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as.mo improvements

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dr. M.S. (Matthijs) Berends
2019-02-25 15:52:32 +01:00
parent 0ec76cfa98
commit c506d2893b
13 changed files with 390 additions and 376 deletions
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53
R/mo.R
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@ -97,7 +97,7 @@
#' The artificial intelligence takes into account microbial prevalence of pathogens in humans. It uses three groups and every (sub)species is in the group it matches first. These groups are:
#' \itemize{
#' \item{1 (most prevalent): class is Gammaproteobacteria \strong{or} genus is one of: \emph{Enterococcus}, \emph{Staphylococcus}, \emph{Streptococcus}.}
#' \item{2: phylum is one of: Proteobacteria, Firmicutes, Actinobacteria, Sarcomastigophora \strong{or} genus is one of: \emph{Aspergillus}, \emph{Bacteroides}, \emph{Candida}, \emph{Capnocytophaga}, \emph{Chryseobacterium}, \emph{Cryptococcus}, \emph{Elisabethkingia}, \emph{Flavobacterium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Leptotrichia}, \emph{Mycoplasma}, \emph{Prevotella}, \emph{Rhodotorula}, \emph{Treponema}, \emph{Trichophyton}.}
#' \item{2: phylum is one of: Proteobacteria, Firmicutes, Actinobacteria, Sarcomastigophora \strong{or} genus is one of: \emph{Aspergillus}, \emph{Bacteroides}, \emph{Candida}, \emph{Capnocytophaga}, \emph{Chryseobacterium}, \emph{Cryptococcus}, \emph{Elisabethkingia}, \emph{Flavobacterium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Leptotrichia}, \emph{Mycoplasma}, \emph{Prevotella}, \emph{Rhodotorula}, \emph{Treponema}, \emph{Trichophyton}, \emph{Ureaplasma}.}
#' \item{3 (least prevalent): all others.}
#' }
#'
@ -167,10 +167,9 @@
#' }
as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE, reference_df = get_mo_source()) {
# will be checked for mo class in validation
mo <- mo_validate(x = x, property = "mo",
Becker = Becker, Lancefield = Lancefield,
allow_uncertain = allow_uncertain, reference_df = reference_df)
structure(.Data = mo, class = "mo")
mo_validate(x = x, property = "mo",
Becker = Becker, Lancefield = Lancefield,
allow_uncertain = allow_uncertain, reference_df = reference_df)
}
#' @rdname as.mo
@ -229,7 +228,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
x <- x[!is.na(x) & !is.null(x) & !identical(x, "")]
# conversion of old MO codes from v0.5.0 (ITIS) to later versions (Catalogue of Life)
if (any(x %like% "^[BFP]_[A-Z]{3,7}")) {
if (any(x %like% "^[BFP]_[A-Z]{3,7}") & !all(x %in% microorganisms$mo)) {
leftpart <- gsub("^([BFP]_[A-Z]{3,7}).*", "\\1", x)
if (any(leftpart %in% names(mo_codes_v0.5.0))) {
rightpart <- gsub("^[BFP]_[A-Z]{3,7}(.*)", "\\1", x)
@ -256,40 +255,52 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
# all empty
if (all(identical(trimws(x_input), "") | is.na(x_input))) {
if (property == "mo") {
return(structure(rep(NA_character_, length(x_input)), class = "mo"))
return(structure(rep(NA_character_, length(x_input)),
class = "mo"))
} else {
return(rep(NA_character_, length(x_input)))
}
} else if (all(x %in% reference_df[, 1])
& all(reference_df[, "mo"] %in% microorganismsDT[, "mo"][[1]])) {
& all(reference_df[, "mo"] %in% AMR::microorganisms$mo)) {
# all in reference df
colnames(reference_df)[1] <- "x"
suppressWarnings(
x <- data.frame(x = x, stringsAsFactors = FALSE) %>%
left_join(reference_df, by = "x") %>%
left_join(microorganisms, by = "mo") %>%
left_join(AMR::microorganisms, by = "mo") %>%
pull(property)
)
} else if (all(x %in% microorganismsDT[, "mo"][[1]])) {
} else if (all(x %in% AMR::microorganisms$mo)) {
# existing mo codes when not looking for property "mo", like mo_genus("B_ESCHR_COL")
x <- microorganismsDT[data.table(mo = x), on = "mo", ..property][[1]]
y <- microorganismsDT[prevalence == 1][data.table(mo = x), on = "mo", ..property][[1]]
if (any(is.na(y))) {
y[is.na(y)] <- microorganismsDT[prevalence == 2][data.table(mo = x[is.na(y)]), on = "mo", ..property][[1]]
}
if (any(is.na(y))) {
y[is.na(y)] <- microorganismsDT[prevalence == 3][data.table(mo = x[is.na(y)]), on = "mo", ..property][[1]]
}
x <- y
} else if (all(x %in% microorganismsDT[prevalence == 1, "fullname"][[1]])) {
} else if (all(x %in% AMR::microorganisms$fullname)) {
# we need special treatment for very prevalent full names, they are likely!
# e.g. as.mo("Staphylococcus aureus")
x <- microorganismsDT[prevalence == 1][data.table(fullname = x), on = "fullname", ..property][[1]]
} else if (all(x %in% microorganismsDT[prevalence == 2, "fullname"][[1]])) {
# same for common full names, they are also likely
x <- microorganismsDT[prevalence == 2][data.table(fullname = x), on = "fullname", ..property][[1]]
y <- microorganismsDT[prevalence == 1][data.table(fullname = x), on = "fullname", ..property][[1]]
if (any(is.na(y))) {
y[is.na(y)] <- microorganismsDT[prevalence == 2][data.table(fullname = x[is.na(y)]), on = "fullname", ..property][[1]]
}
if (any(is.na(y))) {
y[is.na(y)] <- microorganismsDT[prevalence == 3][data.table(fullname = x[is.na(y)]), on = "fullname", ..property][[1]]
}
x <- y
} else if (all(toupper(x) %in% microorganisms.codes[, "code"])) {
} else if (all(toupper(x) %in% AMR::microorganisms.codes$code)) {
# commonly used MO codes
y <- as.data.table(microorganisms.codes)[data.table(code = toupper(x)), on = "code", ]
y <- as.data.table(AMR::microorganisms.codes)[data.table(code = toupper(x)), on = "code", ]
x <- microorganismsDT[data.table(mo = y[["mo"]]), on = "mo", ..property][[1]]
} else if (!all(x %in% microorganismsDT[, ..property][[1]])) {
} else if (!all(x %in% AMR::microorganisms[, property])) {
x_backup <- x
@ -504,8 +515,8 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
}
# TRY OTHER SOURCES ----
if (toupper(x_backup[i]) %in% microorganisms.codes[, 1]) {
mo_found <- microorganisms.codes[toupper(x_backup[i]) == microorganisms.codes[, 1], "mo"][1L]
if (toupper(x_backup[i]) %in% AMR::microorganisms.codes[, 1]) {
mo_found <- AMR::microorganisms.codes[toupper(x_backup[i]) == AMR::microorganisms.codes[, 1], "mo"][1L]
if (length(mo_found) > 0) {
x[i] <- microorganismsDT[mo == mo_found, ..property][[1]][1L]
next