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180 lines
7.6 KiB
180 lines
7.6 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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# all four methods |
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expect_equal(sum(first_isolate(x = example_isolates, method = "isolate-based", info = TRUE), na.rm = TRUE), |
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1984) |
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expect_equal(sum(first_isolate(x = example_isolates, method = "patient-based", info = TRUE), na.rm = TRUE), |
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1265) |
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expect_equal(sum(first_isolate(x = example_isolates, method = "episode-based", info = TRUE), na.rm = TRUE), |
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1300) |
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expect_equal(sum(first_isolate(x = example_isolates, method = "phenotype-based", info = TRUE), na.rm = TRUE), |
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1379) |
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# Phenotype-based, using key antimicrobials |
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expect_equal(sum(first_isolate(x = example_isolates, |
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method = "phenotype-based", |
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type = "keyantimicrobials", |
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antifungal = NULL, info = TRUE), na.rm = TRUE), |
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1395) |
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expect_equal(sum(first_isolate(x = example_isolates, |
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method = "phenotype-based", |
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type = "keyantimicrobials", |
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antifungal = NULL, info = TRUE, ignore_I = FALSE), na.rm = TRUE), |
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1418) |
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# first non-ICU isolates |
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expect_equal( |
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sum( |
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first_isolate(example_isolates, |
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col_mo = "mo", |
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col_date = "date", |
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col_patient_id = "patient_id", |
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col_icu = "ward_icu", |
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info = TRUE, |
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icu_exclude = TRUE), |
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na.rm = TRUE), |
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941) |
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# set 1500 random observations to be of specimen type 'Urine' |
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random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE) |
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x <- example_isolates |
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x$specimen <- "Other" |
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x[random_rows, "specimen"] <- "Urine" |
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expect_true( |
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sum(first_isolate(x = x, |
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col_date = "date", |
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col_patient_id = "patient_id", |
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col_mo = "mo", |
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col_specimen = "specimen", |
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filter_specimen = "Urine", |
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info = TRUE), na.rm = TRUE) < 1501) |
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# same, but now exclude ICU |
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expect_true( |
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sum(first_isolate(x = x, |
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col_date = "date", |
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col_patient_id = "patient_id", |
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col_mo = "mo", |
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col_specimen = "specimen", |
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filter_specimen = "Urine", |
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col_icu = "ward_icu", |
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icu_exclude = TRUE, |
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info = TRUE), na.rm = TRUE) < 1501) |
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# "No isolates found" |
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test_iso <- example_isolates |
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test_iso$specimen <- "test" |
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expect_message(first_isolate(test_iso, |
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"date", |
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"patient_id", |
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col_mo = "mo", |
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col_specimen = "specimen", |
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filter_specimen = "something_unexisting", |
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info = TRUE)) |
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# printing of exclusion message |
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expect_message(first_isolate(example_isolates, |
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col_date = "date", |
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col_mo = "mo", |
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col_patient_id = "patient_id", |
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col_testcode = "gender", |
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testcodes_exclude = "M", |
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info = TRUE)) |
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# errors |
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expect_error(first_isolate("date", "patient_id", col_mo = "mo")) |
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expect_error(first_isolate(example_isolates, |
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col_date = "non-existing col", |
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col_mo = "mo")) |
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) { |
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# if mo is not an mo class, result should be the same |
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expect_identical(example_isolates %>% |
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mutate(mo = as.character(mo)) %>% |
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first_isolate(col_date = "date", |
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col_mo = "mo", |
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col_patient_id = "patient_id", |
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info = FALSE), |
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example_isolates %>% |
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first_isolate(col_date = "date", |
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col_mo = "mo", |
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col_patient_id = "patient_id", |
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info = FALSE)) |
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# support for WHONET |
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expect_message(example_isolates %>% |
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select(-patient_id) %>% |
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mutate(`First name` = "test", |
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`Last name` = "test", |
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Sex = "Female") %>% |
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first_isolate(info = TRUE)) |
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# groups |
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x <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate()) |
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y <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate(.)) |
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expect_identical(x, y) |
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} |
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# missing dates should be no problem |
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df <- example_isolates |
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df[1:100, "date"] <- NA |
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expect_equal( |
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sum( |
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first_isolate(x = df, |
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col_date = "date", |
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col_patient_id = "patient_id", |
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col_mo = "mo", |
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info = TRUE), |
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na.rm = TRUE), |
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1382) |
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# unknown MOs |
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test_unknown <- example_isolates |
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test_unknown$mo <- ifelse(test_unknown$mo == "B_ESCHR_COLI", "UNKNOWN", test_unknown$mo) |
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expect_equal(sum(first_isolate(test_unknown, include_unknown = FALSE)), |
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1108) |
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expect_equal(sum(first_isolate(test_unknown, include_unknown = TRUE)), |
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1591) |
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test_unknown$mo <- ifelse(test_unknown$mo == "UNKNOWN", NA, test_unknown$mo) |
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expect_equal(sum(first_isolate(test_unknown)), |
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1108) |
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# empty rsi results |
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expect_equal(sum(first_isolate(example_isolates, include_untested_rsi = FALSE)), |
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1366) |
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# shortcuts |
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expect_identical(filter_first_isolate(example_isolates), |
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subset(example_isolates, first_isolate(example_isolates))) |
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# notice that all mo's are distinct, so all are TRUE |
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expect_true(all(first_isolate(AMR:::pm_distinct(example_isolates, mo, .keep_all = TRUE), info = TRUE) == TRUE)) |
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# only one isolate, so return fast |
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expect_true(first_isolate(data.frame(mo = "Escherichia coli", date = Sys.Date(), patient = "patient"), info = TRUE))
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