Merge branch 'release-1.0.1' into develop

* release-1.0.1:
  Updated CRAN-SUBMISSION
  Updated cran-comments.md
  Updated comments
  Increment version number to 1.0.1

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

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: permChacko
 Title: Chacko Test for Order-Restriction with Permutation
-Version: 1.0.0.9002
-Date: 2024-04-17
+Version: 1.0.1
+Date: 2024-09-18
 Authors@R:
     c(
         person(

NEWS.md

@@ -1,4 +1,4 @@
-# permChacko (development version)
+# permChacko 1.0.1
 
 * Improved validation
 * Optimized `chackoStatistic()`

R/chackoStatistic.R

@@ -1,8 +1,8 @@
 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],  # current implementation
-    x_t[!duplicated(x_t[, "x"]), , drop = FALSE], # new idea (hidden)
+    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)
 }

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