AMR/tests/testthat/test-resistance_predict.R

95 lines
4.9 KiB
R
Raw Normal View History

2018-12-22 22:39:34 +01:00
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
2018-12-22 22:39:34 +01:00
# #
2019-01-02 23:24:07 +01:00
# SOURCE #
2020-07-08 14:48:06 +02:00
# https://github.com/msberends/AMR #
2018-12-22 22:39:34 +01:00
# #
# LICENCE #
2020-12-27 00:30:28 +01:00
# (c) 2018-2021 Berends MS, Luz CF et al. #
2020-10-08 11:16:03 +02:00
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
2018-12-22 22:39:34 +01:00
# #
2019-01-02 23:24:07 +01:00
# 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. #
2020-10-08 11:16:03 +02:00
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
2018-12-22 22:39:34 +01:00
# ==================================================================== #
2019-07-11 16:08:56 +02:00
context("resistance_predict.R")
2018-12-22 22:39:34 +01:00
test_that("prediction of rsi works", {
2020-07-31 10:50:08 +02:00
skip_on_cran()
2021-01-18 18:45:43 +01:00
library(dplyr)
expect_output(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`
2019-07-11 16:08:56 +02:00
expect_true(AMX_R[3] < AMX_R[20])
2021-01-18 18:45:43 +01:00
expect_output(x <- suppressMessages(resistance_predict(example_isolates, col_ab = "AMX", year_min = 2010, model = "binomial", info = TRUE)))
2020-09-19 15:15:57 +02:00
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(plot(x))
expect_silent(ggplot_rsi_predict(x))
expect_error(ggplot_rsi_predict(example_isolates))
2019-01-15 12:45:24 +01:00
2019-09-18 15:46:09 +02:00
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
2018-12-22 22:39:34 +01:00
model = "binomial",
2019-05-10 16:44:59 +02:00
col_ab = "AMX",
2018-12-22 22:39:34 +01:00
col_date = "date",
info = TRUE))
2019-09-18 15:46:09 +02:00
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
2018-12-22 22:39:34 +01:00
model = "loglin",
2019-05-10 16:44:59 +02:00
col_ab = "AMX",
2018-12-22 22:39:34 +01:00
col_date = "date",
info = TRUE))
2019-09-18 15:46:09 +02:00
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
2018-12-22 22:39:34 +01:00
model = "lin",
2019-05-10 16:44:59 +02:00
col_ab = "AMX",
2018-12-22 22:39:34 +01:00
col_date = "date",
info = TRUE))
2019-09-18 15:46:09 +02:00
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
2018-12-22 22:39:34 +01:00
model = "INVALID MODEL",
2019-05-10 16:44:59 +02:00
col_ab = "AMX",
2018-12-22 22:39:34 +01:00
col_date = "date",
info = TRUE))
2019-09-18 15:46:09 +02:00
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
2019-08-07 15:37:39 +02:00
model = "binomial",
2018-12-22 22:39:34 +01:00
col_ab = "NOT EXISTING COLUMN",
col_date = "date",
info = TRUE))
2019-09-18 15:46:09 +02:00
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
2019-08-07 15:37:39 +02:00
model = "binomial",
2019-05-10 16:44:59 +02:00
col_ab = "AMX",
2018-12-22 22:39:34 +01:00
col_date = "NOT EXISTING COLUMN",
info = TRUE))
2019-09-18 15:46:09 +02:00
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
2019-08-07 15:37:39 +02:00
col_ab = "AMX",
col_date = "NOT EXISTING COLUMN",
info = TRUE))
2019-09-18 15:46:09 +02:00
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
2019-08-07 15:37:39 +02:00
col_ab = "AMX",
col_date = "date",
info = TRUE))
2019-05-10 16:44:59 +02:00
# almost all E. coli are MEM S in the Netherlands :)
2019-09-18 15:46:09 +02:00
expect_error(resistance_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
2019-08-07 15:37:39 +02:00
model = "binomial",
2019-05-10 16:44:59 +02:00
col_ab = "MEM",
2018-12-22 22:39:34 +01:00
col_date = "date",
info = TRUE))
})