(v1.3.0.9008) also tibble printing for ab

R/aa_helper_functions.R

@@ -575,9 +575,9 @@ isFALSE <- function(x) {
 deparse1 <- function(expr, collapse = " ", width.cutoff = 500L, ...) {
   paste(deparse(expr, width.cutoff, ...), collapse = collapse)
 }
-file.size <- function (...) {
+file.size <- function(...) {
   base::file.info(...)$size
 }
-file.mtime <- function (...) {
+file.mtime <- function(...) {
   base::file.info(...)$mtime
 }

R/ab.R

@@ -467,6 +467,26 @@ is.ab <- function(x) {
   inherits(x, "ab")
 }
 
+
+#' @method pillar_shaft ab
+#' @export
+pillar_shaft.ab <- function(x, ...) {
+  # import from the pillar package, without being dependent on it!
+  style_na <- import_fn("style_na", "pillar", error_on_fail = FALSE)
+  new_pillar_shaft_simple <- import_fn("new_pillar_shaft_simple", "pillar", error_on_fail = FALSE)
+  out <- format(x)
+  out[is.na(x)] <- style_na(NA)
+  new_pillar_shaft_simple(out,
+                          align = "left", 
+                          min_width = 4)
+}
+
+#' @method type_sum ab
+#' @export
+type_sum.ab <- function(x, ...) {
+  "ab"
+}
+
 #' @method print ab
 #' @export
 #' @noRd

R/eucast_rules.R

@@ -40,17 +40,12 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
 #' **Note:** This function does not translate MIC values to RSI values. Use [as.rsi()] for that. \cr
 #' **Note:** When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.
 #'
-#' Before further processing, some non-EUCAST rules can be applied to improve the efficacy of the EUCAST rules. These non-EUCAST rules, that are then applied to all isolates, are:
-#' - Inherit amoxicillin (AMX) from ampicillin (AMP), where amoxicillin (AMX) is unavailable;
-#' - Inherit ampicillin (AMP) from amoxicillin (AMX), where ampicillin (AMP) is unavailable;
-#' - Set amoxicillin (AMX) = R where amoxicillin/clavulanic acid (AMC) = R;
-#' - Set piperacillin (PIP) = R where piperacillin/tazobactam (TZP) = R;
-#' - Set trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R;
-#' - Set amoxicillin/clavulanic acid (AMC) = S where amoxicillin (AMX) = S;
-#' - Set piperacillin/tazobactam (TZP) = S where piperacillin (PIP) = S;
-#' - Set trimethoprim/sulfamethoxazole (SXT) = S where trimethoprim (TMP) = S.
+#' Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules. These rules are:
 #' 
-#' These rules are not applied at default, since they are not approved by EUCAST. To use these rules, please use `eucast_rules(..., rules = "all")`, or set the default behaviour of the `[eucast_rules()]` function with `options(AMR.eucast_rules = "all")` (or any other valid input value(s) to the `rules` parameter).
+#' 1. A drug **with** enzyme inhibitor will be set to S if the drug **without** enzyme inhibitor is S
+#' 2. A drug **without** enzyme inhibitor will be set to R if the drug **with** enzyme inhibitor is R
+#' 
+#' These rules are not applied at default, since they are not approved by EUCAST. To use these rules, use `eucast_rules(..., rules = "all")`, or set the default behaviour of the `[eucast_rules()]` function with `options(AMR.eucast_rules = "all")` (or any other valid input value(s) to the `rules` parameter).
 #'
 #' The file containing all EUCAST rules is located here: <https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv>.
 #'

R/globals.R

@@ -19,9 +19,11 @@
 # Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
-globalVariables(c("ab",
+globalVariables(c(".rowid",
+                  "ab",
                   "ab_txt",
                   "angle",
+                  "antibiotic",
                   "antibiotics",
                   "atc_group1",
                   "atc_group2",
@@ -35,9 +37,11 @@ globalVariables(c("ab",
                   "group",
                   "hjust",
                   "input",
+                  "intrinsic_resistant",
                   "isolates",
                   "lang",
                   "lookup",
+                  "microorganism",
                   "microorganisms",
                   "microorganisms.codes",
                   "microorganisms.old",

R/zzz.R

@@ -29,6 +29,8 @@
          envir = asNamespace("AMR"))
   
   # support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
+  s3_register("pillar::pillar_shaft", "ab")
+  s3_register("tibble::type_sum", "ab")
   s3_register("pillar::pillar_shaft", "mo")
   s3_register("tibble::type_sum", "mo")
   s3_register("pillar::pillar_shaft", "rsi")
@@ -87,7 +89,7 @@ create_MO.old_lookup <- function() {
 }
 
 # copied from vctrs::s3_register
-s3_register <- function (generic, class, method = NULL) {
+s3_register <- function(generic, class, method = NULL) {
   stopifnot(is.character(generic), length(generic) == 1)
   stopifnot(is.character(class), length(class) == 1)
   pieces <- strsplit(generic, "::")[[1]]