website syntax update

This commit is contained in:
dr. M.S. (Matthijs) Berends 2023-02-17 11:39:00 +01:00
parent 714a048fa9
commit e890360986
6 changed files with 24 additions and 11 deletions

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

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@ -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!)* *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*

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@ -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 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 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 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 object an [antibiogram()] object
#' @param ... when used in [print()]: arguments passed on to [knitr::kable()] (otherwise, has no use) #' @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. #' @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(), language = get_AMR_locale(),
minimum = 30, minimum = 30,
combine_SI = TRUE, combine_SI = TRUE,
sep = " + ") { sep = " + ",
info = interactive()) {
meet_criteria(x, allow_class = "data.frame", contains_column_class = "sir") 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(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) 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(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(combine_SI, allow_class = "logical", has_length = 1)
meet_criteria(sep, allow_class = "character", 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 # try to find columns based on type
if (is.null(col_mo)) { if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo", info = interactive()) col_mo <- search_type_in_df(x = x, type = "mo", info = interactive())
@ -368,11 +371,13 @@ antibiogram <- function(x,
out$numerator <- out$S out$numerator <- out$S
} }
if (any(out$total < minimum, na.rm = TRUE)) { if (any(out$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>% out <- out %pm>%
subset(total >= minimum) subset(total >= minimum)
} }
# regroup for summarising # regroup for summarising
if (isTRUE(has_syndromic_group)) { if (isTRUE(has_syndromic_group)) {
colnames(out)[1] <- "syndromic_group" colnames(out)[1] <- "syndromic_group"

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@ -41,6 +41,10 @@ template:
# the green "success" colour of this bootstrap theme should be the same as the green in our logo # the green "success" colour of this bootstrap theme should be the same as the green in our logo
success: "#128f76" success: "#128f76"
link-color: "#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" navbar-padding-y: "0.5rem"
opengraph: opengraph:
twitter: twitter:

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@ -27,7 +27,8 @@ antibiogram(
language = get_AMR_locale(), language = get_AMR_locale(),
minimum = 30, minimum = 30,
combine_SI = TRUE, combine_SI = TRUE,
sep = " + " sep = " + ",
info = interactive()
) )
\method{plot}{antibiogram}(x, ...) \method{plot}{antibiogram}(x, ...)
@ -63,6 +64,8 @@ antibiogram(
\item{sep}{a separating character for antibiotic columns in combination antibiograms} \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{...}{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} \item{object}{an \code{\link[=antibiogram]{antibiogram()}} object}

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