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new EUCAST rules algorithm

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-04-05 18:47:39 +02:00
parent 56d4b4719f
commit fbc9191b13
115 changed files with 1340 additions and 2174 deletions
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2
tests/testthat/test-abname.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("abname.R")

2
tests/testthat/test-age.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("age.R")

2
tests/testthat/test-atc.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("atc.R")

2
tests/testthat/test-atc_property.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("atc_property.R")

2
tests/testthat/test-availability.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("availability.R")

2
tests/testthat/test-count.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("count.R")

35
tests/testthat/test-data.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("data.R")
@ -27,36 +27,13 @@ test_that("data sets are valid", {
expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
# there should be no diacritics (i.e. non ASCII) characters in the datasets
library(dplyr)
# check only character variables:
test_microorganisms <- microorganisms %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE)
test_microorganisms.old <- microorganisms.old %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE)
test_antibiotics <- antibiotics %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE)
test_septic_patients <- septic_patients %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE)
# and compare them with their transformed version:
expect_identical(test_microorganisms,
test_microorganisms %>%
lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
as.data.frame(stringsAsFactors = FALSE))
expect_identical(test_microorganisms.old,
test_microorganisms.old %>%
lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
as.data.frame(stringsAsFactors = FALSE))
expect_identical(test_antibiotics,
test_antibiotics %>%
lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
as.data.frame(stringsAsFactors = FALSE))
expect_identical(test_septic_patients,
test_septic_patients %>%
lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
as.data.frame(stringsAsFactors = FALSE))
datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item"]
for (i in 1:length(datasets)) {
dataset <- get(datasets[i], envir = asNamespace("AMR"))
expect_identical(dataset_UTF8_to_ASCII(dataset), dataset)
}
})
test_that("creation of data sets is valid", {
df <- make()
expect_lt(nrow(df[which(df$prevalence == 1), ]), nrow(df[which(df$prevalence == 2), ]))

4
tests/testthat/test-deprecated.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("deprecated.R")
@ -30,8 +30,6 @@ test_that("deprecated functions work", {
expect_identical(suppressWarnings(ratio(c(772, 1611, 737), ratio = "1:2:1")), c(780, 1560, 780))
expect_identical(suppressWarnings(ratio(c(1752, 1895), ratio = c(1, 1))), c(1823.5, 1823.5))
expect_warning(guess_mo("esco"))
expect_warning(guess_atc("amox"))
expect_warning(ab_property("amox"))
expect_warning(ab_atc("amox"))
expect_warning(ab_official("amox"))

12
tests/testthat/test-eucast_rules.R
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@ -16,13 +16,22 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("eucast_rules.R")
test_that("EUCAST rules work", {
# thoroughly check input table
expect_true(file.exists(EUCAST_RULES_FILE_LOCATION))
eucast_input_file <- eucast_rules_file()
expect_equal(colnames(eucast_input_file),
c("if_mo_property", "like_is_one_of", "this_value",
"and_these_antibiotics", "have_these_values",
"then_change_these_antibiotics", "to_value",
"reference.rule", "reference.rule_group"))
expect_error(suppressWarnings(eucast_rules(septic_patients, col_mo = "Non-existing")))
expect_identical(colnames(septic_patients),
@ -40,7 +49,6 @@ test_that("EUCAST rules work", {
stringsAsFactors = FALSE)
expect_identical(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
expect_identical(suppressWarnings(eucast_rules(a, "mo", info = TRUE)), b)
expect_identical(suppressWarnings(interpretive_reading(a, "mo", info = TRUE)), b)
a <- data.frame(mo = c("Staphylococcus aureus",
"Streptococcus group A"),

2
tests/testthat/test-filter_ab_class.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("filter_ab_class.R")

2
tests/testthat/test-first_isolate.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("first_isolate.R")

2
tests/testthat/test-freq.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("freq.R")

2
tests/testthat/test-g.test.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("g.test.R")

2
tests/testthat/test-get_locale.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("get_locale.R")

2
tests/testthat/test-ggplot_rsi.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("ggplot_rsi.R")

2
tests/testthat/test-guess_ab_col.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("guess_ab_col.R")

2
tests/testthat/test-join_microorganisms.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("join_microorganisms.R")

2
tests/testthat/test-key_antibiotics.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("key_antibiotics.R")

2
tests/testthat/test-kurtosis.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("kurtosis.R")

2
tests/testthat/test-like.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("like.R")

2
tests/testthat/test-mdro.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("mdro.R")

2
tests/testthat/test-mic.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("mic.R")

2
tests/testthat/test-misc.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("misc.R")

2
tests/testthat/test-mo.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("mo.R")

2
tests/testthat/test-mo_history.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
# context("mo_history.R")

2
tests/testthat/test-mo_property.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("mo_property.R")

2
tests/testthat/test-p.symbol.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("p.symbol.R")

2
tests/testthat/test-portion.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("portion.R")

2
tests/testthat/test-read.4d.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("read.4d.R")

2
tests/testthat/test-resistance_predict.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("portion.R")

2
tests/testthat/test-rsi.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("rsi.R")

2
tests/testthat/test-skewness.R
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@ -16,7 +16,7 @@
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
context("skewness.R")