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(v0.8.0.9002) eucast_rules() fix for S. maltophilia

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dr. M.S. (Matthijs) Berends
2019-10-23 14:48:25 +02:00
parent 666126cd5e
commit 3e5ab53209
21 changed files with 210 additions and 184 deletions
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20
R/mo.R
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@ -240,8 +240,8 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
left_join(microorganismsDT, by = "fullname_lower") %>%
pull(mo)
# save them to history
set_mo_history(x, y, 0, force = isTRUE(list(...)$force_mo_history), disable = isTRUE(list(...)$disable_mo_history))
# don't save valid fullnames to history (i.e. values that are in microorganisms$fullname)
# set_mo_history(x, y, 0, force = isTRUE(list(...)$force_mo_history), disable = isTRUE(list(...)$disable_mo_history))
} else {
# will be checked for mo class in validation and uses exec_as.mo internally if necessary
@ -482,6 +482,7 @@ exec_as.mo <- function(x,
trimmed
}
x_backup_untouched <- x
x <- strip_whitespace(x, dyslexia_mode)
x_backup <- x
@ -618,13 +619,24 @@ exec_as.mo <- function(x,
next
}
}
if (toupper(x_backup_untouched[i]) %in% microorganisms.codes$code) {
# is a WHONET code, like "HA-"
found <- microorganismsDT[mo == microorganisms.codes[which(microorganisms.codes$code == toupper(x_backup_untouched[i])), "mo"][1L], ..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
# don't save to history, as all items are already in microorganisms.codes
next
}
}
found <- reference_data_to_use[fullname_lower %in% tolower(c(x_backup[i], x_backup_without_spp[i])), ..property][[1]]
# most probable: is exact match in fullname
if (length(found) > 0) {
x[i] <- found[1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
# don't save valid fullnames to history (i.e. values that are in microorganisms$fullname)
# set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
@ -1759,7 +1771,7 @@ pillar_shaft.mo <- function(x, ...) {
out[is.na(x)] <- pillar::style_na(" NA")
out[x == "UNKNOWN"] <- pillar::style_na(" UNKNOWN")
pillar::new_pillar_shaft_simple(out, align = "left", min_width = 12)
pillar::new_pillar_shaft_simple(out, align = "left", width = max(nchar(x)))
}
#' @exportMethod summary.mo