(v1.6.0.9031) tinytest unit tests

2025-07-13 05:21:50 +02:00 · 2021-05-15 21:36:22 +02:00
parent 9a381c8d18
commit d8c91d5876
71 changed files with 2671 additions and 2901 deletions
--- a/inst/tinytest/test-g.test.R
+++ b/inst/tinytest/test-g.test.R
@ -0,0 +1,63 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Data Analysis for R                   #
+#                                                                      #
+# SOURCE                                                               #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# Developed at the University of Groningen, the Netherlands, in        #
+# collaboration with non-profit organisations Certe Medical            #
+# Diagnostics & Advice, and University Medical Center Groningen.       # 
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+# We created this package for both routine data analysis and academic  #
+# research and it was publicly released in the hope that it will be    #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+#                                                                      #
+# Visit our website for the full manual and a complete tutorial about  #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
+# ==================================================================== #
+
+# GOODNESS-OF-FIT
+
+# example 1: clearfield rice vs. red rice
+x <- c(772, 1611, 737)
+expect_equal(g.test(x, p = c(0.25, 0.50, 0.25))$p.value,
+             0.12574,
+             tolerance = 0.0001)
+
+# example 2: red crossbills
+x <- c(1752, 1895)
+expect_equal(g.test(x)$p.value,
+             0.017873,
+             tolerance = 0.0001)
+
+expect_error(g.test(0))
+expect_error(g.test(c(0, 1), 0))
+expect_error(g.test(c(1, 2, 3, 4), p = c(0.25, 0.25)))
+expect_error(g.test(c(1, 2, 3, 4), p = c(0.25, 0.25, 0.25, 0.24)))
+expect_warning(g.test(c(1, 2, 3, 4), p = c(0.25, 0.25, 0.25, 0.24), rescale.p = TRUE))
+
+# INDEPENDENCE
+
+x <- as.data.frame(
+  matrix(data = round(runif(4) * 100000, 0),
+         ncol = 2,
+         byrow = TRUE)
+)
+
+# fisher.test() is always better for 2x2 tables:
+expect_warning(g.test(x))
+expect_true(suppressWarnings(g.test(x)$p.value) < 1)
+
+expect_warning(g.test(x = c(772, 1611, 737),
+                      y = c(780, 1560, 780),
+                      rescale.p = TRUE))
+
+expect_error(g.test(matrix(data = c(-1, -2, -3, -4), ncol = 2, byrow = TRUE)))
+expect_error(g.test(matrix(data = c(0, 0, 0, 0), ncol = 2, byrow = TRUE)))