Merge branch 'release-3.0.0' into develop

ocbe-uio · Mar 14, 2024 · 70c6d9a · 70c6d9a
2 parents 45e22ad + 1f22f8e
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diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 2.2.1
-Date: 2024-01-11 12:34:46 UTC
-SHA: b4e1ca06ab4213586968a25db8bdf598c1693e9a
+Version: 3.0.0
+Date: 2024-03-14 14:47:43 UTC
+SHA: ecbbd5150e7ab951fded4a2bfe4ab4e072a04b68
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: contingencytables
 Title: Statistical Analysis of Contingency Tables
-Version: 2.2.1.9010
+Version: 3.0.0
 Authors@R:
     c(
         person(
@@ -45,4 +45,4 @@ URL: https://contingencytables.com/ https://ocbe-uio.github.io/contingencytables
 BugReports: https://github.com/ocbe-uio/contingencytables/issues
 Imports: MASS, boot, methods
 Suggests: testthat
-Date: 2024-01-11
+Date: 2024-03-14
diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# contingencytables (development version)
+# contingencytables 3.0.0
 
 * Reached 100% test coverage (#52)
 * Removed unused code

diff --git a/R/MiettinenNurminen_asymptotic_score_CI_OR_2x2.R b/R/MiettinenNurminen_asymptotic_score_CI_OR_2x2.R
@@ -67,7 +67,7 @@ MiettinenNurminen_asymptotic_score_CI_OR_2x2 <- function(n, alpha = 0.05) {
     contingencytables_result(
       list("lower" = L, "upper" = U, "estimate" = estimate),
       sprintf(
-        "Mietinen-Nurminen asymptotic score CI: estimate = %6.4f (%g%% CI %6.4f to %6.4f)",
+        "Miettinen-Nurminen asymptotic score CI: estimate = %6.4f (%g%% CI %6.4f to %6.4f)",
         estimate, 100 * (1 - alpha), L, U
       )
     )

diff --git a/R/MiettinenNurminen_asymptotic_score_CI_difference_2x2.R b/R/MiettinenNurminen_asymptotic_score_CI_difference_2x2.R
@@ -1,5 +1,5 @@
-#' @title The Mietinen-Nurminen asymptotic score confidence interval for the
-#' @description The Mietinen-Nurminen asymptotic score confidence interval for the
+#' @title The Miettinen-Nurminen asymptotic score confidence interval for the
+#' @description The Miettinen-Nurminen asymptotic score confidence interval for the
 #' @description difference between probabilities
 #' @description Described in Chapter 4 "The 2x2 Table"
 #' @param n the observed counts (a 2x2 matrix)
@@ -56,7 +56,7 @@ MiettinenNurminen_asymptotic_score_CI_difference_2x2 <- function(n, alpha = 0.05
     contingencytables_result(
       list("lower" = L, "upper" = U, "estimate" = estimate),
       sprintf(
-        "Mietinen-Nurminen asymptotic score CI: estimate = %6.4f (%g%% CI %6.4f to %6.4f)",
+        "Miettinen-Nurminen asymptotic score CI: estimate = %6.4f (%g%% CI %6.4f to %6.4f)",
         estimate, 100 * (1 - alpha), L, U
       )
     )

diff --git a/R/MiettinenNurminen_asymptotic_score_CI_ratio_2x2.R b/R/MiettinenNurminen_asymptotic_score_CI_ratio_2x2.R
@@ -72,7 +72,7 @@ MiettinenNurminen_asymptotic_score_CI_ratio_2x2 <- function(n, alpha = 0.05) {
     contingencytables_result(
       list("lower" = L, "upper" = U, "estimate" = estimate),
       sprintf(
-        "Mietinen-Nurminen asymptotic score CI: estimate = %6.4f (%g%% CI %6.4f to %6.4f)",
+        "Miettinen-Nurminen asymptotic score CI: estimate = %6.4f (%g%% CI %6.4f to %6.4f)",
         estimate, 100 * (1 - alpha), L, U
       )
     )

diff --git a/R/Scheffe_type_CIs_paired_cxc.R b/R/Scheffe_type_CIs_paired_cxc.R
@@ -1,5 +1,5 @@
-#' @title ScheffE-type confidence intervals for differences of marginal probabilities
-#' @description ScheffE-type confidence intervals for differences of marginal probabilities
+#' @title Scheffe-type confidence intervals for differences of marginal probabilities
+#' @description Scheffe-type confidence intervals for differences of marginal probabilities
 #' @description Described in Chapter 9 "The Paired kxk Table"
 #' @param n the observed table (a cxc matrix)
 #' @param alpha the nominal level, e.g. 0.05 for 95% CIs

diff --git a/R/Scheffe_type_CIs_rxc.R b/R/Scheffe_type_CIs_rxc.R
@@ -1,5 +1,5 @@
-#' @title The ScheffE-type simultaneous confidence intervals for the differences pi_1|i - pi_1|j
-#' @description The ScheffE-type simultaneous confidence intervals for the differences pi_1|i - pi_1|j
+#' @title The Scheffe-type simultaneous confidence intervals for the differences pi_1|i - pi_1|j
+#' @description The Scheffe-type simultaneous confidence intervals for the differences pi_1|i - pi_1|j
 #' @description Described in Chapter 7 "The rxc Table"
 #' @param n the observed counts (an rx2 vector)
 #' @param alpha the nominal level, e.g. 0.05 for 95# CIs
@@ -27,7 +27,7 @@ Scheffe_type_CIs_rxc <- function(n, alpha = 0.05) {
     }
   }
 
-  # Simultaneous confidence intervals with ScheffE adjustment
+  # Simultaneous confidence intervals with Scheffe adjustment
   L <- rep(0, C)
   U <- rep(0, C)
   Scheffe <- qchisq(1 - alpha, r - 1)

diff --git a/R/the_paired_cxc_table_nominal.R b/R/the_paired_cxc_table_nominal.R
@@ -51,7 +51,7 @@ the_paired_cxc_table_nominal <- function(n, alpha = 0.05) {
 
 
   cat_sprintf("\nTests and confidence intervals for individual categories:\n")
-  cat_sprintf("\nCategory        Estimate    ScheffE 95%%CI         Bonferroni 95%%CI     P-value*\n")
+  cat_sprintf("\nCategory        Estimate    Scheffe 95%%CI         Bonferroni 95%%CI     P-value*\n")
   cat_sprintf("-------------------------------------------------------------------------------\n")
   for (i in 1:c) {
     tmp <- Scheffe_type_CIs_paired_cxc(n, alpha)

diff --git a/R/validateArguments.R b/R/validateArguments.R
@@ -3,7 +3,7 @@
 #' validate their arguments.
 #' @param x named list containing function arguments and their values
 #' @param types named vector of types for `x`
-#' @return Nothing if all aguments fit their type. An error message otherwise.
+#' @return Nothing if all arguments fit their type. An error message otherwise.
 #' @author Waldir Leoncio
 #' @details Accepted validation types are:
 #' \itemize{

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,6 +1,47 @@
-## R CMD check results
+# contingencytables 3.0.0
 
-0 errors | 0 warnings | 1 note
+* Reached 100% test coverage (#52)
+* Removed unused code
+* Improved handling of edge cases
+* Restricted `Cumulative_models_for_rxc()` and `Cumulative_models_for_2xc()` to 2 columns
+* Added `plot()` method for `Exact_unconditional_test_2x2()` and `McNemar_exact_unconditional_test_paired_2x2()` (#53)
+* Standardized names of objects in the output (#35)
 
-* Improved internals:refactoring (#41), increased test coverage (#52)
-* Fixed upper CI limit on `stratified_2x2_tables()` (thanks to Zhen Wang)
+# Test environments
+- R-hub windows-x86_64-devel (r-devel)
+- R-hub ubuntu-gcc-release (r-release)
+- R-hub fedora-clang-devel (r-devel)
+
+# R CMD check results
+❯ On windows-x86_64-devel (r-devel)
+  checking for non-standard things in the check directory ... NOTE
+  Found the following files/directories:
+    ''NULL''
+
+❯ On windows-x86_64-devel (r-devel)
+  checking for detritus in the temp directory ... NOTE
+  Found the following files/directories:
+    'lastMiKTeXException'
+
+❯ On ubuntu-gcc-release (r-release)
+  checking examples ... [34s/93s] NOTE
+  Examples with CPU (user + system) or elapsed time > 5s
+                                             user system elapsed
+  MidP_multinomial_test_1xc                 3.908  0.001  11.123
+  Exact_multinomial_test_1xc                3.810  0.004  10.800
+  CochranArmitage_exact_cond_midP_tests_rx2 3.323  0.007   8.749
+
+❯ On ubuntu-gcc-release (r-release), fedora-clang-devel (r-devel)
+  checking HTML version of manual ... NOTE
+  Skipping checking HTML validation: no command 'tidy' found
+
+❯ On fedora-clang-devel (r-devel)
+  checking examples ... [35s/98s] NOTE
+  Examples with CPU (user + system) or elapsed time > 5s
+                                             user system elapsed
+  MidP_multinomial_test_1xc                 4.161  0.008  11.308
+  Exact_multinomial_test_1xc                4.079  0.012  10.254
+  CochranArmitage_exact_cond_midP_tests_rx2 3.521  0.003  10.113
+  the_rxc_table                             2.002  0.008   5.574
+
+0 errors ✔ | 0 warnings ✔ | 5 notes ✖
diff --git a/man/MiettinenNurminen_asymptotic_score_CI_difference_2x2.Rd b/man/MiettinenNurminen_asymptotic_score_CI_difference_2x2.Rd
diff --git a/man/Scheffe_type_CIs_paired_cxc.Rd b/man/Scheffe_type_CIs_paired_cxc.Rd
diff --git a/man/Scheffe_type_CIs_rxc.Rd b/man/Scheffe_type_CIs_rxc.Rd
diff --git a/man/validateArguments.Rd b/man/validateArguments.Rd
diff --git a/tests/testthat/test-ch4.R b/tests/testthat/test-ch4.R
@@ -152,11 +152,11 @@ test_that("Chapter 4 functions basically work", {
   )
   expect_output(
     object = print(MiettinenNurminen_asymptotic_score_CI_difference_2x2(matrix(c(2e6, 2, 2, 2e6), 2))),
-    regexp = "Mietinen-Nurminen .+ 1.0000 \\(95% CI 1.0000 to 1.0000\\)"
+    regexp = "Miettinen-Nurminen .+ 1.0000 \\(95% CI 1.0000 to 1.0000\\)"
   )
   expect_output(
     object = print(MiettinenNurminen_asymptotic_score_CI_difference_2x2(matrix(c(2, 2e6, 2e6, 2), 2))),
-    regexp = "Mietinen-Nurminen .+ -1.0000 \\(95% CI -1.0000 to -1.0000\\)"
+    regexp = "Miettinen-Nurminen .+ -1.0000 \\(95% CI -1.0000 to -1.0000\\)"
   )
   expect_output(
     object = print(MiettinenNurminen_asymptotic_score_CI_OR_2x2(lampasona_2013)),