Merge branch 'release-1.0.0' into release

ocbe-uio · Apr 17, 2024 · 1f599e0 · 1f599e0
2 parents f05b622 + 33d0cbb
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diff --git a/.github/workflows/check-standard.yaml b/.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
 

diff --git a/.github/workflows/lint.yaml b/.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
 

diff --git a/.github/workflows/rhub.yaml b/.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 }}
diff --git a/CRAN-SUBMISSION b/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
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: permChacko
 Title: Chacko Test for Order-Restriction with Permutation
-Version: 0.2.0
-Date: 2023-11-07
+Version: 1.0.0
+Date: 2024-04-17
 Authors@R:
     c(
         person(
@@ -25,7 +25,7 @@ Description: Implements an extension of the Chacko chi-square test for
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Suggests:
     knitr,
     rmarkdown,

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# 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)).
+
 # permChacko 0.2.0
 
 * Replaced `verbose` with `verbosity` in functions to allow for more control over the output ([issue #3](https://github.com/ocbe-uio/permChacko/issues/3)).

diff --git a/R/permChacko.R b/R/permChacko.R
@@ -52,7 +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
+  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,
@@ -70,6 +74,7 @@ permChacko <- function(x, n_perm = 1000L, verbosity = 0) {
   p_values <- c(
     "analytic" = anal_p_value,
     "numeric" = perm_p_value,
+    "numeric_mid" = perm_mid_p_value,
     "tabular" = table_p_value
   )
   out <- list(

diff --git a/R/print.R b/R/print.R
@@ -11,12 +11,16 @@ print.chacko_test <- function(x, ...) {
         "p-values:\n",
         "  Analytic p-value        : %f\n",
         "  Numeric p-value         : %f (%d permutations)\n",
+        "  Numeric mid-p value     : %f (%d permutations)\n",
         "  Tabular p-value         : %f\n"
       ),
-      paste0("p", seq_along(x$observed_data), collapse = " == "),
-      paste0("p", seq_along(x$observed_data), collapse = " <= "),
-      x[["statistic"]], p_values[["analytic"]],
-      p_values[["numeric"]], x[["n_perm"]], p_values[["tabular"]]
+      printHypothesis("p", seq_along(x$observed_data), "=="),
+      printHypothesis("p", seq_along(x$observed_data), "<="),
+      x[["statistic"]],
+      p_values[["analytic"]],
+      p_values[["numeric"]], x[["n_perm"]],
+      p_values[["numeric_mid"]], x[["n_perm"]],
+      p_values[["tabular"]]
     )
   )
 }
@@ -35,3 +39,16 @@ print.reduced_vector <- function(x, details = TRUE, ...) {
     )
   )
 }
+
+printHypothesis <- function(x_name, x_indices, operator = "==") {
+  operator <- paste0(" ", operator, " ")
+  if (length(x_indices) < 6) {
+    return(paste0(x_name, x_indices, collapse = operator))
+  } else {
+    first_idx <- 1:2
+    last_idx <- seq(length(x_indices) - 1, length(x_indices))
+    first_x <- paste0(x_name, x_indices[first_idx], collapse = operator)
+    last_x <- paste0(x_name, x_indices[last_idx], collapse = operator)
+    paste0(first_x, operator, "...", operator, last_x)
+  }
+}
diff --git a/README.md b/README.md
@@ -1,7 +1,6 @@
-
 # permChacko
 
-permChacko is an R package that implements a modified version of the Chacko (1966) algorithm for order restriction.
+permChacko is an R package that implements a modified version of the [Chacko (1966)](https://www.jstor.org/stable/25051572) algorithm for order restriction.
 
 ## Installation
 
@@ -32,10 +31,16 @@ library(permChacko)
 permChacko(chacko66_sec3) # example 5 from Chacko (1966)
 ```
 
+## References
+
+Chacko, V. J. "Testing homogeneity against ordered alternatives." The Annals of Mathematical Statistics (1963): 945-956. https://www.jstor.org/stable/2238476
+
+Chacko, V. J. (1966). Modified Chi-Square Test for Ordered Alternatives. Sankhyā: The Indian Journal of Statistics, Series B (1960-2002), 28(3/4), 185–190. http://www.jstor.org/stable/25051572
+
 ## Badges
 
 <!-- badges: start -->
-[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![CodeFactor](https://www.codefactor.io/repository/github/ocbe-uio/permChacko/badge)](https://www.codefactor.io/repository/github/ocbe-uio/permChacko)
 [![R build status](https://github.com/ocbe-uio/permChacko/workflows/R-CMD-check/badge.svg)](https://github.com/ocbe-uio/permChacko/actions)
 [![Codecov](https://codecov.io/gh/ocbe-uio/permChacko/branch/develop/graph/badge.svg)](https://codecov.io/gh/ocbe-uio/permChacko)

diff --git a/cran-comments.md b/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)
diff --git a/man/permChacko-package.Rd b/man/permChacko-package.Rd
diff --git a/tests/testthat/test-print-and-summary.R b/tests/testthat/test-print-and-summary.R
@@ -13,9 +13,13 @@ test_that("print.chacko_test() works as expected", {
   y <- permChacko(rpois(3, 5), n_perm = 30L)
   expect_output(print(y), "Test statistic \\(chisq_bar\\): 0\\.500000")
   expect_output(print(y), "Analytic p-value\\s+: 0\\.778801")
-  expect_output(print(y), "Numeric p-value\\s+: 0\\.400000 \\(30 permutation")
+  expect_output(print(y), "Numeric p-value.+: 0\\.400000 \\(30 permutation")
   expect_output(print(y), "Tabular p-value\\s+: 0\\.369550")
 })
 test_that("summary.reduced_vector() works as expected", {
   expect_output(summary(reduceVector(rpois(7, 7))), "has been reduced 3 times")
 })
+test_that("Hypothesis suppression works as expected", {
+  expect_output(print(permChacko(4:1)), "p1 == p2 == p3 == p4")
+  expect_output(print(permChacko(6:1)), "p1 == p2 == ... == p5 == p6")
+})