Merge branch 'issue-13' into develop (close #13)

* issue-13: Updated NEWS.md Increment version number to 0.2.0.9001 Removed alternative numeric p-value (#13) Removed feature version Updated feature version Added calculation of mid-P value (#13) Updated RoxygenNote version Adjusted unit test expectations (#13) Added calculation of alternative numeric p-value (#13) Increment version number to 0.2.0.9000-1709818294
ocbe-uio · Apr 5, 2024 · 2af89f6 · 2af89f6
2 parents 3c263d4 + fe17834
commit 2af89f6
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: permChacko
 Title: Chacko Test for Order-Restriction with Permutation
-Version: 0.2.0.9000
+Version: 0.2.0.9001
 Date: 2023-11-07
 Authors@R:
     c(
@@ -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
@@ -1,6 +1,7 @@
 # permChacko (development version)
 
 * 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
 

diff --git a/R/permChacko.R b/R/permChacko.R
@@ -53,6 +53,7 @@ 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
   m <- nrow(x_t)
   anal_p_value <- ifelse(
     test = m > 1L,
@@ -70,6 +71,7 @@ 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"
       ),
       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[["tabular"]]
+      x[["statistic"]],
+      p_values[["analytic"]],
+      p_values[["numeric"]], x[["n_perm"]],
+      p_values[["numeric_mid"]], x[["n_perm"]],
+      p_values[["tabular"]]
     )
   )
 }

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
@@ -13,7 +13,7 @@ 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", {