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speed improvement as.mo, freq title
This commit is contained in:
204
R/mo.R
204
R/mo.R
@ -49,7 +49,15 @@
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#'
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#' Use the \code{\link{mo_property}} functions to get properties based on the returned code, see Examples.
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#'
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#' This function uses Artificial Intelligence (AI) to help getting more logical results, based on type of input and known prevalence of human pathogens. For example:
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#' This function uses Artificial Intelligence (AI) to help getting fast and logical results. It tries to find matches in this order:
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#' \itemize{
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#' \item{Taxonomic kingdom: it first searches in bacteria, then fungi, then protozoa}
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#' \item{Human pathogenic prevalence: it first searches in more prevalent microorganisms, then less prevalent ones}
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#' \item{Valid MO codes and full names: it first searches in already valid MO code and genus/species combinations}
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#' \item{Breakdown of input values: from here it starts to breakdown input values to find possible matches}
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#' }
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#'
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#' A couple of effects because of these rules
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#' \itemize{
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#' \item{\code{"E. coli"} will return the ID of \emph{Escherichia coli} and not \emph{Entamoeba coli}, although the latter would alphabetically come first}
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#' \item{\code{"H. influenzae"} will return the ID of \emph{Haemophilus influenzae} and not \emph{Haematobacter influenzae} for the same reason}
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@ -63,10 +71,11 @@
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#' \if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
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#' This package contains the \strong{complete microbial taxonomic data} (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
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#'
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#' All (sub)species from the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens.
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#' All (sub)species from the \strong{taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This \strong{allows users to use authoritative taxonomic information} for their data analysis on any microorganism, not only human pathogens. It also helps to \strong{quickly determine the Gram stain of bacteria}, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
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#'
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#' ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
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# (source as a section, so it can be inherited by other man pages:)
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#'
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# (source as a section, so it can be inherited by other man pages)
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#' @section Source:
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#' [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}
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#'
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@ -129,9 +138,10 @@
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#' mutate(mo = guess_mo(paste(genus, species)))
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#' }
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as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE, reference_df = NULL) {
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exec_as.mo(x = x, Becker = Becker, Lancefield = Lancefield,
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allow_uncertain = allow_uncertain, reference_df = reference_df,
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property = "mo")
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structure(mo_validate(x = x, property = "mo",
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Becker = Becker, Lancefield = Lancefield,
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allow_uncertain = allow_uncertain, reference_df = reference_df),
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class = "mo")
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}
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#' @rdname as.mo
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@ -147,8 +157,15 @@ is.mo <- function(x) {
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guess_mo <- as.mo
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#' @importFrom dplyr %>% pull left_join
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#' @importFrom data.table as.data.table setkey
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#' @importFrom data.table data.table as.data.table setkey
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exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE, reference_df = NULL, property = "mo") {
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# These data.tables are available as data sets when the AMR package is loaded:
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# microorganismsDT # this one is sorted by kingdom (B<F<P), prevalence, TSN
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# microorganisms.prevDT # same as microorganismsDT, but with prevalence != 9999
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# microorganisms.unprevDT # same as microorganismsDT, but with prevalence == 9999
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# microorganisms.oldDT # old taxonomic names, sorted by name (genus+species), TSN
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if (NCOL(x) == 2) {
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# support tidyverse selection like: df %>% select(colA, colB)
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# paste these columns together
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@ -176,12 +193,6 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
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# remove empty values (to later fill them in again)
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x <- x[!is.na(x) & !is.null(x) & !identical(x, "")]
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# These data.tables are available because of .onAttach:
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# MOs
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# MOs_mostprevalent
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# MOs_allothers
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# MOs_old
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# defined df to check for
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if (!is.null(reference_df)) {
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if (!is.data.frame(reference_df) | NCOL(reference_df) < 2) {
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@ -193,18 +204,12 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
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)
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}
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if (all(x %in% AMR::microorganisms[, property])) {
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# already existing mo
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} else if (all(x %in% AMR::microorganisms[, "mo"])) {
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# existing mo codes when not looking for property "mo"
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suppressWarnings(
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x <- data.frame(mo = x, stringsAsFactors = FALSE) %>%
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left_join(AMR::microorganisms, by = "mo") %>%
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pull(property)
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)
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if (all(x %in% microorganismsDT[["mo"]])) {
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# existing mo codes when not looking for property "mo", like mo_genus("B_ESCHR_COL")
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x <- microorganismsDT[data.table(mo = x), on = "mo", ..property][[1]]
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} else if (!is.null(reference_df)
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& all(x %in% reference_df[, 1])
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& all(reference_df[, 2] %in% AMR::microorganisms$mo)) {
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& all(reference_df[, 2] %in% microorganismsDT[["mo"]])) {
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# manually defined reference
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colnames(reference_df)[1] <- "x"
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colnames(reference_df)[2] <- "mo"
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@ -214,24 +219,12 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
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left_join(AMR::microorganisms, by = "mo") %>%
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pull(property)
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)
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} else if (all(x %in% AMR::microorganisms.certe[, "certe"])) {
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} else if (all(toupper(x) %in% AMR::microorganisms.certe[, "certe"])) {
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# old Certe codes
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suppressWarnings(
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x <- data.frame(certe = x, stringsAsFactors = FALSE) %>%
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left_join(AMR::microorganisms.certe, by = "certe") %>%
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left_join(AMR::microorganisms, by = "mo") %>%
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pull(property)
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)
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} else if (all(x %in% AMR::microorganisms.umcg[, "umcg"])) {
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# old UMCG codes
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suppressWarnings(
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x <- data.frame(umcg = x, stringsAsFactors = FALSE) %>%
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left_join(AMR::microorganisms.umcg, by = "umcg") %>%
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left_join(AMR::microorganisms.certe, by = "certe") %>%
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left_join(AMR::microorganisms, by = "mo") %>%
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pull(property)
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)
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} else {
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y <- as.data.table(AMR::microorganisms.certe)[data.table(certe = toupper(x)), on = "certe", ]
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x <- microorganismsDT[data.table(mo = y[["mo"]]), on = "mo", ..property][[1]]
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} else if (!all(x %in% microorganismsDT[[property]])) {
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x_backup <- trimws(x, which = "both")
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x_species <- paste(x_backup, "species")
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@ -280,36 +273,36 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
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| toupper(x_trimmed[i]) == 'MSSA'
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| toupper(x_trimmed[i]) == 'VISA'
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| toupper(x_trimmed[i]) == 'VRSA') {
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x[i] <- MOs[mo == 'B_STPHY_AUR', ..property][[1]][1L]
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x[i] <- microorganismsDT[mo == 'B_STPHY_AUR', ..property][[1]][1L]
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next
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}
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if (toupper(x_trimmed[i]) == 'MRSE'
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| toupper(x_trimmed[i]) == 'MSSE') {
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x[i] <- MOs[mo == 'B_STPHY_EPI', ..property][[1]][1L]
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x[i] <- microorganismsDT[mo == 'B_STPHY_EPI', ..property][[1]][1L]
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next
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}
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if (toupper(x_trimmed[i]) == 'VRE') {
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x[i] <- MOs[mo == 'B_ENTRC', ..property][[1]][1L]
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x[i] <- microorganismsDT[mo == 'B_ENTRC', ..property][[1]][1L]
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next
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}
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if (toupper(x_trimmed[i]) == 'MRPA') {
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# multi resistant P. aeruginosa
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x[i] <- MOs[mo == 'B_PDMNS_AER', ..property][[1]][1L]
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x[i] <- microorganismsDT[mo == 'B_PDMNS_AER', ..property][[1]][1L]
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next
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}
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if (toupper(x_trimmed[i]) == 'CRS'
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| toupper(x_trimmed[i]) == 'CRSM') {
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# co-trim resistant S. maltophilia
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x[i] <- MOs[mo == 'B_STNTR_MAL', ..property][[1]][1L]
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x[i] <- microorganismsDT[mo == 'B_STNTR_MAL', ..property][[1]][1L]
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next
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}
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if (toupper(x_trimmed[i]) %in% c('PISP', 'PRSP', 'VISP', 'VRSP')) {
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# peni I, peni R, vanco I, vanco R: S. pneumoniae
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x[i] <- MOs[mo == 'B_STRPTC_PNE', ..property][[1]][1L]
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x[i] <- microorganismsDT[mo == 'B_STRPTC_PNE', ..property][[1]][1L]
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next
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}
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if (toupper(x_trimmed[i]) %like% '^G[ABCDFGHK]S$') {
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x[i] <- MOs[mo == gsub("G([ABCDFGHK])S", "B_STRPTC_GR\\1", x_trimmed[i]), ..property][[1]][1L]
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x[i] <- microorganismsDT[mo == gsub("G([ABCDFGHK])S", "B_STRPTC_GR\\1", x_trimmed[i]), ..property][[1]][1L]
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next
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}
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# CoNS/CoPS in different languages (support for German, Dutch, Spanish, Portuguese) ----
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@ -317,14 +310,14 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
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| tolower(x_trimmed[i]) %like% '[ck]oagulas[ea] negatie?[vf]'
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| tolower(x[i]) %like% '[ck]o?ns[^a-z]?$') {
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# coerce S. coagulase negative
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x[i] <- MOs[mo == 'B_STPHY_CNS', ..property][[1]][1L]
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x[i] <- microorganismsDT[mo == 'B_STPHY_CNS', ..property][[1]][1L]
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next
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}
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if (tolower(x[i]) %like% '[ck]oagulas[ea] positie?[vf]'
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| tolower(x_trimmed[i]) %like% '[ck]oagulas[ea] positie?[vf]'
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| tolower(x[i]) %like% '[ck]o?ps[^a-z]?$') {
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# coerce S. coagulase positive
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x[i] <- MOs[mo == 'B_STPHY_CPS', ..property][[1]][1L]
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x[i] <- microorganismsDT[mo == 'B_STPHY_CPS', ..property][[1]][1L]
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next
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}
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}
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@ -332,14 +325,14 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
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# FIRST TRY FULLNAMES AND CODES
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# if only genus is available, return only genus
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if (all(!c(x[i], x_trimmed[i]) %like% " ")) {
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found <- MOs[tolower(fullname) %in% tolower(c(x_species[i], x_trimmed_species[i])), ..property][[1]]
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found <- microorganismsDT[tolower(fullname) %in% tolower(c(x_species[i], x_trimmed_species[i])), ..property][[1]]
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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}
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if (nchar(x_trimmed[i]) > 4) {
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# not when abbr is esco, stau, klpn, etc.
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found <- MOs[tolower(fullname) %like% gsub(" ", ".*", x_trimmed_species[i], fixed = TRUE), ..property][[1]]
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found <- microorganismsDT[tolower(fullname) %like% gsub(" ", ".*", x_trimmed_species[i], fixed = TRUE), ..property][[1]]
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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@ -348,20 +341,22 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
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}
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# TRY OTHER SOURCES ----
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if (x_backup[i] %in% AMR::microorganisms.certe[, 1]) {
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x[i] <- MOs[mo == AMR::microorganisms.certe[AMR::microorganisms.certe[, 1] == x_backup[i], 2], ..property][[1]][1L]
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next
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if (x_backup[i] %in% AMR::microorganisms.certe$certe) {
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x[i] <- microorganismsDT[mo == AMR::microorganisms.certe[AMR::microorganisms.certe[, 1] == x_backup[i], 2], ..property][[1]][1L]
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# x[i] <- exec_as.mo(x = AMR::microorganisms.certe[AMR::microorganisms.certe$certe == x_backup[i], "mo"],
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# property = property)
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# next
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}
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if (x_backup[i] %in% AMR::microorganisms.umcg[, 1]) {
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ref_certe <- AMR::microorganisms.umcg[AMR::microorganisms.umcg[, 1] == x_backup[i], 2]
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ref_mo <- AMR::microorganisms.certe[AMR::microorganisms.certe[, 1] == ref_certe, 2]
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x[i] <- MOs[mo == ref_mo, ..property][[1]][1L]
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x[i] <- microorganismsDT[mo == ref_mo, ..property][[1]][1L]
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next
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}
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if (x_backup[i] %in% reference_df[, 1]) {
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ref_mo <- reference_df[reference_df[, 1] == x_backup[i], 2]
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if (ref_mo %in% MOs[, mo]) {
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x[i] <- MOs[mo == ref_mo, ..property][[1]][1L]
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if (ref_mo %in% microorganismsDT[, mo]) {
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x[i] <- microorganismsDT[mo == ref_mo, ..property][[1]][1L]
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next
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} else {
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warning("Value '", x_backup[i], "' was found in reference_df, but '", ref_mo, "' is not a valid MO code.", call. = FALSE)
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@ -369,20 +364,19 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
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}
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# TRY FIRST THOUSAND MOST PREVALENT IN HUMAN INFECTIONS ----
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found <- MOs_mostprevalent[tolower(fullname) %in% tolower(c(x_backup[i], x_trimmed[i])), ..property][[1]]
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found <- microorganisms.prevDT[tolower(fullname) %in% tolower(c(x_backup[i], x_trimmed[i])), ..property][[1]]
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# most probable: is exact match in fullname
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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}
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found <- MOs_mostprevalent[tsn == x_trimmed[i], ..property][[1]]
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found <- microorganisms.prevDT[tsn == x_trimmed[i], ..property][[1]]
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# is a valid TSN
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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}
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found <- MOs_mostprevalent[mo == toupper(x_backup[i]), ..property][[1]]
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found <- microorganisms.prevDT[mo == toupper(x_backup[i]), ..property][[1]]
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# is a valid mo
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if (length(found) > 0) {
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x[i] <- found[1L]
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@ -390,21 +384,21 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
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}
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# try any match keeping spaces ----
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found <- MOs_mostprevalent[fullname %like% x_withspaces[i], ..property][[1]]
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found <- microorganisms.prevDT[fullname %like% x_withspaces[i], ..property][[1]]
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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}
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# try any match keeping spaces, not ending with $ ----
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found <- MOs_mostprevalent[fullname %like% x_withspaces_start[i], ..property][[1]]
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found <- microorganisms.prevDT[fullname %like% x_withspaces_start[i], ..property][[1]]
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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}
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# try any match diregarding spaces ----
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found <- MOs_mostprevalent[fullname %like% x[i], ..property][[1]]
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found <- microorganisms.prevDT[fullname %like% x[i], ..property][[1]]
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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@ -412,7 +406,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
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# try fullname without start and stop regex, to also find subspecies ----
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# like "K. pneu rhino" -> "Klebsiella pneumoniae (rhinoscleromatis)" = KLEPNERH
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found <- MOs_mostprevalent[fullname %like% x_withspaces_start[i], ..property][[1]]
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found <- microorganisms.prevDT[fullname %like% x_withspaces_start[i], ..property][[1]]
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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@ -427,7 +421,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
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x_split[i] <- paste0(x_trimmed[i] %>% substr(1, x_length / 2) %>% trimws(),
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'.* ',
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x_trimmed[i] %>% substr((x_length / 2) + 1, x_length) %>% trimws())
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found <- MOs_mostprevalent[fullname %like% paste0('^', x_split[i]), ..property][[1]]
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found <- microorganisms.prevDT[fullname %like% paste0('^', x_split[i]), ..property][[1]]
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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@ -442,7 +436,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
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# x_trimmed[i] <- trimws(x_trimmed[i], which = "both")
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# }
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# if (!is.na(x_trimmed[i])) {
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# found <- MOs_mostprevalent[fullname %like% x_trimmed[i], ..property][[1]]
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# found <- microorganisms.prevDT[fullname %like% x_trimmed[i], ..property][[1]]
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# if (length(found) > 0) {
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# x[i] <- found[1L]
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# next
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@ -450,25 +444,25 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
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# }
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# THEN TRY ALL OTHERS ----
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found <- MOs_allothers[tolower(fullname) == tolower(x_backup[i]), ..property][[1]]
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found <- microorganisms.unprevDT[tolower(fullname) == tolower(x_backup[i]), ..property][[1]]
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# most probable: is exact match in fullname
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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}
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found <- MOs_allothers[tolower(fullname) == tolower(x_trimmed[i]), ..property][[1]]
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found <- microorganisms.unprevDT[tolower(fullname) == tolower(x_trimmed[i]), ..property][[1]]
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# most probable: is exact match in fullname
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if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
}
|
||||
found <- MOs_allothers[tsn == x_trimmed[i], ..property][[1]]
|
||||
found <- microorganisms.unprevDT[tsn == x_trimmed[i], ..property][[1]]
|
||||
# is a valid TSN
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
}
|
||||
found <- MOs_allothers[mo == toupper(x_backup[i]), ..property][[1]]
|
||||
found <- microorganisms.unprevDT[mo == toupper(x_backup[i]), ..property][[1]]
|
||||
# is a valid mo
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
@ -476,21 +470,21 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
|
||||
}
|
||||
|
||||
# try any match keeping spaces ----
|
||||
found <- MOs_allothers[fullname %like% x_withspaces[i], ..property][[1]]
|
||||
found <- microorganisms.unprevDT[fullname %like% x_withspaces[i], ..property][[1]]
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
}
|
||||
|
||||
# try any match keeping spaces, not ending with $ ----
|
||||
found <- MOs_allothers[fullname %like% x_withspaces_start[i], ..property][[1]]
|
||||
found <- microorganisms.unprevDT[fullname %like% x_withspaces_start[i], ..property][[1]]
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
}
|
||||
|
||||
# try any match diregarding spaces ----
|
||||
found <- MOs_allothers[fullname %like% x[i], ..property][[1]]
|
||||
found <- microorganisms.unprevDT[fullname %like% x[i], ..property][[1]]
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
@ -498,7 +492,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
|
||||
|
||||
# try fullname without start and stop regex, to also find subspecies ----
|
||||
# like "K. pneu rhino" -> "Klebsiella pneumoniae (rhinoscleromatis)" = KLEPNERH
|
||||
found <- MOs_allothers[fullname %like% x_withspaces_start[i], ..property][[1]]
|
||||
found <- microorganisms.unprevDT[fullname %like% x_withspaces_start[i], ..property][[1]]
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
@ -513,7 +507,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
|
||||
x_split[i] <- paste0(x_trimmed[i] %>% substr(1, x_length / 2) %>% trimws(),
|
||||
'.* ',
|
||||
x_trimmed[i] %>% substr((x_length / 2) + 1, x_length) %>% trimws())
|
||||
found <- MOs_allothers[fullname %like% paste0('^', x_split[i]), ..property][[1]]
|
||||
found <- microorganisms.unprevDT[fullname %like% paste0('^', x_split[i]), ..property][[1]]
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
@ -528,7 +522,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
|
||||
# x_trimmed[i] <- trimws(x_trimmed[i], which = "both")
|
||||
# }
|
||||
# if (!is.na(x_trimmed[i])) {
|
||||
# found <- MOs_allothers[fullname %like% x_trimmed[i], ..property][[1]]
|
||||
# found <- microorganisms.unprevDT[fullname %like% x_trimmed[i], ..property][[1]]
|
||||
# if (length(found) > 0) {
|
||||
# x[i] <- found[1L]
|
||||
# next
|
||||
@ -538,33 +532,33 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
|
||||
# MISCELLANEOUS ----
|
||||
|
||||
# look for old taxonomic names ----
|
||||
found <- MOs_old[tolower(name) == tolower(x_backup[i])
|
||||
| tsn == x_trimmed[i]
|
||||
| name %like% x_withspaces[i],]
|
||||
found <- microorganisms.oldDT[tolower(name) == tolower(x_backup[i])
|
||||
| tsn == x_trimmed[i]
|
||||
| name %like% x_withspaces[i],]
|
||||
if (NROW(found) > 0) {
|
||||
x[i] <- MOs[tsn == found[1, tsn_new], ..property][[1]]
|
||||
x[i] <- microorganismsDT[tsn == found[1, tsn_new], ..property][[1]]
|
||||
renamed_note(name_old = found[1, name],
|
||||
name_new = MOs[tsn == found[1, tsn_new], fullname],
|
||||
name_new = microorganismsDT[tsn == found[1, tsn_new], fullname],
|
||||
ref_old = found[1, ref],
|
||||
ref_new = MOs[tsn == found[1, tsn_new], ref])
|
||||
ref_new = microorganismsDT[tsn == found[1, tsn_new], ref])
|
||||
next
|
||||
}
|
||||
|
||||
# check for uncertain results ----
|
||||
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],]
|
||||
found <- microorganisms.oldDT[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], ..property][[1]]
|
||||
x[i] <- microorganismsDT[tsn == found[1, tsn_new], ..property][[1]]
|
||||
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],
|
||||
name_new = microorganismsDT[tsn == found[1, tsn_new], fullname],
|
||||
ref_old = found[1, ref],
|
||||
ref_new = MOs[tsn == found[1, tsn_new], ref])
|
||||
ref_new = microorganismsDT[tsn == found[1, tsn_new], ref])
|
||||
next
|
||||
}
|
||||
|
||||
@ -574,7 +568,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
|
||||
x[i] <- suppressWarnings(suppressMessages(as.mo(x_strip)))
|
||||
if (!is.na(x[i])) {
|
||||
warning("Uncertain interpretation: '",
|
||||
x_backup[i], "' -> '", MOs[mo == x[i], fullname], "' (", x[i], ")",
|
||||
x_backup[i], "' -> '", microorganismsDT[mo == x[i], fullname], "' (", x[i], ")",
|
||||
call. = FALSE, immediate. = TRUE)
|
||||
next
|
||||
}
|
||||
@ -599,7 +593,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
|
||||
if (Becker == TRUE | Becker == "all") {
|
||||
# See Source. It's this figure:
|
||||
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187637/figure/F3/
|
||||
MOs_staph <- MOs[genus == "Staphylococcus"]
|
||||
MOs_staph <- microorganismsDT[genus == "Staphylococcus"]
|
||||
setkey(MOs_staph, species)
|
||||
CoNS <- MOs_staph[species %in% c("arlettae", "auricularis", "capitis",
|
||||
"caprae", "carnosus", "cohnii", "condimenti",
|
||||
@ -617,35 +611,35 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
|
||||
"hyicus", "intermedius",
|
||||
"pseudintermedius", "pseudointermedius",
|
||||
"schleiferi"), ..property][[1]]
|
||||
x[x %in% CoNS] <- MOs[mo == 'B_STPHY_CNS', ..property][[1]][1L]
|
||||
x[x %in% CoPS] <- MOs[mo == 'B_STPHY_CPS', ..property][[1]][1L]
|
||||
x[x %in% CoNS] <- microorganismsDT[mo == 'B_STPHY_CNS', ..property][[1]][1L]
|
||||
x[x %in% CoPS] <- microorganismsDT[mo == 'B_STPHY_CPS', ..property][[1]][1L]
|
||||
if (Becker == "all") {
|
||||
x[x == MOs[mo == 'B_STPHY_AUR', ..property][[1]][1L]] <- MOs[mo == 'B_STPHY_CPS', ..property][[1]][1L]
|
||||
x[x == microorganismsDT[mo == 'B_STPHY_AUR', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STPHY_CPS', ..property][[1]][1L]
|
||||
}
|
||||
}
|
||||
|
||||
# Lancefield ----
|
||||
if (Lancefield == TRUE | Lancefield == "all") {
|
||||
# group A - S. pyogenes
|
||||
x[x == MOs[mo == 'B_STRPTC_PYO', ..property][[1]][1L]] <- MOs[mo == 'B_STRPTC_GRA', ..property][[1]][1L]
|
||||
x[x == microorganismsDT[mo == 'B_STRPTC_PYO', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STRPTC_GRA', ..property][[1]][1L]
|
||||
# group B - S. agalactiae
|
||||
x[x == MOs[mo == 'B_STRPTC_AGA', ..property][[1]][1L]] <- MOs[mo == 'B_STRPTC_GRB', ..property][[1]][1L]
|
||||
x[x == microorganismsDT[mo == 'B_STRPTC_AGA', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STRPTC_GRB', ..property][[1]][1L]
|
||||
# group C
|
||||
S_groupC <- MOs %>% filter(genus == "Streptococcus",
|
||||
species %in% c("equisimilis", "equi",
|
||||
"zooepidemicus", "dysgalactiae")) %>%
|
||||
S_groupC <- microorganismsDT %>% filter(genus == "Streptococcus",
|
||||
species %in% c("equisimilis", "equi",
|
||||
"zooepidemicus", "dysgalactiae")) %>%
|
||||
pull(property)
|
||||
x[x %in% S_groupC] <- MOs[mo == 'B_STRPTC_GRC', ..property][[1]][1L]
|
||||
x[x %in% S_groupC] <- microorganismsDT[mo == 'B_STRPTC_GRC', ..property][[1]][1L]
|
||||
if (Lancefield == "all") {
|
||||
# all Enterococci
|
||||
x[x %like% "^(Enterococcus|B_ENTRC)"] <- MOs[mo == 'B_STRPTC_GRD', ..property][[1]][1L]
|
||||
x[x %like% "^(Enterococcus|B_ENTRC)"] <- microorganismsDT[mo == 'B_STRPTC_GRD', ..property][[1]][1L]
|
||||
}
|
||||
# group F - S. anginosus
|
||||
x[x == MOs[mo == 'B_STRPTC_ANG', ..property][[1]][1L]] <- MOs[mo == 'B_STRPTC_GRF', ..property][[1]][1L]
|
||||
x[x == microorganismsDT[mo == 'B_STRPTC_ANG', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STRPTC_GRF', ..property][[1]][1L]
|
||||
# group H - S. sanguinis
|
||||
x[x == MOs[mo == 'B_STRPTC_SAN', ..property][[1]][1L]] <- MOs[mo == 'B_STRPTC_GRH', ..property][[1]][1L]
|
||||
x[x == microorganismsDT[mo == 'B_STRPTC_SAN', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STRPTC_GRH', ..property][[1]][1L]
|
||||
# group K - S. salivarius
|
||||
x[x == MOs[mo == 'B_STRPTC_SAL', ..property][[1]][1L]] <- MOs[mo == 'B_STRPTC_GRK', ..property][[1]][1L]
|
||||
x[x == microorganismsDT[mo == 'B_STRPTC_SAL', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STRPTC_GRK', ..property][[1]][1L]
|
||||
}
|
||||
|
||||
# comply to x, which is also unique and without empty values
|
||||
@ -700,7 +694,7 @@ print.mo <- function(x, ...) {
|
||||
#' @export
|
||||
#' @noRd
|
||||
as.data.frame.mo <- function (x, ...) {
|
||||
# same as as.data.frame.character but with removed stringsAsFactors
|
||||
# same as as.data.frame.character but with removed stringsAsFactors, since it will be class "mo"
|
||||
nm <- paste(deparse(substitute(x), width.cutoff = 500L),
|
||||
collapse = " ")
|
||||
if (!"nm" %in% names(list(...))) {
|
||||
|
||||
Reference in New Issue
Block a user