Merge branch 'issue-16' into develop (close #16)

* issue-16:
  Increment version number to 1.0.0.9002
  Updated NEWS.md (#16)
  Adjusted unit tests affected by #16
  Defaulting to new agreement regarding #16

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: permChacko
 Title: Chacko Test for Order-Restriction with Permutation
-Version: 1.0.0.9001
+Version: 1.0.0.9002
 Date: 2024-04-17
 Authors@R:
     c(

NEWS.md

@@ -2,6 +2,7 @@
 
 * 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
 

R/chackoStatistic.R

@@ -1,5 +1,5 @@
-chackoStatistic <- function(x_t, n, k, uniqueness_method = 1) {
-  m <- length(unique(x_t[, "x"])) # TODO: check what Chacko really means by m
+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)

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
+})

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")