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(v0.7.0.9013) mo_synonym fix

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dr. M.S. (Matthijs) Berends
2019-06-22 14:49:12 +02:00
parent 409397a337
commit c9156c004a
75 changed files with 465 additions and 507 deletions
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45
R/mo.R
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@ -148,9 +148,10 @@
#' as.mo("Staphylococcus aureus")
#' as.mo("Staphylococcus aureus (MRSA)")
#' as.mo("Sthafilokkockus aaureuz") # handles incorrect spelling
#' as.mo("MRSA") # Methicillin Resistant S. aureus
#' as.mo("VISA") # Vancomycin Intermediate S. aureus
#' as.mo("VRSA") # Vancomycin Resistant S. aureus
#' as.mo("MRSA") # Methicillin Resistant S. aureus
#' as.mo("VISA") # Vancomycin Intermediate S. aureus
#' as.mo("VRSA") # Vancomycin Resistant S. aureus
#' as.mo(22242419) # Catalogue of Life ID
#'
#' # Dyslexia is no problem - these all work:
#' as.mo("Ureaplasma urealyticum")
@ -232,11 +233,11 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
& isFALSE(Lancefield)) {
y <- x
# } else if (!any(is.na(mo_hist))
# & isFALSE(Becker)
# & isFALSE(Lancefield)) {
# # check previously found results
# y <- mo_hist
# } else if (!any(is.na(mo_hist))
# & isFALSE(Becker)
# & isFALSE(Lancefield)) {
# # check previously found results
# y <- mo_hist
} else if (all(tolower(x) %in% microorganismsDT$fullname_lower)
& isFALSE(Becker)
@ -564,6 +565,17 @@ exec_as.mo <- function(x,
next
}
found <- microorganismsDT[col_id == x_backup[i], ..property][[1]]
# is a valid Catalogue of Life ID
if (NROW(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)
}
next
}
# WHONET: xxx = no growth
if (tolower(as.character(paste0(x_backup_without_spp[i], ""))) %in% c("", "xxx", "na", "nan")) {
x[i] <- NA_character_
@ -642,6 +654,18 @@ exec_as.mo <- function(x,
}
next
}
# support for:
# - AIEC (Adherent-Invasive E. coli)
# - ATEC (Atypical Entero-pathogenic E. coli)
# - DAEC (Diffusely Adhering E. coli)
# - EAEC (Entero-Aggresive E. coli)
# - EHEC (Entero-Haemorrhagic E. coli)
# - EIEC (Entero-Invasive E. coli)
# - EPEC (Entero-Pathogenic E. coli)
# - ETEC (Entero-Toxigenic E. coli)
# - NMEC (Neonatal Meningitis‐causing E. coli)
# - STEC (Shiga-toxin producing E. coli)
# - UPEC (Uropathogenic E. coli)
if (toupper(x_backup_without_spp[i]) %in% c("AIEC", "ATEC", "DAEC", "EAEC", "EHEC", "EIEC", "EPEC", "ETEC", "NMEC", "STEC", "UPEC")
| x_backup_without_spp[i] %like% "O?(26|103|104|104|111|121|145|157)") {
x[i] <- microorganismsDT[mo == 'B_ESCHR_COL', ..property][[1]][1L]
@ -770,7 +794,7 @@ exec_as.mo <- function(x,
}
}
# FIRST TRY FULLNAMES AND CODES
# FIRST TRY FULLNAMES AND CODES ----
# if only genus is available, return only genus
if (all(!c(x[i], x_trimmed[i]) %like% " ")) {
found <- microorganismsDT[fullname_lower %in% tolower(c(x_species[i], x_trimmed_species[i])), ..property][[1]]
@ -1465,6 +1489,9 @@ unregex <- function(x) {
}
get_mo_code <- function(x, property) {
# don't use right now
return(NULL)
if (property == "mo") {
unique(x)
} else {