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52 lines
2.7 KiB
52 lines
2.7 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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test_df <- rbind( |
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data.frame( |
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date = as.Date(c("2015-01-01", "2015-10-01", "2016-02-04", "2016-12-31", "2017-01-01", "2017-02-01", "2017-02-05", "2020-01-01")), |
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patient_id = "A" |
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), |
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data.frame( |
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date = as.Date(c("2015-01-01", "2016-02-01", "2016-12-31", "2017-01-01", "2017-02-03")), |
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patient_id = "B" |
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)) |
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expect_equal(get_episode(test_df$date, 365), |
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c(1, 1, 2, 2, 2, 3, 3, 4, 1, 2, 2, 2, 3)) |
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) { |
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expect_identical(test_df %>% group_by(patient_id) %>% mutate(f = is_new_episode(date, 365)) %>% pull(f), |
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c(TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE)) |
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suppressMessages( |
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x <- example_isolates %>% |
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mutate(out = first_isolate(., include_unknown = TRUE, method = "episode-based", info = FALSE)) |
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) |
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y <- example_isolates %>% |
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group_by(patient_id, mo) %>% |
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mutate(out = is_new_episode(date, 365)) |
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expect_identical(which(x$out), which(y$out)) |
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}
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