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(v.1.5.0.9000) implementation of EUCAST rules v11 (2021)

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dr. M.S. (Matthijs) Berends
2021-01-12 22:08:04 +01:00
parent 3b84b8be75
commit d014955ce0
93 changed files with 3631 additions and 374 deletions
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26
R/mo.R
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@ -756,7 +756,7 @@ exec_as.mo <- function(x,
x[i] <- lookup(mo == "B_STRPT_HAEM", uncertainty = -1)
next
}
# CoNS/CoPS in different languages (support for German, Dutch, Spanish, Portuguese) ----
# CoNS/CoPS in different languages (support for German, Dutch, Spanish, Portuguese)
if (x_backup_without_spp[i] %like_case% "[ck]oagulas[ea] negatie?[vf]"
| x_trimmed[i] %like_case% "[ck]oagulas[ea] negatie?[vf]"
| x_backup_without_spp[i] %like_case% "[ck]o?ns[^a-z]?$") {
@ -841,8 +841,17 @@ exec_as.mo <- function(x,
x[i] <- lookup(fullname == "Streptococcus pneumoniae", uncertainty = -1)
next
}
# }
if (x_backup[i] %in% pkg_env$mo_failed) {
# previously failed already in this session ----
# (at this point the latest reference_df has also be checked)
x[i] <- lookup(mo == "UNKNOWN")
if (initial_search == TRUE) {
failures <- c(failures, x_backup[i])
}
next
}
# NOW RUN THROUGH DIFFERENT PREVALENCE LEVELS
check_per_prevalence <- function(data_to_check,
data.old_to_check,
@ -1397,6 +1406,7 @@ exec_as.mo <- function(x,
failures <- failures[!failures %in% c(NA, NULL, NaN)]
if (length(failures) > 0 & initial_search == TRUE) {
pkg_env$mo_failures <- sort(unique(failures))
pkg_env$mo_failed <- c(pkg_env$mo_failed, pkg_env$mo_failures)
plural <- c("value", "it", "was")
if (pm_n_distinct(failures) > 1) {
plural <- c("values", "them", "were")
@ -1412,7 +1422,7 @@ exec_as.mo <- function(x,
}
msg <- paste0(msg,
".\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",
"You can also use your own reference data with set_mo_source() or directly, e.g.:\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),
@ -1430,7 +1440,7 @@ exec_as.mo <- function(x,
plural <- c("s", "them", "were")
}
msg <- paste0("Translation to ", nr2char(length(uncertainties$input)), " microorganism", plural[1],
" ", plural[3], " guessed with uncertainty. Use mo_uncertainties() to review ", plural[2], ".")
" was guessed with uncertainty. Use mo_uncertainties() to review ", plural[2], ".")
message_(msg)
}
@ -1960,12 +1970,12 @@ replace_old_mo_codes <- function(x, property) {
x[which(!is.na(matched))] <- mo_new[which(!is.na(matched))]
n_matched <- length(matched[!is.na(matched)])
if (property != "mo") {
message_(font_blue("NOTE: The input contained old microbial codes (from previous package versions). Please update your MO codes with as.mo()."))
message_(font_blue("The input contained old microbial codes (from previous package versions). Please update your MO codes with as.mo()."))
} else {
if (n_matched == 1) {
message_(font_blue("NOTE: 1 old microbial code (from previous package versions) was updated to a current used MO code."))
message_(font_blue("1 old microbial code (from previous package versions) was updated to a current used MO code."))
} else {
message_(font_blue("NOTE:", n_matched, "old microbial codes (from previous package versions) were updated to current used MO codes."))
message_(font_blue(n_matched, "old microbial codes (from previous package versions) were updated to current used MO codes."))
}
}
}