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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# LICENCE #
# This program is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# ==================================================================== #
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#' Transform to microorganism ID
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#'
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#' Use this function to determine a valid microorganism ID (\code{mo}). Determination is done using Artificial Intelligence (AI) and the complete taxonomic kingdoms \emph{Bacteria}, \emph{Fungi} and \emph{Protozoa} (see Source), so the input can be almost anything: a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), an abbreviation known in the field (like \code{"MRSA"}), or just a genus. You could also \code{\link{select}} a genus and species column, zie Examples.
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#' @param x a character vector or a \code{data.frame} with one or two columns
#' @param Becker a logical to indicate whether \emph{Staphylococci} should be categorised into Coagulase Negative \emph{Staphylococci} ("CoNS") and Coagulase Positive \emph{Staphylococci} ("CoPS") instead of their own species, according to Karsten Becker \emph{et al.} [1].
#'
#' This excludes \emph{Staphylococcus aureus} at default, use \code{Becker = "all"} to also categorise \emph{S. aureus} as "CoPS".
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#' @param Lancefield a logical to indicate whether beta-haemolytic \emph{Streptococci} should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield [2]. These \emph{Streptococci} will be categorised in their first group, e.g. \emph{Streptococcus dysgalactiae} will be group C, although officially it was also categorised into groups G and L.
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#'
#' This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.
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#' @param allow_uncertain a logical to indicate whether empty results should be checked for only a part of the input string. When results are found, a warning will be given about the uncertainty and the result.
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#' @rdname as.mo
#' @aliases mo
#' @keywords mo Becker becker Lancefield lancefield guess
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#' @details
#' A microbial ID (class: \code{mo}) typically looks like these examples:\cr
#' \preformatted{
#' Code Full name
#' --------------- --------------------------------------
#' B_KLBSL Klebsiella
#' B_KLBSL_PNE Klebsiella pneumoniae
#' B_KLBSL_PNE_RHI Klebsiella pneumoniae rhinoscleromatis
#' | | | |
#' | | | |
#' | | | ----> subspecies, a 3-4 letter acronym
#' | | ----> species, a 3-4 letter acronym
#' | ----> genus, a 5-7 letter acronym, mostly without vowels
#' ----> taxonomic kingdom, either Bacteria (B), Fungi (F) or Protozoa (P)
#' }
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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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#' \itemize{
#' \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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#' \item{Something like \code{"p aer"} will return the ID of \emph{Pseudomonas aeruginosa} and not \emph{Pasteurella aerogenes}}
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#' \item{Something like \code{"stau"} or \code{"S aur"} will return the ID of \emph{Staphylococcus aureus} and not \emph{Staphylococcus auricularis}}
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#' }
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#' This means that looking up human non-pathogenic microorganisms takes a longer time compares to human pathogenic microorganisms.
#'
#' \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}
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#' 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, \url{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.
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# (source as section, so it can be inherited by mo_property:)
#' @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}
#'
#' [2] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571– 95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
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#'
#' [3] Integrated Taxonomic Information System (ITIS). Retrieved September 2018. \url{http://www.itis.gov}
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#' @export
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#' @return Character (vector) with class \code{"mo"}. Unknown values will return \code{NA}.
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#' @seealso \code{\link{microorganisms}} for the \code{data.frame} with ITIS content that is being used to determine ID's. \cr
#' The \code{\link{mo_property}} functions (like \code{\link{mo_genus}}, \code{\link{mo_gramstain}}) to get properties based on the returned code.
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#' @examples
#' # These examples all return "STAAUR", the ID of S. aureus:
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#' as.mo("stau")
#' as.mo("STAU")
#' as.mo("staaur")
#' as.mo("S. aureus")
#' as.mo("S aureus")
#' as.mo("Staphylococcus aureus")
#' as.mo("MRSA") # Methicillin Resistant S. aureus
#' as.mo("VISA") # Vancomycin Intermediate S. aureus
#' as.mo("VRSA") # Vancomycin Resistant S. aureus
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#' as.mo(369) # Search on TSN (Taxonomic Serial Number), a unique identifier
#' # for the Integrated Taxonomic Information System (ITIS)
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#'
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#' as.mo("Streptococcus group A")
#' as.mo("GAS") # Group A Streptococci
#' as.mo("GBS") # Group B Streptococci
#'
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#' # guess_mo is an alias of as.mo and works the same
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#' guess_mo("S. epidermidis") # will remain species: B_STPHY_EPI
#' guess_mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CNS
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#'
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#' guess_mo("S. pyogenes") # will remain species: B_STRPTC_PYO
#' guess_mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPTC_GRA
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#'
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#' # Use mo_* functions to get a specific property based on `mo`
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#' Ecoli <- as.mo("E. coli") # returns `B_ESCHR_COL`
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#' mo_genus(Ecoli) # returns "Escherichia"
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#' mo_gramstain(Ecoli) # returns "Gram negative"
#' # but it uses as.mo internally too, so you could also just use:
#' mo_genus("E. coli") # returns "Escherichia"
#'
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#'
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#' \dontrun{
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#' df$mo <- as.mo(df$microorganism_name)
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#'
#' # the select function of tidyverse is also supported:
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#' library(dplyr)
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#' df$mo <- df %>%
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#' select(microorganism_name) %>%
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#' guess_mo()
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#'
#' # and can even contain 2 columns, which is convenient for genus/species combinations:
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#' df$mo <- df %>%
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#' select(genus, species) %>%
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#' guess_mo()
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#'
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#' # same result:
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#' df <- df %>%
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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 ) {
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exec_as.mo ( x = x , Becker = Becker , Lancefield = Lancefield ,
allow_uncertain = allow_uncertain , property = " mo" )
}
#' @rdname as.mo
#' @export
is.mo <- function ( x ) {
# bactid for older releases
# remove when is.bactid will be removed
identical ( class ( x ) , " mo" ) | identical ( class ( x ) , " bactid" )
}
#' @rdname as.mo
#' @export
guess_mo <- as.mo
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#' @importFrom dplyr %>% pull left_join
#' @importFrom data.table as.data.table setkey
exec_as.mo <- function ( x , Becker = FALSE , Lancefield = FALSE , allow_uncertain = FALSE , property = " mo" ) {
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if ( NCOL ( x ) == 2 ) {
# support tidyverse selection like: df %>% select(colA, colB)
# paste these columns together
x_vector <- vector ( " character" , NROW ( x ) )
for ( i in 1 : NROW ( x ) ) {
x_vector [i ] <- paste ( pull ( x [i , ] , 1 ) , pull ( x [i , ] , 2 ) , sep = " " )
}
x <- x_vector
} else {
if ( NCOL ( x ) > 2 ) {
stop ( ' `x` can be 2 columns at most' , call. = FALSE )
}
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x [is.null ( x ) ] <- NA
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# support tidyverse selection like: df %>% select(colA)
if ( ! is.vector ( x ) ) {
x <- pull ( x , 1 )
}
}
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failures <- character ( 0 )
x_input <- x
# only check the uniques, which is way faster
x <- unique ( x )
MOs <- NULL # will be set later, if needed
MOs_mostprevalent <- NULL # will be set later, if needed
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MOs_allothers <- NULL # will be set later, if needed
MOs_old <- NULL # will be set later, if needed
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if ( all ( x %in% AMR :: microorganisms [ , property ] ) ) {
# already existing mo
} else if ( all ( x %in% AMR :: microorganisms.certe [ , " certe" ] ) ) {
# old Certe codes
suppressWarnings (
x <- data.frame ( certe = x , stringsAsFactors = FALSE ) %>%
left_join ( AMR :: microorganisms.certe , by = " certe" ) %>%
left_join ( AMR :: microorganisms , by = " mo" ) %>%
pull ( property )
)
} else if ( all ( x %in% AMR :: microorganisms.umcg [ , " umcg" ] ) ) {
# old UMCG codes
suppressWarnings (
x <- data.frame ( umcg = x , stringsAsFactors = FALSE ) %>%
left_join ( AMR :: microorganisms.umcg , by = " umcg" ) %>%
left_join ( AMR :: microorganisms.certe , by = " certe" ) %>%
left_join ( AMR :: microorganisms , by = " mo" ) %>%
pull ( property )
)
} else {
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MOs <- as.data.table ( AMR :: microorganisms )
setkey ( MOs , prevalence , tsn )
MOs_mostprevalent <- MOs [prevalence != 9999 , ]
x_backup <- trimws ( x , which = " both" )
x_species <- paste ( x_backup , " species" )
# translate to English for supported languages of mo_property
x <- gsub ( " (Gruppe|gruppe|groep|grupo|gruppo|groupe)" , " group" , x )
# remove 'empty' genus and species values
x <- gsub ( " (no MO)" , " " , x , fixed = TRUE )
# remove dots and other non-text in case of "E. coli" except spaces
x <- gsub ( " [^a-zA-Z0-9/ \\-]+" , " " , x )
# but spaces before and after should be omitted
x <- trimws ( x , which = " both" )
x_trimmed <- x
x_trimmed_species <- paste ( x_trimmed , " species" )
# replace space by regex sign
x_withspaces <- gsub ( " " , " .* " , x , fixed = TRUE )
x <- gsub ( " " , " .*" , x , fixed = TRUE )
# add start en stop regex
x <- paste0 ( ' ^' , x , ' $' )
x_withspaces_all <- x_withspaces
x_withspaces_start <- paste0 ( ' ^' , x_withspaces )
x_withspaces <- paste0 ( ' ^' , x_withspaces , ' $' )
# cat(paste0('x "', x, '"\n'))
# cat(paste0('x_species "', x_species, '"\n'))
# cat(paste0('x_withspaces_all "', x_withspaces_all, '"\n'))
# cat(paste0('x_withspaces_start "', x_withspaces_start, '"\n'))
# cat(paste0('x_withspaces "', x_withspaces, '"\n'))
# cat(paste0('x_backup "', x_backup, '"\n'))
# cat(paste0('x_trimmed "', x_trimmed, '"\n'))
# cat(paste0('x_trimmed_species "', x_trimmed_species, '"\n'))
for ( i in 1 : length ( x ) ) {
if ( identical ( x_trimmed [i ] , " " ) | is.na ( x_trimmed [i ] ) ) {
# empty values
x [i ] <- NA
next
}
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# translate known trivial abbreviations to genus + species ----
if ( ! is.na ( x_trimmed [i ] ) ) {
if ( toupper ( x_trimmed [i ] ) == ' MRSA'
| toupper ( x_trimmed [i ] ) == ' VISA'
| toupper ( x_trimmed [i ] ) == ' VRSA' ) {
x [i ] <- MOs [mo == ' B_STPHY_AUR' , ..property ] [ [1 ] ] [1L ]
next
}
if ( toupper ( x_trimmed [i ] ) == ' MRSE' ) {
x [i ] <- MOs [mo == ' B_STPHY_EPI' , ..property ] [ [1 ] ] [1L ]
next
}
if ( toupper ( x_trimmed [i ] ) == ' VRE' ) {
x [i ] <- MOs [mo == ' B_ENTRC' , ..property ] [ [1 ] ] [1L ]
next
}
if ( toupper ( x_trimmed [i ] ) == ' MRPA' ) {
# multi resistant P. aeruginosa
x [i ] <- MOs [mo == ' B_PDMNS_AER' , ..property ] [ [1 ] ] [1L ]
next
}
if ( toupper ( x_trimmed [i ] ) %in% c ( ' PISP' , ' PRSP' , ' VISP' , ' VRSP' ) ) {
# peni I, peni R, vanco I, vanco R: S. pneumoniae
x [i ] <- MOs [mo == ' B_STRPTC_PNE' , ..property ] [ [1 ] ] [1L ]
next
}
if ( toupper ( x_trimmed [i ] ) %like% ' ^G[ABCDFGHK]S$' ) {
x [i ] <- MOs [mo == gsub ( " G([ABCDFGHK])S" , " B_STRPTC_GR\\1" , x_trimmed [i ] ) , ..property ] [ [1 ] ] [1L ]
next
}
# CoNS/CoPS in different languages (support for German, Dutch, Spanish, Portuguese) ----
if ( tolower ( x [i ] ) %like% ' [ck]oagulas[ea] negatie?[vf]'
| tolower ( x_trimmed [i ] ) %like% ' [ck]oagulas[ea] negatie?[vf]'
| tolower ( x [i ] ) %like% ' [ck]o?ns[^a-z]?$' ) {
# coerce S. coagulase negative
x [i ] <- MOs [mo == ' B_STPHY_CNS' , ..property ] [ [1 ] ] [1L ]
next
}
if ( tolower ( x [i ] ) %like% ' [ck]oagulas[ea] positie?[vf]'
| tolower ( x_trimmed [i ] ) %like% ' [ck]oagulas[ea] positie?[vf]'
| tolower ( x [i ] ) %like% ' [ck]o?ps[^a-z]?$' ) {
# coerce S. coagulase positive
x [i ] <- MOs [mo == ' B_STPHY_CPS' , ..property ] [ [1 ] ] [1L ]
next
}
}
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# FIRST TRY FULLNAMES AND CODES
# if only genus is available, don't select species
if ( all ( ! c ( x [i ] , x_trimmed [i ] ) %like% " " ) ) {
found <- MOs [tolower ( fullname ) %in% tolower ( c ( x_species [i ] , x_trimmed_species [i ] ) ) , ..property ] [ [1 ] ]
if ( length ( found ) > 0 ) {
x [i ] <- found [1L ]
next
}
if ( nchar ( x_trimmed [i ] ) > 4 ) {
# not when abbr is esco, stau, klpn, etc.
found <- MOs [tolower ( fullname ) %like% gsub ( " " , " .*" , x_trimmed_species [i ] , fixed = TRUE ) , ..property ] [ [1 ] ]
if ( length ( found ) > 0 ) {
x [i ] <- found [1L ]
next
}
}
}
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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 ] ]
# most probable: is exact match in fullname
if ( length ( found ) > 0 ) {
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 ] ]
# is a valid TSN
if ( length ( found ) > 0 ) {
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 ] ]
# is a valid mo
if ( length ( found ) > 0 ) {
x [i ] <- found [1L ]
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next
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}
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# try any match keeping spaces ----
found <- MOs_mostprevalent [fullname %like% x_withspaces [i ] , ..property ] [ [1 ] ]
if ( length ( found ) > 0 ) {
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 $ ----
found <- MOs_mostprevalent [fullname %like% x_withspaces_start [i ] , ..property ] [ [1 ] ]
if ( length ( found ) > 0 ) {
x [i ] <- found [1L ]
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next
}
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# try any match diregarding spaces ----
found <- MOs_mostprevalent [fullname %like% x [i ] , ..property ] [ [1 ] ]
if ( length ( found ) > 0 ) {
x [i ] <- found [1L ]
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next
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}
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# try fullname without start and stop regex, to also find subspecies ----
# like "K. pneu rhino" -> "Klebsiella pneumoniae (rhinoscleromatis)" = KLEPNERH
found <- MOs_mostprevalent [fullname %like% x_withspaces_start [i ] , ..property ] [ [1 ] ]
if ( length ( found ) > 0 ) {
x [i ] <- found [1L ]
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next
}
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# try splitting of characters and then find ID ----
# like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus
x_split <- x
x_length <- nchar ( x_trimmed [i ] )
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_mostprevalent [fullname %like% paste0 ( ' ^' , x_split [i ] ) , ..property ] [ [1 ] ]
if ( length ( found ) > 0 ) {
x [i ] <- found [1L ]
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next
}
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# try any match with text before and after original search string ----
# so "negative rods" will be "GNR"
# if (x_trimmed[i] %like% "^Gram") {
# x_trimmed[i] <- gsub("^Gram", "", x_trimmed[i], ignore.case = TRUE)
# # remove leading and trailing spaces again
# x_trimmed[i] <- trimws(x_trimmed[i], which = "both")
# }
# if (!is.na(x_trimmed[i])) {
# found <- MOs_mostprevalent[fullname %like% x_trimmed[i], ..property][[1]]
# if (length(found) > 0) {
# x[i] <- found[1L]
# next
# }
# }
# THEN TRY ALL OTHERS ----
if ( is.null ( MOs_allothers ) ) {
MOs_allothers <- MOs [prevalence == 9999 , ]
}
found <- MOs_allothers [tolower ( fullname ) == tolower ( x_backup [i ] ) , ..property ] [ [1 ] ]
# most probable: is exact match in fullname
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if ( length ( found ) > 0 ) {
x [i ] <- found [1L ]
next
}
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found <- MOs_allothers [tolower ( fullname ) == tolower ( x_trimmed [i ] ) , ..property ] [ [1 ] ]
# most probable: is exact match in fullname
if ( length ( found ) > 0 ) {
x [i ] <- found [1L ]
next
}
found <- MOs_allothers [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 ] ]
# is a valid mo
if ( length ( found ) > 0 ) {
x [i ] <- found [1L ]
next
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}
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# try any match keeping spaces ----
found <- MOs_allothers [fullname %like% x_withspaces [i ] , ..property ] [ [1 ] ]
if ( length ( found ) > 0 ) {
x [i ] <- found [1L ]
next
}
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# try any match keeping spaces, not ending with $ ----
found <- MOs_allothers [fullname %like% x_withspaces_start [i ] , ..property ] [ [1 ] ]
if ( length ( found ) > 0 ) {
x [i ] <- found [1L ]
next
}
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# try any match diregarding spaces ----
found <- MOs_allothers [fullname %like% x [i ] , ..property ] [ [1 ] ]
if ( length ( found ) > 0 ) {
x [i ] <- found [1L ]
next
}
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# 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 ] ]
if ( length ( found ) > 0 ) {
x [i ] <- found [1L ]
next
}
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# try splitting of characters and then find ID ----
# like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus
x_split <- x
x_length <- nchar ( x_trimmed [i ] )
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 ] ]
if ( length ( found ) > 0 ) {
x [i ] <- found [1L ]
next
}
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# # try any match with text before and after original search string ----
# # so "negative rods" will be "GNR"
# if (x_trimmed[i] %like% "^Gram") {
# x_trimmed[i] <- gsub("^Gram", "", x_trimmed[i], ignore.case = TRUE)
# # remove leading and trailing spaces again
# 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]]
# if (length(found) > 0) {
# x[i] <- found[1L]
# next
# }
# }
# MISCELLANEOUS ----
# look for old taxonomic names ----
if ( is.null ( MOs_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 ] , ]
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if ( NROW ( found ) > 0 ) {
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x [i ] <- MOs [tsn == found [1 , tsn_new ] , ..property ] [ [1 ] ]
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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
}
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# 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 ] , ]
if ( NROW ( found ) > 0 ) {
x [i ] <- MOs [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 ] ,
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 interpretation: '" ,
x_backup [i ] , " ' -> '" , MOs [mo == x [i ] , fullname ] , " ' (" , x [i ] , " )" ,
call. = FALSE , immediate. = TRUE )
next
}
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}
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# not found ----
x [i ] <- NA_character_
failures <- c ( failures , x_backup [i ] )
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}
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}
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failures <- failures [ ! failures %in% c ( NA , NULL , NaN ) ]
if ( length ( failures ) > 0 ) {
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warning ( " These " , length ( failures ) , " values could not be coerced (try again with allow_uncertain = TRUE):\n" ,
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paste ( ' "' , unique ( failures ) , ' "' , sep = " " , collapse = ' , ' ) ,
" ." ,
call. = FALSE )
}
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# Becker ----
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if ( Becker == TRUE | Becker == " all" ) {
# See Source. It's this figure:
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187637/figure/F3/
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if ( is.null ( MOs ) ) {
MOs <- as.data.table ( AMR :: microorganisms )
setkey ( MOs , prevalence , tsn )
}
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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" ,
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" vitulinus" , " warneri" , " xylosus" ) , ..property ] [ [1 ] ]
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CoPS <- MOs_staph [species %in% c ( " simiae" , " agnetis" , " chromogenes" ,
" delphini" , " felis" , " lutrae" ,
" hyicus" , " intermedius" ,
" pseudintermedius" , " pseudointermedius" ,
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" 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 ]
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if ( Becker == " all" ) {
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x [x == MOs [mo == ' B_STPHY_AUR' , ..property ] [ [1 ] ] [1L ] ] <- MOs [mo == ' B_STPHY_CPS' , ..property ] [ [1 ] ] [1L ]
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}
}
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# Lancefield ----
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if ( Lancefield == TRUE | Lancefield == " all" ) {
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if ( is.null ( MOs ) ) {
MOs <- as.data.table ( AMR :: microorganisms )
setkey ( MOs , prevalence , tsn )
}
# group A - S. pyogenes
x [x == MOs [mo == ' B_STRPTC_PYO' , ..property ] [ [1 ] ] [1L ] ] <- MOs [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 ]
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# group C
S_groupC <- MOs %>% filter ( genus == " Streptococcus" ,
species %in% c ( " equisimilis" , " equi" ,
" zooepidemicus" , " dysgalactiae" ) ) %>%
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pull ( property )
x [x %in% S_groupC ] <- MOs [mo == ' B_STRPTC_GRC' , ..property ] [ [1 ] ] [1L ]
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if ( Lancefield == " all" ) {
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# all Enterococci
x [x %like% " ^(Enterococcus|B_ENTRC)" ] <- MOs [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 ]
# group H - S. sanguinis
x [x == MOs [mo == ' B_STRPTC_SAN' , ..property ] [ [1 ] ] [1L ] ] <- MOs [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 ]
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}
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# left join the found results to the original input values (x_input)
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df_found <- data.frame ( input = as.character ( unique ( x_input ) ) ,
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found = x ,
stringsAsFactors = FALSE )
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df_input <- data.frame ( input = as.character ( x_input ) ,
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stringsAsFactors = FALSE )
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x <- df_input %>%
left_join ( df_found ,
by = " input" ) %>%
pull ( found )
if ( property == " mo" ) {
class ( x ) <- " mo"
attr ( x , ' package' ) <- ' AMR'
attr ( x , ' ITIS' ) <- TRUE
} else if ( property == " tsn" ) {
x <- as.integer ( x )
}
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x
}
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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 )
}
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#' @exportMethod print.mo
#' @export
#' @noRd
print.mo <- function ( x , ... ) {
cat ( " Class 'mo'\n" )
print.default ( as.character ( x ) , quote = FALSE )
}
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#' @exportMethod as.data.frame.mo
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#' @export
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#' @noRd
as.data.frame.mo <- function ( x , ... ) {
# same as as.data.frame.character but with removed stringsAsFactors
nm <- paste ( deparse ( substitute ( x ) , width.cutoff = 500L ) ,
collapse = " " )
if ( ! " nm" %in% names ( list ( ... ) ) ) {
as.data.frame.vector ( x , ... , nm = nm )
} else {
as.data.frame.vector ( x , ... )
}
}
#' @exportMethod pull.mo
#' @export
#' @importFrom dplyr pull
#' @noRd
pull.mo <- function ( .data , ... ) {
pull ( as.data.frame ( .data ) , ... )
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}