2018-12-22 22:39:34 +01:00
|
|
|
# ==================================================================== #
|
|
|
|
|
# TITLE #
|
|
|
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
|
|
|
# #
|
2019-01-02 23:24:07 +01:00
|
|
|
# SOURCE #
|
|
|
|
|
# https://gitlab.com/msberends/AMR #
|
2018-12-22 22:39:34 +01:00
|
|
|
# #
|
|
|
|
|
# LICENCE #
|
2019-01-02 23:24:07 +01:00
|
|
|
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
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. #
|
|
|
|
|
# #
|
|
|
|
|
# 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. #
|
2018-12-22 22:39:34 +01:00
|
|
|
# ==================================================================== #
|
|
|
|
|
|
|
|
|
|
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])
|
|
|
|
|
|
2019-01-15 12:45:24 +01:00
|
|
|
x <- resistance_predict(septic_patients, col_ab = "amox", year_min = 2010)
|
|
|
|
|
plot(x)
|
|
|
|
|
ggplot_rsi_predict(x)
|
|
|
|
|
expect_error(ggplot_rsi_predict(septic_patients))
|
|
|
|
|
|
2018-12-22 22:39:34 +01:00
|
|
|
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"]))
|
|
|
|
|
})
|
