Develop

.github/workflows/test-coverage.yaml

@@ -1,50 +1,63 @@
-# 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: [master, develop]
   pull_request:
+    branches: [master, develop]
 
-name: test-coverage
+name: test-coverage-new
+
+permissions: read-all
 
 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@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-
+
+      - name: Install devtools
+        run: install.packages("devtools")
+        shell: Rscript {0}
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v5
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          files: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
-          path: ${{ runner.temp }}/package
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,8 +1,7 @@
 Package: DDD
 Type: Package
 Title: Diversity-Dependent Diversification
-Version: 5.2.3
-Date: 2024-11-26
+Version: 5.2.4
 Depends: R (>= 3.5.0)
 Imports:
   deSolve,

R/RcppExports.R

@@ -8,6 +8,13 @@ dd_integrate_bw_odeint <- function(ry, times, pars, atol, rtol, stepper) {
 #' @useDynLib DDD
 NULL
 
+dd_integrate_log_odeint <- function(ry, times, pars, atol, rtol, stepper) {
+    .Call('_DDD_dd_integrate_log_odeint', PACKAGE = 'DDD', ry, times, pars, atol, rtol, stepper)
+}
+
+#' @useDynLib DDD
+NULL
+
 dd_integrate_odeint <- function(ry, times, pars, atol, rtol, stepper) {
     .Call('_DDD_dd_integrate_odeint', PACKAGE = 'DDD', ry, times, pars, atol, rtol, stepper)
 }

R/bd_ML.R

@@ -57,7 +57,7 @@
 #' @param changeloglikifnoconv if TRUE the loglik will be set to -Inf if ML
 #' does not converge
 #' @param optimmethod Method used in optimization of the likelihood. Current
-#' default is 'subplex'. Alternative is 'simplex' (default of previous
+#' default is 'simplex'. Alternative is 'subplex' (default of previous
 #' versions)
 #' @param num_cycles the number of cycles of opimization. If set at Inf, it will
 #' do as many cycles as needed to meet the tolerance set for the target function.
@@ -102,7 +102,7 @@ bd_ML = function(brts,
     tol = c(1E-3, 1E-4, 1E-6),
     maxiter = 1000 * round((1.25)^length(idparsopt)),
     changeloglikifnoconv = FALSE,
-    optimmethod = 'subplex',
+    optimmethod = 'simplex',
     num_cycles = 1,
     methode = 'odeint::runge_kutta_cash_karp54',
     verbose = FALSE)

R/dd_KI_ML.R

@@ -78,7 +78,7 @@
 #' @param changeloglikifnoconv if TRUE the loglik will be set to -Inf if ML
 #' does not converge
 #' @param optimmethod Method used in optimization of the likelihood. Current
-#' default is 'subplex'. Alternative is 'simplex' (default of previous
+#' default is 'simplex'. Alternative is 'subplex' (default of previous
 #' versions)
 #' @param num_cycles the number of cycles of opimization. If set at Inf, it will
 #' do as many cycles as needed to meet the tolerance set for the target function.
@@ -140,7 +140,7 @@ dd_KI_ML = function(brtsM,
     tol = c(1E-3, 1E-4, 1E-6),
     maxiter = 1000 * round((1.25)^length(idparsopt)),
     changeloglikifnoconv = FALSE,
-    optimmethod = 'subplex',
+    optimmethod = 'simplex',
     num_cycles = 1,
     methode = 'analytical',
     correction = TRUE,

R/dd_LR.R

@@ -60,7 +60,7 @@
 #' @param changeloglikifnoconv if TRUE the loglik will be set to -Inf if ML
 #' does not converge
 #' @param optimmethod Method used in optimization of the likelihood. Current
-#' default is 'subplex'. Alternative is 'simplex' (default of previous
+#' default is 'simplex'. Alternative is 'subplex' (default of previous
 #' versions)
 #' @param methode The method used to solve the master equation, default is
 #' 'analytical' which uses matrix exponentiation; alternatively numerical ODE
@@ -120,7 +120,7 @@ dd_LR = function(
    tol = c(1E-3,1E-4,1E-6),
    maxiter = 2000,
    changeloglikifnoconv = FALSE,
-   optimmethod = 'subplex',
+   optimmethod = 'simplex',
    methode = 'analytical'   
    )
 {

R/dd_ML.R

@@ -91,15 +91,20 @@ parsfixdefault = function(ddmodel,brts,missnumspec,idparsopt)
 #' @param btorph Sets whether the likelihood is for the branching times (0) or
 #' the phylogeny (1)
 #' @param soc Sets whether stem or crown age should be used (1 or 2)
-#' @param tol Sets the tolerances in the optimization. Consists of: \cr reltolx
-#' = relative tolerance of parameter values in optimization \cr reltolf =
-#' relative tolerance of function value in optimization \cr abstolx = absolute
-#' tolerance of parameter values in optimization
+#' @param tol Sets the tolerances in the optimization. Consists of:\cr
+#' reltolx = relative tolerance of parameter values in optimization \cr
+#' reltolf = relative tolerance of function value in optimization \cr
+#' abstolx = absolute tolerance of parameter values in optimization
+#' @param tolint Sets the tolerance of the numerical integration. Consists of: \cr
+#' absoltint = absolute tolerance and \cr
+#' reltolint = relative tolerance.
+#' @param probs_threshold Sets the threshold of the probability below which
+#' logarithmic integration must be used. Default is 0.
 #' @param maxiter Sets the maximum number of iterations in the optimization
 #' @param changeloglikifnoconv if TRUE the loglik will be set to -Inf if ML
 #' does not converge
 #' @param optimmethod Method used in optimization of the likelihood. Current
-#' default is 'subplex'. Alternative is 'simplex' (default of previous
+#' default is 'simplex'. Alternative is 'subplex' (default of previous
 #' versions)
 #' @param num_cycles the number of cycles of opimization. If set at Inf, it will
 #' do as many cycles as needed to meet the tolerance set for the target function.
@@ -145,9 +150,11 @@ dd_ML = function(
   btorph = 1,
   soc = 2,
   tol = c(1E-3, 1E-4, 1E-6),
+  tolint = c(1E-10,1E-8),
+  probs_threshold = 0,
   maxiter = 1000 * round((1.25)^length(idparsopt)),
   changeloglikifnoconv = FALSE,
-  optimmethod = 'subplex',
+  optimmethod = 'simplex',
   num_cycles = 1,
   methode = 'analytical',
   verbose = FALSE)
@@ -183,7 +190,7 @@ dd_ML = function(
       trparsopt[which(initparsopt == Inf)] = 1
       trparsfix = parsfix/(1 + parsfix)
       trparsfix[which(parsfix == Inf)] = 1
-      pars2 = c(res,ddmodel,cond,btorph,verbose,soc,tol,maxiter)
+      pars2 = c(res,ddmodel,cond,btorph,verbose,soc,tol,maxiter,abstolint = tolint[1],reltolint = tolint[2],probs_threshold = probs_threshold)
       optimpars = c(tol,maxiter)
       initloglik = dd_loglik_choosepar(trparsopt = trparsopt,trparsfix = trparsfix,idparsopt = idparsopt,idparsfix = idparsfix,pars2 = pars2,brts = brts,missnumspec = missnumspec, methode = methode)
       cat("The loglikelihood for the initial parameter values is",initloglik,"\n")

R/dd_MS_ML.R

@@ -78,7 +78,7 @@
 #' @param changeloglikifnoconv if TRUE the loglik will be set to -Inf if ML
 #' does not converge
 #' @param optimmethod Method used in optimization of the likelihood. Current
-#' default is 'subplex'. Alternative is 'simplex' (default of previous
+#' default is 'simplex'. Alternative is 'subplex' (default of previous
 #' versions)
 #' @param num_cycles the number of cycles of opimization. If set at Inf, it will
 #' do as many cycles as needed to meet the tolerance set for the target function.
@@ -136,7 +136,7 @@ dd_MS_ML = function(brtsM,
     tol = c(1E-3, 1E-4, 1E-6),
     maxiter = 1000 * round((1.25)^length(idparsopt)),
     changeloglikifnoconv = FALSE,
-    optimmethod = 'subplex',
+    optimmethod = 'simplex',
     num_cycles = 1,
     methode = 'ode45',
     correction = FALSE,

R/dd_SR_ML.R

@@ -71,7 +71,7 @@
 #' @param changeloglikifnoconv if TRUE the loglik will be set to -Inf if ML
 #' does not converge
 #' @param optimmethod Method used in optimization of the likelihood. Current
-#' default is 'subplex'. Alternative is 'simplex' (default of previous
+#' default is 'simplex'. Alternative is 'subplex' (default of previous
 #' versions)
 #' @param num_cycles the number of cycles of opimization. If set at Inf, it will
 #' do as many cycles as needed to meet the tolerance set for the target function.
@@ -128,7 +128,7 @@ dd_SR_ML = function(brts,
     tol = c(1E-3, 1E-4, 1E-6),
     maxiter = 1000 * round((1.25)^length(idparsopt)),
     changeloglikifnoconv = FALSE,
-    optimmethod = 'subplex',
+    optimmethod = 'simplex',
     num_cycles = 1,
     methode = 'analytical',
     verbose = FALSE)