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95 lines
5.0 KiB
95 lines
5.0 KiB
# ==================================================================== # |
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# TITLE # |
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# Antimicrobial Resistance (AMR) Data Analysis for R # |
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# # |
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# SOURCE # |
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# https://github.com/msberends/AMR # |
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# # |
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# LICENCE # |
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# (c) 2018-2021 Berends MS, Luz CF et al. # |
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# Developed at the University of Groningen, the Netherlands, in # |
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# collaboration with non-profit organisations Certe Medical # |
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# Diagnostics & Advice, and University Medical Center Groningen. # |
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# # |
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# This R package is free software; you can freely use and distribute # |
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# it for both personal and commercial purposes under the terms of the # |
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# GNU General Public License version 2.0 (GNU GPL-2), as published by # |
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# the Free Software Foundation. # |
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# We created this package for both routine data analysis and academic # |
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# research and it was publicly released in the hope that it will be # |
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # |
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# # |
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# Visit our website for the full manual and a complete tutorial about # |
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ # |
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# ==================================================================== # |
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) { |
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expect_stdout(AMX_R <- example_isolates %>% |
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filter(mo == "B_ESCHR_COLI") %>% |
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rsi_predict(col_ab = "AMX", |
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col_date = "date", |
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model = "binomial", |
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minimum = 10, |
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info = TRUE) %>% |
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pull("value")) |
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# 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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} |
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expect_stdout(x <- suppressMessages(resistance_predict(example_isolates, |
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col_ab = "AMX", |
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year_min = 2010, |
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model = "binomial", |
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info = TRUE))) |
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pdf(NULL) # prevent Rplots.pdf being created |
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expect_silent(plot(x)) |
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if (AMR:::pkg_is_available("ggplot2")) { |
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expect_silent(ggplot_rsi_predict(x)) |
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expect_silent(autoplot(x)) |
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expect_error(ggplot_rsi_predict(example_isolates)) |
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} |
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expect_stdout(rsi_predict(x = subset(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", |
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info = TRUE)) |
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expect_stdout(rsi_predict(x = subset(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", |
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info = TRUE)) |
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expect_stdout(rsi_predict(x = subset(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", |
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info = TRUE)) |
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expect_error(rsi_predict(x = subset(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", |
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info = TRUE)) |
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expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"), |
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model = "binomial", |
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col_ab = "NOT EXISTING COLUMN", |
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col_date = "date", |
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info = TRUE)) |
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expect_error(rsi_predict(x = subset(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", |
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info = TRUE)) |
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expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"), |
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col_ab = "AMX", |
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col_date = "NOT EXISTING COLUMN", |
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info = TRUE)) |
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expect_error(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"), |
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col_ab = "AMX", |
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col_date = "date", |
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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 = subset(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", |
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info = TRUE))
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