Merge pull request #162 from rsetienne/develop

v4.4.1

.Rbuildignore

@@ -19,3 +19,6 @@
 ^\.vscode$
 ^dummy\.R
 ^LICENSE\.md$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# 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:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -16,3 +16,4 @@ src/*.gcno
 **/.DS_Store
 **/Rplots.pdf
 Meta
+docs

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: DAISIE
 Type: Package
 Title: Dynamical Assembly of Islands by Speciation, Immigration and Extinction
-Version: 4.4.0
-Date: 2023-03-29
+Version: 4.4.1
+Date: 2023-10-20
 Depends: R (>= 4.2.0)
 biocViews:
 Imports: 
@@ -114,6 +114,7 @@ NeedsCompilation: yes
 SystemRequirements: C++17
 Encoding: UTF-8
 VignetteBuilder: knitr
-URL: https://github.com/rsetienne/DAISIE
+URL: https://github.com/rsetienne/DAISIE,
+    https://rsetienne.github.io/DAISIE/
 BugReports: https://github.com/rsetienne/DAISIE/issues
 RoxygenNote: 7.2.3

NEWS.md

@@ -1,3 +1,12 @@
+# DAISIE 4.4.1
+
+* Fix bug in the calculation of shift loglikelihoods.
+* Fix bug where parameters being optimized could incorrectly be `Inf` #159 #160 (@joshwlambert).
+* `DAISIE_SR_loglik_CS_M1()` is now `DAISIE_loglik_CS_shift()`.
+* New pkgdown website.
+* Several improvements to the relaxed rate code.
+
+
 # DAISIE 4.4.0
 
 * No longer include patched version of `boost/numeric/odeint/stepper/bulirsch_stoer.hpp`,

R/DAISIE_ML1.R

@@ -25,7 +25,7 @@ DAISIE_loglik_all_choosepar <- function(trparsopt,
   } else {
     trpars1 <- rep(0, 6)
     prop_type2_present <- which(idparsfix == 11)
-    if(!is.null(prop_type2_present)) {
+    if (length(prop_type2_present) > 0) {
        trparsfix <- trparsfix[-prop_type2_present]
        idparsfix <- idparsfix[-prop_type2_present]
     }

R/DAISIE_ML_CS.R

@@ -49,7 +49,7 @@
 #' \code{\link{DAISIE_sim_cr_shift}}
 #' @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. <DOI:10.1111/ele.12461>.
+#' Galapagos islands. Ecology Letters 18: 844-852. <doi:10.1111/ele.12461>.
 #' @keywords models
 #' @examples
 #'

R/DAISIE_SR_loglik_CS.R

@@ -356,15 +356,17 @@ DAISIE_SR_loglik_CS <- DAISIE_SR_loglik_all <- function(
     return(check_shift_loglik)
   }
   cond = pars2[3]
-  logp0 = DAISIE_SR_loglik_CS_M1(
-    pars1 = pars1,
+  logp0 = DAISIE_loglik_CS_shift(
+    pars1 = pars1[1:10],
     pars2 = pars2,
     brts = datalist[[1]]$island_age,
     stac = 0,
     missnumspec = 0,
     methode = methode,
     abstolint = abstolint,
-    reltolint = reltolint
+    reltolint = reltolint,
+    verbose = verbose,
+    tshift = pars1[11]
   )
   if (is.null(datalist[[1]]$not_present)) {
     not_present <- (datalist[[1]]$not_present_type1 + datalist[[1]]$not_present_type2)
@@ -377,15 +379,17 @@ DAISIE_SR_loglik_CS <- DAISIE_SR_loglik_all <- function(
   loglik <- loglik - logcond
   if (length(datalist) > 1) {
     for (i in 2:length(datalist)) {
-      loglik <- loglik + DAISIE_SR_loglik_CS_M1(
-        pars1 = pars1,
+      loglik <- loglik + DAISIE_loglik_CS_shift(
+        pars1 = pars1[1:10],
         pars2 = pars2,
         brts = datalist[[i]]$branching_times,
         stac = datalist[[i]]$stac,
         missnumspec = datalist[[i]]$missing_species,
         methode = methode,
         abstolint = abstolint,
-        reltolint = reltolint
+        reltolint = reltolint,
+        verbose = verbose,
+        tshift = pars1[11]
       )
     }
   }

R/DAISIE_loglik_CS.R

@@ -1034,9 +1034,11 @@ DAISIE_loglik_CS <- DAISIE_loglik_all <- function(
         reltolint = reltolint)
     }
   }
+
   print_parameters_and_loglik(pars = pars,
                               loglik = loglik,
                               verbose = pars2[4],
+                              parnames = c("lambda^c", "mu", "K", "gamma", "lambda^a", "prob_init_pres"),
                               type = 'island_loglik')
   return(loglik)
 }