website syntax update

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.2.9132
+Version: 1.8.2.9133
 Date: 2023-02-17
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.2.9132
+# AMR 1.8.2.9133
 
 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
 

R/antibiogram.R

@@ -43,6 +43,7 @@
 #' @param minimum the minimum allowed number of available (tested) isolates. Any isolate count lower than `minimum` will return `NA` with a warning. The default number of `30` isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see *Source*.
 #' @param combine_SI a [logical] to indicate whether all susceptibility should be determined by results of either S or I, instead of only S (defaults to `TRUE`)
 #' @param sep a separating character for antibiotic columns in combination antibiograms
+#' @param info 	a [logical] to indicate info should be printed, defaults to `TRUE` only in interactive mode
 #' @param object an [antibiogram()] object
 #' @param ... when used in [print()]: arguments passed on to [knitr::kable()] (otherwise, has no use)
 #' @details This function returns a table with values between 0 and 100 for *susceptibility*, not resistance.
@@ -253,7 +254,8 @@ antibiogram <- function(x,
                         language = get_AMR_locale(),
                         minimum = 30,
                         combine_SI = TRUE,
-                        sep = " + ") {
+                        sep = " + ",
+                        info = interactive()) {
   meet_criteria(x, allow_class = "data.frame", contains_column_class = "sir")
   meet_criteria(mo_transform, allow_class = "character", has_length = 1, is_in = c("name", "shortname", "gramstain", colnames(AMR::microorganisms)), allow_NULL = TRUE)
   meet_criteria(ab_transform, allow_class = "character", has_length = 1, is_in = colnames(AMR::antibiotics), allow_NULL = TRUE)
@@ -266,7 +268,8 @@ antibiogram <- function(x,
   meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_positive_or_zero = TRUE, is_finite = TRUE)
   meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
   meet_criteria(sep, allow_class = "character", has_length = 1)
-
+  meet_criteria(info, allow_class = "logical", has_length = 1)
+  
   # try to find columns based on type
   if (is.null(col_mo)) {
     col_mo <- search_type_in_df(x = x, type = "mo", info = interactive())
@@ -368,11 +371,13 @@ antibiogram <- function(x,
     out$numerator <- out$S
   }
   if (any(out$total < minimum, na.rm = TRUE)) {
-    message_("NOTE: ", sum(out$total < minimum, na.rm = TRUE), " combinations had less than `minimum = ", minimum, "` results and were ignored", add_fn = font_red)
+    if (isTRUE(info)) {
+      message_("NOTE: ", sum(out$total < minimum, na.rm = TRUE), " combinations had less than `minimum = ", minimum, "` results and were ignored", add_fn = font_red)
+    }
     out <- out %pm>%
       subset(total >= minimum)
   }
-  
+
   # regroup for summarising
   if (isTRUE(has_syndromic_group)) {
     colnames(out)[1] <- "syndromic_group"

_pkgdown.yml

@@ -41,6 +41,10 @@ template:
     # the green "success" colour of this bootstrap theme should be the same as the green in our logo
     success: "#128f76"
     link-color: "#128f76"
+    light: "#128f76a6" # this is success with 60% alpha
+    # the template "info" is blue - this should be a green fitting our theme
+    info: "#60a799"
+    # make top bar a bit wider
     navbar-padding-y: "0.5rem"
   opengraph:
     twitter:

man/antibiogram.Rd

@@ -27,7 +27,8 @@ antibiogram(
   language = get_AMR_locale(),
   minimum = 30,
   combine_SI = TRUE,
-  sep = " + "
+  sep = " + ",
+  info = interactive()
 )
 
 \method{plot}{antibiogram}(x, ...)
@@ -63,6 +64,8 @@ antibiogram(
 
 \item{sep}{a separating character for antibiotic columns in combination antibiograms}
 
+\item{info}{a \link{logical} to indicate info should be printed, defaults to \code{TRUE} only in interactive mode}
+
 \item{...}{when used in \code{\link[=print]{print()}}: arguments passed on to \code{\link[knitr:kable]{knitr::kable()}} (otherwise, has no use)}
 
 \item{object}{an \code{\link[=antibiogram]{antibiogram()}} object}

pkgdown/extra.css

@@ -51,7 +51,7 @@
 
 /* marked words for after using the search box */
 mark, .mark {
-  background: rgba(17, 143, 118, 0.25) !important;
+  background: var(--bs-light) !important;
 }
 
 /* smaller tables */
@@ -82,17 +82,18 @@ pre .fu, .fu {
 }
 pre .st, .st {
   /* strings, regular text */
-  color: #60a799 !important;
+  color: var(--bs-info) !important;
 }
 pre .co, .co {
   /* comments */
-  color: #999999 !important;
+  color: var(--bs-success) !important;
   font-style: italic !important;
 }
 pre code .r-out,
 pre code .r-msg {
   /* output of functions */
-  color: #555555 !important;
+  color: var(--bs-gray-600) !important;
+  font-style: normal !important;
 }
 code a[href],
 a[href] code,