fixes

.github/workflows/codecovr.yaml

@@ -61,6 +61,6 @@ jobs:
           R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
           R_RUN_TINYTEST: true
         run: |
-          x <- covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
+          x <- covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/zz_deprecated.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
           print(x)
         shell: Rscript {0}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
 Version: 1.8.2.9096
-Date: 2023-01-20
+Date: 2023-01-21
 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

NAMESPACE

@@ -27,6 +27,7 @@ S3method("[<-",av)
 S3method("[<-",disk)
 S3method("[<-",mic)
 S3method("[<-",mo)
+S3method("[<-",rsi)
 S3method("[<-",sir)
 S3method("[[",ab)
 S3method("[[",av)
@@ -38,6 +39,7 @@ S3method("[[<-",av)
 S3method("[[<-",disk)
 S3method("[[<-",mic)
 S3method("[[<-",mo)
+S3method("[[<-",rsi)
 S3method("[[<-",sir)
 S3method("^",mic)
 S3method("|",ab_selector)
@@ -73,6 +75,7 @@ S3method(atan,mic)
 S3method(atanh,mic)
 S3method(barplot,disk)
 S3method(barplot,mic)
+S3method(barplot,rsi)
 S3method(barplot,sir)
 S3method(c,ab)
 S3method(c,ab_selector)
@@ -82,6 +85,7 @@ S3method(c,custom_mdro_guideline)
 S3method(c,disk)
 S3method(c,mic)
 S3method(c,mo)
+S3method(c,rsi)
 S3method(c,sir)
 S3method(ceiling,mic)
 S3method(close,progress_bar)
@@ -94,6 +98,7 @@ S3method(cumprod,mic)
 S3method(cumsum,mic)
 S3method(digamma,mic)
 S3method(droplevels,mic)
+S3method(droplevels,rsi)
 S3method(droplevels,sir)
 S3method(exp,mic)
 S3method(expm1,mic)
@@ -121,6 +126,7 @@ S3method(min,mic)
 S3method(plot,disk)
 S3method(plot,mic)
 S3method(plot,resistance_predict)
+S3method(plot,rsi)
 S3method(plot,sir)
 S3method(print,ab)
 S3method(print,av)
@@ -143,6 +149,7 @@ S3method(rep,av)
 S3method(rep,disk)
 S3method(rep,mic)
 S3method(rep,mo)
+S3method(rep,rsi)
 S3method(rep,sir)
 S3method(round,mic)
 S3method(sign,mic)
@@ -159,6 +166,7 @@ S3method(sum,mic)
 S3method(summary,mic)
 S3method(summary,mo)
 S3method(summary,pca)
+S3method(summary,rsi)
 S3method(summary,sir)
 S3method(tan,mic)
 S3method(tanh,mic)
@@ -170,6 +178,7 @@ S3method(unique,av)
 S3method(unique,disk)
 S3method(unique,mic)
 S3method(unique,mo)
+S3method(unique,rsi)
 S3method(unique,sir)
 export("%like%")
 export("%like_case%")

R/zz_deprecated.R

@@ -162,6 +162,34 @@ print.rsi <- function(x, ...) {
   print(as.character(x), quote = FALSE)
 }
 
+#' @noRd
+#' @export
+`[<-.rsi` <- `[<-.sir`
+#' @noRd
+#' @export
+`[[<-.rsi` <- `[[<-.sir`
+#' @noRd
+#' @export
+barplot.rsi <- barplot.sir
+#' @noRd
+#' @export
+c.rsi <- c.sir
+#' @noRd
+#' @export
+droplevels.rsi <- droplevels.sir
+#' @noRd
+#' @export
+plot.rsi <- plot.sir
+#' @noRd
+#' @export
+rep.rsi <- rep.sir
+#' @noRd
+#' @export
+summary.rsi <- summary.sir
+#' @noRd
+#' @export
+unique.rsi <- unique.sir
+
 deprecation_warning <- function(old = NULL, new = NULL, extra_msg = NULL) {
   if (is.null(old)) {
     warning_(extra_msg)