mirror of https://github.com/msberends/AMR.git
201 lines
7.3 KiB
R
Executable File
201 lines
7.3 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (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 #
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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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# #
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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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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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context("first_isolate.R")
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test_that("first isolates work", {
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skip_on_cran()
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# first isolates
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expect_equal(
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sum(
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first_isolate(x = example_isolates,
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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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1317)
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# first weighted isolates
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ex_iso_with_keyab <- example_isolates
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ex_iso_with_keyab$keyab <- key_antibiotics(example_isolates, warnings = FALSE)
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expect_equal(
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suppressWarnings(
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sum(
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first_isolate(x = ex_iso_with_keyab,
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# let syntax determine arguments automatically
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type = "keyantibiotics",
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info = TRUE),
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na.rm = TRUE)),
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1413)
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# when not ignoring I
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expect_equal(
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suppressWarnings(
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sum(
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first_isolate(x = ex_iso_with_keyab,
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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_keyantibiotics = "keyab",
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ignore_I = FALSE,
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type = "keyantibiotics",
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info = TRUE),
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na.rm = TRUE)),
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1436)
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# when using points
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expect_equal(
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suppressWarnings(
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sum(
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first_isolate(x = ex_iso_with_keyab,
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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_keyantibiotics = "keyab",
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type = "points",
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info = TRUE),
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na.rm = TRUE)),
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1417)
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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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891)
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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_lt(
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sum(
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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),
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na.rm = TRUE),
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1501)
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# same, but now exclude ICU
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expect_lt(
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sum(
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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),
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na.rm = TRUE),
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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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# look for columns itself
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expect_message(first_isolate(example_isolates))
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expect_message(first_isolate(example_isolates %>%
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mutate(mo = as.character(mo)) %>%
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left_join_microorganisms()))
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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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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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# 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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1322)
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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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1062)
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expect_equal(sum(first_isolate(test_unknown, include_unknown = TRUE)),
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1529)
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test_unknown$mo <- ifelse(test_unknown$mo == "UNKNOWN", NA, test_unknown$mo)
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expect_equal(sum(first_isolate(test_unknown)),
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1062)
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# shortcuts
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expect_identical(filter_first_isolate(example_isolates),
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subset(example_isolates, first_isolate(example_isolates)))
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ex <- example_isolates
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ex$keyab <- key_antibiotics(ex)
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expect_identical(filter_first_weighted_isolate(example_isolates),
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subset(example_isolates, first_isolate(ex)))
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})
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