AMR/inst/tinytest/test-resistance_predict.R

# ==================================================================== #
# 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/   #
# ==================================================================== #

if (AMR:::pkg_is_available("dplyr")) {
  expect_stdout(AMX_R <- example_isolates %>%
                  filter(mo == "B_ESCHR_COLI") %>%
                  rsi_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_rsi_predict(x))
  expect_silent(autoplot(x))
  expect_error(ggplot_rsi_predict(example_isolates))
}
expect_stdout(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
                          model = "binomial",
                          col_ab = "AMX",
                          col_date = "date",
                          info = TRUE))
expect_stdout(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
                          model = "loglin",
                          col_ab = "AMX",
                          col_date = "date",
                          info = TRUE))
expect_stdout(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
                          model = "lin",
                          col_ab = "AMX",
                          col_date = "date",
                          info = TRUE))

expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
                         model = "INVALID MODEL",
                         col_ab = "AMX",
                         col_date = "date",
                         info = TRUE))
expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
                         model = "binomial",
                         col_ab = "NOT EXISTING COLUMN",
                         col_date = "date",
                         info = TRUE))
expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
                         model = "binomial",
                         col_ab = "AMX",
                         col_date = "NOT EXISTING COLUMN",
                         info = TRUE))
expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
                         col_ab = "AMX",
                         col_date = "NOT EXISTING COLUMN",
                         info = TRUE))
expect_error(rsi_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))