Bug fixes in IW model (brt table)

.github/workflows/R-CMD-check.yaml

@@ -6,6 +6,8 @@ on:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -22,13 +24,14 @@ jobs:
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -46,3 +49,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/test-coverage.yaml

@@ -6,45 +6,55 @@ on:
 
 name: test-coverage
 
+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') || github.event.pull_request"
-
     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
 
       - 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@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./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

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: DAISIE
 Type: Package
 Title: Dynamical Assembly of Islands by Speciation, Immigration and Extinction
-Version: 4.4.1
+Version: 4.4.1.9000
 Date: 2023-10-20
 Depends: R (>= 4.2.0)
 biocViews:

NEWS.md

@@ -1,3 +1,5 @@
+# DAISIE (development version)
+
 # DAISIE 4.4.1
 
 * Fix bug in the calculation of shift loglikelihoods.

R/DAISIE_ML1.R

@@ -107,7 +107,8 @@ DAISIE_ML1 <- function(
   tolint = c(1E-16, 1E-10),
   island_ontogeny = NA,
   jitter = 0,
-  num_cycles = 1) {
+  num_cycles = 1,
+  function_to_optimize = 'DAISIE_exact') {
   # datalist = list of all data: branching times, status of clade, and numnber of missing species
   # datalist[[,]][1] = list of branching times (positive, from present to past)
   # - max(brts) = age of the island
@@ -156,6 +157,12 @@ DAISIE_ML1 <- function(
   #  . eqmodel = 4 : equilibrium is assumed on immigrants using deterministic equation for endemics and immigrants
   #  . eqmodel = 5 : equilibrium is assumed on endemics and immigrants using deterministic equation for endemics and immigrants
 
+  if(function_to_optimize == 'DAISIE_exact') {
+    function_to_optimize <- DAISIE_loglik_all_choosepar
+  } else
+  {
+    DAISIE_loglik_all_choosepar_approx
+  }
 
   out2err <- data.frame(
     lambda_c = NA,
@@ -288,7 +295,7 @@ DAISIE_ML1 <- function(
   )
 
   optimpars <- c(tol, maxiter)
-  initloglik <- DAISIE_loglik_all_choosepar(
+  initloglik <- function_to_optimize(
     trparsopt = trparsopt,
     trparsfix = trparsfix,
     idparsopt = idparsopt,

R/DAISIE_ML_CS.R

@@ -183,7 +183,8 @@ DAISIE_ML_CS <- DAISIE_ML <- function(
   verbose = 0,
   tolint = c(1E-16, 1E-10),
   jitter = 0,
-  num_cycles = 1) {
+  num_cycles = 1,
+  function_to_optimize = 'DAISIE_exact') {
 
   if (datatype == "single") {
     if (is.na(island_ontogeny)) {
@@ -229,7 +230,8 @@ DAISIE_ML_CS <- DAISIE_ML <- function(
                           verbose = verbose,
                           tolint = tolint,
                           jitter = jitter,
-                          num_cycles = num_cycles)
+                          num_cycles = num_cycles,
+                          function_to_optimize = function_to_optimize)
       }
     } else {
         stop(

R/DAISIE_ML_IW.R

@@ -104,7 +104,7 @@ DAISIE_ML_IW <- function(
   }
   np = datalist[[1]]$not_present
   if (is.null(np)) {
-    np = datalist[[1]]$not_present_type1 + datalist[[1]]$not_present_type2
+    np <- datalist[[1]]$not_present_type1 + datalist[[1]]$not_present_type2
     warning('Number of species not present is misspecified.\n')
     return(invisible(out2err))
   }
@@ -130,6 +130,18 @@ DAISIE_ML_IW <- function(
     verbose = verbose
   )
 
+  pars1 <- rep(0, 5)
+  pars1[idparsopt] <- initparsopt
+  if (length(idparsfix) != 0) {
+    pars1[idparsfix] <- parsfix
+  }
+  if (pars1[4] == 0) {
+    warning('You have chosen a zero immigration rate; an empty island will never be colonized')
+  }
+  if (pars1[2] == 0) {
+    warning('You have chosen a zero extinction rate; this might create problems in optimization; please use a number close to 0 instead')
+  }
+
   trparsopt <- initparsopt / (1 + initparsopt)
   trparsopt[which(initparsopt == Inf)] <- 1
   trparsfix <- parsfix / (1 + parsfix)

R/DAISIE_SR_sim_core.R

@@ -83,8 +83,10 @@ DAISIE_SR_sim_core <- function(time,mainland_n,pars)
     immig_rate <- max(c(mainland_n * gam * (1 - length(island_spec[,1])/K),0),na.rm = T)
 
     totalrate <- ext_rate + clado_rate + ana_rate + immig_rate
-    dt <- stats::rexp(1,totalrate)
-
+    dt <- stats::rexp(1, totalrate)
+    if (is.nan(dt)) {
+      dt <- total_time - timeval
+    }
     if ( timeval < pars[11] & ((timeval + dt) >= pars[11])  )
     {
       lac <- pars[6]
@@ -98,6 +100,9 @@ DAISIE_SR_sim_core <- function(time,mainland_n,pars)
       immig_rate <- max( c(mainland_n * gam * (1 - length(island_spec[,1])/K), 0), na.rm = TRUE )
       totalrate <- ext_rate + clado_rate + ana_rate + immig_rate
       dt <- stats::rexp(1, totalrate)
+      if (is.nan(dt)) {
+        dt <- total_time - pars[11]
+      }
       timeval <- pars[11] + dt
     } else
     {
@@ -107,7 +112,7 @@ DAISIE_SR_sim_core <- function(time,mainland_n,pars)
     possible_event <- sample(1:4,1,replace = FALSE,c(immig_rate,ext_rate,ana_rate,clado_rate))
 
     ##############
-    if(timeval <= total_time)
+    if(timeval < total_time)
     {
       new_state <- DAISIE_sim_update_state_cr(timeval = timeval,
                                               total_time = total_time,

R/DAISIE_data.R

@@ -565,3 +565,43 @@ NULL
 #' }
 #' @keywords datasets
 NULL
+
+#' @name frogs_sim_datalist
+#' @title Colonization and branching times of a data set simulated with the
+#' MLE parameters of frogs_datalist
+#' @docType data
+#' @format A list with the first element containing 2 elements and the following
+#'elements containing 5 components.
+#' @description A list containing the colonization and branching times
+#' of a simulated data set using the MLE parameters of IW model for the
+#' frogs_datalist. It is an R list object with the following elements.\cr \cr
+#' The first element of the list has two components: \cr \cr
+#' \code{$island_age} - the island age \cr
+#' \code{$not_present} - the number of mainland lineages that are not present
+#' on the island \cr \cr
+#' The following elements of the list each contains
+#' information on a single colonist lineage on the island and has 5
+#' components:\cr \cr
+#' \code{$colonist_name} - the name of the species or clade
+#' that colonized the island \cr
+#' \code{$branching_times} - island age followed by stem age of the population/species
+#' in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close
+#' relatives on the island. For endemic clades with more than one species on the island
+#' (cladogenetic clades/ radiations) these should be island age followed by the
+#' branching times of the island clade including the stem age of the clade.\cr
+#' \code{$stac} - the status of the colonist \cr \cr
+#' * Non_endemic_MaxAge: 1 \cr
+#' * Endemic: 2 \cr
+#' * Endemic&Non_Endemic: 3 \cr
+#' * Non_endemic: 4 \cr
+#' * Endemic_MaxAge: 5 or 6 \cr \cr
+#' \code{$missing_species} - number of island species
+#' that were not sampled for particular clade (only applicable for endemic
+#' clades) \cr
+#' \code{$type1or2} - whether the colonist belongs to type 1 or
+#' type 2. In this dataset all are equal to 1. \cr
+#' @seealso \code{\link{DAISIE_ML}}, \code{\link{DAISIE_SR_ML}}
+#' @source Etienne RS, Haegeman B, Dugo-Cota A, Vila C, Gonzalez-Voyer A &
+#' Valente L. The limits to ecological limits to diversification.\cr
+#' @keywords datasets
+NULL

R/DAISIE_format_IW.R

@@ -117,7 +117,7 @@ DAISIE_format_IW_trait <- function(island_replicates,
   return(several_islands)
 }
 
-add_brt_table <- function(island, full_table = FALSE) {
+add_brt_table_old <- function(island, full_table = FALSE) {
   island_age <- island[[1]]$island_age
   island_top <- island[[1]]
   if (length(island) == 1) {
@@ -175,7 +175,7 @@ add_brt_table <- function(island, full_table = FALSE) {
           for (k in 1:length(island[[i]]$all_colonisations)) {
             the_brts <- island[[i]]$all_colonisations[[k]]$event_times[-1]
             pos2 <- pos1 + length(the_brts)
-            ff <- matrix(ncol = 5, nrow = pos2 - pos1 + 1)
+            ff <- matrix(ncol = 5, nrow = pos2 - pos1)
             ff[1:(pos2 - pos1), 1] <- the_brts
             ff[1:(pos2 - pos1), 2] <- j
             ff[1:(pos2 - pos1), 3] <- seq(1, length(the_brts))
@@ -203,3 +203,88 @@ add_brt_table <- function(island, full_table = FALSE) {
   colnames(island[[1]]$brts_table) <- c("brt", "clade", "event", "endemic", "col")
   return(island)
 }
+
+add_brt_table <- function(island, full_table = TRUE) {
+  island_age <- island[[1]]$island_age
+  island_top <- island[[1]]
+  if (length(island) == 1) {
+    brts_table <- matrix(ncol = 5, nrow = 1)
+    brts_table[1, ] <-  c(island_age, 0, 0, NA, NA)
+    island[[1]]$brts_table <- brts_table
+  } else {
+    island_top <- island[[1]]
+    island[[1]] <- NULL
+    btimes <- list()
+    for (i in 1:length(island)) {
+      btimes[[i]] <- island[[i]]$branching_times[-1]
+    }
+    island <- island[rev(order(sapply(btimes, "[", 1)))]
+    il <- unlist(island)
+    stac1s <- which(il[which(names(il) == "stac")] == "1")
+    stac5s <- which(il[which(names(il) == "stac")] == "5")
+    stac1_5s <- sort(c(stac1s, stac5s))
+    if (length(stac1_5s) != 0) {
+      if (length(stac1_5s) == length(island)) {
+        brts_table <- matrix(ncol = 5, nrow = 1)
+        brts_table[1, ] <- c(island_age, 0, 0, NA, NA)
+        island_no_stac1or5 <- NULL
+      } else {
+        island_no_stac1or5 <- island[-stac1_5s]
+      }
+    }
+    if (length(stac1_5s) == 0) {
+      island_no_stac1or5 <- island
+    }
+    if (length(island_no_stac1or5) != 0) {
+      btimes <- list()
+      for (i in 1:length(island_no_stac1or5)) {
+        btimes[[i]] <- island_no_stac1or5[[i]]$branching_times[-1]
+      }
+      brts <- rev(sort(unlist(btimes)))
+      brts_IWK <- NULL
+      pos1 <- 0
+      for (i in 1:length(btimes)) {
+        the_stac <- island_no_stac1or5[[i]]$stac
+        if(!is.null(island[[i]]$all_colonisations) & full_table == TRUE) {
+          #if(length(island[[i]]$all_colonisations) > 0) print(i)
+          for (k in 1:length(island[[i]]$all_colonisations)) {
+            the_brts <- island[[i]]$all_colonisations[[k]]$event_times[-1]
+            pos2 <- pos1 + length(the_brts)
+            ff <- matrix(ncol = 5, nrow = pos2 - pos1)
+            ff[1:(pos2 - pos1), 1] <- the_brts
+            ff[1:(pos2 - pos1), 2] <- i
+            ff[1:(pos2 - pos1), 3] <- seq(1, length(the_brts))
+            ff[1:(pos2 - pos1), 4] <- (the_stac == 2) + (the_stac == 3)
+            ff[1:(pos2 - pos1), 5] <- k
+            brts_IWK <- rbind(brts_IWK,ff)
+            pos1 <- pos2
+          }
+        } else {
+          the_brts <- btimes[[i]]
+          pos2 <- pos1 + length(the_brts)
+          ff <- matrix(ncol = 5, nrow = pos2 - pos1)
+          ff[1:(pos2 - pos1), 1] <- the_brts
+          ff[1:(pos2 - pos1), 2] <- i
+          ff[1:(pos2 - pos1), 3] <- seq(1, length(the_brts))
+          ff[1:(pos2 - pos1), 4] <- (the_stac == 2) + (the_stac == 3)
+          ff[1:(pos2 - pos1), 5] <- 1
+          brts_IWK <- rbind(brts_IWK,ff)
+          pos1 <- pos2
+        }
+      }
+      brts_table <- brts_IWK[rev(order(brts_IWK[, 1])), ]
+      brts_table <- rbind(c(island_age, 0, 0, NA, NA), brts_table)
+    }
+    island_top$brts_table <- brts_table
+    if (length(stac1_5s) != 0) {
+      for (i in 1:length(stac1_5s)) {
+        island[[length(island) + 1]] <- island[[stac1_5s[i]]]
+        island[[stac1_5s[i]]] <- NULL
+        stac1_5s <- stac1_5s - 1
+      }
+    }
+    island <- append(list(island_top), island)
+  }
+  colnames(island[[1]]$brts_table) <- c("brt", "clade", "event", "endemic", "col")
+  return(island)
+}

R/DAISIE_loglik_CS.R

@@ -545,14 +545,14 @@ DAISIE_loglik_CS_M1 <- DAISIE_loglik <- function(pars1,
           # means that any colonization that took place before this maximum
           # colonization time (including presence in the non-oceanic scenario)
           # does not count and should be followed by another colonization.
-          # To allow this we introduce a third set of equations for the
-          # probability that colonization might have happened before but
-          # recolonization has not taken place yet (Q_M,n).
+          # To allow this we introduce a third and fourth set of equations for
+          # the probability that colonization might have happened before but
+          # recolonization has not taken place yet (Q_M,n and Q^M_{M,n}).
           epss <- 1.01E-5 #We're taking the risk
           if (abs(brts[2] - brts[1]) >= epss) {
             probs[(2 * lx + 1):(4 * lx)] <- probs[1:(2 * lx)]
             probs[1:(2 * lx)] <- 0
-          } else {
+          } else { #max age equals island age
             probs[(2 * lx + 1):(4 * lx)] <- 0
           }