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/av.R

@@ -52,7 +52,7 @@
 #' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
 #'
 #' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
-#' @aliases ab
+#' @aliases av
 #' @return A [character] [vector] with additional class [`ab`]
 #' @seealso
 #' * [antivirals] for the [data.frame] that is being used to determine ATCs

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))
 

man/as.av.Rd

@@ -2,7 +2,7 @@
 % Please edit documentation in R/av.R
 \name{as.av}
 \alias{as.av}
-\alias{ab}
+\alias{av}
 \alias{is.av}
 \title{Transform Input to an Antiviral Agent ID}
 \usage{

vignettes/datasets.Rmd

@@ -156,7 +156,7 @@ microorganisms %>%
 ```
 
 
-## `antibiotics`: Antibiotic Agents
+## `antibiotics`: Antibiotic (+Antifungal) Drugs
 
 `r structure_txt(antibiotics)`
 
@@ -173,6 +173,7 @@ This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET,
 * [ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology](https://www.whocc.no/atc_ddd_index/) (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)
 * [PubChem by the US National Library of Medicine](https://pubchem.ncbi.nlm.nih.gov)
 * [WHONET software 2019](https://whonet.org)
+* [LOINC (Logical Observation Identifiers Names and Codes)](https://loinc.org)
 
 ### Example content
 
@@ -183,7 +184,7 @@ antibiotics %>%
 ```
 
 
-## `antivirals`: Antiviral Agents
+## `antivirals`: Antiviral Drugs
 
 `r structure_txt(antivirals)`
 
@@ -191,7 +192,7 @@ This data set is in R available as `antivirals`, after you load the `AMR` packag
 
 `r download_txt("antivirals")`
 
-The tab-separated text file and Microsoft Excel workbook, and SAS, SPSS and Stata files all contain the trade names as comma separated values.
+The tab-separated text file and Microsoft Excel workbook, and SAS, SPSS and Stata files all contain the trade names and LOINC codes as comma separated values.
 
 ### Source
 
@@ -199,6 +200,7 @@ This data set contains all ATC codes gathered from WHO and all compound IDs from
 
 * [ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology](https://www.whocc.no/atc_ddd_index/) (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)
 * [PubChem by the US National Library of Medicine](https://pubchem.ncbi.nlm.nih.gov)
+* [LOINC (Logical Observation Identifiers Names and Codes)](https://loinc.org)
 
 ### Example content