Merge commit 'fe63fe14' into release

ocbe-uio · Sep 18, 2024 · b7c23a7 · b7c23a7
2 parents 1f599e0 + fe63fe1
commit b7c23a7
Show file tree

Hide file tree

Showing 15 changed files with 56 additions and 34 deletions.
diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
@@ -29,7 +29,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -14,7 +14,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -18,7 +18,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 1.0.0
-Date: 2024-04-17 09:04:51 UTC
-SHA: 6a30f4384d9d15cb292b9d25e45a868477d30606
+Version: 1.0.1
+Date: 2024-09-18 06:43:47 UTC
+SHA: b1a16105f7008089bce6302cb9c54c41f40eb088
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: permChacko
 Title: Chacko Test for Order-Restriction with Permutation
-Version: 1.0.0
-Date: 2024-04-17
+Version: 1.0.1
+Date: 2024-09-18
 Authors@R:
     c(
         person(
@@ -25,7 +25,8 @@ Description: Implements an extension of the Chacko chi-square test for
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
+Imports: methods
 Suggests:
     knitr,
     rmarkdown,

diff --git a/NAMESPACE b/NAMESPACE
@@ -9,5 +9,6 @@ export(chacko66_sec5)
 export(permChacko)
 export(reduceVector)
 export(ruxton221207)
+importFrom(methods,is)
 importFrom(stats,pchisq)
 importFrom(stats,weighted.mean)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# permChacko 1.0.1
+
+* Improved validation
+* Optimized `chackoStatistic()`
+* Revised calculation of unique values in `chackoStatistic()` ([issue #16](https://github.com/ocbe-uio/permChacko/issues/16)).
+
 # permChacko 1.0.0
 
 * Improved printing of hypothesis ([issue #11](https://github.com/ocbe-uio/permChacko/issues/11)).

diff --git a/R/chackoStatistic.R b/R/chackoStatistic.R
@@ -1,10 +1,8 @@
-chackoStatistic <- function(x_t, n, k) {
-  x_bar <- x_t[, "x"]
-  t <- x_t[, "t"]
-  m <- length(unique(x_bar))
-  power_sum <- 0
-  for (j in seq_len(m)) {
-    power_sum <- power_sum + t[[j]] * (x_bar[[j]] - n / k) ^ 2
-  }
-  return(k / n * power_sum)
+chackoStatistic <- function(x_t, n, k, uniqueness_method = 2) {
+  m <- length(x_t[, "x"])
+  x_t_unique <- switch(uniqueness_method,
+    x_t[seq_len(m), , drop = FALSE],  # legacy code (hidden)
+    x_t[!duplicated(x_t[, "x"]), , drop = FALSE], # current implementation
+  )
+  k / n * sum(x_t_unique[, "t"] * (x_t_unique[, "x"] - n / k) ^ 2)
 }
diff --git a/R/permChacko-package.R b/R/permChacko-package.R
@@ -1,7 +1,4 @@
 #' @keywords internal
 #' @aliases permChacko-package
+#' @importFrom methods is
 "_PACKAGE"
-
-## usethis namespace: start
-## usethis namespace: end
-NULL
diff --git a/R/permChacko.R b/R/permChacko.R
@@ -24,7 +24,7 @@
 #' permChacko(chacko66_sec5)
 #' @export
 permChacko <- function(x, n_perm = 1000L, verbosity = 0) {
-  if (!is.null(dim(x))) stop("Input must be a vector")
+  if (!is(x, "numeric")) stop("Input must be a vector")
   if (verbosity >= 1L) message("Reducing original vector")
   # Ordering and reducing vector
   x_t <- reduceVector(x, verbosity)[["x_t"]]

diff --git a/R/reduceVector.R b/R/reduceVector.R
@@ -21,7 +21,7 @@
 #' reduceVector(chacko66_sec5)
 #' reduceVector(chacko66_sec5, verbosity = 1)
 reduceVector <- function(x, verbosity = 0L) {
-  if (!is.null(dim(x))) stop("Input must be a vector")
+  if (!is(x, "numeric")) stop("Input must be a vector")
   x_t <- cbind("x" = unname(x), "t" = unname(x) ^ 0L)
   reductions <- 0L
   while (nrow(x_t) > 1L && isMonotoneIncreasing(x_t[, "x"])) {

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,19 +1,25 @@
 Dear CRAN Team,
 this is a resubmission of package 'permChacko'. I have added the following changes:
 
-* 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)).
+* Improved validation
+* Optimized `chackoStatistic()`
+* Revised calculation of unique values in `chackoStatistic()` ([issue #16](https://github.com/ocbe-uio/permChacko/issues/16)).
 
 Please upload to CRAN.
 Best, Waldir
 
-# Package permChacko 1.0.0
+# Package permChacko 1.0.1
 
 Reporting is done by packager version 1.15.2
 
+
 ## Test environments
-- R version 4.3.1 (2023-06-16)
+- R version 4.3.3 (2024-02-29)
    Platform: x86_64-pc-linux-gnu (64-bit)
-   Running under: Ubuntu 23.10
+   Running under: Ubuntu 24.04.1 LTS
    ERROR: No check log found!
 - win-builder (devel)
+
+## Local test results
+
+## Local meta results
diff --git a/tests/testthat/test-customExamples.R b/tests/testthat/test-customExamples.R
@@ -64,3 +64,12 @@ test_that("Verbosity works as expected", {
     "Comparing 3.5 and 1.5. Replacing."
   )
 })
+
+test_that("m is properly calculated on reduced vectors with duplicates", {
+  x <- c(12, 12, 16, 17, 13)
+  y <- reduceVector(x)
+  expect_equal(chackoStatistic(y$x_t, sum(x), length(x)), 2 / 3) # equiv to m=3
+  expect_equal(
+    chackoStatistic(y$x_t, sum(x), length(x), 1L), .95238095
+  ) # equiv to m = 2
+})
diff --git a/tests/testthat/test-print-and-summary.R b/tests/testthat/test-print-and-summary.R
@@ -8,17 +8,21 @@ test_that("print.reduced_vector() works as expected", {
   x <- reduceVector(rpois(6, 6))
   expect_output(print(x), "Reduced vector : 4\\t4\\t4\\t5\\t8")
 })
+
 test_that("print.chacko_test() works as expected", {
   expect_output(permChacko(rpois(8, 6), n_perm = 50L), NA)
   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.+: 0\\.400000 \\(30 permutation")
-  expect_output(print(y), "Tabular p-value\\s+: 0\\.369550")
+  expect_output(print(y), "Test statistic \\(chisq_bar\\): 1\\.250000")
+  expect_output(print(y), "Analytic p-value\\s+: 0\\.535261")
+  expect_output(print(y), "Numeric p-value.+: 0\\.366667 \\(30 permutation")
+  expect_output(print(y), "Numeric mid-p value.+: 0\\.283333 \\(30 permutation")
+  expect_output(print(y), "Tabular p-value\\s+: 0\\.220987")
 })
+
 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")