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(v1.4.0.9043) documentation update

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dr. M.S. (Matthijs) Berends
2020-12-22 00:51:17 +01:00
parent ee70883246
commit 128ebcfd62
107 changed files with 518 additions and 475 deletions
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12
R/mo.R
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@ -38,7 +38,7 @@
#' @param reference_df a [data.frame] to be used for extra reference when translating `x` to a valid [`mo`]. See [set_mo_source()] and [get_mo_source()] to automate the usage of your own codes (e.g. used in your analysis or organisation).
#' @param ignore_pattern a regular expression (case-insensitive) of which all matches in `x` must return `NA`. This can be convenient to exclude known non-relevant input and can also be set with the option `AMR_ignore_pattern`, e.g. `options(AMR_ignore_pattern = "(not reported|contaminated flora)")`.
#' @param language language to translate text like "no growth", which defaults to the system language (see [get_locale()])
#' @param ... other parameters passed on to functions
#' @param ... other arguments passed on to functions
#' @rdname as.mo
#' @aliases mo
#' @keywords mo Becker becker Lancefield lancefield guess
@ -200,7 +200,7 @@ as.mo <- function(x,
uncertainty_level <- translate_allow_uncertain(allow_uncertain)
if (!is.null(reference_df)
&& mo_source_isvalid(reference_df)
&& check_validity_mo_source(reference_df)
&& isFALSE(Becker)
&& isFALSE(Lancefield)
&& all(x %in% unlist(reference_df), na.rm = TRUE)) {
@ -388,7 +388,7 @@ exec_as.mo <- function(x,
# defined df to check for
if (!is.null(reference_df)) {
mo_source_isvalid(reference_df)
check_validity_mo_source(reference_df)
reference_df <- repair_reference_df(reference_df)
}
@ -1408,10 +1408,10 @@ exec_as.mo <- function(x,
msg <- paste0(msg, ": ", paste('"', unique(failures), '"', sep = "", collapse = ", "))
}
msg <- paste0(msg,
".\nUse mo_failures() to review ", plural[2], ". Edit the `allow_uncertain` parameter if needed (see ?as.mo).\n",
".\nUse mo_failures() to review ", plural[2], ". Edit the `allow_uncertain` argument if needed (see ?as.mo).\n",
"You can also use your own reference data, e.g.:\n",
' as.mo("mycode", reference_df = data.frame(own = "mycode", mo = "B_ESCHR_COLI"))\n',
' mo_name("mycode", reference_df = data.frame(own = "mycode", mo = "B_ESCHR_COLI"))\n')
' as.mo("mycode", reference_df = data.frame(own = "mycode", mo = "', MO_lookup$mo[match("Escherichia coli", MO_lookup$fullname)], '"))\n',
' mo_name("mycode", reference_df = data.frame(own = "mycode", mo = "', MO_lookup$mo[match("Escherichia coli", MO_lookup$fullname)], '"))\n')
warning_(paste0("\n", msg),
add_fn = font_red,
call = FALSE,