mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 17:26:12 +01:00
121 lines
4.3 KiB
R
121 lines
4.3 KiB
R
# ==================================================================== #
|
|
# 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
|
|
))
|