(v1.0.1.9001) PCA unit tests

tests/testthat/test-pca.R

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+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://gitlab.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+#                                                                      #
+# 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 more info: https://msberends.gitlab.io/AMR.    #
+# ==================================================================== #
+
+context("pca.R")
+
+test_that("PCA works", {
+  library(dplyr)
+  resistance_data <- example_isolates %>% 
+    filter(mo %in% as.mo(c("E. coli", "K. pneumoniae", "S. aureus"))) %>% 
+    select(mo, AMC, CXM, CTX, TOB, TMP) %>% 
+    group_by(order = mo_order(mo),       # group on anything, like order
+             genus = mo_genus(mo)) %>%   #  and genus as we do here
+    summarise_if(is.rsi, resistance, minimum = 0)
+  
+  expect_s3_class(pca(resistance_data), "prcomp")
+  expect_s3_class(prcomp(resistance_data), "prcomp")
+  
+  ggplot_pca(pca(resistance_data), ellipse = TRUE)
+})