Merge branch 'release/v0.7.1'

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# /~https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

CITATION.cff

@@ -8,7 +8,7 @@ message: 'To cite package "multinma" in publications use:'
 type: software
 license: GPL-3.0-only
 title: 'multinma: Bayesian Network Meta-Analysis of Individual and Aggregate Data'
-version: 0.7.0
+version: 0.7.1
 doi: 10.5281/zenodo.3904454
 abstract: Network meta-analysis and network meta-regression models for aggregate data,
   individual patient data, and mixtures of both individual and aggregate data using
@@ -28,7 +28,7 @@ preferred-citation:
     email: david.phillippo@bristol.ac.uk
     orcid: https://orcid.org/0000-0003-2672-7841
   year: '2023'
-  notes: R package version 0.7.0
+  notes: R package version 0.7.1
   url: https://dmphillippo.github.io/multinma/
   doi: 10.5281/zenodo.3904454
 repository: https://CRAN.R-project.org/package=multinma

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: multinma
 Title: Bayesian Network Meta-Analysis of Individual and Aggregate Data
-Version: 0.7.0
+Version: 0.7.1
 Authors@R: 
     person(given = c("David", "M."),
            family = "Phillippo",
@@ -51,7 +51,7 @@ LinkingTo:
     RcppEigen (>= 0.3.3.3.0),
     RcppParallel (>= 5.0.1),
     rstan (>= 2.26.0),
-    StanHeaders (>= 2.26.0)
+    StanHeaders (>= 2.32.9)
 SystemRequirements: GNU make
 RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)

NEWS.md

@@ -1,3 +1,11 @@
+# multinma 0.7.1
+
+* Fix: Producing survival/hazard/cumulative hazard predictions for survival 
+models with `predict()` outside of a `plot()` call no longer gives an error 
+(#40).
+* Fix: Increased StanHeaders version requirement to version 2.32.9 or later, to 
+avoid CRAN sanitizer warnings (caused by stan-dev/rstan#1111).
+
 # multinma 0.7.0
 
 * Feature: The new `marginal_effects()` function produces marginal treatment

R/predict.R

@@ -1663,7 +1663,9 @@ predict.stan_nma <- function(object, ...,
           if (packageVersion("dplyr") > "1.1.0") {
             pd_undups <- dplyr::filter(preddat, .data$.study == studies[s], .data$.trt == treatments[trt]) %>%
               dplyr::distinct(dplyr::pick(dplyr::all_of(collapse_by))) %>%
-              dplyr::mutate(.dup_id = 1:dplyr::n())
+              dplyr::mutate(.dup_id = seq_len(dplyr::n()))
+
+            if (nrow(pd_undups) == 0) next
 
             pd_col <- dplyr::filter(preddat, .data$.study == studies[s], .data$.trt == treatments[trt]) %>%
               dplyr::left_join(pd_undups, by = collapse_by) %>%
@@ -1673,7 +1675,9 @@ predict.stan_nma <- function(object, ...,
           } else {
             pd_undups <- dplyr::filter(preddat, .data$.study == studies[s], .data$.trt == treatments[trt]) %>%
               dplyr::distinct(dplyr::across(dplyr::all_of(collapse_by))) %>%
-              dplyr::mutate(.dup_id = 1:dplyr::n())
+              dplyr::mutate(.dup_id = seq_len(dplyr::n()))
+
+            if (nrow(pd_undups) == 0) next
 
             pd_col <- dplyr::filter(preddat, .data$.study == studies[s], .data$.trt == treatments[trt]) %>%
               dplyr::left_join(pd_undups, by = collapse_by) %>%
@@ -2054,8 +2058,7 @@ predict.stan_nma_surv <- function(object, times = NULL,
 
   # Set times_seq by default if called within plot()
   if (is.null(times_seq) && type %in% c("survival", "hazard", "cumhaz") &&
-       (deparse(sys.call(-2)[[1]]) == "plot" ||
-        deparse(sys.call(-3)[[1]]) == "marginal_effects" && deparse(sys.call(-4)[[1]]) == "plot"))
+      "plot" %in% unlist(lapply(sys.calls(), function(x) deparse(x[[1]]))))
     times_seq <- 50
 
   # Other checks (including times, aux) in predict.stan_nma()

README.md

@@ -78,7 +78,7 @@ papers:
 The `multinma` package can be cited as follows:
 
 > Phillippo, D. M. (2024). *multinma: Bayesian Network Meta-Analysis of
-> Individual and Aggregate Data*. R package version 0.7.0, doi:
+> Individual and Aggregate Data*. R package version 0.7.1, doi:
 > [10.5281/zenodo.3904454](https://doi.org/10.5281/zenodo.3904454).
 
 When fitting ML-NMR models, please cite the methods paper:

cran-comments.md

@@ -1,6 +1,12 @@
-This release adds new features and fixes a few bugs.
+Require StanHeaders version 2.32.9 or later in LinkingTo, as requested, which 
+fixes the UBSAN warnings.
+
+Confirmed that this fixes the sanitizer warnings with rocker/r-devel-san and 
+rhub clang-asan.
 
 ## Test environments
+* rocker/r-devel-san
+* rhub clang-asan
 * local R installation (Windows 10), R 4.4.0
 * win-builder (release, devel)
 * Ubuntu 22.04.4 on GitHub Actions (release, devel, oldrel)