addSpecies() now correctly preserves all species_params of the ex…

…isting model.

DESCRIPTION

@@ -19,7 +19,7 @@ Authors@R: c(person("Gustav", "Delius", email="gustav.delius@york.ac.uk",
                     comment = c(ORCID = "0000-0002-8478-3430")),
              person("Richard", "Southwell", email="richard.southwell@york.ac.uk",
                     role=c("ctb", "cph")))
-Version: 2.5.1.9003
+Version: 2.5.1.9004
 License: GPL-3
 Imports:
     assertthat,

NEWS.md

@@ -1,5 +1,7 @@
-# mizer 2.5.1.9003
+# mizer 2.5.1.9004
 
+- `addSpecies()` now correctly preserves all `species_params` of the existing
+  model.
 - New species parameter `w_repro_max` giving the size at which a species 
   invests 100% of its energy into reproduction. Set to `w_max` by default.
 - `getDiet()` now also includes the contribution of the external encounter rate
@@ -17,6 +19,8 @@
   to observed biomass as default (`ratio = T`), as this is more useful visually
   to see how far off modelled biomass is from observed biomass.
 - Deprecated `matchYields()` and `calibrateYield()`.
+- Improved some unit tests.
+- Some improvements to documentation.
 
 # mizer 2.5.1
 

R/manipulate_species.R

@@ -85,7 +85,7 @@ addSpecies <- function(params, species_params,
              "has its catchability array protected by a comment.")
     }
 
-    # set interaction
+    # set interaction ----
     no_old_sp <- nrow(params@species_params)
     old_sp <- 1:no_old_sp
     no_new_sp <- nrow(species_params)
@@ -112,9 +112,9 @@ addSpecies <- function(params, species_params,
     # combine species params ----
 
     # Move linecolour and linetype into species_params
-    params@given_species_params$linetype <-
+    params@species_params$linetype <-
         params@linetype[as.character(params@species_params$species)]
-    params@given_species_params$linecolour <-
+    params@species_params$linecolour <-
         params@linecolour[as.character(params@species_params$species)]
 
     # Make sure that all columns exist in both data frames
@@ -123,9 +123,16 @@ addSpecies <- function(params, species_params,
     missing <- setdiff(names(given_species_params), names(params@given_species_params))
     params@given_species_params[missing] <- NA
 
+    missing <- setdiff(names(params@species_params), names(species_params))
+    species_params[missing] <- NA
+    missing <- setdiff(names(species_params), names(params@species_params))
+    params@species_params[missing] <- NA
+
     # add the new species (with parameters described by species_params),
     # to make a larger species_params dataframe.
-    combi_species_params <- rbind(params@given_species_params, given_species_params,
+    combi_species_params <- rbind(params@species_params, species_params,
+                                  stringsAsFactors = FALSE)
+    combi_given_species_params <- rbind(params@given_species_params, given_species_params,
                                   stringsAsFactors = FALSE)
 
     # combine gear params ----
@@ -194,6 +201,7 @@ addSpecies <- function(params, species_params,
         lambda = params@resource_params$lambda,
         w_pp_cutoff = params@resource_params$w_pp_cutoff
     )
+    p@given_species_params <- combi_given_species_params
 
     # Set effort ----
     new_gear <- setdiff(unique(gear_params$gear),

tests/testthat/test-manipulate_species.R

@@ -6,7 +6,7 @@ test_that("addSpecies works when adding a second identical species", {
     species_params <- p@species_params[5, ]
     species_params$species <- "new"
     # Adding species 5 again should lead two copies of the species
-    expect_message(pa <- addSpecies(p, species_params))
+    pa <- addSpecies(p, species_params)
     expect_identical(pa@metab[5, ], pa@metab[no_sp + 1, ])
     expect_identical(pa@psi[5, ], pa@psi[no_sp + 1, ])
     expect_identical(pa@ft_pred_kernel_e[5, ], pa@ft_pred_kernel_e[no_sp + 1, ])
@@ -160,9 +160,25 @@ test_that("Added species stay at low abundance", {
     expect_message(params <- addSpecies(params, species_params))
     no_sp <- nrow(params@species_params)
     sim <- project(params, t_max = 1, progress_bar = FALSE)
-    expect_lt(finalN(sim)[no_sp, 1] / initialN(sim)[no_sp, 1], 1.04)
+    expect_lt(finalN(sim)[no_sp, 1] / initialN(sim)[no_sp, 1], 1.05)
 })
 
+test_that("addSpecies preserves both given and other species params", {
+
+    params <- newTraitParams()
+    params@given_species_params$b <- 3
+    params@species_params$w_mat25 <- params@species_params$w_mat25 * 1.01
+    sp <- data.frame(species = "new",
+                     w_max = 10, test = "test")
+    expect_message(p <- addSpecies(params, sp))
+    no_sp <- nrow(params@species_params)
+    expect_identical(p@species_params$w_mat25[1:no_sp],
+                     params@species_params$w_mat25[1:no_sp])
+    expect_identical(p@given_species_params$b[1:no_sp],
+                     params@given_species_params$b[1:no_sp])
+    expect_in("test", names(p@species_params))
+    expect_in("test", names(p@given_species_params))
+})
 
 # removeSpecies ----
 test_that("removeSpecies works", {
@@ -209,7 +225,7 @@ test_that("adding and then removing species leaves params unaltered", {
     # two arbitrary species
     sp <- data.frame(species = c("new1", "new2"),
                      w_max = c(10, 100),
-                     k_vb = c(4, 1),
+                     k_vb = c(4, 2),
                      stringsAsFactors = FALSE)
     # add comments to test that they will be preserved as well
     comment(params) <- "test"