(v3.0.1.9022) add ceftibuten/avibactam (CTA), kasugamycin (KAS), ostreogrycin (OST), thiostrepton (THS), xeruborbactam (XER), zorbamycin (ZOR)

R/amr_selectors.R

@@ -417,6 +417,14 @@ penicillins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
   amr_select_exec("penicillins", only_sir_columns = only_sir_columns, return_all = return_all)
 }
 
+#' @rdname antimicrobial_selectors
+#' @export
+peptides <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
+  meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
+  meet_criteria(return_all, allow_class = "logical", has_length = 1)
+  amr_select_exec("peptides", only_sir_columns = only_sir_columns, return_all = return_all)
+}
+
 #' @rdname antimicrobial_selectors
 #' @export
 phenicols <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {

R/mic.R

@@ -126,7 +126,7 @@ COMMON_MIC_VALUES <- c(
 #' # this can also coerce combined MIC/SIR values:
 #' as.mic("<=0.002; S")
 #'
-#' # mathematical processing treats MICs as numeric values
+#' # mathematical processing treats MICs as, and returns, numeric values
 #' fivenum(mic_data)
 #' quantile(mic_data)
 #' all(mic_data < 512)
@@ -134,6 +134,10 @@ COMMON_MIC_VALUES <- c(
 #' # rescale MICs using rescale_mic()
 #' rescale_mic(mic_data, mic_range = c(4, 16))
 #'
+#' # round up to nearest log2 level, e.g. for CLSI breakpoint interpretation:
+#' c(1:8)
+#' as.mic(c(1:8), round_to_next_log2 = TRUE)
+#'
 #' # interpret MIC values
 #' as.sir(
 #'   x = as.mic(2),

R/zzz.R

@@ -118,18 +118,12 @@ AMR_env$cross_icon <- if (isTRUE(base::l10n_info()$`UTF-8`)) "\u00d7" else "x"
   if (interactive() && is.null(getOption("AMR_guideline"))) {
     packageStartupMessage(
       word_wrap(
-        "Welcome to AMR v", format(utils::packageVersion("AMR")), ". ",
-        "You have not set the 'AMR_guideline' option to either \"CLSI\" or \"EUCAST\". ",
-        "You can set it using either:\n",
-        "  options(AMR_guideline = \"CLSI\")\n",
-        "  options(AMR_guideline = \"EUCAST\")\n",
-        "See `?AMR-options`. While unset, the AMR package uses the current default guideline: ", AMR::clinical_breakpoints$guideline[1], ".",
+        "Assuming ", AMR::clinical_breakpoints$guideline[1], " as the default AMR guideline, see `?AMR-options` to change this.",
         add_fn = NULL
       )
     )
   }
 
-
   # if custom ab option is available, load it
   if (!is.null(getOption("AMR_custom_ab")) && file.exists(getOption("AMR_custom_ab", default = ""))) {
     if (getOption("AMR_custom_ab") %unlike% "[.]rds$") {