Merge branch 'release-1.0.0' into develop

.github/workflows/check-standard.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [develop, release]
+    branches: [develop, release*]
   pull_request:
-    branches: [develop, release]
+    branches: [develop, release*]
 
 name: R-CMD-check
 

.github/workflows/lint.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [develop, release, fix-linter]
+    branches: [develop, release*, fix-linter]
   pull_request:
-    branches: [develop, release]
+    branches: [develop, release*]
 
 name: lint
 

.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 }}

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 0.2.0
-Date: 2023-11-07 08:27:25 UTC
-SHA: 543f1ca2fb82489effd0178f2be3f9fec5e9f68b
+Version: 1.0.0
+Date: 2024-04-17 09:04:51 UTC
+SHA: 6a30f4384d9d15cb292b9d25e45a868477d30606

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: permChacko
 Title: Chacko Test for Order-Restriction with Permutation
-Version: 0.2.0.9001
-Date: 2023-11-07
+Version: 1.0.0
+Date: 2024-04-17
 Authors@R:
     c(
         person(

NEWS.md

@@ -1,4 +1,4 @@
-# permChacko (development version)
+# permChacko 1.0.0
 
 * Improved printing of hypothesis ([issue #11](https://github.com/ocbe-uio/permChacko/issues/11)).
 * Added calculation of mid-P values ([issue #13](https://github.com/ocbe-uio/permChacko/issues/13)).

R/permChacko.R

@@ -52,8 +52,11 @@ permChacko <- function(x, n_perm = 1000L, verbosity = 0) {
 
   # The p-value is simply the fraction of such permutations that yield a test
   # statistic equal to or greater than the one we originally observed.
-  perm_p_value <- sum(perm_chisq_bar >= chisq_bar) / n_perm
-  perm_mid_p_value <- (sum(perm_chisq_bar > chisq_bar) + 0.5 * sum(perm_chisq_bar == chisq_bar)) / n_perm
+  sum_eq <- sum(perm_chisq_bar == chisq_bar)
+  sum_gt <- sum(perm_chisq_bar > chisq_bar)
+  sum_gte <- sum(perm_chisq_bar >= chisq_bar)
+  perm_p_value <- sum_gte / n_perm
+  perm_mid_p_value <- (sum_gt + 0.5 * sum_eq) / n_perm
   m <- nrow(x_t)
   anal_p_value <- ifelse(
     test = m > 1L,

cran-comments.md

@@ -1,5 +1,19 @@
-## R CMD check results
+Dear CRAN Team,
+this is a resubmission of package 'permChacko'. I have added the following changes:
 
-0 errors | 0 warnings | 1 note
+* Improved printing of hypothesis ([issue #11](https://github.com/ocbe-uio/permChacko/issues/11)).
+* Added calculation of mid-P values ([issue #13](https://github.com/ocbe-uio/permChacko/issues/13)).
 
-* This is a new release.
+Please upload to CRAN.
+Best, Waldir
+
+# Package permChacko 1.0.0
+
+Reporting is done by packager version 1.15.2
+
+## Test environments
+- R version 4.3.1 (2023-06-16)
+   Platform: x86_64-pc-linux-gnu (64-bit)
+   Running under: Ubuntu 23.10
+   ERROR: No check log found!
+- win-builder (devel)