AMR/tests/testthat/test-resistance_predict.R

80 lines
3.8 KiB
R
Raw Normal View History

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. #
2019-04-05 18:47:39 +02:00
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
2018-12-22 22:39:34 +01:00
# ==================================================================== #
context("portion.R")
test_that("prediction of rsi works", {
2019-05-10 16:44:59 +02:00
AMX_R <- septic_patients %>%
2018-12-22 22:39:34 +01:00
filter(mo == "B_ESCHR_COL") %>%
2019-05-10 16:44:59 +02:00
rsi_predict(col_ab = "AMX",
2018-12-22 22:39:34 +01:00
col_date = "date",
minimum = 10,
info = TRUE) %>%
pull("value")
2019-05-10 16:44:59 +02:00
# AMX resistance will increase according to data set `septic_patients`
expect_true(AMX_R[3] < AMX_R[20])
2018-12-22 22:39:34 +01:00
2019-05-10 16:44:59 +02:00
x <- resistance_predict(septic_patients, col_ab = "AMX", year_min = 2010)
2019-01-15 12:45:24 +01:00
plot(x)
ggplot_rsi_predict(x)
expect_error(ggplot_rsi_predict(septic_patients))
2018-12-22 22:39:34 +01:00
library(dplyr)
2019-05-13 20:16:51 +02:00
expect_output(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
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))
2019-05-13 20:16:51 +02:00
expect_output(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
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))
2019-05-13 20:16:51 +02:00
expect_output(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
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))
2019-05-13 20:16:51 +02:00
expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
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))
2019-05-13 20:16:51 +02:00
expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
2018-12-22 22:39:34 +01:00
col_ab = "NOT EXISTING COLUMN",
col_date = "date",
info = TRUE))
2019-05-13 20:16:51 +02:00
expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
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))
2019-05-10 16:44:59 +02:00
# almost all E. coli are MEM S in the Netherlands :)
2019-05-13 20:16:51 +02:00
expect_error(resistance_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
2019-05-10 16:44:59 +02:00
col_ab = "MEM",
2018-12-22 22:39:34 +01:00
col_date = "date",
info = TRUE))
expect_error(portion_df(c("A", "B", "C")))
expect_error(portion_df(septic_patients[,"date"]))
})