Prep for new release

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

@@ -2,7 +2,7 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
+  workflow_dispatch:
 
 name: R-CMD-check
 
@@ -31,7 +31,7 @@ jobs:
 
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -56,7 +56,7 @@ jobs:
           key: ${{ runner.os }}-jags-4.3.1
           restore-keys: |
             ${{ runner.os }}-jags-
-            
+
       # Install JAGS on Windows
       - name: Install JAGS (Windows)
         if: runner.os == 'Windows'
@@ -71,18 +71,14 @@ jobs:
             echo "JAGS found in cache, skipping installation"
           )
 
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
-
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: |
+            any::survival
+            any::rcmdcheck
+          upgrade: 'TRUE'
+          cache-version: 2
           needs: check
 
 

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: JointAI
-Version: 1.0.6.9000
+Version: 1.1.0
 Title: Joint Analysis and Imputation of Incomplete Data
 Authors@R: c(person("Nicole S.", "Erler", email = "n.s.erler@umcutrecht.nl",
                   role = c("aut", "cre"),

NEWS.md

@@ -1,4 +1,4 @@
-# JointAI (development version)
+# JointAI 1.1.0
 
 ## New features
 * Added functions `crosscorr()`, `crosscorr_plot()`, `autocorr()` and `autocorr_plot()`
@@ -20,6 +20,9 @@
 * Fix in identifying the number of workers used in parallel computation
   with the **future** package.
 * Fix `summary()` printout showing the wrong MCMC settings when using thinning.
+* `rd_vcov()`: fixed issue resulting in error when extracting random effects
+  variance-covariance matrix from fitted model in case of a multivariate mixed
+  model.
 
 
 --------------------------------------------------------------------------------

R/helpfunctions_checks.R

@@ -150,7 +150,7 @@ resolve_family_obj <- function(family) {
   return(thefamily)
 }
 
-#' Check wheather fixed or formula contains a random effects specification
+#' Check whether fixed or formula contains a random effects specification
 #'
 #' Checks if the objects provided to the `formula` and `fixed` arguments contain
 #' a random effects specification. This function is used in random effects

R/helpfunctions_melt.R

@@ -30,29 +30,38 @@ melt_list <- function(l, varname = "L1", valname = "value") {
 
   # Check for elements that cannot be converted to a data.frame or would
   # result in differing numbers of columns e.g., formulas, arrays, lists, ...
-  if (any(lvapply(l, function(x) !is.atomic(x) | !is.vector(x)))) {
+  if (all(lvapply(l, function(x) is.atomic(x) & is.vector(x)))) {
+    do.call(
+      rbind,
+      lapply(seq_along(l), function(k) {
+        df <- as.data.frame(
+          list(l[[k]]),
+          col.names = valname,
+          stringsAsFactors = FALSE
+        )
+
+        df[, varname] <- names(l)[k]
+        df
+      })
+    )
+  } else if (all(lvapply(l, function(x) is.atomic(x) & inherits(x, "matrix")))) {
+    do.call(
+      rbind,
+      lapply(seq_along(l), function(k) {
+        df <- as.data.frame(
+          list(l[[k]]),
+          stringsAsFactors = FALSE
+        )
+        df[, varname] <- names(l)[k]
+        df
+      })
+    )
+  } else {
     errormsg(
-      "In melt_list(): Not all elements are atomic vectors (%s).",
-      paste_and(
-        names(Filter(function(x) !is.atomic(x) | !is.vector(x), l)),
-        dQ = TRUE
-      )
+      "In melt_list(): Not all elements are atomic vectors or matrices (%s).
+      I don't know how to convert this."
     )
   }
-
-  do.call(
-    rbind,
-    lapply(seq_along(l), function(k) {
-      df <- as.data.frame(
-        list(l[[k]]),
-        col.names = valname,
-        stringsAsFactors = FALSE
-      )
-
-      df[, varname] <- names(l)[k]
-      df
-    })
-  )
 }
 
 

cran-comments.md

@@ -1,3 +1,32 @@
+# JointAI (version 1.1.0)
+
+## Round 1
+
+### Test environments
+* local macOS Darwin 25.2.0, R 4.5.2
+* windows server 2022 x64 (via github actions), R 4.5.2
+* ubuntu 24.04.3 LTS (via github actions), R 4.4.3, R 4.5.2, devel
+* macOS Sequoia 15.7.2 (via github actions), R 4.5.2
+* win-builder (oldrelease, devel and release)
+
+
+### R CMD check results
+0 errors | 0 warnings | 1-2 NOTES on win-builder
+
+#### NOTES
+* The Maintainer e-mail address has changed from  `n.erler@erasmusmc.nl` to
+  `n.s.erler@umcutrecht.nl`. This is intentional.
+* oldrel-only: “Author field differs from that derived from Authors@R”
+  This NOTE appears only on R-oldrelease, likely due to differences in how older
+  R formats ORCID information.
+
+
+### Reverse dependencies
+One reverse dependency: "remiod"; passed the check.
+
+---  
+
+
 # JointAI (version 1.0.6)
 
 ## Round 1