cleanup

DESCRIPTION

@@ -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

R/mdro.R

@@ -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 ---------------------------------------------------

inst/tinytest/test-ab_property.R

@@ -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(

inst/tinytest/test-av_property.R

@@ -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)
 

inst/tinytest/test-mdro.R

@@ -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))