AMR/tests/testthat/test-resistance_predict.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
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# SOURCE #
# https://gitlab.com/msberends/AMR #
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# #
# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# 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. #
# #
# This R package was created for academic research and 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.gitab.io/AMR. #
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# ==================================================================== #
context("portion.R")
test_that("prediction of rsi works", {
amox_R <- septic_patients %>%
filter(mo == "B_ESCHR_COL") %>%
rsi_predict(col_ab = "amox",
col_date = "date",
minimum = 10,
info = TRUE) %>%
pull("value")
# amox resistance will increase according to data set `septic_patients`
expect_true(amox_R[3] < amox_R[20])
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x <- resistance_predict(septic_patients, col_ab = "amox", year_min = 2010)
plot(x)
ggplot_rsi_predict(x)
expect_error(ggplot_rsi_predict(septic_patients))
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library(dplyr)
expect_output(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"),
model = "binomial",
col_ab = "amox",
col_date = "date",
info = TRUE))
expect_output(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"),
model = "loglin",
col_ab = "amox",
col_date = "date",
info = TRUE))
expect_output(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"),
model = "lin",
col_ab = "amox",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"),
model = "INVALID MODEL",
col_ab = "amox",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"),
col_ab = "NOT EXISTING COLUMN",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"),
col_ab = "amox",
col_date = "NOT EXISTING COLUMN",
info = TRUE))
# almost all E. coli are mero S in the Netherlands :)
expect_error(resistance_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"),
col_ab = "mero",
col_date = "date",
info = TRUE))
expect_error(portion_df(c("A", "B", "C")))
expect_error(portion_df(septic_patients[,"date"]))
})