 + i + 1] * xx4[ix3 + i]
-        - (lacvec[il3in3 + i] + muvec[il3in3 + i]) * nn[il3in3 + i] * xx3[ix3 + i]
-        - gamvec[il3in3 + i] * xx3[ix3 + i];
-        dx4[i] = lacvec[il1 + i + 1] * nn[in1 + i] * xx4[in4ix1 + i]
-        + muvec[il2 + i + 1] * nn[in2ix2 + i] * xx4[in2ix2 + i]
-        - (lacvec[il3in3 + i + 1] + muvec[il3in3 + i + 1]) * nn[il3in3 + i + 1] * xx4[ix3 + i]
-        - gamvec[il3in3 + i + 1] * xx4[ix3 + i];
+        dx1[i] = lacvec[il1 + i] * nn[in1 + i] * xx1[ix1 + i]
+               + laavec[il1 + i + 1] * xx2[ix1 + i]
+               + lacvec[il4 + i + 1] * xx2[ix4 + i]
+               + muvec[il2 + i] * nn[in2 + i] * xx1[ix2 + i]
+               + muvec[il3 + i + 1] * xx2[ix3 + i]
+               - (muvec[il3 + i] + lacvec[il3 + i]) * nn[in3 + i] * xx1[ix3 + i]
+               - gamvec[il3 + i] * xx1[ix3 + i];
+        dx2[i] = gamvec[il3 + i] * xx1[ix3 + i]
+               + gamvec[il3 + i] * xx3[ix3 + i]
+               + gamvec[il3 + i + 1] * xx4[ix3 + i]
+               + lacvec[il1 + i + 1] * nn[in1 + i] * xx2[ix1 + i]
+               + muvec[il2 + i + 1] * nn[in2 + i] * xx2[ix2 + i]
+               - (muvec[il3 + 1 + i] + lacvec[il3 + 1 + i]) * nn[in3 + i + 1] * xx2[ix3 + i]
+               - laavec[il3 + i] * xx2[ix3 + i];
+        dx3[i] = lacvec[il1 + i] * nn[in1 + i] * xx3[ix1 + i]
+               + laavec[il1 + i + 1] * xx4[ix1 + i]
+               + lacvec[il4 + i + 1] * xx4[ix4 + i]
+               + muvec[il2 + i] * nn[in2 + i] * xx3[ix2 + i]
+               + muvec[il3 + i + 1] * xx4[ix3 + i]
+               - (lacvec[il3 + i] + muvec[il3 + i]) * nn[in3 + i] * xx3[ix3 + i]
+               - gamvec[il3 + i] * xx3[ix3 + i];
+        dx4[i] = lacvec[il1 + i + 1] * nn[in1 + i] * xx4[ix1 + i]
+               + muvec[il2 + i + 1] * nn[in2 + i] * xx4[ix2 + i]
+               - (lacvec[il3 + i + 1] + muvec[il3 + i + 1]) * nn[in3 + i + 1] * xx4[ix3 + i]
+               - gamvec[il3 + i + 1] * xx4[ix3 + i];
       }
     }
 
@@ -309,8 +183,8 @@ namespace {
   class cpp_daisie_cs_runmod_2
   {
   public:
-    cpp_daisie_cs_runmod_2(param_t&& p) :
-      p_(p)
+    cpp_daisie_cs_runmod_2(param_t&& par) :
+      p_(std::move(par))
     {
     }
 
@@ -319,22 +193,10 @@ namespace {
     {
       if (++p_.steps > max_cs_steps) throw std::runtime_error("cpp_daisie_cs_runmod_2: too many steps");
 
-      // xx1 = c(0,0,x[1:lx],0)
-      // xx2 = c(0,0,x[(lx + 1):(2 * lx)],0)
-      // xx3 = c(0,0,x[(2 * lx + 1):(3 * lx)],0)
-      // using padded views instead of vectors:
-      const auto xx1 = padded_vector_view(2, x.data().begin(), p_.lx);
-      const auto xx2 = padded_vector_view(2, x.data().begin() + p_.lx, p_.lx);
-      const auto xx3 = padded_vector_view(2, x.data().begin() + 2 * p_.lx, p_.lx);
-
-      // DO I = 1, N + 4 + 2 * kk
-      //   laavec(I) = P(I)
-      //   lacvec(I) = P(I + N + 4 + 2 * kk)
-      //   muvec(I)  = P(I + 2 * (N + 4 + 2 * kk))
-      //   gamvec(I) = P(I + 3 * (N + 4 + 2 * kk))
-      //   nn(I)     = P(I + 4 * (N + 4 + 2 * kk))
-      // ENDDO
-      // using views instead of vectors:
+      const auto xx1 = padded_vector_view<2>(x.data().begin(), p_.lx);
+      const auto xx2 = padded_vector_view<2>(x.data().begin() + p_.lx, p_.lx);
+      const auto xx3 = padded_vector_view<2>(x.data().begin() + 2 * p_.lx, p_.lx);
+
       const auto chunk = p_.lx + 4 + 2 * p_.kk;
       const auto laavec = p_.P.data().begin();
       const auto lacvec = p_.P.data().begin() + chunk;
@@ -342,81 +204,47 @@ namespace {
       const auto gamvec = p_.P.data().begin() + 3 * chunk;
       const auto nn = p_.P.data().begin() + 4 * chunk;
 
-      // DO I = 3, N + 2
-      //   il1(I - 2) = I + kk - 1
-      //   il2(I - 2) = I + kk + 1
-      //   il3in3(I - 2) = I + kk
-      //   il4(I - 2) = I + kk - 2
-      //   in1(I - 2) = I + 2 * kk - 1
-      //   in2ix2(I - 2) = I + 1
-      //   in4ix1(I - 2) = I - 1
-      //   ix3(I - 2) = I
-      //   ix4(I - 2) = I - 2
-      // ENDDO
       // using offsets into our views instead of vectors:
-      const int il1 = 2 + p_.kk - 1;
-      const int il2 = 2 + p_.kk + 1;
-      const int il3in3 = 2 + p_.kk;
-      const int il4 = 2 + p_.kk - 2;
-      const int in1 = 2 + 2 * p_.kk - 1;
-      const int in2ix2 = 2 + 1;   // spilt in in2, ix2 at no cost?
-      const int in4ix1 = 2 - 1;   // split in in4, ix1 at no cost?
-      const int ix3 = 2;
-      const int ix4 = 2 - 2;
-
-      // DO I = 1, N
-      //   FF1 = laavec(il1(I) + 1) * xx2(in4ix1(I))
-      //   FF1 = FF1 + lacvec(il4(I) + 1) * xx2(ix4(I))
-      //   FF1 = FF1 + muvec(il2(I) + 1) * xx2(ix3(I))
-      //   FF1 = FF1 + lacvec(il1(I)) * nn(in1(I)) * xx1(in4ix1(I))
-      //   FF1 = FF1 + muvec(il2(I)) * nn(in2ix2(I)) * xx1(in2ix2(I))
-      //   FFF = muvec(il3in3(I)) + lacvec(il3in3(I))
-      //   FF1 = FF1 - FFF * nn(il3in3(I)) * xx1(ix3(I))
-      //   FF1 = FF1 - gamvec(il3in3(I)) * xx1(ix3(I))
-      //   FFF = 0
-      //   IF(kk .EQ. 1) THEN
-      //     FFF = laavec(il3in3(I)) * xx3(ix3(I))
-      //     FFF = FFF + 2 * lacvec(il1(I)) * xx3(in4ix1(I))
-      //   ENDIF
-      //   dConc(I) = FF1 + FFF
-      //   FF1 = gamvec(il3in3(I)) * xx1(ix3(I))
-      //   FF1 = FF1 + lacvec(il1(I) + 1) * nn(in1(I)) * xx2(in4ix1(I))
-      //   FF1 = FF1 + muvec(il2(I)+1) * nn(in2ix2(I)) * xx2(in2ix2(I))
-      //   FFF = muvec(il3in3(I) + 1) + lacvec(il3in3(I) + 1)
-      //   FF1 = FF1 - FFF * nn(il3in3(I) + 1) * xx2(ix3(I))
-      //   FF1 = FF1 - laavec(il3in3(I) + 1) * xx2(ix3(I))
-      //   dConc(N + I) = FF1
-      //   FF1 = lacvec(il1(I)) * nn(in4ix1(I)) * xx3(in4ix1(I))
-      //   FF1 = FF1 + muvec(il2(I)) * nn(in2ix2(I)) * xx3(in2ix2(I))
-      //   FFF = lacvec(il3in3(I)) + muvec(il3in3(I))
-      //   FF1 = FF1 - FFF * nn(il3in3(I)) * xx3(ix3(I))
-      //   FF1 = FF1-(laavec(il3in3(I))+gamvec(il3in3(I)))*xx3(ix3(I))
-      //   dConc(2 * N + I) = FF1
-      // ENDDO
+      const int nil2lx = 2;
+      const int il1 = nil2lx + p_.kk - 1;
+      const int il2 = nil2lx + p_.kk + 1;
+      const int il3 = nil2lx + p_.kk;
+      const int il4 = nil2lx + p_.kk - 2;
+
+      const int in1 = nil2lx + 2 * p_.kk - 1;
+      const int in2 = nil2lx + 1;
+      const int in3 = nil2lx + p_.kk;
+      const int in4 = nil2lx-1;
+
+      const int ix1 = nil2lx - 1;
+      const int ix2 = nil2lx + 1;
+      const int ix3 = nil2lx;
+      const int ix4 = nil2lx - 2;
+
       // using views into output vector:
       auto dx1 = dx.data().begin();
       auto dx2 = dx1 + p_.lx;
       auto dx3 = dx2 + p_.lx;
       for (int i = 0; i < p_.lx; ++i) {
-        dx1[i] = laavec[il1 + i + 1] * xx2[in4ix1 + i]
+        dx1[i] = laavec[il1 + i + 1] * xx2[ix1 + i]
                + lacvec[il4 + i + 1] * xx2[ix4 + i]
                + muvec[il2 + i + 1] * xx2[ix3 + i]
-               + lacvec[il1 + i] * nn[in1 + i] * xx1[in4ix1 + i]
-               + muvec[il2 + i] * nn[in2ix2 + i] * xx1[in2ix2 + i]
-               - (muvec[il3in3 + i] + lacvec[il3in3 + i]) * nn[il3in3 + i] * xx1[ix3 + i]
-               - gamvec[il3in3 + i] * xx1[ix3 + i];
+               + lacvec[il1 + i] * nn[in1 + i] * xx1[ix1 + i]
+               + muvec[il2 + i] * nn[in2 + i] * xx1[ix2 + i]
+               - (muvec[il3 + i] + lacvec[il3 + i]) * nn[in3 + i] * xx1[ix3 + i]
+               - gamvec[il3 + i] * xx1[ix3 + i];
         if (1 == p_.kk) {
-          dx1[i] += laavec[il3in3 + i] * xx3[ix3 + i] + 2.0 * lacvec[il1 + i] * xx3[in4ix1 + i];
+          dx1[i] += laavec[il3 + i] * xx3[ix3 + i] + 2.0 * lacvec[il1 + i] * xx3[ix1 + i];
         }
-        dx2[i] = gamvec[il3in3 + i] * xx1[ix3 + i]
-               + lacvec[il1 + i + 1] * nn[in1 + i] * xx2[in4ix1 + i]
-               + muvec[il2 + i + 1] * nn[in2ix2 + i] * xx2[in2ix2 + i]
-               - (muvec[il3in3 + 1 + i] + lacvec[il3in3 + 1 + i]) * nn[il3in3 + i + 1] * xx2[ix3 + i]
-               - laavec[il3in3 + i] * xx2[ix3 + i];
-        dx3[i] = lacvec[il1 + i] * nn[in4ix1 + i] * xx3[in4ix1 + i]
-               + muvec[il2 + i] * nn[in2ix2 + i] * xx3[in2ix2 + i]
-               - (lacvec[il3in3 + i] + muvec[il3in3 + i]) * nn[il3in3 + i] * xx3[ix3 + i]
-               - (laavec[il3in3 + i] + gamvec[il3in3 + i]) * xx3[ix3 + i];
+        dx2[i] = gamvec[il3 + i] * xx1[ix3 + i]
+               + lacvec[il1 + i + 1] * nn[in1 + i] * xx2[ix1 + i]
+               + muvec[il2 + i + 1] * nn[in2 + i] * xx2[ix2 + i]
+               - (muvec[il3 + 1 + i] + lacvec[il3 + 1 + i]) * nn[in3 + i + 1] * xx2[ix3 + i]
+               - laavec[il3 + i] * xx2[ix3 + i];
+        dx3[i] = lacvec[il1 + i] * nn[in4 + i] * xx3[ix1 + i]
+               + muvec[il2 + i] * nn[in2 + i] * xx3[ix2 + i]
+               - (lacvec[il3 + i] + muvec[il3 + i]) * nn[in3 + i] * xx3[ix3 + i]
+               - (laavec[il3 + i] + gamvec[il3 + i]) * xx3[ix3 + i];
       }
     }
 
@@ -430,7 +258,7 @@ namespace {
 //' Driver for the boost::odeint solver
 //'
 //' @name daisie_odeint_cs
-RcppExport SEXP daisie_odeint_cs(SEXP rrunmod, SEXP ry, SEXP rtimes, SEXP rlx, SEXP rkk, SEXP rpar, SEXP Stepper, SEXP atolint, SEXP reltolint) {
+RcppExport SEXP daisie_odeint_cs(SEXP rrunmod, SEXP ry, SEXP rtimes, SEXP rlx, SEXP rkk, SEXP rpar, SEXP Stepper, SEXP ratol, SEXP rrtol) {
 BEGIN_RCPP
   Rcpp::RObject rcpp_result_gen;
   Rcpp::RNGScope rcpp_rngScope_gen;
@@ -440,9 +268,10 @@ BEGIN_RCPP
   auto lx = as<int>(rlx);
   auto kk = as<int>(rkk);
   auto stepper = as<std::string>(Stepper);
-  auto atol = as<double>(atolint);
-  auto rtol = as<double>(reltolint);
+  auto atol = as<double>(ratol);
+  auto rtol = as<double>(rrtol);
 
+  Rprintf("length(y): %u  ", y.size());
   auto p = param_t(lx, kk, as<state_type>(rpar));
   if (runmod == "daisie_runmod") {
     cpp_daisie_cs_runmod rhs(std::move(p));
diff --git a/src/DAISIE_odeint.h b/src/DAISIE_odeint.h
index c24a1d32..cb58fc5f 100644
--- a/src/DAISIE_odeint.h
+++ b/src/DAISIE_odeint.h
@@ -17,6 +17,28 @@ using namespace boost::numeric::odeint;
 using state_type = vector_t<double>;
 
 
+// zero-value padded view into vector
+template <int Pad>
+class padded_vector_view
+{
+public:
+  padded_vector_view(const double* data, int n) :
+    data_(data), n_(n)
+  {
+  }
+
+  // return 0.0 for indices 'i' outside [Pad, Pad + n)
+  double operator[](int i) const
+  {
+    const auto ii = i - Pad;
+    return (ii >= 0 && ii < n_) ? *(data_ + ii) : 0.0;
+  }
+
+private:
+  const double* data_ = nullptr;  // this->operator[Pad_] == *data_
+  int n_ = 0;
+};
+
 
 namespace daisie_odeint {
 

From 2a0fbd4314300810e53985ea6f1ae8dc94757700 Mon Sep 17 00:00:00 2001
From: Hanno Hildenbrandt <h.hildenbrandt@rug.nl>
Date: Fri, 23 Dec 2022 10:19:29 +0100
Subject: [PATCH 43/73] minor optimizations

Signed-off-by: Hanno Hildenbrandt <h.hildenbrandt@rug.nl>
---
 src/DAISIE_CS.cpp   | 11 ++++++-----
 src/DAISIE_odeint.h | 11 +++++------
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/DAISIE_CS.cpp b/src/DAISIE_CS.cpp
index 0cb7be55..0e3dcc03 100644
--- a/src/DAISIE_CS.cpp
+++ b/src/DAISIE_CS.cpp
@@ -78,7 +78,7 @@ namespace {
       auto dx1 = dx.data().begin();
       auto dx2 = dx1 + p_.lx;
       auto dx3 = dx2 + p_.lx;
-      // Note: in C++, '+1' is dealt with by the compiler
+
       for (int i = 0; i < p_.lx; ++i) {
         dx1[i] = laavec[il1 + i + 1] * xx2[ix1 + i]
                + lacvec[il4 + i + 1] * xx2[ix4 + i]
@@ -146,6 +146,7 @@ namespace {
       auto dx2 = dx1 + p_.lx;
       auto dx3 = dx2 + p_.lx;
       auto dx4 = dx3 + p_.lx;
+
       for (int i = 0; i < p_.lx; ++i) {
         dx1[i] = lacvec[il1 + i] * nn[in1 + i] * xx1[ix1 + i]
                + laavec[il1 + i + 1] * xx2[ix1 + i]
@@ -225,6 +226,8 @@ namespace {
       auto dx1 = dx.data().begin();
       auto dx2 = dx1 + p_.lx;
       auto dx3 = dx2 + p_.lx;
+
+      const auto kk = (1 == p_.kk) ? 1.0 : 0.0;         // make the loop body branch-free
       for (int i = 0; i < p_.lx; ++i) {
         dx1[i] = laavec[il1 + i + 1] * xx2[ix1 + i]
                + lacvec[il4 + i + 1] * xx2[ix4 + i]
@@ -232,10 +235,8 @@ namespace {
                + lacvec[il1 + i] * nn[in1 + i] * xx1[ix1 + i]
                + muvec[il2 + i] * nn[in2 + i] * xx1[ix2 + i]
                - (muvec[il3 + i] + lacvec[il3 + i]) * nn[in3 + i] * xx1[ix3 + i]
-               - gamvec[il3 + i] * xx1[ix3 + i];
-        if (1 == p_.kk) {
-          dx1[i] += laavec[il3 + i] * xx3[ix3 + i] + 2.0 * lacvec[il1 + i] * xx3[ix1 + i];
-        }
+               - gamvec[il3 + i] * xx1[ix3 + i]
+               + kk * (laavec[il3 + i] * xx3[ix3 + i] + 2.0 * lacvec[il1 + i] * xx3[ix1 + i]);
         dx2[i] = gamvec[il3 + i] * xx1[ix3 + i]
                + lacvec[il1 + i + 1] * nn[in1 + i] * xx2[ix1 + i]
                + muvec[il2 + i + 1] * nn[in2 + i] * xx2[ix2 + i]
diff --git a/src/DAISIE_odeint.h b/src/DAISIE_odeint.h
index cb58fc5f..748055c4 100644
--- a/src/DAISIE_odeint.h
+++ b/src/DAISIE_odeint.h
@@ -23,20 +23,19 @@ class padded_vector_view
 {
 public:
   padded_vector_view(const double* data, int n) :
-    data_(data), n_(n)
+    sdata_(data - Pad), sn_(n + Pad)
   {
   }
 
-  // return 0.0 for indices 'i' outside [Pad, Pad + n)
+  // returns 0.0 for indices 'i' outside [Pad, Pad + n)
   double operator[](int i) const
   {
-    const auto ii = i - Pad;
-    return (ii >= 0 && ii < n_) ? *(data_ + ii) : 0.0;
+    return (i >= Pad && i < sn_) ? *(sdata_ + i) : 0.0;
   }
 
 private:
-  const double* data_ = nullptr;  // this->operator[Pad_] == *data_
-  int n_ = 0;
+  const double* sdata_ = nullptr;  // sdata_[Pad] == data[0]
+  const int sn_ = 0;
 };
 
 

From 165140738cf99519cb2563d9d235bbff0ddd9da0 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Fri, 23 Dec 2022 16:01:00 +0100
Subject: [PATCH 44/73] Add test_odeint.R

---
 tests/testthat/test_odeint.R | 70 ++++++++++++++++++++++++++++++++++++
 1 file changed, 70 insertions(+)
 create mode 100644 tests/testthat/test_odeint.R

diff --git a/tests/testthat/test_odeint.R b/tests/testthat/test_odeint.R
new file mode 100644
index 00000000..43a2c9cd
--- /dev/null
+++ b/tests/testthat/test_odeint.R
@@ -0,0 +1,70 @@
+test_that("odeint solvers give the same result as desolve solvers", {
+  utils::data(Galapagos_datalist_2types)
+  pars1 <- c(
+    0.195442017,
+    0.087959583,
+    Inf,
+    0.002247364,
+    0.873605049,
+    3755.202241,
+    8.909285094,
+    14.99999923,
+    0.002247364,
+    0.873605049,
+    0.163
+  )
+  pars2 <- c(40, 11, 0, 1)
+  methode <- 'deSolve_R::lsodes'
+  loglik_lsodes_R <- DAISIE_loglik_all(pars1, pars2, Galapagos_datalist_2types, methode = methode)
+  methode <- 'deSolve_R::lsoda'
+  loglik_lsodes_R <- DAISIE_loglik_all(pars1, pars2, Galapagos_datalist_2types, methode = methode)
+  methode <- 'lsodes'
+  loglik_lsodes <- DAISIE_loglik_all(pars1, pars2, Galapagos_datalist_2types, methode = methode)
+  methode <- 'lsoda'
+  loglik_lsoda <- DAISIE_loglik_all(pars1, pars2, Galapagos_datalist_2types, methode = methode)
+  expect_equal(loglik_lsoda_R,loglik_lsoda)
+  expect_equal(loglik_lsodes_R,loglik_lsodes)
+  expect_equal(loglik_lsoda,loglik_lsodes)
+  methode <- 'odeint::runge_kutta_cash_karp54'
+  loglik_rkck54 <- DAISIE_loglik_all(pars1, pars2, Galapagos_datalist_2types, methode = methode)
+  methode <- 'odeint::runge_kutta_fehlberg78'
+  loglik_rkf78 <- DAISIE_loglik_all(pars1, pars2, Galapagos_datalist_2types, methode = methode)
+  methode <- 'odeint::runge_kutta_dopri5'
+  loglik_rkd5 <- DAISIE_loglik_all(pars1, pars2, Galapagos_datalist_2types, methode = methode)
+  methode <- 'odeint::bulirsch_stoer'
+  loglik_bs <- DAISIE_loglik_all(pars1, pars2, Galapagos_datalist_2types, methode = methode)
+  methode <- 'odeint::rosenbrock4'
+  loglik_rb <- DAISIE_loglik_all(pars1, pars2, Galapagos_datalist_2types, methode = methode)
+  methode <- 'odeint::adams_bashforth_moulton_1'
+  DAISIE_CS_max_steps(100000000)
+  DAISIE_abm_factor(0.000001)
+  loglik_abm <- DAISIE_loglik_all(pars1, pars2, Galapagos_datalist_2types, methode = methode)
+  logliks <- list(loglik_lsodes = loglik_lsodes,
+                  loglik_lsoda = loglik_lsoda,
+                  loglik_rkck54 = loglik_rkck54,
+                  loglik_rkf78 = loglik_rkf78,
+                  loglik_rkd5 = loglik_rkd5,
+                  loglik_bs = loglik_bs,
+                  loglik_rb = loglik_rb,
+                  loglik_abm = loglik_abm)
+  expect_equal(loglik_lsodes, loglik_rkck54)
+  expect_equal(loglik_lsodes, loglik_rkf78)
+  expect_equal(loglik_lsodes, loglik_rkd5)
+  expect_equal(loglik_lsodes, loglik_bs)
+  expect_equal(loglik_lsodes, loglik_rb)
+  expect_equal(loglik_lsodes, loglik_abm)
+
+  pars1a <- pars1
+  pars1a[6] <- Inf
+  methode <- 'deSolve_R::lsoda'
+  loglik_lsoda_R_Inf <- DAISIE_loglik_all(pars1a, pars2, Galapagos_datalist_2types, methode = methode)
+  methode <- 'lsoda'
+  loglik_lsoda_F_Inf <- DAISIE_loglik_all(pars1a, pars2, Galapagos_datalist_2types, methode = methode)
+  expect_equal(loglik_lsoda_R_Inf,loglik_lsoda_F_Inf)
+
+  methode <- 'deSolve_R::lsodes'
+  loglik_lsodes_R_Inf <- DAISIE_loglik_all(pars1a, pars2, Galapagos_datalist_2types, methode = methode)
+  methode <- 'lsodes'
+  loglik_lsodes_F_Inf <- DAISIE_loglik_all(pars1a, pars2, Galapagos_datalist_2types, methode = methode)
+  expect_equal(loglik_lsodes_R_Inf,loglik_lsodes_F_Inf)
+})

From 1557fe3a185636fc7ac17854b7d1807b21b5e9aa Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Fri, 23 Dec 2022 16:04:03 +0100
Subject: [PATCH 45/73] Test analytical approximation for high lambda

---
 tests/testthat/test_odeint.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test_odeint.R b/tests/testthat/test_odeint.R
index 43a2c9cd..078273a2 100644
--- a/tests/testthat/test_odeint.R
+++ b/tests/testthat/test_odeint.R
@@ -17,7 +17,7 @@ test_that("odeint solvers give the same result as desolve solvers", {
   methode <- 'deSolve_R::lsodes'
   loglik_lsodes_R <- DAISIE_loglik_all(pars1, pars2, Galapagos_datalist_2types, methode = methode)
   methode <- 'deSolve_R::lsoda'
-  loglik_lsodes_R <- DAISIE_loglik_all(pars1, pars2, Galapagos_datalist_2types, methode = methode)
+  loglik_lsoda_R <- DAISIE_loglik_all(pars1, pars2, Galapagos_datalist_2types, methode = methode)
   methode <- 'lsodes'
   loglik_lsodes <- DAISIE_loglik_all(pars1, pars2, Galapagos_datalist_2types, methode = methode)
   methode <- 'lsoda'
@@ -67,4 +67,7 @@ test_that("odeint solvers give the same result as desolve solvers", {
   methode <- 'lsodes'
   loglik_lsodes_F_Inf <- DAISIE_loglik_all(pars1a, pars2, Galapagos_datalist_2types, methode = methode)
   expect_equal(loglik_lsodes_R_Inf,loglik_lsodes_F_Inf)
+
+  expect_equal(loglik_lsoda_R_Inf,loglik_lsoda_R, tol = 1E-4)
+  expect_equal(loglik_lsodes_R_Inf,loglik_lsodes_R, tol = 1E-4)
 })

From c007fec872c61308558e1020d61379d36783f20e Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Fri, 23 Dec 2022 16:05:53 +0100
Subject: [PATCH 46/73] typo

---
 tests/testthat/test_odeint.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test_odeint.R b/tests/testthat/test_odeint.R
index 078273a2..4a9945ba 100644
--- a/tests/testthat/test_odeint.R
+++ b/tests/testthat/test_odeint.R
@@ -1,4 +1,4 @@
-test_that("odeint solvers give the same result as desolve solvers", {
+test_that("odeint solvers give the same result as deSolve solvers", {
   utils::data(Galapagos_datalist_2types)
   pars1 <- c(
     0.195442017,

From db1bcfb7ddcc27f87b04eb1642b95f44cd0016ab Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Fri, 23 Dec 2022 16:51:36 +0100
Subject: [PATCH 47/73] Adding tolerance for abm-lsodes comparison

---
 tests/testthat/test_odeint.R | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/tests/testthat/test_odeint.R b/tests/testthat/test_odeint.R
index 4a9945ba..6a47f4a9 100644
--- a/tests/testthat/test_odeint.R
+++ b/tests/testthat/test_odeint.R
@@ -39,20 +39,12 @@ test_that("odeint solvers give the same result as deSolve solvers", {
   DAISIE_CS_max_steps(100000000)
   DAISIE_abm_factor(0.000001)
   loglik_abm <- DAISIE_loglik_all(pars1, pars2, Galapagos_datalist_2types, methode = methode)
-  logliks <- list(loglik_lsodes = loglik_lsodes,
-                  loglik_lsoda = loglik_lsoda,
-                  loglik_rkck54 = loglik_rkck54,
-                  loglik_rkf78 = loglik_rkf78,
-                  loglik_rkd5 = loglik_rkd5,
-                  loglik_bs = loglik_bs,
-                  loglik_rb = loglik_rb,
-                  loglik_abm = loglik_abm)
   expect_equal(loglik_lsodes, loglik_rkck54)
   expect_equal(loglik_lsodes, loglik_rkf78)
   expect_equal(loglik_lsodes, loglik_rkd5)
   expect_equal(loglik_lsodes, loglik_bs)
   expect_equal(loglik_lsodes, loglik_rb)
-  expect_equal(loglik_lsodes, loglik_abm)
+  expect_equal(loglik_lsodes, loglik_abm, tol = 1E-6)
 
   pars1a <- pars1
   pars1a[6] <- Inf

From 6c67ef0401a6222cbd26827cb492ffcaa4da8e19 Mon Sep 17 00:00:00 2001
From: Hanno Hildenbrandt <h.hildenbrandt@rug.nl>
Date: Fri, 23 Dec 2022 17:06:44 +0100
Subject: [PATCH 48/73] length(y) removed

Signed-off-by: Hanno Hildenbrandt <h.hildenbrandt@rug.nl>
---
 src/DAISIE_CS.cpp | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/DAISIE_CS.cpp b/src/DAISIE_CS.cpp
index 0e3dcc03..9d70391c 100644
--- a/src/DAISIE_CS.cpp
+++ b/src/DAISIE_CS.cpp
@@ -272,7 +272,6 @@ BEGIN_RCPP
   auto atol = as<double>(ratol);
   auto rtol = as<double>(rrtol);
 
-  Rprintf("length(y): %u  ", y.size());
   auto p = param_t(lx, kk, as<state_type>(rpar));
   if (runmod == "daisie_runmod") {
     cpp_daisie_cs_runmod rhs(std::move(p));

From a7ea6af9b5d15d85e4507cfc316d744e83f193d8 Mon Sep 17 00:00:00 2001
From: Hanno Hildenbrandt <h.hildenbrandt@rug.nl>
Date: Mon, 26 Dec 2022 21:49:26 +0100
Subject: [PATCH 49/73] jacobian policy

---
 src/DAISIE_CS.cpp   |  8 ++++++
 src/DAISIE_IW.cpp   |  3 +++
 src/DAISIE_odeint.h | 60 ++++++++++++++++++++++++---------------------
 3 files changed, 43 insertions(+), 28 deletions(-)

diff --git a/src/DAISIE_CS.cpp b/src/DAISIE_CS.cpp
index 9d70391c..8ecb47d0 100644
--- a/src/DAISIE_CS.cpp
+++ b/src/DAISIE_CS.cpp
@@ -7,6 +7,8 @@
 
 #include "DAISIE_odeint.h"
 
+using namespace daisie_odeint::jacobian_policy;
+
 
 namespace {
 
@@ -39,6 +41,8 @@ namespace {
   class cpp_daisie_cs_runmod
   {
   public:
+    using jacobian = const_from_linear_rhs<cpp_daisie_cs_runmod>;
+
     cpp_daisie_cs_runmod(param_t&& par) :
       p_(std::move(par))
     {
@@ -103,6 +107,8 @@ namespace {
   class cpp_daisie_cs_runmod_1
   {
   public:
+    using jacobian = const_from_linear_rhs<cpp_daisie_cs_runmod_1>;
+
     cpp_daisie_cs_runmod_1(param_t&& par) :
       p_(std::move(par))
     {
@@ -184,6 +190,8 @@ namespace {
   class cpp_daisie_cs_runmod_2
   {
   public:
+    using jacobian = const_from_linear_rhs<cpp_daisie_cs_runmod_2>;
+
     cpp_daisie_cs_runmod_2(param_t&& par) :
       p_(std::move(par))
     {
diff --git a/src/DAISIE_IW.cpp b/src/DAISIE_IW.cpp
index e6f55b53..27d39945 100644
--- a/src/DAISIE_IW.cpp
+++ b/src/DAISIE_IW.cpp
@@ -19,6 +19,7 @@ using namespace Eigen;
 
 // num_threads
 unsigned daisie_odeint_iw_num_threads_ = std::max(1u, std::thread::hardware_concurrency());
+using namespace daisie_odeint::jacobian_policy;
 
 
 namespace {
@@ -178,6 +179,8 @@ namespace {
 
   struct daisie_iw_wrapper
   {
+    using jacobian = const_from_linear_rhs<daisie_iw_wrapper>;
+
     std::unique_ptr<ThreadPool> pool;
     std::unique_ptr<ThreadPoolDevice> dev;
 
diff --git a/src/DAISIE_odeint.h b/src/DAISIE_odeint.h
index 748055c4..af595928 100644
--- a/src/DAISIE_odeint.h
+++ b/src/DAISIE_odeint.h
@@ -44,7 +44,7 @@ namespace daisie_odeint {
 
   extern double abm_factor;
 
-
+  
   template <typename Stepper, typename Rhs>
   inline void do_integrate(double atol, double rtol, Rhs rhs, state_type& y, double t0, double t1)
   {
@@ -70,37 +70,41 @@ namespace daisie_odeint {
   }
 
 
-  // Evaluator of the Jacobian for linear, time independent systems 
-  // dxdt = Ax => Jacobian = t(A)
-  template <typename RHS>
-  struct const_jacobian_from_linear_rhs
-  {
-    explicit const_jacobian_from_linear_rhs(RHS& rhs) : rhs_(rhs)
-    {
-    }
+  namespace jacobian_policy {
 
-    void operator()(const vector_t<double>& x, matrix_t<double>& J, double t, vector_t<double>& /*dfdt*/)
+    // Evaluator of the Jacobian for linear, time independent systems 
+    // dxdt = Ax => Jacobian = t(A)
+    template <typename RHS>
+    struct const_from_linear_rhs
     {
-      if (!J_) {
-        // once-only, generic evaluation
-        J_ = std::make_unique<matrix_t<double>>(J.size1(), J.size2());
-        auto single = vector_t<double>(x.size(), 0);
-        auto dxdt = vector_t<double>(x.size());
-        for (size_t i = 0; i < J.size1(); ++i) {
-          single[i] = 1.0;
-          auto col = ublas::matrix_column<matrix_t<double>>(*J_, i);
-          std::copy(col.begin(), col.end(), dxdt.begin());
-          rhs_(single, dxdt, 0);
-          std::copy(dxdt.begin(), dxdt.end(), col.begin());
-          single[i] = 0.0;
+      explicit const_from_linear_rhs(RHS& rhs) : rhs_(rhs)
+      {
+      }
+
+      void operator()(const vector_t<double>& x, matrix_t<double>& J, double t, vector_t<double>& /*dfdt*/)
+      {
+        if (!J_) {
+          // once-only, generic evaluation
+          J_ = std::make_unique<matrix_t<double>>(J.size1(), J.size2());
+          auto single = vector_t<double>(x.size(), 0);
+          auto dxdt = vector_t<double>(x.size());
+          for (size_t i = 0; i < J.size1(); ++i) {
+            single[i] = 1.0;
+            auto col = ublas::matrix_column<matrix_t<double>>(*J_, i);
+            std::copy(col.begin(), col.end(), dxdt.begin());
+            rhs_(single, dxdt, 0);
+            std::copy(dxdt.begin(), dxdt.end(), col.begin());
+            single[i] = 0.0;
+          }
         }
+        J = *J_;
       }
-      J = *J_;
-    }
 
-    RHS& rhs_;
-    std::unique_ptr<matrix_t<double>> J_;
-  };
+      RHS& rhs_;
+      std::unique_ptr<matrix_t<double>> J_;
+    };
+
+  }
 
 
   // wrapper around odeint::integrate
@@ -161,7 +165,7 @@ namespace daisie_odeint {
       // another outlier in calling convention
       using stepper_t = rosenbrock4<double>;
       using controlled_stepper_t = rosenbrock4_controller<stepper_t>;
-      auto jac = const_jacobian_from_linear_rhs<Rhs>{rhs};
+      auto jac = typename Rhs::type::jacobian(rhs);
       auto sys = std::make_pair(std::ref(rhs), std::ref(jac));
       integrate_adaptive(controlled_stepper_t(atol, rtol), sys, y, t0, t1, 0.1 * (t1 - t0));
     }

From 409098614ab3249838459e484bb1a986dcf027c5 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Fri, 20 Jan 2023 17:55:55 +0100
Subject: [PATCH 50/73] Revert 79f2b1b Replacing sprintf by format

---
 R/DAISIE_ML1.R          |  60 ++++++++-------
 R/DAISIE_ML2.R          |  11 +--
 R/DAISIE_ML4.R          |  21 +++---
 R/DAISIE_ML_IW.R        |  11 +--
 R/DAISIE_MW_ML.R        | 162 ++++++++++++++++++++--------------------
 R/DAISIE_SR_ML_CS.R     |  17 +----
 R/DAISIE_SR_loglik_CS.R |   8 +-
 R/DAISIE_loglik_CS.R    |  34 ++++-----
 8 files changed, 153 insertions(+), 171 deletions(-)

diff --git a/R/DAISIE_ML1.R b/R/DAISIE_ML1.R
index 945013b6..0f51918e 100644
--- a/R/DAISIE_ML1.R
+++ b/R/DAISIE_ML1.R
@@ -399,18 +399,20 @@ DAISIE_ML1 <- function(
       df = length(initparsopt),
       conv = unlist(out$conv)
     )
-    s1 <- c('Maximum likelihood parameter estimates:',
-            '\n lambda_c:', format(MLpars1[1], format = 'f', digits = 6),
-            '\n mu:', format(MLpars1[2], format = 'f', digits = 6),
-            '\n K:', format(MLpars1[3], format = 'f', digits = 6),
-            '\n gamma:', format(MLpars1[4], format = 'f', digits = 6),
-            '\n lambda_a:', format(MLpars1[5], format = 'f', digits = 6),
-            '\n lambda_c2:', format(MLpars1[6], format = 'f', digits = 6),
-            '\n mu2:', format(MLpars1[7], format = 'f', digits = 6),
-            '\n K2:', format(MLpars1[8], format = 'f', digits = 6),
-            '\n gamma2:', format(MLpars1[9], format = 'f', digits = 6),
-            '\n lambda_a2:', format(MLpars1[10], format = 'f', digits = 6),
-            '\n prop_type2:', format(MLpars1[11], format = 'f', digits = 6))
+    s1 <- sprintf(
+      "Maximum likelihood parameter estimates:\n lambda_c: %f\n mu: %f\n K: %f\n gamma: %f\n lambda_a: %f\n lambda_c2: %f\n mu2: %f\n K2: %f\n gamma2: %f\n lambda_a2: %f\n prop_type2: %f",
+      MLpars1[1],
+      MLpars1[2],
+      MLpars1[3],
+      MLpars1[4],
+      MLpars1[5],
+      MLpars1[6],
+      MLpars1[7],
+      MLpars1[8],
+      MLpars1[9],
+      MLpars1[10],
+      MLpars1[11]
+    )
   } else if (all(all_no_shift == 7:11)) {
     out2 <- data.frame(
       lambda_c = MLpars1[1],
@@ -423,13 +425,15 @@ DAISIE_ML1 <- function(
       df = length(initparsopt),
       conv = unlist(out$conv)
     )
-    s1 <- c('Maximum likelihood parameter estimates:',
-            '\n lambda_c:', format(MLpars1[1], format = 'f', digits = 6),
-            '\n mu:', format(MLpars1[2], format = 'f', digits = 6),
-            '\n K:', format(MLpars1[3], format = 'f', digits = 6),
-            '\n gamma:', format(MLpars1[4], format = 'f', digits = 6),
-            '\n lambda_a:', format(MLpars1[5], format = 'f', digits = 6),
-            '\n prop_init_pres:', format(MLpars1[6], format = 'f', digits = 6))
+    s1 <- sprintf(
+      "Maximum likelihood parameter estimates:\n lambda_c: %f\n mu: %f\n K: %f\n gamma: %f\n lambda_a: %f\n prob_init_pres: %f",
+      MLpars1[1],
+      MLpars1[2],
+      MLpars1[3],
+      MLpars1[4],
+      MLpars1[5],
+      MLpars1[6]
+    )
   } else {
     out2 <- data.frame(
       lambda_c = MLpars1[1],
@@ -441,15 +445,17 @@ DAISIE_ML1 <- function(
       df = length(initparsopt),
       conv = unlist(out$conv)
     )
-    s1 <- c('Maximum likelihood parameter estimates:',
-            '\n lambda_c:', format(MLpars1[1], format = 'f', digits = 6),
-            '\n mu:', format(MLpars1[2], format = 'f', digits = 6),
-            '\n K:', format(MLpars1[3], format = 'f', digits = 6),
-            '\n gamma:', format(MLpars1[4], format = 'f', digits = 6),
-            '\n lambda_a:', format(MLpars1[5], format = 'f', digits = 6))
+    s1 <- sprintf(
+      "Maximum likelihood parameter estimates:\n lambda_c: %f\n mu: %f\n K: %f\n gamma: %f\n lambda_a: %f\n",
+      MLpars1[1],
+      MLpars1[2],
+      MLpars1[3],
+      MLpars1[4],
+      MLpars1[5]
+    )
   }
-  s2 <- c('Maximum loglikelihood:', format(ML, format = 'f', digits = 6))
-  cat("\n", s1, "\n", s2, "\n", sep = ' ')
+  s2 <- sprintf("Maximum loglikelihood: %f", ML)
+  cat("\n", s1, "\n", s2, "\n")
   if (eqmodel > 0) {
     M <- calcMN(datalist, MLpars1)
     ExpEIN <- DAISIE_ExpEIN(datalist[[1]]$island_age, MLpars1, M) # nolint start
diff --git a/R/DAISIE_ML2.R b/R/DAISIE_ML2.R
index 11972681..3cff782b 100644
--- a/R/DAISIE_ML2.R
+++ b/R/DAISIE_ML2.R
@@ -197,13 +197,8 @@ DAISIE_ML2 <- function(
     }
   }
   out2 <- data.frame(lambda_c = MLpars1[, 1], mu = MLpars1[, 2], K = MLpars1[, 3], gamma = MLpars1[, 4], lambda_a = MLpars1[, 5], loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
-  s1 <- c('Maximum likelihood parameter estimates:',
-          '\n lambda_c:', format(MLpars1[1], format = 'f', digits = 6),
-          '\n mu:', format(MLpars1[2], format = 'f', digits = 6),
-          '\n K:', format(MLpars1[3], format = 'f', digits = 6),
-          '\n gamma:', format(MLpars1[4], format = 'f', digits = 6),
-          '\n lambda_a:', format(MLpars1[5], format = 'f', digits = 6))
-  s2 <- c('Maximum loglikelihood:', format(ML, format = 'f', digits = 6))
-  cat("\n", s1, "\n", s2, "\n", sep = ' ')
+  s1 <- sprintf("Maximum likelihood parameter estimates: %f", MLpars1)
+  s2 <- sprintf("Maximum loglikelihood: %f", ML)
+  cat("\n", s1, "\n", s2, "\n")
   return(invisible(out2))
 }
diff --git a/R/DAISIE_ML4.R b/R/DAISIE_ML4.R
index dc0ecccf..4b75f572 100644
--- a/R/DAISIE_ML4.R
+++ b/R/DAISIE_ML4.R
@@ -236,14 +236,17 @@ DAISIE_ML4 <- function(
     df = length(initparsopt),
     conv = unlist(out$conv)
   )
-  s1 <- c('Maximum likelihood parameter estimates:',
-          '\n lambda_c:', format(MLpars1[1], format = 'f', digits = 6),
-          '\n mu:', format(MLpars1[2], format = 'f', digits = 6),
-          '\n K:', format(MLpars1[3], format = 'f', digits = 6),
-          '\n gamma:', format(MLpars1[4], format = 'f', digits = 6),
-          '\n lambda_a:', format(MLpars1[5], format = 'f', digits = 6),
-          '\n sd:', format(MLpars1[6], format = 'f', digits = 6))
-  s2 <- c('Maximum loglikelihood:', format(ML, format = 'f', digits = 6))
-  cat("\n", s1, "\n", s2, "\n", sep = ' ')
+  s1 <- sprintf(
+    "Maximum likelihood parameter estimates: lambda_c: %f, mu: %f, K: %f,
+      gamma: %f, lambda_a: %f, sd: %f",
+    MLpars1[1],
+    MLpars1[2],
+    MLpars1[3],
+    MLpars1[4],
+    MLpars1[5],
+    MLpars1[6]
+  )
+  s2 <- sprintf("Maximum loglikelihood: %f", ML)
+  cat("\n", s1, "\n", s2, "\n")
   return(invisible(out2))
 }
diff --git a/R/DAISIE_ML_IW.R b/R/DAISIE_ML_IW.R
index e7a6b943..c130e12b 100644
--- a/R/DAISIE_ML_IW.R
+++ b/R/DAISIE_ML_IW.R
@@ -171,13 +171,8 @@ DAISIE_ML_IW <- function(
   if (length(idparsfix) != 0) { MLpars1[idparsfix] <- parsfix }
   if (MLpars1[3] > 10 ^ 7){ MLpars1[3] <- Inf }
   out2 <- data.frame(lambda_c = MLpars1[1], mu = MLpars1[2], K = MLpars1[3], gamma = MLpars1[4], lambda_a = MLpars1[5], loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
-  s1 <- c('Maximum likelihood parameter estimates:',
-          '\n lambda_c:', format(MLpars1[1], format = 'f', digits = 6),
-          '\n mu:', format(MLpars1[2], format = 'f', digits = 6),
-          '\n K:', format(MLpars1[3], format = 'f', digits = 6),
-          '\n gamma:', format(MLpars1[4], format = 'f', digits = 6),
-          '\n lambda_a:', format(MLpars1[5], format = 'f', digits = 6))
-  s2 <- c('Maximum loglikelihood:', format(ML, format = 'f', digits = 6))
-  cat("\n", s1, "\n", s2, "\n", sep = ' ')
+  s1 <- sprintf("Maximum likelihood parameter estimates: lambda_c: %f, mu: %f, K: %f, gamma: %f, lambda_a: %f", MLpars1[1], MLpars1[2], MLpars1[3], MLpars1[4], MLpars1[5])
+  s2 <- sprintf("Maximum loglikelihood: %f", ML)
+  cat("\n", s1, "\n", s2, "\n")
   return(invisible(out2))
 }
diff --git a/R/DAISIE_MW_ML.R b/R/DAISIE_MW_ML.R
index 60511399..3b2ae608 100644
--- a/R/DAISIE_MW_ML.R
+++ b/R/DAISIE_MW_ML.R
@@ -477,84 +477,85 @@ DAISIE_MW_ML = function(
   MLpars1[idparsopt] = MLpars
   if(length(idparsfix) != 0) { MLpars1[idparsfix] = parsfix }
   if(MLpars1[5] > 10^7){ MLpars1[5] = Inf }
-#  s1output <- function(MLpars1,distance_dep)
-#  {
-#    s1 <- switch(distance_dep,
-#                 power = sprintf('Maximum likelihood parameter estimates:\n
-#               lambda_c = %f * A^ %f\n
-#               mu = %f * A^ -%f\n
-#               K = %f * A^ %f\n
-#               M * gamma = %f * d^ -%f\n
-#               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-#                 signoidal_col = sprintf('Maximum likelihood parameter estimates:\n
-#               lambda_c = %f * A^ %f\n
-#               mu = %f * A^ -%f\n
-#               K = %f * A^ %f\n
-#               M * gamma = %f * (1 - (d/%f)^%f / (1 + (d/%f)^%f )\n
-#               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[11],MLpars1[8],MLpars1[11],MLpars1[8],MLpars1[9],MLpars1[10]),
-#                 sigmoidal_ana = sprintf('Maximum likelihood parameter estimates:\n
-#               lambda_c = %f * A^ %f\n
-#               mu = %f * A^ -%f\n
-#               K = %f * A^ %f\n
-#               M * gamma = %f * d^ -%f\n
-#               lambda_a = %f * (d/%f)^%f / (1 + (d/%f)^%f )\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[11],MLpars1[10],MLpars1[11],MLpars1[10]),
-#                 sigmoidal_clado = sprintf('Maximum likelihood parameter estimates:\n
-#               lambda_c = %f * (d/%f)^%f / (1 + (d/%f)^%f )\n
-#               mu = %f * A^ -%f\n
-#               K = %f * A^ %f\n
-#               M * gamma = %f * d^ -%f\n
-#               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[11],MLpars1[2],MLpars1[11],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-#                 sigmoidal_col_ana = sprintf('Maximum likelihood parameter estimates:\n
-#               lambda_c = %f * A^ %f\n
-#               mu = %f * A^ -%f\n
-#               K = %f * A^ %f\n
-#               M * gamma = %f * (1 - (d/%f)^%f / (1 + (d/%f)^%f )\n
-#               lambda_a = %f * (d/%f)^%f / (1 + (d/%f)^%f )\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[11],MLpars1[8],MLpars1[11],MLpars1[8],MLpars1[9],MLpars1[12],MLpars1[10],MLpars1[12],MLpars1[10]),
-#                 area_additive_clado = sprintf('Maximum likelihood parameter estimates:\n
-#               lambda_c = %f * A^ %f * d^ %f \n
-#               mu = %f * A^ -%f\n
-#               K = %f * A^ %f\n
-#               M * gamma = %f * d^ -%f\n
-#               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-#                 area_interactive_clado = sprintf('Maximum likelihood parameter estimates:\n
-#               lambda_c = %f * A^ (%f + %f * log(d)) \n
-#               mu = %f * A^ -%f\n
-#               K = %f * A^ %f\n
-#               M * gamma = %f * d^ -%f\n
-#               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-#                 area_interactive_clado0 = sprintf('Maximum likelihood parameter estimates:\n
-#               lambda_c = %f * A^ (%f + %f * log(d)) \n
-#               mu = %f * A^ -%f\n
-#               K = %f * A^ %f\n
-#               M * gamma = %f * d^ -%f\n
-#               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-#                 area_interactive_clado1 = sprintf('Maximum likelihood parameter estimates:\n
-#               lambda_c = %f * A^ (%f + d/%f)) \n
-#               mu = %f * A^ -%f\n
-#               K = %f * A^ %f\n
-#               M * gamma = %f * d^ -%f\n
-#               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-#                 area_interactive_clado2 = sprintf('Maximum likelihood parameter estimates:\n
-#               lambda_c = %f * A^ (%f + d/(d + %f)) \n
-#               mu = %f * A^ -%f\n
-#               K = %f * A^ %f\n
-#               M * gamma = %f * d^ -%f\n
-#               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-#                 area_interactive_clado3 = sprintf('Maximum likelihood parameter estimates:\n
-#               lambda_c = %f * (A + d/%f)^ %f\n \n
-#               mu = %f * A^ -%f\n
-#               K = %f * A^ %f\n
-#               M * gamma = %f * d^ -%f\n
-#               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[11],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-#                 area_interactive_clado4 = sprintf('Maximum likelihood parameter estimates:\n
-#               lambda_c = %f * A^ (%f * d/(d + %f)) \n
-#               mu = %f * A^ -%f\n
-#               K = %f * A^ %f\n
-#               M * gamma = %f * d^ -%f\n
-#               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10])
-#    )
-#    return(s1)
-# }
+  s1output <- function(MLpars1,distance_dep)
+  {
+    s1 <- switch(distance_dep,
+                 power = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * A^ %f\n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * d^ -%f\n
+               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+                 signoidal_col = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * A^ %f\n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * (1 - (d/%f)^%f / (1 + (d/%f)^%f )\n
+               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[11],MLpars1[8],MLpars1[11],MLpars1[8],MLpars1[9],MLpars1[10]),
+                 sigmoidal_ana = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * A^ %f\n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * d^ -%f\n
+               lambda_a = %f * (d/%f)^%f / (1 + (d/%f)^%f )\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[11],MLpars1[10],MLpars1[11],MLpars1[10]),
+                 sigmoidal_clado = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * (d/%f)^%f / (1 + (d/%f)^%f )\n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * d^ -%f\n
+               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[11],MLpars1[2],MLpars1[11],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+                 sigmoidal_col_ana = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * A^ %f\n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * (1 - (d/%f)^%f / (1 + (d/%f)^%f )\n
+               lambda_a = %f * (d/%f)^%f / (1 + (d/%f)^%f )\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[11],MLpars1[8],MLpars1[11],MLpars1[8],MLpars1[9],MLpars1[12],MLpars1[10],MLpars1[12],MLpars1[10]),
+                 area_additive_clado = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * A^ %f * d^ %f \n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * d^ -%f\n
+               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+                 area_interactive_clado = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * A^ (%f + %f * log(d)) \n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * d^ -%f\n
+               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+                 area_interactive_clado0 = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * A^ (%f + %f * log(d)) \n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * d^ -%f\n
+               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+                 area_interactive_clado1 = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * A^ (%f + d/%f)) \n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * d^ -%f\n
+               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+                 area_interactive_clado2 = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * A^ (%f + d/(d + %f)) \n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * d^ -%f\n
+               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+                 area_interactive_clado3 = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * (A + d/%f)^ %f\n \n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * d^ -%f\n
+               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[11],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+                 area_interactive_clado4 = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * A^ (%f * d/(d + %f)) \n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * d^ -%f\n
+               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10])
+    )
+    return(s1)
+  }
+  s2 = sprintf('Maximum loglikelihood: %f',ML)
   if(is.element(distance_dep,distance_dep_options1))
   {
     out2 = data.frame(lambda_c0 = MLpars1[1], y = MLpars1[2], mu_0 = MLpars1[3], x = MLpars1[4], K_0 = MLpars1[5], z = MLpars1[6], gamma_0 = MLpars1[7], alpha = MLpars1[8], lambda_a0 = MLpars1[9], beta = MLpars1[10], d_0 = MLpars1[11], loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
@@ -566,9 +567,6 @@ DAISIE_MW_ML = function(
     {
       out2 = data.frame(lambda_c0 = MLpars1[1], y = MLpars1[2], mu_0 = MLpars1[3], x = MLpars1[4], K_0 = MLpars1[5], z = MLpars1[6], gamma_0 = MLpars1[7], alpha = MLpars1[8], lambda_a0 = MLpars1[9], beta = MLpars1[10], loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
     }
-  #cat("\n",s1output(MLpars1,distance_dep),"\n",s2,"\n")
-  s1 <- c('Parameters:', format(MLpars1, format = 'f', digits = 6))
-  s2 <- c('Maximum loglikelihood:',format(ML, format = 'f', digits = 6))
-  cat("\n",s1,"\n",s2,"\n", sep = ' ')
+  cat("\n",s1output(MLpars1,distance_dep),"\n",s2,"\n")
   return(invisible(out2))
 }
diff --git a/R/DAISIE_SR_ML_CS.R b/R/DAISIE_SR_ML_CS.R
index 83b522ad..76b0b3fd 100644
--- a/R/DAISIE_SR_ML_CS.R
+++ b/R/DAISIE_SR_ML_CS.R
@@ -427,19 +427,8 @@ DAISIE_SR_ML_CS <- DAISIE_SR_ML <- function(
     MLpars1[8] <- Inf
   }
   out2 <- data.frame(lambda_c = MLpars1[1], mu = MLpars1[2], K = MLpars1[3], gamma = MLpars1[4], lambda_a = MLpars1[5], lambda_c2 = MLpars1[6], mu2 = MLpars1[7], K2 = MLpars1[8], gamma2 = MLpars1[9], lambda_a2 = MLpars1[10], tshift = MLpars1[11], loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
-  s1 <- c('Maximum likelihood parameter estimates:',
-          '\n lambda_c:', format(MLpars1[1], format = 'f', digits = 6),
-          '\n mu:', format(MLpars1[2], format = 'f', digits = 6),
-          '\n K:', format(MLpars1[3], format = 'f', digits = 6),
-          '\n gamma:', format(MLpars1[4], format = 'f', digits = 6),
-          '\n lambda_a:', format(MLpars1[5], format = 'f', digits = 6),
-          '\n lambda_c2:', format(MLpars1[6], format = 'f', digits = 6),
-          '\n mu2:', format(MLpars1[7], format = 'f', digits = 6),
-          '\n K2:', format(MLpars1[8], format = 'f', digits = 6),
-          '\n gamma2:', format(MLpars1[9], format = 'f', digits = 6),
-          '\n lambda_a2:', format(MLpars1[10], format = 'f', digits = 6),
-          '\n time of shift:', format(MLpars1[11], format = 'f', digits = 6))
-  s2 <- c('Maximum loglikelihood:', format(ML, format = 'f', digits = 6))
-  cat("\n", s1, "\n", s2, "\n", sep = ' ')
+  s1 <- sprintf("Maximum likelihood parameter estimates: lambda_c: %f, mu: %f, K: %f, gamma: %f, lambda_a: %f, lambda_c2: %f, mu2: %f, K2: %f, gamma2: %f, lambda_a2: %f, time of shift: %f", MLpars1[1], MLpars1[2], MLpars1[3], MLpars1[4], MLpars1[5], MLpars1[6], MLpars1[7], MLpars1[8], MLpars1[9], MLpars1[10], MLpars1[11])
+  s2 <- sprintf("Maximum loglikelihood: %f", ML)
+  cat("\n", s1, "\n", s2, "\n")
   return(invisible(out2))
 }
diff --git a/R/DAISIE_SR_loglik_CS.R b/R/DAISIE_SR_loglik_CS.R
index e0d04012..adc596c0 100644
--- a/R/DAISIE_SR_loglik_CS.R
+++ b/R/DAISIE_SR_loglik_CS.R
@@ -234,13 +234,9 @@ DAISIE_SR_loglik_CS_M1 <- DAISIE_SR_loglik <- function(
   #print(head(probs,n = 15))
   if (pars2[4] >= 1) {
     # if (length(pars1 > 5)) {
-    s1 <- c('Status of colonist:',
-              format(stac, format = 'd'),
-              '\n Parameters:',
-              format(pars1[1:5], format = 'f', digits = 6))
+      s1 <- sprintf("Status of colonist: %d, Parameters: %f %f %f %f %f ", stac, pars1[1], pars1[2], pars1[3], pars1[4], pars1[5])
     # }
-    s2 <- c('\n Loglikelihood:',
-            format(loglik, format = 'f', digits = 6))
+    s2 <- sprintf(", Loglikelihood: %f", loglik)
     cat(s1, s2, "\n", sep = "")
     utils::flush.console()
   }
diff --git a/R/DAISIE_loglik_CS.R b/R/DAISIE_loglik_CS.R
index 7c555c21..2188f4e4 100644
--- a/R/DAISIE_loglik_CS.R
+++ b/R/DAISIE_loglik_CS.R
@@ -677,19 +677,20 @@ DAISIE_loglik_CS_M1 <- DAISIE_loglik <- function(pars1,
   if(pars2[4] >= 1)
   {
     if (length(pars1) == 11) { # CHANGE
-      s1 <- c('Status of colonist:',
-              format(stac, format = 'd'),
-              '\n Parameters:',
-              format(pars1[6:11], format = 'f', digits = 6))
+      s1 <- sprintf('Status of colonist: %d, Parameters: %f %f %f %f %f %f', stac, pars1[5], pars1[6], pars1[7], pars1[8], pars1[9], pars1[10])
     } else {
-      s1 <- c('Status of colonist:',
-              format(stac, format = 'd'),
-              '\n Parameters:',
-              format(pars1[1:5], format = 'f', digits = 6))
+      s1 <- sprintf(
+        "Status of colonist: %d, Parameters: %f %f %f %f %f ",
+        stac,
+        pars1[1],
+        pars1[2],
+        pars1[3],
+        pars1[4],
+        pars1[5]
+      )
     }
-    s2 <- c('\n Loglikelihood:',
-             format(loglik, format = 'f', digits = 6))
-    cat(s1, s2, "\n", sep = " ")
+    s2 <- sprintf(", Loglikelihood: %f", loglik)
+    cat(s1, s2, "\n", sep = "")
     utils::flush.console()
   }
   if (is.na(loglik)) {
@@ -1042,14 +1043,13 @@ DAISIE_loglik_CS <- DAISIE_loglik_all <- function(
   return(loglik)
 }
 
-print_parameters_and_loglik <- function(pars, loglik, verbose, dgts = 6)
+print_parameters_and_loglik <- function(pars, loglik, verbose)
 {
   if (verbose >= 1) {
-    s1 <- c('Parameters:',
-            format(pars, format = 'f', digits = dgts))
-    s2 <- c('Loglikelihood:',
-            format(loglik, format = 'f', digits = dgts))
-    cat(s1, "\n", s2, "\n", sep = " ")
+    s1 <- sprintf("Parameters: ")
+    s2 <- sprintf("%f ", pars)
+    s3 <- sprintf(", Loglikelihood: %f", loglik)
+    cat(s1, s2, s3, "\n", sep = "")
     utils::flush.console()
   }
 }

From 91712e6249984ae7829649f119838d0afe20e585 Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Fri, 20 Jan 2023 18:23:41 +0100
Subject: [PATCH 51/73] Auto GHA check only on main and develop

---
 .github/workflows/R-CMD-check.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index fe099a77..2fd0756b 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -2,7 +2,9 @@
 # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
 on:
   push:
+    branches: [main, master, develop]
   pull_request:
+    branches: [main, master, develop]
   schedule:
   - cron: "0 0 * * *"
 

From 957bd6adf29849e499fd706c1b3ae53f6a379b64 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Mon, 23 Jan 2023 11:04:04 +0100
Subject: [PATCH 52/73] Printing all in one function
 print_parameters_and_loglik

---
 R/DAISIE_ML1.R                 |  44 +++------
 R/DAISIE_ML2.R                 |  16 +++-
 R/DAISIE_ML4.R                 |  17 +---
 R/DAISIE_ML_IW.R               |   7 +-
 R/DAISIE_MW_ML.R               |  88 ++---------------
 R/DAISIE_SR_loglik_CS.R        |  13 +--
 R/DAISIE_loglik_CS.R           | 167 ++++++++++++++++++++++++++++-----
 R/DAISIE_loglik_IW.R           |   5 +-
 tests/testthat/test_printing.R |   7 ++
 9 files changed, 196 insertions(+), 168 deletions(-)
 create mode 100644 tests/testthat/test_printing.R

diff --git a/R/DAISIE_ML1.R b/R/DAISIE_ML1.R
index 0f51918e..2f0df0d7 100644
--- a/R/DAISIE_ML1.R
+++ b/R/DAISIE_ML1.R
@@ -399,20 +399,8 @@ DAISIE_ML1 <- function(
       df = length(initparsopt),
       conv = unlist(out$conv)
     )
-    s1 <- sprintf(
-      "Maximum likelihood parameter estimates:\n lambda_c: %f\n mu: %f\n K: %f\n gamma: %f\n lambda_a: %f\n lambda_c2: %f\n mu2: %f\n K2: %f\n gamma2: %f\n lambda_a2: %f\n prop_type2: %f",
-      MLpars1[1],
-      MLpars1[2],
-      MLpars1[3],
-      MLpars1[4],
-      MLpars1[5],
-      MLpars1[6],
-      MLpars1[7],
-      MLpars1[8],
-      MLpars1[9],
-      MLpars1[10],
-      MLpars1[11]
-    )
+    pars_to_print <- MLpars1[1:11]
+    parnames <- c('lambda^c','mu','K','gamma','lambda^a','lambda^c2','mu2','K2','gamma2','lambda^a2','prop_type2')
   } else if (all(all_no_shift == 7:11)) {
     out2 <- data.frame(
       lambda_c = MLpars1[1],
@@ -425,15 +413,8 @@ DAISIE_ML1 <- function(
       df = length(initparsopt),
       conv = unlist(out$conv)
     )
-    s1 <- sprintf(
-      "Maximum likelihood parameter estimates:\n lambda_c: %f\n mu: %f\n K: %f\n gamma: %f\n lambda_a: %f\n prob_init_pres: %f",
-      MLpars1[1],
-      MLpars1[2],
-      MLpars1[3],
-      MLpars1[4],
-      MLpars1[5],
-      MLpars1[6]
-    )
+    pars_to_print <- MLpars1[1:6]
+    parnames <- c('lambda^c','mu','K','gamma','lambda^a','prob_init_pres')
   } else {
     out2 <- data.frame(
       lambda_c = MLpars1[1],
@@ -445,17 +426,14 @@ DAISIE_ML1 <- function(
       df = length(initparsopt),
       conv = unlist(out$conv)
     )
-    s1 <- sprintf(
-      "Maximum likelihood parameter estimates:\n lambda_c: %f\n mu: %f\n K: %f\n gamma: %f\n lambda_a: %f\n",
-      MLpars1[1],
-      MLpars1[2],
-      MLpars1[3],
-      MLpars1[4],
-      MLpars1[5]
-    )
+    pars_to_print <- MLpars1[1:5]
+    parnames <- c('lambda^c','mu','K','gamma','lambda^a')
   }
-  s2 <- sprintf("Maximum loglikelihood: %f", ML)
-  cat("\n", s1, "\n", s2, "\n")
+  print_parameters_and_loglik(pars = pars_to_print,
+                              loglik = ML,
+                              verbose = TRUE,
+                              parnames = parnames,
+                              type = 'island_ML')
   if (eqmodel > 0) {
     M <- calcMN(datalist, MLpars1)
     ExpEIN <- DAISIE_ExpEIN(datalist[[1]]$island_age, MLpars1, M) # nolint start
diff --git a/R/DAISIE_ML2.R b/R/DAISIE_ML2.R
index 3cff782b..c50ff4d4 100644
--- a/R/DAISIE_ML2.R
+++ b/R/DAISIE_ML2.R
@@ -196,9 +196,17 @@ DAISIE_ML2 <- function(
       MLpars1[i, 3] <- Inf
     }
   }
-  out2 <- data.frame(lambda_c = MLpars1[, 1], mu = MLpars1[, 2], K = MLpars1[, 3], gamma = MLpars1[, 4], lambda_a = MLpars1[, 5], loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
-  s1 <- sprintf("Maximum likelihood parameter estimates: %f", MLpars1)
-  s2 <- sprintf("Maximum loglikelihood: %f", ML)
-  cat("\n", s1, "\n", s2, "\n")
+  out2 <- data.frame(lambda_c = MLpars1[, 1],
+                     mu = MLpars1[, 2],
+                     K = MLpars1[, 3],
+                     gamma = MLpars1[, 4],
+                     lambda_a = MLpars1[, 5],
+                     loglik = ML,
+                     df = length(initparsopt),
+                     conv = unlist(out$conv))
+  print_parameters_and_loglik(pars = MLpars1,
+                              loglik = ML,
+                              verbose = TRUE,
+                              ML = TRUE)
   return(invisible(out2))
 }
diff --git a/R/DAISIE_ML4.R b/R/DAISIE_ML4.R
index 4b75f572..cc76e033 100644
--- a/R/DAISIE_ML4.R
+++ b/R/DAISIE_ML4.R
@@ -236,17 +236,10 @@ DAISIE_ML4 <- function(
     df = length(initparsopt),
     conv = unlist(out$conv)
   )
-  s1 <- sprintf(
-    "Maximum likelihood parameter estimates: lambda_c: %f, mu: %f, K: %f,
-      gamma: %f, lambda_a: %f, sd: %f",
-    MLpars1[1],
-    MLpars1[2],
-    MLpars1[3],
-    MLpars1[4],
-    MLpars1[5],
-    MLpars1[6]
-  )
-  s2 <- sprintf("Maximum loglikelihood: %f", ML)
-  cat("\n", s1, "\n", s2, "\n")
+  print_parameters_and_loglik(pars = MLpars1[1:6],
+                              loglik = ML,
+                              verbose = TRUE,
+                              parnames = c('lambda^c','mu','K','gamma','lambda^a','sd'),
+                              type = 'island_ML')
   return(invisible(out2))
 }
diff --git a/R/DAISIE_ML_IW.R b/R/DAISIE_ML_IW.R
index c130e12b..8fd289c4 100644
--- a/R/DAISIE_ML_IW.R
+++ b/R/DAISIE_ML_IW.R
@@ -171,8 +171,9 @@ DAISIE_ML_IW <- function(
   if (length(idparsfix) != 0) { MLpars1[idparsfix] <- parsfix }
   if (MLpars1[3] > 10 ^ 7){ MLpars1[3] <- Inf }
   out2 <- data.frame(lambda_c = MLpars1[1], mu = MLpars1[2], K = MLpars1[3], gamma = MLpars1[4], lambda_a = MLpars1[5], loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
-  s1 <- sprintf("Maximum likelihood parameter estimates: lambda_c: %f, mu: %f, K: %f, gamma: %f, lambda_a: %f", MLpars1[1], MLpars1[2], MLpars1[3], MLpars1[4], MLpars1[5])
-  s2 <- sprintf("Maximum loglikelihood: %f", ML)
-  cat("\n", s1, "\n", s2, "\n")
+  print_parameters_and_loglik(pars = MLpars1[1:5],
+                              loglik = ML,
+                              verbose = TRUE,
+                              type = 'island_ML')
   return(invisible(out2))
 }
diff --git a/R/DAISIE_MW_ML.R b/R/DAISIE_MW_ML.R
index 3b2ae608..cf36cf04 100644
--- a/R/DAISIE_MW_ML.R
+++ b/R/DAISIE_MW_ML.R
@@ -477,89 +477,10 @@ DAISIE_MW_ML = function(
   MLpars1[idparsopt] = MLpars
   if(length(idparsfix) != 0) { MLpars1[idparsfix] = parsfix }
   if(MLpars1[5] > 10^7){ MLpars1[5] = Inf }
-  s1output <- function(MLpars1,distance_dep)
-  {
-    s1 <- switch(distance_dep,
-                 power = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * A^ %f\n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * d^ -%f\n
-               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-                 signoidal_col = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * A^ %f\n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * (1 - (d/%f)^%f / (1 + (d/%f)^%f )\n
-               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[11],MLpars1[8],MLpars1[11],MLpars1[8],MLpars1[9],MLpars1[10]),
-                 sigmoidal_ana = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * A^ %f\n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * d^ -%f\n
-               lambda_a = %f * (d/%f)^%f / (1 + (d/%f)^%f )\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[11],MLpars1[10],MLpars1[11],MLpars1[10]),
-                 sigmoidal_clado = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * (d/%f)^%f / (1 + (d/%f)^%f )\n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * d^ -%f\n
-               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[11],MLpars1[2],MLpars1[11],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-                 sigmoidal_col_ana = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * A^ %f\n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * (1 - (d/%f)^%f / (1 + (d/%f)^%f )\n
-               lambda_a = %f * (d/%f)^%f / (1 + (d/%f)^%f )\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[11],MLpars1[8],MLpars1[11],MLpars1[8],MLpars1[9],MLpars1[12],MLpars1[10],MLpars1[12],MLpars1[10]),
-                 area_additive_clado = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * A^ %f * d^ %f \n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * d^ -%f\n
-               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-                 area_interactive_clado = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * A^ (%f + %f * log(d)) \n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * d^ -%f\n
-               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-                 area_interactive_clado0 = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * A^ (%f + %f * log(d)) \n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * d^ -%f\n
-               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-                 area_interactive_clado1 = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * A^ (%f + d/%f)) \n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * d^ -%f\n
-               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-                 area_interactive_clado2 = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * A^ (%f + d/(d + %f)) \n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * d^ -%f\n
-               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-                 area_interactive_clado3 = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * (A + d/%f)^ %f\n \n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * d^ -%f\n
-               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[11],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
-                 area_interactive_clado4 = sprintf('Maximum likelihood parameter estimates:\n
-               lambda_c = %f * A^ (%f * d/(d + %f)) \n
-               mu = %f * A^ -%f\n
-               K = %f * A^ %f\n
-               M * gamma = %f * d^ -%f\n
-               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10])
-    )
-    return(s1)
-  }
-  s2 = sprintf('Maximum loglikelihood: %f',ML)
   if(is.element(distance_dep,distance_dep_options1))
   {
     out2 = data.frame(lambda_c0 = MLpars1[1], y = MLpars1[2], mu_0 = MLpars1[3], x = MLpars1[4], K_0 = MLpars1[5], z = MLpars1[6], gamma_0 = MLpars1[7], alpha = MLpars1[8], lambda_a0 = MLpars1[9], beta = MLpars1[10], d_0 = MLpars1[11], loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
-  } else
+  } else {
     if(distance_dep == 'sigmoidal_col_ana')
     {
       out2 = data.frame(lambda_c0 = MLpars1[1], y = MLpars1[2], mu_0 = MLpars1[3], x = MLpars1[4], K_0 = MLpars1[5], z = MLpars1[6], gamma_0 = MLpars1[7], alpha = MLpars1[8], lambda_a0 = MLpars1[9], beta = MLpars1[10], d0_col = MLpars1[11], d0_ana = MLpars1[12], loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
@@ -567,6 +488,11 @@ DAISIE_MW_ML = function(
     {
       out2 = data.frame(lambda_c0 = MLpars1[1], y = MLpars1[2], mu_0 = MLpars1[3], x = MLpars1[4], K_0 = MLpars1[5], z = MLpars1[6], gamma_0 = MLpars1[7], alpha = MLpars1[8], lambda_a0 = MLpars1[9], beta = MLpars1[10], loglik = ML, df = length(initparsopt), conv = unlist(out$conv))
     }
-  cat("\n",s1output(MLpars1,distance_dep),"\n",s2,"\n")
+  }
+  print_parameters_and_loglik(pars = MLpars1,
+                              loglik = ML,
+                              verbose = TRUE,
+                              type = 'global_ML',
+                              distance_dep = distance_dep)
   return(invisible(out2))
 }
diff --git a/R/DAISIE_SR_loglik_CS.R b/R/DAISIE_SR_loglik_CS.R
index adc596c0..e8a35ea7 100644
--- a/R/DAISIE_SR_loglik_CS.R
+++ b/R/DAISIE_SR_loglik_CS.R
@@ -231,15 +231,10 @@ DAISIE_SR_loglik_CS_M1 <- DAISIE_SR_loglik <- function(
       }
     }
   }
-  #print(head(probs,n = 15))
-  if (pars2[4] >= 1) {
-    # if (length(pars1 > 5)) {
-      s1 <- sprintf("Status of colonist: %d, Parameters: %f %f %f %f %f ", stac, pars1[1], pars1[2], pars1[3], pars1[4], pars1[5])
-    # }
-    s2 <- sprintf(", Loglikelihood: %f", loglik)
-    cat(s1, s2, "\n", sep = "")
-    utils::flush.console()
-  }
+  print_parameters_and_loglik(pars = c(stac,pars1[1:5]),
+                              loglik = loglik,
+                              verbose = pars2[4],
+                              type = 'clade_loglik')
   return(as.numeric(loglik))
 }
 
diff --git a/R/DAISIE_loglik_CS.R b/R/DAISIE_loglik_CS.R
index 2188f4e4..435cc981 100644
--- a/R/DAISIE_loglik_CS.R
+++ b/R/DAISIE_loglik_CS.R
@@ -674,24 +674,16 @@ DAISIE_loglik_CS_M1 <- DAISIE_loglik <- function(pars1,
     }
   }
 
-  if(pars2[4] >= 1)
-  {
-    if (length(pars1) == 11) { # CHANGE
-      s1 <- sprintf('Status of colonist: %d, Parameters: %f %f %f %f %f %f', stac, pars1[5], pars1[6], pars1[7], pars1[8], pars1[9], pars1[10])
-    } else {
-      s1 <- sprintf(
-        "Status of colonist: %d, Parameters: %f %f %f %f %f ",
-        stac,
-        pars1[1],
-        pars1[2],
-        pars1[3],
-        pars1[4],
-        pars1[5]
-      )
-    }
-    s2 <- sprintf(", Loglikelihood: %f", loglik)
-    cat(s1, s2, "\n", sep = "")
-    utils::flush.console()
+ if (length(pars1) == 11) { # CHANGE
+    print_parameters_and_loglik(pars = c(stac, pars1[5:10]), # should this be 6:10, or 6:11?
+                                loglik = loglik,
+                                verbose = pars2[4],
+                                type = 'clade_loglik')
+  } else {
+    print_parameters_and_loglik(pars = c(stac, pars1[1:5]),
+                                loglik = loglik,
+                                verbose = pars2[4],
+                                type = 'clade_loglik')
   }
   if (is.na(loglik)) {
     message("NA in loglik encountered. Changing to -Inf.")
@@ -935,7 +927,10 @@ DAISIE_loglik_CS <- DAISIE_loglik_all <- function(
     {
       message('Positive values of loglik encountered without possibility for approximation. Setting loglik to -Inf.')
       loglik <- -Inf
-      print_parameters_and_loglik(pars = pars, loglik = loglik, verbose = pars2[4])
+      print_parameters_and_loglik(pars = pars,
+                                  loglik = loglik,
+                                  verbose = pars2[4],
+                                  type = 'island_loglik')
       return(loglik)
     }
     if (is.null(datalist[[1]]$not_present)) {
@@ -1039,21 +1034,143 @@ DAISIE_loglik_CS <- DAISIE_loglik_all <- function(
         reltolint = reltolint)
     }
   }
-  print_parameters_and_loglik(pars = pars, loglik = loglik, verbose = pars2[4])
+  print_parameters_and_loglik(pars = pars,
+                              loglik = loglik,
+                              verbose = pars2[4],
+                              type = 'island_loglik')
   return(loglik)
 }
 
-print_parameters_and_loglik <- function(pars, loglik, verbose)
+print_parameters_and_loglik <- function(pars,
+                                        loglik,
+                                        verbose,
+                                        parnames = c("lambda^c", "mu", "K", "gamma", "lambda^a"),
+                                        type = 'island_loglik',
+                                        distance_dep = NULL)
 {
   if (verbose >= 1) {
-    s1 <- sprintf("Parameters: ")
-    s2 <- sprintf("%f ", pars)
-    s3 <- sprintf(", Loglikelihood: %f", loglik)
-    cat(s1, s2, s3, "\n", sep = "")
+    if(type == 'clade_loglik') {
+      s1a <- sprintf("Status of colonist: %d", pars[1])
+      s1b <- sprintf("Parameters:")
+      s1 <- paste(s1a, s1b, sep = ', ')
+      s2 <- paste(sprintf("%f", pars[-1]), collapse = ', ')
+      s12 <- paste(s1, s2, collapse = ' ')
+      s3 <- paste(sprintf("Loglikelihood: %f", loglik), collapse = '')
+      cat(s12, s3, sep = ', ')
+    } else {
+      if(type == 'global_ML') {
+        s1 <- s1output(pars, distance_dep)
+        s3 <- sprintf("Maximum Loglikelihood: %f", loglik)
+        cat(s1,s3,sep = '\n')
+      } else {
+        if(length(pars) != length(parnames))
+        {
+          warning('The vectors of parameters and parameter names have different lengths.')
+          parnames <- NULL
+        } else {
+          parnames <- paste(parnames, collapse = ', ')
+        }
+        if(type == 'island_ML') {
+          s1 <- sprintf("Maximum likelihood parameters: ")
+          s2 <- paste(sprintf("%f", pars), collapse = ', ')
+          s3 <- sprintf("Maximum Loglikelihood: %f", loglik)
+          cat(s1, parnames, s2, s3, sep = '\n')
+        } else {
+          if(type == 'island_loglik') {
+            s1 <- sprintf("Parameters: ")
+            s2 <- paste(sprintf("%f", pars), collapse = ', ')
+            s3 <- sprintf("Loglikelihood: %f", loglik)
+            cat(s1, parnames, s2, s3, sep = '\n')
+          } else {
+            stop('Type of printing output unknown')
+          }
+        }
+      }
+    }
+    cat('\n')
     utils::flush.console()
   }
 }
 
+s1output <- function(MLpars1,distance_dep)
+{
+  s1 <- switch(distance_dep,
+               power = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * A^ %f\n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * d^ -%f\n
+               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+               sigmoidal_col = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * A^ %f\n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * (1 - (d/%f)^%f / (1 + (d/%f)^%f )\n
+               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[11],MLpars1[8],MLpars1[11],MLpars1[8],MLpars1[9],MLpars1[10]),
+               sigmoidal_ana = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * A^ %f\n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * d^ -%f\n
+               lambda_a = %f * (d/%f)^%f / (1 + (d/%f)^%f )\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[11],MLpars1[10],MLpars1[11],MLpars1[10]),
+               sigmoidal_clado = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * (d/%f)^%f / (1 + (d/%f)^%f )\n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * d^ -%f\n
+               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[11],MLpars1[2],MLpars1[11],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+               sigmoidal_col_ana = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * A^ %f\n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * (1 - (d/%f)^%f / (1 + (d/%f)^%f )\n
+               lambda_a = %f * (d/%f)^%f / (1 + (d/%f)^%f )\n',MLpars1[1],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[11],MLpars1[8],MLpars1[11],MLpars1[8],MLpars1[9],MLpars1[12],MLpars1[10],MLpars1[12],MLpars1[10]),
+               area_additive_clado = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * A^ %f * d^ %f \n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * d^ -%f\n
+               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+               area_interactive_clado = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * A^ (%f + %f * log(d)) \n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * d^ -%f\n
+               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+               area_interactive_clado0 = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * A^ (%f + %f * log(d)) \n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * d^ -%f\n
+               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+               area_interactive_clado1 = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * A^ (%f + d/%f)) \n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * d^ -%f\n
+               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+               area_interactive_clado2 = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * A^ (%f + d/(d + %f)) \n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * d^ -%f\n
+               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+               area_interactive_clado3 = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * (A + d/%f)^ %f\n \n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * d^ -%f\n
+               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[11],MLpars1[2],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10]),
+               area_interactive_clado4 = sprintf('Maximum likelihood parameter estimates:\n
+               lambda_c = %f * A^ (%f * d/(d + %f)) \n
+               mu = %f * A^ -%f\n
+               K = %f * A^ %f\n
+               M * gamma = %f * d^ -%f\n
+               lambda_a = %f * d^ %f\n',MLpars1[1],MLpars1[2],MLpars1[11],MLpars1[3],MLpars1[4],MLpars1[5],MLpars1[6],MLpars1[7],MLpars1[8],MLpars1[9],MLpars1[10])
+  )
+  return(s1)
+}
+
 DAISIE_integrate <- function(initprobs,
                              tvec,
                              rhs_func,
diff --git a/R/DAISIE_loglik_IW.R b/R/DAISIE_loglik_IW.R
index e55b5c94..72c7aa50 100644
--- a/R/DAISIE_loglik_IW.R
+++ b/R/DAISIE_loglik_IW.R
@@ -522,6 +522,9 @@ DAISIE_loglik_IW <- function(
         loglik <- loglik - logcond
     }
   }
-  print_parameters_and_loglik(pars = pars1, loglik = loglik, verbose = pars2[4])
+  print_parameters_and_loglik(pars = pars1,
+                              loglik = loglik,
+                              verbose = pars2[4],
+                              type = 'island_loglik')
   return(as.numeric(loglik))
 }
diff --git a/tests/testthat/test_printing.R b/tests/testthat/test_printing.R
new file mode 100644
index 00000000..b7cab1a6
--- /dev/null
+++ b/tests/testthat/test_printing.R
@@ -0,0 +1,7 @@
+test_that("printing is done", {
+  print_parameters_and_loglik(pars = c(1,2:6), loglik = -3, verbose = T, type = 'clade_loglik')
+  print_parameters_and_loglik(pars = c(2:6), loglik = -3, verbose = T, type = 'island_loglik')
+  print_parameters_and_loglik(pars = c(2:6), loglik = -3, verbose = T, type = 'island_ML')
+  print_parameters_and_loglik(pars = c(1:11), loglik = -3, verbose = T, type = 'global_ML', distance_dep = 'power')
+  print_parameters_and_loglik(pars = c(1:11), loglik = -3, verbose = T, type = 'global_ML', distance_dep = 'sigmoidal_col')
+})

From 992d6f50e52a9e163c68e7035da4a270877819ef Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Mon, 23 Jan 2023 17:13:47 +0100
Subject: [PATCH 53/73] Update GHA check

---
 .github/workflows/R-CMD-check.yaml | 79 ++++++++----------------------
 1 file changed, 20 insertions(+), 59 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 2fd0756b..1e3c1216 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -1,12 +1,10 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, develop]
+    branches: [main, master, develop, src_fix]
   pull_request:
-    branches: [main, master, develop]
-  schedule:
-  - cron: "0 0 * * *"
+    branches: [main, master, develop, src_fix]
 
 name: R-CMD-check
 
@@ -20,69 +18,32 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          if (.Platform$OS.type == "unix") remotes::install_cran("doMC")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true

From 043f39980dd745cbc4148b0434fee97ef745f8c1 Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Mon, 23 Jan 2023 17:50:08 +0100
Subject: [PATCH 54/73] ignore doMC on GHA

---
 .github/workflows/R-CMD-check.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 1e3c1216..5f4dcc32 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -41,7 +41,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: any::rcmdcheck, doMC=?ignore
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

From c8a551c3272f8bb5e3eeab32d5c8d825c59e3e58 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Tue, 24 Jan 2023 09:03:15 +0100
Subject: [PATCH 55/73] bug fix in print call from DAISIE_ML2

---
 R/DAISIE_ML2.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/DAISIE_ML2.R b/R/DAISIE_ML2.R
index c50ff4d4..9c578f82 100644
--- a/R/DAISIE_ML2.R
+++ b/R/DAISIE_ML2.R
@@ -207,6 +207,6 @@ DAISIE_ML2 <- function(
   print_parameters_and_loglik(pars = MLpars1,
                               loglik = ML,
                               verbose = TRUE,
-                              ML = TRUE)
+                              type = 'island_ML')
   return(invisible(out2))
 }

From 456b4b5cab38f814e043af0cc4141c9f2e19886d Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Tue, 24 Jan 2023 11:12:15 +0100
Subject: [PATCH 56/73] Add code and test for multiple island case (ML2)

---
 R/DAISIE_ML2.R                 |  2 +-
 R/DAISIE_loglik_CS.R           | 24 +++++++++++++++++-------
 tests/testthat/test_printing.R |  1 +
 3 files changed, 19 insertions(+), 8 deletions(-)

diff --git a/R/DAISIE_ML2.R b/R/DAISIE_ML2.R
index 9c578f82..3bd3702c 100644
--- a/R/DAISIE_ML2.R
+++ b/R/DAISIE_ML2.R
@@ -207,6 +207,6 @@ DAISIE_ML2 <- function(
   print_parameters_and_loglik(pars = MLpars1,
                               loglik = ML,
                               verbose = TRUE,
-                              type = 'island_ML')
+                              type = 'multiple_island_ML')
   return(invisible(out2))
 }
diff --git a/R/DAISIE_loglik_CS.R b/R/DAISIE_loglik_CS.R
index 435cc981..b60619c4 100644
--- a/R/DAISIE_loglik_CS.R
+++ b/R/DAISIE_loglik_CS.R
@@ -1063,7 +1063,7 @@ print_parameters_and_loglik <- function(pars,
         s3 <- sprintf("Maximum Loglikelihood: %f", loglik)
         cat(s1,s3,sep = '\n')
       } else {
-        if(length(pars) != length(parnames))
+        if(ncol(pars) != length(parnames))
         {
           warning('The vectors of parameters and parameter names have different lengths.')
           parnames <- NULL
@@ -1076,13 +1076,23 @@ print_parameters_and_loglik <- function(pars,
           s3 <- sprintf("Maximum Loglikelihood: %f", loglik)
           cat(s1, parnames, s2, s3, sep = '\n')
         } else {
-          if(type == 'island_loglik') {
-            s1 <- sprintf("Parameters: ")
-            s2 <- paste(sprintf("%f", pars), collapse = ', ')
-            s3 <- sprintf("Loglikelihood: %f", loglik)
-            cat(s1, parnames, s2, s3, sep = '\n')
+          if(type == 'multiple_island_ML') {
+            s1 <- sprintf("Maximum likelihood parameters: ")
+            s2 <- parnames
+            for(i in 1:nrow(pars)) {
+               s2 <- paste(s2,paste(sprintf("%f", pars[i,]), collapse = ', '), sep = '\n')
+            }
+            s3 <- sprintf("Maximum Loglikelihood: %f", loglik)
+            cat(s1, s2, s3, sep = '\n')
           } else {
-            stop('Type of printing output unknown')
+            if(type == 'island_loglik') {
+              s1 <- sprintf("Parameters: ")
+              s2 <- paste(sprintf("%f", pars), collapse = ', ')
+              s3 <- sprintf("Loglikelihood: %f", loglik)
+              cat(s1, parnames, s2, s3, sep = '\n')
+            } else {
+              stop('Type of printing output unknown')
+            }
           }
         }
       }
diff --git a/tests/testthat/test_printing.R b/tests/testthat/test_printing.R
index b7cab1a6..4d331126 100644
--- a/tests/testthat/test_printing.R
+++ b/tests/testthat/test_printing.R
@@ -4,4 +4,5 @@ test_that("printing is done", {
   print_parameters_and_loglik(pars = c(2:6), loglik = -3, verbose = T, type = 'island_ML')
   print_parameters_and_loglik(pars = c(1:11), loglik = -3, verbose = T, type = 'global_ML', distance_dep = 'power')
   print_parameters_and_loglik(pars = c(1:11), loglik = -3, verbose = T, type = 'global_ML', distance_dep = 'sigmoidal_col')
+  print_parameters_and_loglik(pars = data.frame(rbind(c(2:6),c(12:16))), loglik = -3, verbose = T, type = 'multiple_island_ML')
 })

From e83868d33b633575526fd12bcc8c6fdc97a96e77 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Tue, 24 Jan 2023 14:29:33 +0100
Subject: [PATCH 57/73] bug fix in print_parameters_and_loglik

---
 R/DAISIE_loglik_CS.R | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/R/DAISIE_loglik_CS.R b/R/DAISIE_loglik_CS.R
index b60619c4..d1c22a13 100644
--- a/R/DAISIE_loglik_CS.R
+++ b/R/DAISIE_loglik_CS.R
@@ -1063,7 +1063,12 @@ print_parameters_and_loglik <- function(pars,
         s3 <- sprintf("Maximum Loglikelihood: %f", loglik)
         cat(s1,s3,sep = '\n')
       } else {
-        if(ncol(pars) != length(parnames))
+        if(is.null(ncol(pars))) {
+          lpars <- length(pars)
+        } else {
+          lpars <- ncol(pars)
+        }
+        if(lpars != length(parnames))
         {
           warning('The vectors of parameters and parameter names have different lengths.')
           parnames <- NULL

From 10571602488234db3c7257b99d8180acbe324cb5 Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Tue, 24 Jan 2023 16:51:35 +0100
Subject: [PATCH 58/73] Update GHA coverage workflow

---
 .github/workflows/test-coverage.yaml | 36 ++++++++++++++++++++++------
 1 file changed, 29 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index a869e0de..2c5bb502 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -1,8 +1,10 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
+    branches: [main, master]
   pull_request:
-  schedule:
-  - cron: "0 0 * * *"
+    branches: [main, master]
 
 name: test-coverage
 
@@ -13,16 +15,36 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: covr
+          extra-packages: any::covr
+          needs: coverage
 
       - name: Test coverage
-        run: covr::codecov()
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
         shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

From 12f38b0ff2f6872ff473d9a83f335960f96b0026 Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Tue, 24 Jan 2023 16:57:36 +0100
Subject: [PATCH 59/73] Coverage CI on develop

---
 .github/workflows/test-coverage.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 2c5bb502..056da9e9 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, develop]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, develop]
 
 name: test-coverage
 

From 64b6cab8267637dae218b928e67d59a095c8416b Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Wed, 25 Jan 2023 13:10:27 +0100
Subject: [PATCH 60/73] Require recent versions

---
 DESCRIPTION | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index bc7fb01e..43d0265f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -11,7 +11,7 @@ Imports:
     graphics,
     stats,
     utils,
-    DDD (>= 4.4),
+    DDD (>= 5.0),
     subplex,
     Matrix,
     tensor,
@@ -21,11 +21,11 @@ Imports:
     doParallel,
     magrittr,
     parallel,
-    Rcpp (>= 1.0.5)
+    Rcpp (>= 1.0.10)
 LinkingTo: 
     Rcpp,
     RcppEigen,
-    BH
+    BH (>= 1.81.0-1)
 Suggests: 
     covr,
     testthat (>= 2.1.0),

From 49bbff1e45b081348262bc6b27daad13351ae413 Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Wed, 25 Jan 2023 13:26:27 +0100
Subject: [PATCH 61/73] Tweak authors

---
 DESCRIPTION           | 7 ++++---
 man/DAISIE-package.Rd | 4 ++--
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 43d0265f..38e3ff5a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -67,7 +67,7 @@ Authors@R: c(
            email = "j.w.l.lambert@rug.nl",
            comment = c(ORCID = "0000-0001-5218-3046")),
     person(given = "Pedro",
-           family = "Neves",
+           family = "Santos Neves",
            role = c("aut"),
            email = "p.m.santos.neves@rug.nl",
            comment = c(ORCID = "0000-0003-2561-4677")),
@@ -84,7 +84,8 @@ Authors@R: c(
     person(given = "Hanno",
            family = "Hildenbrandt",
            email = "h.hildenbrandt@rug.nl",
-           role = c("aut")),
+           role = c("aut"),
+           comment = c(ORCID = "0000-0002-6784-1037")),
     person(given = "Torsten",
            family = "Hauffe",
            email = "torsten.hauffe@gmail.com",
@@ -115,4 +116,4 @@ Encoding: UTF-8
 VignetteBuilder: knitr
 URL: https://github.com/rsetienne/DAISIE
 BugReports: https://github.com/rsetienne/DAISIE/issues
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
diff --git a/man/DAISIE-package.Rd b/man/DAISIE-package.Rd
index 9260d5d4..a20b0803 100644
--- a/man/DAISIE-package.Rd
+++ b/man/DAISIE-package.Rd
@@ -45,10 +45,10 @@ Authors:
   \item Albert B. Phillimore (\href{https://orcid.org/0000-0002-6553-1553}{ORCID})
   \item Bart Haegeman (\href{https://orcid.org/0000-0003-2325-4727}{ORCID})
   \item Joshua W. Lambert \email{j.w.l.lambert@rug.nl} (\href{https://orcid.org/0000-0001-5218-3046}{ORCID})
-  \item Pedro Neves \email{p.m.santos.neves@rug.nl} (\href{https://orcid.org/0000-0003-2561-4677}{ORCID})
+  \item Pedro Santos Neves \email{p.m.santos.neves@rug.nl} (\href{https://orcid.org/0000-0003-2561-4677}{ORCID})
   \item Shu Xie \email{s.xie@rug.nl} (\href{https://orcid.org/0000-0001-9594-946X}{ORCID})
   \item Richèl J.C. Bilderbeek \email{richel@richelbilderbeek.nl} (\href{https://orcid.org/0000-0003-1107-7049}{ORCID})
-  \item Hanno Hildenbrandt \email{h.hildenbrandt@rug.nl}
+  \item Hanno Hildenbrandt \email{h.hildenbrandt@rug.nl} (\href{https://orcid.org/0000-0002-6784-1037}{ORCID})
 }
 
 Other contributors:

From fd92c146297b9d51d27a30af456b492ba5d3958d Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Wed, 25 Jan 2023 13:31:35 +0100
Subject: [PATCH 62/73] Update refs

---
 R/DAISIE-package.R    | 4 ++--
 man/DAISIE-package.Rd | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/DAISIE-package.R b/R/DAISIE-package.R
index 66572b99..dabb6fdf 100644
--- a/R/DAISIE-package.R
+++ b/R/DAISIE-package.R
@@ -14,9 +14,9 @@
 #' \item Valente, L., Phillimore, A. B., Melo, M., Warren, B. H., Clegg, S. M., Havenstein, K., & Etienne, R. S. (2020). A simple dynamic model explains the diversity of island birds worldwide. Nature 579: 92-96. \doi{10.1038/s41586-020-2022-5}.\cr
 #' \item Hauffe, T., Delicado, D., Etienne, R.S., & Valente, L. (2020). Lake expansion elevates equilibrium diversity via increasing colonization. Journal of Biogeography 47: 1849–1860. \doi{10.1111/jbi.13914}.\cr
 #' \item Valente, L., Kristensen, N., Phillimore, A. B., & Etienne, R. S. (2021). Report of programming bugs in the DAISIE R package: consequences and correction. EcoEvoRxiv. \doi{10.32942/osf.io/w5ntf}.\cr
-#' \item Santos Neves, P., Lambert, J. W., Valente, L., & Etienne, R. S. (2021).The robustness of a simple dynamic model of island biodiversity to geological and eustatic change. bioRxiv. \doi{10.1101/2021.07.26.453064}.\cr
+#' \item Santos Neves, P., Lambert, J. W., Valente, L., & Etienne, R. S. (2022). The robustness of a simple dynamic model of island biodiversity to geological and sea-level change. Journal of Biogeography. \doi{10.1111/jbi.14519}.\cr
 #' \item Lambert, J. W., Santos Neves, P., Bilderbeek, R. L. C., Valente, L., Etienne, R. S. (2022). The effect of mainland dynamics on data and parameter estimates in island biogeography. bioRxiv. \doi{10.1101/2022.01.13.476210}.\cr
-#' \item Xie, S., Valente, L., Etienne, R. S. (2022). A simple island biodiversity model is robust to trait dependence in diversification and colonization rates. biRrxiv. \doi{10.1101/2022.01.01.474685}.\cr
+#' \item Xie, S., Valente, L., Etienne, R. S. (2023). Can we ignore trait-dependent colonization and diversification in island biogeography? biRrxiv. \doi{10.1093/evolut/qpad006}.\cr
 #' }
 #' @keywords internal
 #' @import Rcpp
diff --git a/man/DAISIE-package.Rd b/man/DAISIE-package.Rd
index a20b0803..18956371 100644
--- a/man/DAISIE-package.Rd
+++ b/man/DAISIE-package.Rd
@@ -23,9 +23,9 @@ Cladogenesis and immigration rates can be dependent on diversity.
 \item Valente, L., Phillimore, A. B., Melo, M., Warren, B. H., Clegg, S. M., Havenstein, K., & Etienne, R. S. (2020). A simple dynamic model explains the diversity of island birds worldwide. Nature 579: 92-96. \doi{10.1038/s41586-020-2022-5}.\cr
 \item Hauffe, T., Delicado, D., Etienne, R.S., & Valente, L. (2020). Lake expansion elevates equilibrium diversity via increasing colonization. Journal of Biogeography 47: 1849–1860. \doi{10.1111/jbi.13914}.\cr
 \item Valente, L., Kristensen, N., Phillimore, A. B., & Etienne, R. S. (2021). Report of programming bugs in the DAISIE R package: consequences and correction. EcoEvoRxiv. \doi{10.32942/osf.io/w5ntf}.\cr
-\item Santos Neves, P., Lambert, J. W., Valente, L., & Etienne, R. S. (2021).The robustness of a simple dynamic model of island biodiversity to geological and eustatic change. bioRxiv. \doi{10.1101/2021.07.26.453064}.\cr
+\item Santos Neves, P., Lambert, J. W., Valente, L., & Etienne, R. S. (2022). The robustness of a simple dynamic model of island biodiversity to geological and sea-level change. Journal of Biogeography. \doi{10.1111/jbi.14519}.\cr
 \item Lambert, J. W., Santos Neves, P., Bilderbeek, R. L. C., Valente, L., Etienne, R. S. (2022). The effect of mainland dynamics on data and parameter estimates in island biogeography. bioRxiv. \doi{10.1101/2022.01.13.476210}.\cr
-\item Xie, S., Valente, L., Etienne, R. S. (2022). A simple island biodiversity model is robust to trait dependence in diversification and colonization rates. biRrxiv. \doi{10.1101/2022.01.01.474685}.\cr
+\item Xie, S., Valente, L., Etienne, R. S. (2023). Can we ignore trait-dependent colonization and diversification in island biogeography? biRrxiv. \doi{10.1093/evolut/qpad006}.\cr
 }
 }
 \seealso{

From d878d308a7494a08eb400e4b69e2841983e6dfe9 Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Wed, 25 Jan 2023 13:35:32 +0100
Subject: [PATCH 63/73] CI needs [run ci]

---
 .github/workflows/R-CMD-check.yaml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 5f4dcc32..87ab87a9 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -2,14 +2,15 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, develop, src_fix]
+    branches: [main, master, develop]
   pull_request:
-    branches: [main, master, develop, src_fix]
+    branches: [main, master, develop]
 
 name: R-CMD-check
 
 jobs:
   R-CMD-check:
+  if: "contains(github.event.head_commit.message, '[run ci]')"
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})

From 6aba12e605e799a083ea2d4f7d6817b68c84f768 Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Wed, 25 Jan 2023 13:36:39 +0100
Subject: [PATCH 64/73] Fix syntax error

---
 .github/workflows/R-CMD-check.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 87ab87a9..ba7e9f5e 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -10,11 +10,12 @@ name: R-CMD-check
 
 jobs:
   R-CMD-check:
-  if: "contains(github.event.head_commit.message, '[run ci]')"
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
 
+    if: "contains(github.event.head_commit.message, '[run ci]')"
+
     strategy:
       fail-fast: false
       matrix:

From fa18dbb01c90facc84127e869d59f63806f7d02a Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Wed, 25 Jan 2023 13:38:23 +0100
Subject: [PATCH 65/73] Condition to coverage too [run ci]

---
 .github/workflows/test-coverage.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 056da9e9..5bd08d71 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -11,6 +11,8 @@ name: test-coverage
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
+    if: "contains(github.event.head_commit.message, '[run ci]')"
+
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 

From 4b2b9deda690c4e8ba2cc8360910cd63f40a65cc Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Wed, 25 Jan 2023 13:42:32 +0100
Subject: [PATCH 66/73] ubunutu-latest r: olderl-1 is not a CRAN check flavor

---
 .github/workflows/R-CMD-check.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index ba7e9f5e..9e4feb39 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -24,7 +24,6 @@ jobs:
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

From bc785b02e31075a2f7a962075ea839a51cf2ad27 Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Thu, 26 Jan 2023 15:12:46 +0100
Subject: [PATCH 67/73] Update NEWS.md

---
 DESCRIPTION |  2 +-
 NEWS.md     | 10 ++++++++--
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 38e3ff5a..28aab8fa 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: DAISIE
 Type: Package
 Title: Dynamical Assembly of Islands by Speciation, Immigration and Extinction
 Version: 4.3.0
-Date: 2022-12-21
+Date: 2023-12-26
 Depends: R (>= 3.5.0)
 biocViews:
 SystemRequirements: C++14
diff --git a/NEWS.md b/NEWS.md
index 7a3a6fcf..c1abcf67 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,7 +1,13 @@
 # DAISIE 4.3.0
 * Add code for the trait-dependent simulations considering two carrying capacities for each trait state.
-* Bug fix in 'DAISIE_sim_cr_iw()', which wrongly computed number of species at present
-* Improve the likelihood calculation.
+* Improvements to the relaxed rate model fitting procedure.
+* Add `DAISIE_count_species()` to count the number of species in a datalist or simulated data.
+* Simply printing code by wrapping multiple instances into `print_parameters_and_loglik()`.
+* Overall documentation improvements and updated references.
+* Bug fix in `DAISIE_sim_cr_iw()`, which wrongly computed number of species at present. #147
+* Improve the likelihood calculation. Fixed incorrect likelihood present for  type 2 case CS model inference if the values of lambda were high, in the C++ implementation.
+* Overhaul GHA workflows to be more up to date and more conservative when to run. Feature branches require the tag
+[run ci] be added to the commit message to run.
 
 # DAISIE 4.2.1
 

From c1ca375cd27dc24a495f72d8868aa5ad46d3cf35 Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Thu, 26 Jan 2023 15:16:14 +0100
Subject: [PATCH 68/73] Try updated GHA conditions

---
 .github/workflows/R-CMD-check.yaml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 9e4feb39..2bbdcbb2 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -2,9 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, develop]
   pull_request:
-    branches: [main, master, develop]
 
 name: R-CMD-check
 
@@ -14,7 +12,7 @@ jobs:
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
 
-    if: "contains(github.event.head_commit.message, '[run ci]')"
+    if: "contains(github.event.head_commit.message, '[run ci]' || (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop')"
 
     strategy:
       fail-fast: false

From b75474e495c69f4939d16d8b50ab3869a389d388 Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Thu, 26 Jan 2023 15:18:17 +0100
Subject: [PATCH 69/73] Fix syntax

---
 .github/workflows/R-CMD-check.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 2bbdcbb2..a3d89ced 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -12,7 +12,7 @@ jobs:
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
 
-    if: "contains(github.event.head_commit.message, '[run ci]' || (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop')"
+    if: "contains(github.event.head_commit.message, '[run ci]') || (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop')"
 
     strategy:
       fail-fast: false

From 62349f246e2a12daf3628d4bbda7c5f6869e0f9d Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Thu, 26 Jan 2023 15:50:17 +0100
Subject: [PATCH 70/73] Flag and conditions for coverage

---
 .github/workflows/test-coverage.yaml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 5bd08d71..952a4f78 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -2,16 +2,14 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, develop]
   pull_request:
-    branches: [main, master, develop]
 
 name: test-coverage
 
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
-    if: "contains(github.event.head_commit.message, '[run ci]')"
+    if: "contains(github.event.head_commit.message, '[run ci]') || (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop')"
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

From e81fdc7e700cb5c502f28591226667bc895e375e Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Thu, 26 Jan 2023 16:04:39 +0100
Subject: [PATCH 71/73] Fix refs

---
 R/DAISIE-package.R    | 2 +-
 man/DAISIE-package.Rd | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/DAISIE-package.R b/R/DAISIE-package.R
index dabb6fdf..95c1c772 100644
--- a/R/DAISIE-package.R
+++ b/R/DAISIE-package.R
@@ -16,7 +16,7 @@
 #' \item Valente, L., Kristensen, N., Phillimore, A. B., & Etienne, R. S. (2021). Report of programming bugs in the DAISIE R package: consequences and correction. EcoEvoRxiv. \doi{10.32942/osf.io/w5ntf}.\cr
 #' \item Santos Neves, P., Lambert, J. W., Valente, L., & Etienne, R. S. (2022). The robustness of a simple dynamic model of island biodiversity to geological and sea-level change. Journal of Biogeography. \doi{10.1111/jbi.14519}.\cr
 #' \item Lambert, J. W., Santos Neves, P., Bilderbeek, R. L. C., Valente, L., Etienne, R. S. (2022). The effect of mainland dynamics on data and parameter estimates in island biogeography. bioRxiv. \doi{10.1101/2022.01.13.476210}.\cr
-#' \item Xie, S., Valente, L., Etienne, R. S. (2023). Can we ignore trait-dependent colonization and diversification in island biogeography? biRrxiv. \doi{10.1093/evolut/qpad006}.\cr
+#' \item Xie, S., Valente, L., Etienne, R. S. (2023). Can we ignore trait-dependent colonization and diversification in island biogeography? Evolution. \doi{10.1093/evolut/qpad006}.\cr
 #' }
 #' @keywords internal
 #' @import Rcpp
diff --git a/man/DAISIE-package.Rd b/man/DAISIE-package.Rd
index 18956371..464c1708 100644
--- a/man/DAISIE-package.Rd
+++ b/man/DAISIE-package.Rd
@@ -25,7 +25,7 @@ Cladogenesis and immigration rates can be dependent on diversity.
 \item Valente, L., Kristensen, N., Phillimore, A. B., & Etienne, R. S. (2021). Report of programming bugs in the DAISIE R package: consequences and correction. EcoEvoRxiv. \doi{10.32942/osf.io/w5ntf}.\cr
 \item Santos Neves, P., Lambert, J. W., Valente, L., & Etienne, R. S. (2022). The robustness of a simple dynamic model of island biodiversity to geological and sea-level change. Journal of Biogeography. \doi{10.1111/jbi.14519}.\cr
 \item Lambert, J. W., Santos Neves, P., Bilderbeek, R. L. C., Valente, L., Etienne, R. S. (2022). The effect of mainland dynamics on data and parameter estimates in island biogeography. bioRxiv. \doi{10.1101/2022.01.13.476210}.\cr
-\item Xie, S., Valente, L., Etienne, R. S. (2023). Can we ignore trait-dependent colonization and diversification in island biogeography? biRrxiv. \doi{10.1093/evolut/qpad006}.\cr
+\item Xie, S., Valente, L., Etienne, R. S. (2023). Can we ignore trait-dependent colonization and diversification in island biogeography? Evolution. \doi{10.1093/evolut/qpad006}.\cr
 }
 }
 \seealso{

From 4cfa5756ee984a82e8b438b9da3d96df9bcc9d56 Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Thu, 26 Jan 2023 16:17:07 +0100
Subject: [PATCH 72/73] Correct references

---
 README.md | 27 +++++++++++++--------------
 1 file changed, 13 insertions(+), 14 deletions(-)

diff --git a/README.md b/README.md
index e01d37ef..e4347b4c 100644
--- a/README.md
+++ b/README.md
@@ -86,29 +86,28 @@ For feature requests or bug-reports or other matters, please submit an [issue](h
 
 ## References
 
-Etienne R. S., Valente, L., Phillimore, A. B., Haegeman, B., Lambert, J. W., Neves, P., Xie, S., Bilderbeek, R. J. C., & Hildenbrandt, H. (2021). DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction. R package version 4.0.2. https://cran.r-project.org/package=DAISIE. https://doi.org/10.5281/zenodo.4054058
+* Etienne R. S., Valente, L., Phillimore, A. B., Haegeman, B., Lambert, J. W., Neves, P., Xie, S., Bilderbeek, R. J. C., & Hildenbrandt, H. (2021). DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction. R package version 4.0.2. https://cran.r-project.org/package=DAISIE. https://doi.org/10.5281/zenodo.4054058
 
-Valente, L., Etienne, R.S., & Phillimore, A.B. (2014). The effects of island ontogeny on species diversity and phylogeny. Proceedings of the Royal Society B: Biological Sciences, 281(1784), 20133227–20133227. http://doi.org/10.1098/rspb.2013.3227
+* Valente, L., Etienne, R.S., & Phillimore, A.B. (2014). The effects of island ontogeny on species diversity and phylogeny. Proceedings of the Royal Society B: Biological Sciences, 281(1784), 20133227–20133227. http://doi.org/10.1098/rspb.2013.3227
 
-Valente, L., Phillimore, A.B., & Etienne, R.S. (2015). Equilibrium and non-equilibrium dynamics simultaneously operate in the Galápagos islands. Ecology Letters, 18(8), 844–852. http://doi.org/10.1111/ele.12461
+* Valente, L., Phillimore, A.B., & Etienne, R.S. (2015). Equilibrium and non-equilibrium dynamics simultaneously operate in the Galápagos islands. Ecology Letters, 18(8), 844–852. http://doi.org/10.1111/ele.12461
 
-Valente, L., Etienne, R.S., & Dávalos, L.M. (2017). Recent extinctions disturb path to equilibrium diversity in Caribbean bats. Nature Ecology & Evolution, 1(2), 0026. http://doi.org/10.1038/s41559-016-0026
+* Valente, L., Etienne, R.S., & Dávalos, L.M. (2017). Recent extinctions disturb path to equilibrium diversity in Caribbean bats. Nature Ecology & Evolution, 1(2), 0026. http://doi.org/10.1038/s41559-016-0026
 
-Valente, L., Illera, J.C., Havenstein, K., Pallien, T., Etienne, R.S., & Tiedemann, R. (2017). Equilibrium Bird Species Diversity in Atlantic Islands. Current Biology, 27(11), 1660-1666. https://doi.org/10.1016/j.cub.2017.04.053
+* Valente, L., Illera, J.C., Havenstein, K., Pallien, T., Etienne, R.S., & Tiedemann, R. (2017). Equilibrium Bird Species Diversity in Atlantic Islands. Current Biology, 27(11), 1660-1666. https://doi.org/10.1016/j.cub.2017.04.053
 
-Valente, L., Phillimore, A.B., & Etienne, R.S. (2018). Using molecular phylogenies in island biogeography: It’s about time. Ecography, 1–3. http://doi.org/10.1111/ecog.03503
+* Valente, L., Phillimore, A.B., & Etienne, R.S. (2018). Using molecular phylogenies in island biogeography: It’s about time. Ecography, 1–3. http://doi.org/10.1111/ecog.03503
 
-Valente, L., Etienne, R.S., & Garcia-R., J.C. (2019). Deep Macroevolutionary Impact of Humans on New Zealand’s Unique Avifauna. Current Biology 29 (15): 2563-2569.e4. https://doi.org/10.1016/j.cub.2019.06.058
+* Valente, L., Etienne, R.S., & Garcia-R., J.C. (2019). Deep Macroevolutionary Impact of Humans on New Zealand’s Unique Avifauna. Current Biology 29 (15): 2563-2569.e4. https://doi.org/10.1016/j.cub.2019.06.058
 
-Valente, L., Phillimore, A.B., Melo, M., Warren, B.H., Clegg, S.M., Havenstein, K., Tiedemann, R., Illera, J.C., Thebaud, C., Aschenbach, T. & Etienne, R.S. (2020). A Simple Dynamic Model Explains the Diversity of Island Birds Worldwide. Nature 579 (7797): 92–96. https://doi.org/10.1038/s41586-020-2022-5
+* Valente, L., Phillimore, A.B., Melo, M., Warren, B.H., Clegg, S.M., Havenstein, K., Tiedemann, R., Illera, J.C., Thebaud, C., Aschenbach, T. & Etienne, R.S. (2020). A Simple Dynamic Model Explains the Diversity of Island Birds Worldwide. Nature 579 (7797): 92–96. https://doi.org/10.1038/s41586-020-2022-5
 
-Hauffe, T., Delicado, D., Etienne, R.S., & Valente, L. (2020). Lake expansion elevates equilibrium diversity via increasing colonization. Journal of Biogeography 47: 1849–1860. https://doi.org/10.1111/jbi.13914
+* Hauffe, T., Delicado, D., Etienne, R.S., & Valente, L. (2020). Lake expansion elevates equilibrium diversity via increasing colonization. Journal of Biogeography 47: 1849–1860. https://doi.org/10.1111/jbi.13914
 
-Valente, L., Kristensen, N., Phillimore, A. B., & Etienne, R. S. (2021). Report of programming bugs in the DAISIE R package: consequences and correction. https://doi.org/10.32942/osf.io/w5ntf
+* Valente, L., Kristensen, N., Phillimore, A. B., & Etienne, R. S. (2021). Report of programming bugs in the DAISIE R package: consequences and correction. https://doi.org/10.32942/osf.io/w5ntf
 
+* Santos Neves, P.\*, Lambert, J. W.\*, Valente, L., & Etienne, R. S. (2022). The robustness of a simple dynamic model of island biodiversity to geological and sea-level change. Journal of Biogeography. https://doi.org/10.1111/jbi.14519
 
-Santos Neves, P.\*, Lambert, J. W.\*, Valente, L., & Etienne, R. S. (2021). The robustness of a simple dynamic model of island biodiversity to geological and eustatic change. bioRxiv. https://doi.org/10.1101/2021.07.26.453064
+* Lambert, J. W., Santos Neves, P., Bilderbeek, R. L. C., Valente, L., Etienne, R. S. (2022). The effect of mainland dynamics on data and parameter estimates in island biogeography. bioRxiv. https://doi.org/10.1101/2022.01.13.476210
 
-Lambert, J. W., Santos Neves, P., Bilderbeek, R. L. C., Valente, L., Etienne, R. S. (2022). The effect of mainland dynamics on data and parameter estimates in island biogeography. bioRxiv. https://doi.org/10.1101/2022.01.13.476210
-
-Xie, S., Valente, L., Etienne, R. S. (2022). A simple island biodiversity model is robust to trait dependence in diversification and colonization rates. biRrxiv. https://doi.org/10.1101/2022.01.01.474685
+* Xie, S., Valente, L., Etienne, R. S. (2023). Can we ignore trait-dependent colonization and diversification in island biogeography? Evolution. https://doi.org/10.1093/evolut/qpad006.

From 362a3a5af418e6969839d52f7df38c763d6d41b6 Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Thu, 26 Jan 2023 16:38:54 +0100
Subject: [PATCH 73/73] NEWS.md updated note on sprintf

---
 NEWS.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index c1abcf67..3edb86f7 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,6 @@
 # DAISIE 4.3.0
+
+* Due to recent changes in CRAN policy that result in warnings due to the use of Rcpp related packages that link to libraries that use `sprintf` ('Rcpp' and 'BH'), 'DAISIE' now requires Rcpp v(>= 1.0.10) and BH v(>= 1.81.0-1). See https://github.com/RcppCore/Rcpp/pull/1236 and https://github.com/eddelbuettel/bh/pull/90 respectively. Also require package 'DDD' v(>= 5.0.0).
 * Add code for the trait-dependent simulations considering two carrying capacities for each trait state.
 * Improvements to the relaxed rate model fitting procedure.
 * Add `DAISIE_count_species()` to count the number of species in a datalist or simulated data.