P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 23:41:57 +02:00
Code Releases Activity

styled, unit test fix

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-08-28 10:31:50 +02:00
parent 4cb1db4554
commit 4d050aef7c
147 changed files with 10897 additions and 8169 deletions
Download Patch File Download Diff File Expand all files Collapse all files

131
inst/tinytest/test-resistance_predict.R
View File

@ -9,7 +9,7 @@
# (c) 2018-2022 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. #
# 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 #
@ -25,22 +25,25 @@
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
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"))
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)))
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")) {
@ -48,48 +51,66 @@ if (AMR:::pkg_is_available("ggplot2")) {
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_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))
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))
expect_error(resistance_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "MEM",
col_date = "date",
info = TRUE
))