P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-01-16 01:21:38 +01:00
Code Releases Activity

cleanup

Browse Source
This commit is contained in:
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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
DESCRIPTION
View File

@ -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
View File

File diff suppressed because it is too large Load Diff

5
R/mdro.R
View File

@ -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
View File

@ -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
View File

@ -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
View File

@ -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))