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. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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context("resistance_predict.R")
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test_that("prediction of rsi works", {
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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plot(x)
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))
})