2018-12-16 22:45:12 +01:00
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# ==================================================================== #
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# TITLE #
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2020-10-08 11:16:03 +02:00
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# Antimicrobial Resistance (AMR) Analysis for R #
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2018-12-16 22:45:12 +01:00
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# #
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2019-01-02 23:24:07 +01:00
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# SOURCE #
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2020-07-08 14:48:06 +02:00
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# https://github.com/msberends/AMR #
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2018-12-16 22:45:12 +01:00
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# #
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# LICENCE #
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2020-01-05 17:22:09 +01:00
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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2020-10-08 11:16:03 +02:00
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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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2018-12-16 22:45:12 +01:00
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# #
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2019-01-02 23:24:07 +01:00
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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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2020-01-05 17:22:09 +01:00
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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 analysis: https://msberends.github.io/AMR/ #
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2018-12-16 22:45:12 +01:00
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# ==================================================================== #
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2018-11-16 20:50:50 +01:00
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context("eucast_rules.R")
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2018-03-27 17:43:42 +02:00
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test_that("EUCAST rules work", {
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2019-10-15 14:35:23 +02:00
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skip_on_cran()
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2020-05-16 13:05:47 +02:00
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2019-04-05 18:47:39 +02:00
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# thoroughly check input table
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2019-06-01 20:54:56 +02:00
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expect_equal(colnames(eucast_rules_file),
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2019-08-06 14:39:22 +02:00
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c("if_mo_property", "like.is.one_of", "this_value",
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2019-04-05 18:47:39 +02:00
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"and_these_antibiotics", "have_these_values",
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"then_change_these_antibiotics", "to_value",
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2020-09-19 15:15:57 +02:00
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"reference.rule", "reference.rule_group",
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2020-09-24 00:30:11 +02:00
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"reference.version",
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"note"))
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MOs_mentioned <- unique(eucast_rules_file$this_value)
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MOs_mentioned <- sort(trimws(unlist(strsplit(MOs_mentioned[!is_possibly_regex(MOs_mentioned)], ",", fixed = TRUE))))
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MOs_test <- suppressWarnings(suppressMessages(mo_name(MOs_mentioned)))
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expect_length(MOs_mentioned[MOs_test != MOs_mentioned], 0)
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expect_error(suppressWarnings(eucast_rules(example_isolates, col_mo = "Non-existing")))
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2019-05-13 12:21:57 +02:00
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expect_error(eucast_rules(x = "text"))
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expect_error(eucast_rules(data.frame(a = "test")))
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expect_error(eucast_rules(data.frame(mo = "test"), rules = "invalid rules set"))
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2019-08-07 15:37:39 +02:00
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2020-04-29 14:33:44 +02:00
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expect_warning(eucast_rules(data.frame(mo = "Escherichia coli", vancomycin = "S", stringsAsFactors = TRUE)))
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expect_identical(colnames(example_isolates),
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colnames(suppressWarnings(eucast_rules(example_isolates))))
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2020-05-16 13:05:47 +02:00
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2019-02-27 17:39:39 +01:00
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a <- data.frame(mo = c("Klebsiella pneumoniae",
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"Pseudomonas aeruginosa",
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"Enterobacter aerogenes"),
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amox = "-", # Amoxicillin
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stringsAsFactors = FALSE)
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b <- data.frame(mo = c("Klebsiella pneumoniae",
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"Pseudomonas aeruginosa",
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"Enterobacter aerogenes"),
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amox = "R", # Amoxicillin
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stringsAsFactors = FALSE)
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expect_identical(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
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expect_identical(suppressWarnings(eucast_rules(a, "mo", info = TRUE)), b)
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2019-02-27 17:39:39 +01:00
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a <- data.frame(mo = c("Staphylococcus aureus",
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"Streptococcus group A"),
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COL = "-", # Colistin
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stringsAsFactors = FALSE)
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b <- data.frame(mo = c("Staphylococcus aureus",
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"Streptococcus group A"),
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COL = "R", # Colistin
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stringsAsFactors = FALSE)
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2018-11-16 20:50:50 +01:00
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expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
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2020-05-16 13:05:47 +02:00
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2018-11-01 20:23:33 +01:00
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# piperacillin must be R in Enterobacteriaceae when tica is R
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2020-09-26 16:26:01 +02:00
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library(dplyr, warn.conflicts = FALSE)
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2018-08-29 16:25:57 +02:00
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expect_equal(suppressWarnings(
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example_isolates %>%
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mutate(TIC = as.rsi("R"),
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PIP = as.rsi("S")) %>%
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2020-09-24 00:30:11 +02:00
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eucast_rules(col_mo = "mo", version_expertrules = 3.1) %>%
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2018-08-29 16:25:57 +02:00
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left_join_microorganisms() %>%
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filter(family == "Enterobacteriaceae") %>%
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pull(PIP) %>%
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unique() %>%
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as.character()),
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"R")
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2020-05-16 13:05:47 +02:00
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2020-09-26 16:26:01 +02:00
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# Azithromycin and Clarythromycin must be equal to Erythromycin
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2020-11-11 16:49:27 +01:00
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a <- suppressWarnings(as.rsi(eucast_rules(data.frame(mo = example_isolates$mo,
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ERY = example_isolates$ERY,
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AZM = as.rsi("R"),
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CLR = factor("R"),
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stringsAsFactors = FALSE),
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version_expertrules = 3.1)$CLR))
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b <- example_isolates$ERY
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2018-10-17 17:32:34 +02:00
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expect_identical(a[!is.na(b)],
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b[!is.na(b)])
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2020-05-16 13:05:47 +02:00
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2018-10-17 17:32:34 +02:00
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# amox is inferred by benzylpenicillin in Kingella kingae
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expect_equal(
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2019-01-03 23:56:19 +01:00
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suppressWarnings(
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as.list(eucast_rules(
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data.frame(mo = as.mo("Kingella kingae"),
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PEN = "S",
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AMX = "-",
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stringsAsFactors = FALSE)
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, info = FALSE))$AMX
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2019-01-03 23:56:19 +01:00
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),
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"S")
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2018-11-30 12:05:59 +01:00
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# also test norf
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2020-02-21 21:13:38 +01:00
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expect_output(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE)))
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2020-05-16 13:05:47 +02:00
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2018-11-30 12:05:59 +01:00
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# check verbose output
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2020-12-11 12:17:23 +01:00
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expect_output(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE, rules = "all", info = TRUE)))
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2020-05-16 13:05:47 +02:00
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2018-03-27 17:43:42 +02:00
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})
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