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(v0.7.1.9072) key_antibiotics() for foreign systems

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dr. M.S. (Matthijs) Berends
2019-09-12 15:08:53 +02:00
parent b5d2a08401
commit cd178ee569
28 changed files with 1640 additions and 119 deletions
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52
R/mo.R
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@ -432,13 +432,13 @@ exec_as.mo <- function(x,
}
x <- y
} else if (all(x %in% read_mo_history(uncertainty_level,
force = force_mo_history)$x)) {
# previously found code
x <- microorganismsDT[data.table(mo = get_mo_history(x,
uncertainty_level,
force = force_mo_history)),
on = "mo", ..property][[1]]
# } else if (all(x %in% read_mo_history(uncertainty_level,
# force = force_mo_history)$x)) {
# # previously found code
# x <- microorganismsDT[data.table(mo = get_mo_history(x,
# uncertainty_level,
# force = force_mo_history)),
# on = "mo", ..property][[1]]
} else if (all(tolower(x) %in% microorganismsDT$fullname_lower)) {
# we need special treatment for very prevalent full names, they are likely!
@ -561,17 +561,17 @@ exec_as.mo <- function(x,
progress$tick()$print()
if (initial_search == TRUE) {
found <- microorganismsDT[mo == get_mo_history(x_backup[i],
uncertainty_level,
force = force_mo_history),
..property][[1]]
# previously found result
if (length(found) > 0) {
x[i] <- found[1L]
next
}
}
# if (initial_search == TRUE) {
# found <- microorganismsDT[mo == get_mo_history(x_backup[i],
# uncertainty_level,
# force = force_mo_history),
# ..property][[1]]
# # previously found result
# if (length(found) > 0) {
# x[i] <- found[1L]
# next
# }
# }
found <- microorganismsDT[mo == toupper(x_backup[i]), ..property][[1]]
# is a valid MO code
@ -826,6 +826,7 @@ exec_as.mo <- function(x,
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
}
next
} else if (grepl("[sS]almonella [A-Z][a-z]+ ?.*", x_backup_without_spp[i], ignore.case = FALSE)) {
# Salmonella with capital letter species like "Salmonella Goettingen" - they're all S. enterica
x[i] <- microorganismsDT[mo == 'B_SLMNL_ENT', ..property][[1]][1L]
@ -833,11 +834,11 @@ exec_as.mo <- function(x,
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
}
uncertainties <- rbind(uncertainties,
data.frame(uncertainty_level = 1,
input = x_backup_without_spp[i],
result_mo = "B_SLMNL_ENT"))
format_uncertainty_as_df(uncertainty_level = 1,
input = x_backup_without_spp[i],
result_mo = "B_SLMNL_ENT"))
next
}
next
}
# trivial names known to the field:
@ -1850,8 +1851,11 @@ mo_renamed <- function() {
#' @export
#' @noRd
print.mo_renamed <- function(x, ...) {
items <- getOption("mo_renamed")
base::message(blue(paste("NOTE:", names(items), "was renamed", items, collapse = "\n"), collapse = "\n"))
items <- x #getOption("mo_renamed")
old <- names(x)
new <- x
cat(blue(paste("NOTE:", italic(names(items)), "was renamed", italic(items), collapse = "\n"), collapse = "\n"))
}
nr2char <- function(x) {