(v2.1.1.9131) implement testthat

2025-07-11 23:42:02 +02:00 · 2025-01-27 21:43:10 +01:00
parent 92166c16e8
commit f03933940c
63 changed files with 172 additions and 267 deletions
--- a/tests/testthat/test-g.test.R
+++ b/tests/testthat/test-g.test.R
@ -0,0 +1,69 @@
+# ==================================================================== #
+# TITLE:                                                               #
+# AMR: An R Package for Working with Antimicrobial Resistance Data     #
+#                                                                      #
+# SOURCE CODE:                                                         #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# PLEASE CITE THIS SOFTWARE AS:                                        #
+# Berends MS, Luz CF, Friedrich AW, et al. (2022).                     #
+# AMR: An R Package for Working with Antimicrobial Resistance Data.    #
+# Journal of Statistical Software, 104(3), 1-31.                       #
+# https://doi.org/10.18637/jss.v104.i03                                #
+#                                                                      #
+# Developed at the University of Groningen and the University Medical  #
+# Center Groningen in The Netherlands, in collaboration with many      #
+# colleagues from around the world, see our website.                   #
+#                                                                      #
+# 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)))