merge bugfix into develop

.Rbuildignore

@@ -17,3 +17,4 @@
 ^\.covrignore$
 ^firebase\.json$
 ^\.github$
+^\.firebaserc$

.firebaserc

@@ -0,0 +1,5 @@
+{
+  "projects": {
+    "default": "ramses-antibiotics"
+  }
+}

.github/workflows/R-CMD-check.yaml

@@ -107,13 +107,13 @@ jobs:
 
       - name: Deploy to Firebase
         if: github.ref == 'refs/heads/master' && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' &&  matrix.config.r == 'release'
-        uses: w9jds/firebase-action@master
+        uses: FirebaseExtended/action-hosting-deploy@v0
         with:
-          args: deploy --only hosting
-        env:
-          PROJECT_ID: ramses-antibiotics
-          FIREBASE_TOKEN: ${{ secrets.FIREBASE_TOKEN }}
-      
+          repoToken: '${{ secrets.GITHUB_TOKEN }}'
+          firebaseServiceAccount: '${{ secrets.FIREBASE_SERVICE_ACCOUNT_RAMSES_ANTIBIOTICS }}'
+          projectId: ramses-antibiotics
+          channelId: live
+
       - uses: r-lib/actions/setup-tinytex@v2
         if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' &&  matrix.config.r == 'release'
 

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Ramses
 Type: Package
 Title: R Package for Antimicrobial Stewardship & Surveillance 
-Version: 0.7.0
+Version: 0.7.2
 Authors@R: c(
     person(given = "Peter",
            family = "Dutey-Magni",
@@ -26,12 +26,12 @@ Encoding: UTF-8
 LazyData: true
 Depends: 
     R (>= 4.0.0),
-    AMR (>= 1.8.0)
+    AMR (>= 2.0.0)
 Imports: 
     DBI,
     rlang,
     dplyr (>= 1.1.0),
-    dbplyr (>= 2.3.2),
+    dbplyr (>= 2.4.0),
     tidyselect (>= 1.2.0),
     magrittr,
     duckdb (>= 0.4.0),
@@ -59,11 +59,12 @@ Suggests:
     R.utils,
     comorbidity,
     RPostgres,
-    gh (>= 1.3.0)
+    gh (>= 1.3.0),
+    vctrs
 Remotes: 
     ramses-antibiotics/snomedizer
 RdMacros: Rdpack    
-RoxygenNote: 7.2.0
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr,rmarkdown
 Collate: 
     'Ramses-deprecated.R'

NEWS.md

@@ -1,4 +1,26 @@
 
+# 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.
+- Unit test maintenance required by `dbplyr` v2.4.0.
+
+
 # Ramses 0.7.0
 
 *11 April 2023* 

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}
 #' }
 #'