mirror of
https://github.com/msberends/AMR.git
synced 2025-07-08 11:11:54 +02:00
new: 1680 old taxonomic names
This commit is contained in:
112
R/mo.R
112
R/mo.R
@ -60,7 +60,7 @@
|
||||
#' \code{guess_mo} is an alias of \code{as.mo}.
|
||||
#' @section ITIS:
|
||||
#' \if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
|
||||
#' This \code{AMR} package contains the \strong{complete microbial taxonomic data} from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa (from subkingdom to the subspecies level) are included in this package.
|
||||
#' This \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
|
||||
# (source as section, so it can be inherited by mo_property:)
|
||||
#' @section Source:
|
||||
#' [1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13}
|
||||
@ -302,7 +302,8 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE
|
||||
next
|
||||
}
|
||||
found <- MOs_mostprevalent[mo.old == toupper(x_backup[i])
|
||||
| (substr(x_backup[i], 4, 6) == "SPP" & mo.old == substr(x_backup[i], 1, 3)), mo]
|
||||
| (substr(x_backup[i], 4, 6) == "SPP" & mo.old == substr(x_backup[i], 1, 3))
|
||||
| mo.old == substr(x_backup[i], 1, 3), mo]
|
||||
# is a valid old mo
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
@ -395,7 +396,9 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
}
|
||||
found <- MOs_allothers[mo.old == toupper(x_backup[i]), mo]
|
||||
found <- MOs_allothers[mo.old == toupper(x_backup[i])
|
||||
| (substr(x_backup[i], 4, 6) == "SPP" & mo.old == substr(x_backup[i], 1, 3))
|
||||
| mo.old == substr(x_backup[i], 1, 3), mo]
|
||||
# is a valid old mo
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
@ -463,27 +466,47 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE
|
||||
|
||||
# look for old taxonomic names ----
|
||||
if (is.null(MOs_old)) {
|
||||
MOs_old <- as.data.table(microorganisms.old)
|
||||
MOs_old <- as.data.table(AMR::microorganisms.old)
|
||||
setkey(MOs_old, name, tsn_new)
|
||||
}
|
||||
found <- MOs_old[tolower(name) == tolower(x_backup[i]) |
|
||||
tsn == x_trimmed[i],]
|
||||
if (NROW(found) > 0) {
|
||||
x[i] <- MOs[tsn == found[1, tsn_new], mo]
|
||||
message("Note: '", found[1, name], "' was renamed to '",
|
||||
MOs[tsn == found[1, tsn_new], fullname], "' by ",
|
||||
found[1, authors], " in ", found[1, year])
|
||||
renamed_note(name_old = found[1, name],
|
||||
name_new = MOs[tsn == found[1, tsn_new], fullname],
|
||||
authors = found[1, authors],
|
||||
year = found[1, year])
|
||||
next
|
||||
}
|
||||
|
||||
# check for uncertain results ----
|
||||
# (1) try to strip off one element and check the remains
|
||||
if (allow_uncertain == TRUE) {
|
||||
# (1) look again for old taxonomic names, now for G. species ----
|
||||
found <- MOs_old[name %like% x_withspaces[i]
|
||||
| name %like% x_withspaces_start[i]
|
||||
| name %like% x[i],]
|
||||
if (NROW(found) > 0) {
|
||||
x[i] <- MOs[tsn == found[1, tsn_new], mo]
|
||||
warning("Uncertain interpretation: '",
|
||||
x_backup[i], "' -> '", found[1, name], "'",
|
||||
call. = FALSE, immediate. = TRUE)
|
||||
renamed_note(name_old = found[1, name],
|
||||
name_new = MOs[tsn == found[1, tsn_new], fullname],
|
||||
authors = found[1, authors],
|
||||
year = found[1, year])
|
||||
|
||||
next
|
||||
}
|
||||
|
||||
# (2) try to strip off one element and check the remains
|
||||
x_strip <- x_backup[i] %>% strsplit(" ") %>% unlist()
|
||||
x_strip <- x_strip[1:length(x_strip) - 1]
|
||||
x[i] <- suppressWarnings(suppressMessages(as.mo(x_strip)))
|
||||
if (!is.na(x[i])) {
|
||||
warning("Uncertain result: '", x_backup[i], "' -> '", MOs[mo == x[i], fullname], "' (", x[i], ")")
|
||||
warning("Uncertain interpretation: '",
|
||||
x_backup[i], "' -> '", MOs[mo == x[i], fullname], "' (", x[i], ")",
|
||||
call. = FALSE, immediate. = TRUE)
|
||||
next
|
||||
}
|
||||
}
|
||||
@ -506,28 +529,24 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE
|
||||
if (Becker == TRUE | Becker == "all") {
|
||||
# See Source. It's this figure:
|
||||
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187637/figure/F3/
|
||||
CoNS <- MOs %>%
|
||||
filter(genus == "Staphylococcus",
|
||||
species %in% c("arlettae", "auricularis", "capitis",
|
||||
"caprae", "carnosus", "cohnii", "condimenti",
|
||||
"devriesei", "epidermidis", "equorum",
|
||||
"fleurettii", "gallinarum", "haemolyticus",
|
||||
"hominis", "jettensis", "kloosii", "lentus",
|
||||
"lugdunensis", "massiliensis", "microti",
|
||||
"muscae", "nepalensis", "pasteuri", "petrasii",
|
||||
"pettenkoferi", "piscifermentans", "rostri",
|
||||
"saccharolyticus", "saprophyticus", "sciuri",
|
||||
"stepanovicii", "simulans", "succinus",
|
||||
"vitulinus", "warneri", "xylosus")) %>%
|
||||
pull(mo)
|
||||
CoPS <- MOs %>%
|
||||
filter(genus == "Staphylococcus",
|
||||
species %in% c("simiae", "agnetis", "chromogenes",
|
||||
"delphini", "felis", "lutrae",
|
||||
"hyicus", "intermedius",
|
||||
"pseudintermedius", "pseudointermedius",
|
||||
"schleiferi")) %>%
|
||||
pull(mo)
|
||||
MOs_staph <- MOs[genus == "Staphylococcus"]
|
||||
setkey(MOs_staph, species)
|
||||
CoNS <- MOs_staph[species %in% c("arlettae", "auricularis", "capitis",
|
||||
"caprae", "carnosus", "cohnii", "condimenti",
|
||||
"devriesei", "epidermidis", "equorum",
|
||||
"fleurettii", "gallinarum", "haemolyticus",
|
||||
"hominis", "jettensis", "kloosii", "lentus",
|
||||
"lugdunensis", "massiliensis", "microti",
|
||||
"muscae", "nepalensis", "pasteuri", "petrasii",
|
||||
"pettenkoferi", "piscifermentans", "rostri",
|
||||
"saccharolyticus", "saprophyticus", "sciuri",
|
||||
"stepanovicii", "simulans", "succinus",
|
||||
"vitulinus", "warneri", "xylosus"), mo]
|
||||
CoPS <- MOs_staph[species %in% c("simiae", "agnetis", "chromogenes",
|
||||
"delphini", "felis", "lutrae",
|
||||
"hyicus", "intermedius",
|
||||
"pseudintermedius", "pseudointermedius",
|
||||
"schleiferi"), mo]
|
||||
x[x %in% CoNS] <- "B_STPHY_CNS"
|
||||
x[x %in% CoPS] <- "B_STPHY_CPS"
|
||||
if (Becker == "all") {
|
||||
@ -559,16 +578,24 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE
|
||||
}
|
||||
|
||||
# left join the found results to the original input values (x_input)
|
||||
df_found <- data.frame(input = as.character(unique(x_input)),
|
||||
DT_found <- data.table(input = as.character(unique(x_input)),
|
||||
found = x,
|
||||
key = "input",
|
||||
stringsAsFactors = FALSE)
|
||||
df_input <- data.frame(input = as.character(x_input),
|
||||
DT_input <- data.table(input = as.character(x_input),
|
||||
key = "input",
|
||||
stringsAsFactors = FALSE)
|
||||
x <- DT_found[DT_input, on = "input", found]
|
||||
|
||||
x <- df_input %>%
|
||||
left_join(df_found,
|
||||
by = "input") %>%
|
||||
pull(found)
|
||||
# df_found <- data.frame(input = as.character(unique(x_input)),
|
||||
# found = x,
|
||||
# stringsAsFactors = FALSE)
|
||||
# df_input <- data.frame(input = as.character(x_input),
|
||||
# stringsAsFactors = FALSE)
|
||||
# x <- df_input %>%
|
||||
# left_join(df_found,
|
||||
# by = "input") %>%
|
||||
# pull(found)
|
||||
|
||||
class(x) <- "mo"
|
||||
attr(x, 'package') <- 'AMR'
|
||||
@ -576,6 +603,17 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE
|
||||
x
|
||||
}
|
||||
|
||||
renamed_note <- function(name_old, name_new, authors, year) {
|
||||
msg <- paste0("Note: '", name_old, "' was renamed to '", name_new, "'")
|
||||
if (!authors %in% c("", NA)) {
|
||||
msg <- paste0(msg, " by ", authors)
|
||||
}
|
||||
if (!year %in% c("", NA)) {
|
||||
msg <- paste0(msg, " in ", year)
|
||||
}
|
||||
base::message(msg)
|
||||
}
|
||||
|
||||
|
||||
#' @rdname as.mo
|
||||
#' @export
|
||||
|
||||
Reference in New Issue
Block a user