Merge pull request #115 from ramses-antibiotics/bugfix/AMR_fn_name

fix AMR deprecated as.rsi()
ramses-antibiotics · Feb 11, 2024 · d31a960 · d31a960
2 parents 62f9657 + d13a573
commit d31a960
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: Ramses
 Type: Package
 Title: R Package for Antimicrobial Stewardship & Surveillance 
-Version: 0.7.1
+Version: 0.7.2
 Authors@R: c(
     person(given = "Peter",
            family = "Dutey-Magni",
@@ -26,7 +26,7 @@ Encoding: UTF-8
 LazyData: true
 Depends: 
     R (>= 4.0.0),
-    AMR (>= 1.8.0)
+    AMR (>= 2.0.0)
 Imports: 
     DBI,
     rlang,
@@ -64,7 +64,7 @@ Suggests:
 Remotes: 
     ramses-antibiotics/snomedizer
 RdMacros: Rdpack    
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr,rmarkdown
 Collate: 
     'Ramses-deprecated.R'

diff --git a/NEWS.md b/NEWS.md
@@ -1,8 +1,20 @@
 
+# Ramses 0.7.2
+
+*11 February 2024* 
+
+
+## Changed
+
+- Now requires minimum `AMR` v2.0.0.
+- Updated function calls and documentation following deprecation of `AMR::as.rsi()`.
+
+
 # Ramses 0.7.1
 
 *19 November 2023* 
 
+
 ## Changed
 
 - Now requires minimum `dbplyr` v2.4.0.

diff --git a/R/validate_data.R b/R/validate_data.R
@@ -1201,7 +1201,7 @@ validate_administrations <- function(data) {
 #'   (can be the same as \code{drug_name})}
 #'   \item{\code{rsi_code}}{\code{"R"} (resistant), \code{"S"} (susceptible), 
 #'    or \code{"I"} (intermediate exposure), as determined by the laboratory or by
-#'   \code{\link[AMR]{as.rsi}()} on the basis of minimum inhibitory concentrations
+#'   \code{\link[AMR]{as.sir}()} on the basis of minimum inhibitory concentrations
 #'   or disk diffusion diameters}
 #' }
 #' 

diff --git a/man/validate_microbiology.Rd b/man/validate_microbiology.Rd
diff --git a/vignettes/load-data.Rmd b/vignettes/load-data.Rmd
@@ -580,7 +580,7 @@ be found in `Ramses::reference_specimen_type`.
 Susceptibility testing results in the example dataset are already
 interpreted as Resistant/Increased exposure/Susceptible (RSI). Where
 needed, minimum inhibitory concentrations and disk diffusion diameters
-can be interpreted as RSI using the `as.rsi()` function provided by the
+can be interpreted as RSI using the `as.sir()` function provided by the
 AMR package.
 
 If possible, use the most specific concept available (eg