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(v0.7.1.9077) mo codes fix

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dr. M.S. (Matthijs) Berends
2019-09-20 14:18:29 +02:00
parent 3596adb295
commit 40e6b3e8f6
26 changed files with 256 additions and 256 deletions
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3
R/data.R
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@ -98,12 +98,13 @@ catalogue_of_life <- list(
#'
#' A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by \code{\link{as.mo}}.
#' @inheritSection catalogue_of_life Catalogue of Life
#' @format A \code{\link{data.frame}} with 24,246 observations and 4 variables:
#' @format A \code{\link{data.frame}} with 24,246 observations and 5 variables:
#' \describe{
#' \item{\code{col_id}}{Catalogue of Life ID that was originally given}
#' \item{\code{col_id_new}}{New Catalogue of Life ID that responds to an entry in the \code{\link{microorganisms}} data set}
#' \item{\code{fullname}}{Old full taxonomic name of the microorganism}
#' \item{\code{ref}}{Author(s) and year of concerning scientific publication}
#' \item{\code{prevalence}}{Prevalence of the microorganism, see \code{?as.mo}}
#' }
#' @source Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
#' @inheritSection AMR Read more on our website!

58
R/mo.R
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@ -71,9 +71,10 @@
#' \itemize{
#' \item{Valid MO codes and full names: it first searches in already valid MO code and known genus/species combinations}
#' \item{Human pathogenic prevalence: it first searches in more prevalent microorganisms, then less prevalent ones (see \emph{Microbial prevalence of pathogens in humans} below)}
#' \item{Taxonomic kingdom: it first searches in Bacteria/Chromista, then Fungi, then Protozoa}
#' \item{Taxonomic kingdom: it first searches in Bacteria, then Fungi, then Protozoa, then Archaea, then others}
#' \item{Breakdown of input values: from here it starts to breakdown input values to find possible matches}
#' }
#'
#'
#' A couple of effects because of these rules:
#' \itemize{
@ -258,7 +259,6 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
y <- mo_validate(x = x, property = "mo",
Becker = Becker, Lancefield = Lancefield,
allow_uncertain = uncertainty_level, reference_df = reference_df,
#force_mo_history = isTRUE(list(...)$force_mo_history),
...)
}
@ -285,7 +285,7 @@ is.mo <- function(x) {
# param force_mo_history logical - whether found result must be saved with set_mo_history (default FALSE on non-interactive sessions)
# param disable_mo_history logical - whether set_mo_history and get_mo_history should be ignored
# param debug logical - show different lookup texts while searching
# param uncertain_check_prevalence integer - the prevalence to check for when running for uncertain results, follows microorganisms$prevalence
# param reference_data_to_use data.frame - the data set to check for
exec_as.mo <- function(x,
Becker = FALSE,
Lancefield = FALSE,
@ -936,6 +936,7 @@ exec_as.mo <- function(x,
# NOW RUN THROUGH DIFFERENT PREVALENCE LEVELS
check_per_prevalence <- function(data_to_check,
data.old_to_check,
a.x_backup,
b.x_trimmed,
c.x_trimmed_without_group,
@ -1065,33 +1066,31 @@ exec_as.mo <- function(x,
}
# MISCELLANEOUS ----
# look for old taxonomic names ----
# wait until prevalence == 2 to run the old taxonomic results on both prevalence == 1 and prevalence == 2
if (nrow(data_to_check) == nrow(microorganismsDT[prevalence == 2])) {
found <- microorganisms.oldDT[fullname_lower == tolower(a.x_backup)
| fullname_lower %like_case% d.x_withspaces_start_end,]
if (NROW(found) > 0) {
col_id_new <- found[1, col_id_new]
# when property is "ref" (which is the case in mo_ref, mo_authors and mo_year), return the old value, so:
# mo_ref("Chlamydia psittaci") = "Page, 1968" (with warning)
# mo_ref("Chlamydophila psittaci") = "Everett et al., 1999"
if (property == "ref") {
x[i] <- found[1, ref]
} else {
x[i] <- microorganismsDT[col_id == found[1, col_id_new], ..property][[1]]
}
options(mo_renamed_last_run = found[1, fullname])
was_renamed(name_old = found[1, fullname],
name_new = microorganismsDT[col_id == found[1, col_id_new], fullname],
ref_old = found[1, ref],
ref_new = microorganismsDT[col_id == found[1, col_id_new], ref],
mo = microorganismsDT[col_id == found[1, col_id_new], mo])
if (initial_search == TRUE) {
set_mo_history(a.x_backup, get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
return(x[i])
found <- data.old_to_check[fullname_lower == tolower(a.x_backup)
| fullname_lower %like_case% d.x_withspaces_start_end,]
if (NROW(found) > 0) {
col_id_new <- found[1, col_id_new]
# when property is "ref" (which is the case in mo_ref, mo_authors and mo_year), return the old value, so:
# mo_ref("Chlamydia psittaci") = "Page, 1968" (with warning)
# mo_ref("Chlamydophila psittaci") = "Everett et al., 1999"
if (property == "ref") {
x[i] <- found[1, ref]
} else {
x[i] <- microorganismsDT[col_id == found[1, col_id_new], ..property][[1]]
}
options(mo_renamed_last_run = found[1, fullname])
was_renamed(name_old = found[1, fullname],
name_new = microorganismsDT[col_id == found[1, col_id_new], fullname],
ref_old = found[1, ref],
ref_new = microorganismsDT[col_id == found[1, col_id_new], ref],
mo = microorganismsDT[col_id == found[1, col_id_new], mo])
if (initial_search == TRUE) {
set_mo_history(a.x_backup, get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
return(x[i])
}
# check for uncertain results ----
@ -1119,7 +1118,7 @@ exec_as.mo <- function(x,
if (isTRUE(debug)) {
message("Running '", d.x_withspaces_start_end, "' and '", e.x_withspaces_start_only, "'")
}
found <- microorganisms.oldDT[fullname_lower %like_case% d.x_withspaces_start_end
found <- data.old_to_check[fullname_lower %like_case% d.x_withspaces_start_end
| fullname_lower %like_case% e.x_withspaces_start_only]
if (NROW(found) > 0 & nchar(g.x_backup_without_spp) >= 6) {
if (property == "ref") {
@ -1521,6 +1520,7 @@ exec_as.mo <- function(x,
# FIRST TRY VERY PREVALENT IN HUMAN INFECTIONS ----
x[i] <- check_per_prevalence(data_to_check = reference_data_to_use[prevalence == 1],
data.old_to_check = microorganisms.oldDT[prevalence == 1],
a.x_backup = x_backup[i],
b.x_trimmed = x_trimmed[i],
c.x_trimmed_without_group = x_trimmed_without_group[i],
@ -1539,6 +1539,7 @@ exec_as.mo <- function(x,
# THEN TRY PREVALENT IN HUMAN INFECTIONS ----
x[i] <- check_per_prevalence(data_to_check = reference_data_to_use[prevalence == 2],
data.old_to_check = microorganisms.oldDT[prevalence == 2],
a.x_backup = x_backup[i],
b.x_trimmed = x_trimmed[i],
c.x_trimmed_without_group = x_trimmed_without_group[i],
@ -1557,6 +1558,7 @@ exec_as.mo <- function(x,
# THEN UNPREVALENT IN HUMAN INFECTIONS ----
x[i] <- check_per_prevalence(data_to_check = reference_data_to_use[prevalence == 3],
data.old_to_check = microorganisms.oldDT[prevalence == 3],
a.x_backup = x_backup[i],
b.x_trimmed = x_trimmed[i],
c.x_trimmed_without_group = x_trimmed_without_group[i],

2
R/mo_history.R
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@ -55,7 +55,7 @@ set_mo_history <- function(x, mo, uncertainty_level, force = FALSE, disable = FA
# if (tryCatch(nrow(getOption("mo_remembered_results")), error = function(e) 1001) > 1000) {
# return(base::invisible())
# }
if (is.null(mo_hist)) {
if (is.null(mo_hist) & interactive()) {
message(blue(paste0("NOTE: results are saved to ", mo_history_file(), ".")))
}
tryCatch(write.csv(rbind(mo_hist,

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R/sysdata.rda
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11
R/zzz.R
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@ -28,7 +28,7 @@
microorganisms.oldDT <- as.data.table(AMR::microorganisms.old)
# for fullname_lower: keep only dots, letters, numbers, slashes, spaces and dashes
microorganisms.oldDT$fullname_lower <- gsub("[^.a-z0-9/ \\-]+", "", tolower(microorganisms.oldDT$fullname))
setkey(microorganisms.oldDT, col_id, fullname)
setkey(microorganisms.oldDT, prevalence, fullname)
assign(x = "microorganismsDT",
value = make_DT(),
@ -81,12 +81,17 @@
#' @importFrom data.table as.data.table setkey
make_DT <- function() {
microorganismsDT <- as.data.table(AMR::microorganisms)
microorganismsDT <- as.data.table(AMR::microorganisms %>%
mutate(kingdom_index = case_when(kingdom == "Bacteria" ~ 1,
kingdom == "Fungi" ~ 2,
kingdom == "Protozoa" ~ 3,
kingdom == "Archaea" ~ 4,
TRUE ~ 6)))
# for fullname_lower: keep only dots, letters, numbers, slashes, spaces and dashes
microorganismsDT$fullname_lower <- gsub("[^.a-z0-9/ \\-]+", "", tolower(microorganismsDT$fullname))
setkey(microorganismsDT,
prevalence,
kingdom,
kingdom_index,
fullname)
microorganismsDT
}