Merge pull request #152 from rsetienne/develop

V4.3.0
rsetienne · Jan 26, 2023 · d0ed3df · d0ed3df
2 parents 58ecf4a + 362a3a5
commit d0ed3df
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,10 +1,8 @@
-# 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:
   pull_request:
-  schedule:
-  - cron: "0 0 * * *"
 
 name: R-CMD-check
 
@@ -14,73 +12,37 @@ 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')"
+
     strategy:
       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'}
 
     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-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - 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, doMC=?ignore
+          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
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -1,28 +1,50 @@
+# 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:
   pull_request:
-  schedule:
-  - cron: "0 0 * * *"
 
 name: test-coverage
 
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
+    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 }}
 
     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
diff --git 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: 4.3.0
+Date: 2023-12-26
 Depends: R (>= 3.5.0)
 biocViews:
 SystemRequirements: C++14
@@ -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),
@@ -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: 7.2.0
+RoxygenNote: 7.2.3
diff --git 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)
@@ -32,12 +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/NEWS.md b/NEWS.md
@@ -1,3 +1,16 @@
+# 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.
+* 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
 
 * Bug fixes in `DAISIE_loglik_CS()`on the likelihood code for the continental sampling (probability of initial presence on the island).

diff --git 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? Evolution. \doi{10.1093/evolut/qpad006}.\cr
 #' }
 #' @keywords internal
 #' @import Rcpp

diff --git 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(
@@ -240,13 +242,19 @@ 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)
@@ -391,20 +399,8 @@ DAISIE_ML1 <- function(
       df = length(initparsopt),
       conv = unlist(out$conv)
     )
-    s1 <- sprintf(
-      "Maximum likelihood parameter estimates:\n lambda_c: %f\n mu: %f\n K: %f\n gamma: %f\n lambda_a: %f\n lambda_c2: %f\n mu2: %f\n K2: %f\n gamma2: %f\n lambda_a2: %f\n prop_type2: %f",
-      MLpars1[1],
-      MLpars1[2],
-      MLpars1[3],
-      MLpars1[4],
-      MLpars1[5],
-      MLpars1[6],
-      MLpars1[7],
-      MLpars1[8],
-      MLpars1[9],
-      MLpars1[10],
-      MLpars1[11]
-    )
+    pars_to_print <- MLpars1[1:11]
+    parnames <- c('lambda^c','mu','K','gamma','lambda^a','lambda^c2','mu2','K2','gamma2','lambda^a2','prop_type2')
   } else if (all(all_no_shift == 7:11)) {
     out2 <- data.frame(
       lambda_c = MLpars1[1],
@@ -417,15 +413,8 @@ DAISIE_ML1 <- function(
       df = length(initparsopt),
       conv = unlist(out$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],
@@ -437,17 +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