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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 Package: AMR
Version: 1.8.2.9049 Version: 1.8.2.9049
Date: 2022-11-12 Date: 2022-11-13
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by 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 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 guideline.bak <- guideline
if (is.list(guideline)) { if (is.list(guideline)) {
# Custom MDRO 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_name("J01CF05", language = NULL), "Flucloxacillin")
expect_identical(ab_ddd("AMX", "oral"), 1.5) 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_units("AMX", "iv"), "g")
expect_identical(ab_ddd("AMX", "iv"), 3) 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(ab_name(x = c("AMC", "PLB"), language = NULL), c("Amoxicillin/clavulanic acid", "Polymyxin B"))
expect_identical( 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_name("J05AB01", language = NULL), "Aciclovir")
expect_identical(av_ddd("ACI", "oral"), 4) 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_units("ACI", "iv"), "g")
expect_identical(av_ddd("ACI", "iv"), 4) 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/ # # 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, guideline = c("BRMO", "MRGN"), info = TRUE))
expect_error(mdro(example_isolates, col_mo = "invalid", info = TRUE)) expect_error(mdro(example_isolates, col_mo = "invalid", info = TRUE))