AMR/tests/testthat/test-resistance_predict.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
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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. #
# #
# 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. #
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# Visit our website for more info: https://msberends.github.io/AMR. #
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# ==================================================================== #
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context("resistance_predict.R")
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test_that("prediction of rsi works", {
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skip_on_cran()
AMX_R <- example_isolates %>%
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filter(mo == "B_ESCHR_COLI") %>%
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rsi_predict(col_ab = "AMX",
col_date = "date",
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model = "binomial",
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minimum = 10,
info = TRUE) %>%
pull("value")
# AMX resistance will increase according to data set `example_isolates`
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expect_true(AMX_R[3] < AMX_R[20])
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x <- resistance_predict(example_isolates, col_ab = "AMX", year_min = 2010, model = "binomial")
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pdf(NULL) # prevent Rplots.pdf being created
expect_silent(plot(x))
expect_silent(ggplot_rsi_predict(x))
expect_error(ggplot_rsi_predict(example_isolates))
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library(dplyr)
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expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
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model = "binomial",
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col_ab = "AMX",
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col_date = "date",
info = TRUE))
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expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
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model = "loglin",
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col_ab = "AMX",
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col_date = "date",
info = TRUE))
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expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
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model = "lin",
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col_ab = "AMX",
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col_date = "date",
info = TRUE))
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expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
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model = "INVALID MODEL",
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col_ab = "AMX",
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col_date = "date",
info = TRUE))
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expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
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model = "binomial",
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col_ab = "NOT EXISTING COLUMN",
col_date = "date",
info = TRUE))
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expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
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model = "binomial",
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col_ab = "AMX",
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col_date = "NOT EXISTING COLUMN",
info = TRUE))
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expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
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col_ab = "AMX",
col_date = "NOT EXISTING COLUMN",
info = TRUE))
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expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
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col_ab = "AMX",
col_date = "date",
info = TRUE))
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# almost all E. coli are MEM S in the Netherlands :)
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expect_error(resistance_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
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model = "binomial",
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col_ab = "MEM",
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col_date = "date",
info = TRUE))
})