(v2.1.1.9131) implement testthat

2025-08-13 12:45:14 +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-resistance_predict.R
+++ b/tests/testthat/test-resistance_predict.R
@ -0,0 +1,120 @@
+# ==================================================================== #
+# 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/   #
+# ==================================================================== #
+
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
+  expect_stdout(AMX_R <- example_isolates %>%
+    filter(mo == "B_ESCHR_COLI") %>%
+    sir_predict(
+      col_ab = "AMX",
+      col_date = "date",
+      model = "binomial",
+      minimum = 10,
+      info = TRUE
+    ) %>%
+    pull("value"))
+  # AMX resistance will increase according to data set `example_isolates`
+  expect_true(AMX_R[3] < AMX_R[20])
+}
+
+expect_stdout(x <- suppressMessages(resistance_predict(example_isolates,
+  col_ab = "AMX",
+  year_min = 2010,
+  model = "binomial",
+  info = TRUE
+)))
+pdf(NULL) # prevent Rplots.pdf being created
+expect_silent(plot(x))
+if (AMR:::pkg_is_available("ggplot2")) {
+  expect_silent(ggplot_sir_predict(x))
+  expect_silent(ggplot2::autoplot(x))
+  expect_error(ggplot_sir_predict(example_isolates))
+}
+expect_stdout(sir_predict(
+  x = subset(example_isolates, mo == "B_ESCHR_COLI"),
+  model = "binomial",
+  col_ab = "AMX",
+  col_date = "date",
+  info = TRUE
+))
+expect_stdout(sir_predict(
+  x = subset(example_isolates, mo == "B_ESCHR_COLI"),
+  model = "loglin",
+  col_ab = "AMX",
+  col_date = "date",
+  info = TRUE
+))
+expect_stdout(sir_predict(
+  x = subset(example_isolates, mo == "B_ESCHR_COLI"),
+  model = "lin",
+  col_ab = "AMX",
+  col_date = "date",
+  info = TRUE
+))
+
+expect_error(sir_predict(
+  x = subset(example_isolates, mo == "B_ESCHR_COLI"),
+  model = "INVALID MODEL",
+  col_ab = "AMX",
+  col_date = "date",
+  info = TRUE
+))
+expect_error(sir_predict(
+  x = subset(example_isolates, mo == "B_ESCHR_COLI"),
+  model = "binomial",
+  col_ab = "NOT EXISTING COLUMN",
+  col_date = "date",
+  info = TRUE
+))
+expect_error(sir_predict(
+  x = subset(example_isolates, mo == "B_ESCHR_COLI"),
+  model = "binomial",
+  col_ab = "AMX",
+  col_date = "NOT EXISTING COLUMN",
+  info = TRUE
+))
+expect_error(sir_predict(
+  x = subset(example_isolates, mo == "B_ESCHR_COLI"),
+  col_ab = "AMX",
+  col_date = "NOT EXISTING COLUMN",
+  info = TRUE
+))
+expect_error(sir_predict(
+  x = subset(example_isolates, mo == "B_ESCHR_COLI"),
+  col_ab = "AMX",
+  col_date = "date",
+  info = TRUE
+))
+# almost all E. coli are MEM S in the Netherlands :)
+expect_error(resistance_predict(
+  x = subset(example_isolates, mo == "B_ESCHR_COLI"),
+  model = "binomial",
+  col_ab = "MEM",
+  col_date = "date",
+  info = TRUE
+))