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AMR
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cleanup

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dr. M.S. (Matthijs) Berends 2022-11-13 07:31:07 +01:00
parent c7bfc47502
commit b142fa12dd
6 changed files with 3 additions and 1321 deletions
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2
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.8.2.9049
Date: 2022-11-12
Date: 2022-11-13
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by

1312
NEWS.md
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5
R/mdro.R
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@ -248,11 +248,6 @@ mdro <- function(x = NULL,
pct_required_classes <- pct_required_classes / 100
}
if (!is.null(list(...)$country)) {
warning_("in `mdro()`: using `country` is deprecated, use `guideline` instead. See ?mdro")
guideline <- list(...)$country
}
guideline.bak <- guideline
if (is.list(guideline)) {
# Custom MDRO guideline ---------------------------------------------------

2
inst/tinytest/test-ab_property.R
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@ -45,10 +45,8 @@ expect_identical(ab_name(21319, language = NULL), "Flucloxacillin")
expect_identical(ab_name("J01CF05", language = NULL), "Flucloxacillin")
expect_identical(ab_ddd("AMX", "oral"), 1.5)
expect_warning(ab_ddd("AMX", "oral", units = TRUE)) # old behaviour
expect_identical(ab_ddd_units("AMX", "iv"), "g")
expect_identical(ab_ddd("AMX", "iv"), 3)
expect_identical(ab_ddd_units("AMX", "iv"), "g")
expect_identical(ab_name(x = c("AMC", "PLB"), language = NULL), c("Amoxicillin/clavulanic acid", "Polymyxin B"))
expect_identical(

1
inst/tinytest/test-av_property.R
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@ -40,7 +40,6 @@ expect_identical(av_name(135398513, language = NULL), "Aciclovir")
expect_identical(av_name("J05AB01", language = NULL), "Aciclovir")
expect_identical(av_ddd("ACI", "oral"), 4)
expect_warning(av_ddd("ACI", "oral", units = TRUE)) # old behaviour
expect_identical(av_ddd_units("ACI", "iv"), "g")
expect_identical(av_ddd("ACI", "iv"), 4)

2
inst/tinytest/test-mdro.R
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@ -27,8 +27,6 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
expect_error(suppressWarnings(mdro(example_isolates, country = "invalid", col_mo = "mo", info = TRUE)))
expect_error(suppressWarnings(mdro(example_isolates, country = "fr", info = TRUE)))
expect_error(mdro(example_isolates, guideline = c("BRMO", "MRGN"), info = TRUE))
expect_error(mdro(example_isolates, col_mo = "invalid", info = TRUE))