Add verbose flag to the simplex function

.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

DDD.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: cbff7951-4a06-4670-bbdf-df0ae63c05bf
 
 RestoreWorkspace: Default
 SaveWorkspace: Default

DESCRIPTION

@@ -2,7 +2,6 @@ Package: DDD
 Type: Package
 Title: Diversity-Dependent Diversification
 Version: 5.2.4
-Date: 2024-03-04
 Depends: R (>= 3.5.0)
 Imports:
   deSolve,

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

@@ -99,7 +99,7 @@ parsfixdefault = function(ddmodel,brts,missnumspec,idparsopt)
 #' @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.
@@ -147,7 +147,7 @@ dd_ML = function(
   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)

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)

R/dd_utils.R

@@ -514,10 +514,12 @@ sample2 = function(x,size,replace = FALSE,prob = NULL)
 #' 
 #' @param fun Function to be optimized
 #' @param trparsopt Initial guess of the parameters to be optimized
-#' @param ... Any other arguments of the function to be optimimzed, or settings
+#' @param ... Any other arguments of the function to be optimimized, or settings
 #' of the optimization routine
 #' @param optimpars Parameters of the optimization: relative tolerance in
 #' function arguments, relative tolerance in function value, absolute tolerance
+#' in function arguments, and maximum number of iterations
+#' @param verbose adds verbose output of intermediate evaluations
 #' in function arguments, maximum number of iterations, and the level of verbosity
 #' @return \item{out}{ A list containing optimal function arguments
 #' (\code{par}, the optimal function value (\code{fvalues}) and whether the
@@ -529,7 +531,8 @@ sample2 = function(x,size,replace = FALSE,prob = NULL)
 #' cat("No examples")
 #' 
 #' @export simplex
-simplex = function(fun,trparsopt,optimpars,...)
+simplex = function(fun,trparsopt,optimpars,
+                   verbose = TRUE,...)
 {
   numpar = length(trparsopt)
   reltolx = optimpars[1]
@@ -570,6 +573,11 @@ simplex = function(fun,trparsopt,optimpars,...)
     cat(string)
     utils::flush.console()
   }
+
+  string = paste(string, -fv[1], how, "\n", sep = " ")
+  if (verbose) cat(string)
+  utils::flush.console()
+
   tmp = order(fv)
   if(numpar == 1)
   {
@@ -678,13 +686,18 @@ simplex = function(fun,trparsopt,optimpars,...)
        cat(string)
        utils::flush.console()
      }
+
+     string = paste(string, -fv[1], how, "\n", sep = " ")
+     if (verbose) cat(string)
+     utils::flush.console()
+
      v2 = t(matrix(rep(v[,1],each = numpar + 1),nrow = numpar + 1))
   }
   if(itercount < maxiter)
   {
-     cat("Optimization has terminated successfully.","\n")
+    if (verbose) cat("Optimization has terminated successfully.","\n")
   } else {
-     cat("Maximum number of iterations has been exceeded.","\n")
+    if (verbose) cat("Maximum number of iterations has been exceeded.","\n")
   }
   out = list(par = v[,1], fvalues = -fv[1], conv = as.numeric(itercount > maxiter))
   invisible(out)
@@ -710,6 +723,7 @@ simplex = function(fun,trparsopt,optimpars,...)
 #' @param jitter Perturbation of an initial parameter value when precisely equal to 0.5;
 #' this is only relevant when subplex is chosen. The default value is 0, so no jitter
 #' is applied. A recommended value when using it is 1E-5.
+#' @param verbose if TRUE, prints intermediate output when using simplex
 #' @param ... Any other arguments of the function to be optimimzed, or settings
 #' of the optimization routine
 #' @return \item{out}{ A list containing optimal function arguments
@@ -729,6 +743,7 @@ optimizer <- function(
     fun,
     trparsopt,
     jitter = 0,
+    verbose = FALSE,
     ...)
 {
   if(num_cycles == Inf)
@@ -747,16 +762,19 @@ optimizer <- function(
   out <- NULL
   while(cy <= max_cycles)
   {
-    if(max_cycles > 1) cat(paste('Cycle ',cy,'\n',sep =''))
+    if(max_cycles > 1) {
+      if (verbose) cat(paste('Cycle ',cy,'\n',sep =''))
+    }
     if(optimmethod == 'simplex')
     {
       outnew <- suppressWarnings(simplex(fun = fun,
                                          trparsopt = trparsopt,
                                          optimpars = optimpars,
+                                         verbose = verbose,
                                          ...))
     } else if(optimmethod == 'subplex')
     {
-      minfun1 <- function(fun,trparsopt,...)
+      minfun1 <- function(fun, trparsopt,...)
       {           
         return(-fun(trparsopt = trparsopt,...))
       }
@@ -818,7 +836,7 @@ optimizer <- function(
     {
       if(abs(fvalue[cy] - fvalue[cy - 1]) < optimpars[3])
       {
-        if(cy < max_cycles) cat('No more cycles needed.\n')
+        if(cy < max_cycles) if (verbose) cat('No more cycles needed.\n')
         cy <- max_cycles
       } else if(cy == max_cycles)
       {