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replaced bactid by mo
This commit is contained in:
22
man/AMR-deprecated.Rd
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22
man/AMR-deprecated.Rd
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@ -0,0 +1,22 @@
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/deprecated.R
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\name{AMR-deprecated}
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\alias{AMR-deprecated}
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\alias{as.bactid}
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\alias{is.bactid}
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\alias{guess_bactid}
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\alias{ratio}
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\title{Deprecated functions}
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\usage{
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as.bactid(...)
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is.bactid(...)
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guess_bactid(...)
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ratio(x, ratio)
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}
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\description{
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These functions are \link{Deprecated}. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by.
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}
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\keyword{internal}
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@ -13,7 +13,7 @@ EUCAST Expert Rules Version 2.0: \cr
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\url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
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}
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\usage{
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EUCAST_rules(tbl, col_bactid = "bactid", info = TRUE, amcl = "amcl",
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EUCAST_rules(tbl, col_mo = "mo", info = TRUE, amcl = "amcl",
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amik = "amik", amox = "amox", ampi = "ampi", azit = "azit",
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azlo = "azlo", aztr = "aztr", cefa = "cefa", cfep = "cfep",
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cfot = "cfot", cfox = "cfox", cfra = "cfra", cfta = "cfta",
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@ -28,18 +28,21 @@ EUCAST_rules(tbl, col_bactid = "bactid", info = TRUE, amcl = "amcl",
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peni = "peni", pita = "pita", poly = "poly", pris = "pris",
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qida = "qida", rifa = "rifa", roxi = "roxi", siso = "siso",
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teic = "teic", tetr = "tetr", tica = "tica", tige = "tige",
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tobr = "tobr", trim = "trim", trsu = "trsu", vanc = "vanc")
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tobr = "tobr", trim = "trim", trsu = "trsu", vanc = "vanc",
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col_bactid = "bactid")
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interpretive_reading(...)
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}
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\arguments{
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\item{tbl}{table with antibiotic columns, like e.g. \code{amox} and \code{amcl}}
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\item{col_bactid}{column name of the bacteria ID in \code{tbl} - values of this column should be present in \code{microorganisms$bactid}, see \code{\link{microorganisms}}}
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\item{col_mo}{column name of the bacteria ID in \code{tbl} - values of this column should be present in \code{microorganisms$mo}, see \code{\link{microorganisms}}}
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\item{info}{print progress}
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\item{amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfep, cfot, cfox, cfra, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, norf, novo, oflo, peni, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc}{column names of antibiotics. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfep, cfot, cfox, cfra, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, norf, novo, oflo, peni, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{col_bactid}{Deprecated. Use \code{col_mo} instead.}
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\item{...}{parameters that are passed on to \code{EUCAST_rules}}
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}
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@ -49,7 +52,7 @@ table with edited variables of antibiotics.
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\description{
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Apply expert rules (like intrinsic resistance), as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}.
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}
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\section{Abbrevations of antibiotics}{
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\section{Antibiotics}{
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Abbrevations of the column containing antibiotics:
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@ -118,16 +121,16 @@ Abbrevations of the column containing antibiotics:
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\examples{
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a <- EUCAST_rules(septic_patients)
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a <- data.frame(bactid = c("STAAUR", # Staphylococcus aureus
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"ENCFAE", # Enterococcus faecalis
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"ESCCOL", # Escherichia coli
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"KLEPNE", # Klebsiella pneumoniae
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"PSEAER"), # Pseudomonas aeruginosa
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vanc = "-", # Vancomycin
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amox = "-", # Amoxicillin
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coli = "-", # Colistin
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cfta = "-", # Ceftazidime
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cfur = "-", # Cefuroxime
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a <- data.frame(mo = c("STAAUR", # Staphylococcus aureus
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"ENCFAE", # Enterococcus faecalis
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"ESCCOL", # Escherichia coli
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"KLEPNE", # Klebsiella pneumoniae
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"PSEAER"), # Pseudomonas aeruginosa
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vanc = "-", # Vancomycin
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amox = "-", # Amoxicillin
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coli = "-", # Colistin
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cfta = "-", # Ceftazidime
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cfur = "-", # Cefuroxime
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stringsAsFactors = FALSE)
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a
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196
man/MDRO.Rd
196
man/MDRO.Rd
@ -7,7 +7,7 @@
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\alias{EUCAST_exceptional_phenotypes}
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\title{Determine multidrug-resistant organisms (MDRO)}
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\usage{
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MDRO(tbl, country = NULL, col_bactid = "bactid", info = TRUE,
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MDRO(tbl, country = NULL, col_mo = "mo", info = TRUE,
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amcl = "amcl", amik = "amik", amox = "amox", ampi = "ampi",
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azit = "azit", aztr = "aztr", cefa = "cefa", cfra = "cfra",
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cfep = "cfep", cfot = "cfot", cfox = "cfox", cfta = "cfta",
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@ -22,7 +22,8 @@ MDRO(tbl, country = NULL, col_bactid = "bactid", info = TRUE,
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peni = "peni", pita = "pita", poly = "poly", qida = "qida",
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rifa = "rifa", roxi = "roxi", siso = "siso", teic = "teic",
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tetr = "tetr", tica = "tica", tige = "tige", tobr = "tobr",
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trim = "trim", trsu = "trsu", vanc = "vanc")
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trim = "trim", trsu = "trsu", vanc = "vanc",
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col_bactid = "bactid")
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BRMO(tbl, country = "nl", ...)
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@ -35,11 +36,129 @@ EUCAST_exceptional_phenotypes(tbl, country = "EUCAST", ...)
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\item{country}{country code to determine guidelines. EUCAST rules will be used when left empty, see Details. Should be or a code from the \href{https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements}{list of ISO 3166-1 alpha-2 country codes}. Case-insensitive. Currently supported are \code{de} (Germany) and \code{nl} (the Netherlands).}
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\item{col_bactid}{column name of the bacteria ID in \code{tbl} - values of this column should be present in \code{microorganisms$bactid}, see \code{\link{microorganisms}}}
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\item{col_mo}{column name of the bacteria ID in \code{tbl} - values of this column should be present in \code{microorganisms$mo}, see \code{\link{microorganisms}}}
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\item{info}{print progress}
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\item{amcl, amik, amox, ampi, azit, aztr, cefa, cfra, cfep, cfot, cfox, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, metr, mino, moxi, nali, neom, neti, nitr, novo, norf, oflo, peni, pita, poly, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc}{column names of antibiotics. column names of antibiotics}
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\item{amcl}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{amik}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{amox}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{ampi}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{azit}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{aztr}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{cefa}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{cfra}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{cfep}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{cfot}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{cfox}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{cfta}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{cftr}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{cfur}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{chlo}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{cipr}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{clar}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{clin}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{clox}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{coli}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{czol}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{dapt}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{doxy}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{erta}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{eryt}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{fosf}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{fusi}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{gent}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{imip}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{kana}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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||||
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\item{levo}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{linc}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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||||
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\item{line}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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\item{mero}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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||||
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||||
\item{metr}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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||||
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\item{mino}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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||||
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\item{moxi}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
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||||
\item{nali}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
|
||||
\item{neom}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
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||||
\item{neti}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
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||||
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||||
\item{nitr}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
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||||
\item{novo}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
|
||||
\item{norf}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
|
||||
\item{oflo}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
|
||||
\item{peni}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
|
||||
\item{pita}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
|
||||
\item{poly}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
|
||||
\item{qida}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
|
||||
\item{rifa}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
|
||||
\item{roxi}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
|
||||
\item{siso}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
|
||||
\item{teic}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
|
||||
\item{tetr}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
|
||||
\item{tica}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
|
||||
\item{tige}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
|
||||
\item{tobr}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
|
||||
\item{trim}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
|
||||
\item{trsu}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
|
||||
\item{vanc}{column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.}
|
||||
|
||||
\item{col_bactid}{Deprecated. Use \code{col_mo} instead.}
|
||||
|
||||
\item{...}{parameters that are passed on to methods}
|
||||
}
|
||||
@ -52,10 +171,77 @@ Determine which isolates are multidrug-resistant organisms (MDRO) according to c
|
||||
\details{
|
||||
When \code{country} will be left blank, guidelines will be taken from EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}).
|
||||
}
|
||||
\section{Antibiotics}{
|
||||
|
||||
Abbrevations of the column containing antibiotics:
|
||||
|
||||
\strong{amcl}: amoxicillin and beta-lactamase inhibitor (\emph{J01CR02}),
|
||||
\strong{amik}: amikacin (\emph{J01GB06}),
|
||||
\strong{amox}: amoxicillin (\emph{J01CA04}),
|
||||
\strong{ampi}: ampicillin (\emph{J01CA01}),
|
||||
\strong{azit}: azithromycin (\emph{J01FA10}),
|
||||
\strong{azlo}: azlocillin (\emph{J01CA09}),
|
||||
\strong{aztr}: aztreonam (\emph{J01DF01}),
|
||||
\strong{cefa}: cefaloridine (\emph{J01DB02}),
|
||||
\strong{cfep}: cefepime (\emph{J01DE01}),
|
||||
\strong{cfot}: cefotaxime (\emph{J01DD01}),
|
||||
\strong{cfox}: cefoxitin (\emph{J01DC01}),
|
||||
\strong{cfra}: cefradine (\emph{J01DB09}),
|
||||
\strong{cfta}: ceftazidime (\emph{J01DD02}),
|
||||
\strong{cftr}: ceftriaxone (\emph{J01DD04}),
|
||||
\strong{cfur}: cefuroxime (\emph{J01DC02}),
|
||||
\strong{chlo}: chloramphenicol (\emph{J01BA01}),
|
||||
\strong{cipr}: ciprofloxacin (\emph{J01MA02}),
|
||||
\strong{clar}: clarithromycin (\emph{J01FA09}),
|
||||
\strong{clin}: clindamycin (\emph{J01FF01}),
|
||||
\strong{clox}: flucloxacillin (\emph{J01CF05}),
|
||||
\strong{coli}: colistin (\emph{J01XB01}),
|
||||
\strong{czol}: cefazolin (\emph{J01DB04}),
|
||||
\strong{dapt}: daptomycin (\emph{J01XX09}),
|
||||
\strong{doxy}: doxycycline (\emph{J01AA02}),
|
||||
\strong{erta}: ertapenem (\emph{J01DH03}),
|
||||
\strong{eryt}: erythromycin (\emph{J01FA01}),
|
||||
\strong{fosf}: fosfomycin (\emph{J01XX01}),
|
||||
\strong{fusi}: fusidic acid (\emph{J01XC01}),
|
||||
\strong{gent}: gentamicin (\emph{J01GB03}),
|
||||
\strong{imip}: imipenem and cilastatin (\emph{J01DH51}),
|
||||
\strong{kana}: kanamycin (\emph{J01GB04}),
|
||||
\strong{levo}: levofloxacin (\emph{J01MA12}),
|
||||
\strong{linc}: lincomycin (\emph{J01FF02}),
|
||||
\strong{line}: linezolid (\emph{J01XX08}),
|
||||
\strong{mero}: meropenem (\emph{J01DH02}),
|
||||
\strong{mezl}: mezlocillin (\emph{J01CA10}),
|
||||
\strong{mino}: minocycline (\emph{J01AA08}),
|
||||
\strong{moxi}: moxifloxacin (\emph{J01MA14}),
|
||||
\strong{nali}: nalidixic acid (\emph{J01MB02}),
|
||||
\strong{neom}: neomycin (\emph{J01GB05}),
|
||||
\strong{neti}: netilmicin (\emph{J01GB07}),
|
||||
\strong{nitr}: nitrofurantoin (\emph{J01XE01}),
|
||||
\strong{norf}: norfloxacin (\emph{J01MA06}),
|
||||
\strong{novo}: novobiocin (an ATCvet code: \emph{QJ01XX95}),
|
||||
\strong{oflo}: ofloxacin (\emph{J01MA01}),
|
||||
\strong{peni}: penicillins, combinations with other antibacterials (\emph{J01RA01}),
|
||||
\strong{pita}: piperacillin and beta-lactamase inhibitor (\emph{J01CR05}),
|
||||
\strong{poly}: polymyxin B (\emph{J01XB02}),
|
||||
\strong{pris}: pristinamycin (\emph{J01FG01}),
|
||||
\strong{qida}: quinupristin/dalfopristin (\emph{J01FG02}),
|
||||
\strong{rifa}: rifampicin (\emph{J04AB02}),
|
||||
\strong{roxi}: roxithromycin (\emph{J01FA06}),
|
||||
\strong{siso}: sisomicin (\emph{J01GB08}),
|
||||
\strong{teic}: teicoplanin (\emph{J01XA02}),
|
||||
\strong{tetr}: tetracycline (\emph{J01AA07}),
|
||||
\strong{tica}: ticarcillin (\emph{J01CA13}),
|
||||
\strong{tige}: tigecycline (\emph{J01AA12}),
|
||||
\strong{tobr}: tobramycin (\emph{J01GB01}),
|
||||
\strong{trim}: trimethoprim (\emph{J01EA01}),
|
||||
\strong{trsu}: sulfamethoxazole and trimethoprim (\emph{J01EE01}),
|
||||
\strong{vanc}: vancomycin (\emph{J01XA01}).
|
||||
}
|
||||
|
||||
\examples{
|
||||
library(dplyr)
|
||||
|
||||
septic_patients \%>\%
|
||||
mutate(EUCAST = MDRO(.),
|
||||
BRMO = MDRO(., "nl"))
|
||||
BRMO = BRMO(.))
|
||||
}
|
||||
|
||||
@ -1,11 +1,11 @@
|
||||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/bactid.R
|
||||
\name{as.bactid}
|
||||
\alias{as.bactid}
|
||||
\alias{bactid}
|
||||
\alias{guess_bactid}
|
||||
\alias{is.bactid}
|
||||
\title{Transform to bacteria ID}
|
||||
% Please edit documentation in R/mo.R
|
||||
\name{as.mo}
|
||||
\alias{as.mo}
|
||||
\alias{mo}
|
||||
\alias{is.mo}
|
||||
\alias{guess_mo}
|
||||
\title{Transform to microorganism ID}
|
||||
\source{
|
||||
[1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \cr
|
||||
\url{https://dx.doi.org/10.1128/CMR.00109-13} \cr
|
||||
@ -13,11 +13,11 @@
|
||||
\url{https://dx.doi.org/10.1084/jem.57.4.571}
|
||||
}
|
||||
\usage{
|
||||
as.bactid(x, Becker = FALSE, Lancefield = FALSE)
|
||||
as.mo(x, Becker = FALSE, Lancefield = FALSE)
|
||||
|
||||
guess_bactid(x, Becker = FALSE, Lancefield = FALSE)
|
||||
is.mo(x)
|
||||
|
||||
is.bactid(x)
|
||||
guess_mo(x, Becker = FALSE, Lancefield = FALSE)
|
||||
}
|
||||
\arguments{
|
||||
\item{x}{a character vector or a dataframe with one or two columns}
|
||||
@ -27,15 +27,15 @@ is.bactid(x)
|
||||
\item{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, i.e. \emph{Streptococcus dysgalactiae} will be group C, although officially it was also categorised into groups G and L. Groups D and E will be ignored, since they are \emph{Enterococci}.}
|
||||
}
|
||||
\value{
|
||||
Character (vector) with class \code{"bactid"}. Unknown values will return \code{NA}.
|
||||
Character (vector) with class \code{"mo"}. Unknown values will return \code{NA}.
|
||||
}
|
||||
\description{
|
||||
Use this function to determine a valid ID based on a genus (and species). This input can be a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), or just a genus. You could also \code{\link{select}} a genus and species column, zie Examples.
|
||||
}
|
||||
\details{
|
||||
\code{guess_bactid} is an alias of \code{as.bactid}.
|
||||
\code{guess_mo} is an alias of \code{as.mo}.
|
||||
|
||||
Use the \code{\link{mo_property}} functions to get properties based on the returned bactid, see Examples.
|
||||
Use the \code{\link{mo_property}} functions to get properties based on the returned mo, see Examples.
|
||||
|
||||
Some exceptions have been built in to get more logical results, based on prevalence of human pathogens. These are:
|
||||
\itemize{
|
||||
@ -49,45 +49,45 @@ For example, \code{"Gram negative rods"} and \code{"GNR"} will both return the I
|
||||
}
|
||||
\examples{
|
||||
# These examples all return "STAAUR", the ID of S. aureus:
|
||||
as.bactid("stau")
|
||||
as.bactid("STAU")
|
||||
as.bactid("staaur")
|
||||
as.bactid("S. aureus")
|
||||
as.bactid("S aureus")
|
||||
as.bactid("Staphylococcus aureus")
|
||||
as.bactid("MRSA") # Methicillin Resistant S. aureus
|
||||
as.bactid("VISA") # Vancomycin Intermediate S. aureus
|
||||
as.bactid("VRSA") # Vancomycin Resistant S. aureus
|
||||
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
|
||||
|
||||
# guess_bactid is an alias of as.bactid and works the same
|
||||
guess_bactid("S. epidermidis") # will remain species: STAEPI
|
||||
guess_bactid("S. epidermidis", Becker = TRUE) # will not remain species: STACNS
|
||||
# guess_mo is an alias of as.mo and works the same
|
||||
guess_mo("S. epidermidis") # will remain species: STAEPI
|
||||
guess_mo("S. epidermidis", Becker = TRUE) # will not remain species: STACNS
|
||||
|
||||
guess_bactid("S. pyogenes") # will remain species: STCAGA
|
||||
guess_bactid("S. pyogenes", Lancefield = TRUE) # will not remain species: STCGRA
|
||||
guess_mo("S. pyogenes") # will remain species: STCAGA
|
||||
guess_mo("S. pyogenes", Lancefield = TRUE) # will not remain species: STCGRA
|
||||
|
||||
# Use mo_* functions to get a specific property based on a bactid
|
||||
Ecoli <- as.bactid("E. coli") # returns `ESCCOL`
|
||||
# Use mo_* functions to get a specific property based on `mo`
|
||||
Ecoli <- as.mo("E. coli") # returns `ESCCOL`
|
||||
mo_genus(Ecoli) # returns "Escherichia"
|
||||
mo_gramstain(Ecoli) # returns "Negative rods"
|
||||
|
||||
\dontrun{
|
||||
df$bactid <- as.bactid(df$microorganism_name)
|
||||
df$mo <- as.mo(df$microorganism_name)
|
||||
|
||||
# the select function of tidyverse is also supported:
|
||||
library(dplyr)
|
||||
df$bactid <- df \%>\%
|
||||
df$mo <- df \%>\%
|
||||
select(microorganism_name) \%>\%
|
||||
guess_bactid()
|
||||
guess_mo()
|
||||
|
||||
# and can even contain 2 columns, which is convenient for genus/species combinations:
|
||||
df$bactid <- df \%>\%
|
||||
df$mo <- df \%>\%
|
||||
select(genus, species) \%>\%
|
||||
guess_bactid()
|
||||
guess_mo()
|
||||
|
||||
# same result:
|
||||
df <- df \%>\%
|
||||
mutate(bactid = guess_bactid(paste(genus, species)))
|
||||
mutate(mo = guess_mo(paste(genus, species)))
|
||||
}
|
||||
}
|
||||
\seealso{
|
||||
@ -95,7 +95,7 @@ df <- df \%>\%
|
||||
}
|
||||
\keyword{Becker}
|
||||
\keyword{Lancefield}
|
||||
\keyword{bactid}
|
||||
\keyword{becker}
|
||||
\keyword{guess}
|
||||
\keyword{lancefield}
|
||||
\keyword{mo}
|
||||
@ -7,13 +7,13 @@
|
||||
Methodology of this function is based on: \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
|
||||
}
|
||||
\usage{
|
||||
first_isolate(tbl, col_date, col_patient_id, col_bactid = NA,
|
||||
first_isolate(tbl, col_date, col_patient_id, col_mo = NA,
|
||||
col_testcode = NA, col_specimen = NA, col_icu = NA,
|
||||
col_keyantibiotics = NA, episode_days = 365,
|
||||
testcodes_exclude = "", icu_exclude = FALSE, filter_specimen = NA,
|
||||
output_logical = TRUE, type = "keyantibiotics", ignore_I = TRUE,
|
||||
points_threshold = 2, info = TRUE, col_genus = NA,
|
||||
col_species = NA)
|
||||
points_threshold = 2, info = TRUE, col_bactid = NA,
|
||||
col_genus = NA, col_species = NA)
|
||||
}
|
||||
\arguments{
|
||||
\item{tbl}{a \code{data.frame} containing isolates.}
|
||||
@ -22,7 +22,7 @@ first_isolate(tbl, col_date, col_patient_id, col_bactid = NA,
|
||||
|
||||
\item{col_patient_id}{column name of the unique IDs of the patients}
|
||||
|
||||
\item{col_bactid}{column name of the unique IDs of the microorganisms: \code{bactid}'s. If this column has another class than \code{"bactid"}, values will be coerced using \code{\link{as.bactid}}.}
|
||||
\item{col_mo}{column name of the unique IDs of the microorganisms, see \code{\link{mo}}. If this column has another class than \code{"mo"}, values will be coerced using \code{\link{as.mo}}.}
|
||||
|
||||
\item{col_testcode}{column name of the test codes. Use \code{col_testcode = NA} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored. Supports tidyverse-like quotation.}
|
||||
|
||||
@ -50,9 +50,11 @@ first_isolate(tbl, col_date, col_patient_id, col_bactid = NA,
|
||||
|
||||
\item{info}{print progress}
|
||||
|
||||
\item{col_genus}{(deprecated, use \code{col_bactid} instead) column name of the genus of the microorganisms}
|
||||
\item{col_bactid}{(deprecated, use \code{col_mo} instead)}
|
||||
|
||||
\item{col_species}{(deprecated, use \code{col_bactid} instead) column name of the species of the microorganisms}
|
||||
\item{col_genus}{(deprecated, use \code{col_mo} instead) column name of the genus of the microorganisms}
|
||||
|
||||
\item{col_species}{(deprecated, use \code{col_mo} instead) column name of the species of the microorganisms}
|
||||
}
|
||||
\value{
|
||||
A vector to add to table, see Examples.
|
||||
@ -84,7 +86,7 @@ my_patients <- septic_patients \%>\%
|
||||
mutate(first_isolate = first_isolate(.,
|
||||
col_date = "date",
|
||||
col_patient_id = "patient_id",
|
||||
col_bactid = "bactid"))
|
||||
col_mo = "mo"))
|
||||
|
||||
# Now let's see if first isolates matter:
|
||||
A <- my_patients \%>\%
|
||||
|
||||
@ -88,7 +88,7 @@ septic_patients \%>\% freq(hospital_id) #<- easiest to remember when you're use
|
||||
# you could also use `select` or `pull` to get your variables
|
||||
septic_patients \%>\%
|
||||
filter(hospital_id == "A") \%>\%
|
||||
select(bactid) \%>\%
|
||||
select(mo) \%>\%
|
||||
freq()
|
||||
|
||||
# multiple selected variables will be pasted together
|
||||
@ -100,7 +100,7 @@ septic_patients \%>\%
|
||||
# get top 10 bugs of hospital A as a vector
|
||||
septic_patients \%>\%
|
||||
filter(hospital_id == "A") \%>\%
|
||||
freq(bactid) \%>\%
|
||||
freq(mo) \%>\%
|
||||
top_freq(10)
|
||||
|
||||
# save frequency table to an object
|
||||
|
||||
@ -119,14 +119,14 @@ septic_patients \%>\%
|
||||
# genuine analysis: check 2 most prevalent microorganisms
|
||||
septic_patients \%>\%
|
||||
# create new bacterial ID's, with all CoNS under the same group (Becker et al.)
|
||||
mutate(bactid = as.bactid(bactid, Becker = TRUE)) \%>\%
|
||||
mutate(mo = as.mo(mo, Becker = TRUE)) \%>\%
|
||||
# filter on top 2 bacterial ID's
|
||||
filter(bactid \%in\% top_freq(freq(.$bactid), 2)) \%>\%
|
||||
filter(mo \%in\% top_freq(freq(.$mo), 2)) \%>\%
|
||||
# determine first isolates
|
||||
mutate(first_isolate = first_isolate(.,
|
||||
col_date = "date",
|
||||
col_patient_id = "patient_id",
|
||||
col_bactid = "bactid")) \%>\%
|
||||
col_mo = "mo")) \%>\%
|
||||
# filter on first isolates
|
||||
filter(first_isolate == TRUE) \%>\%
|
||||
# join the `microorganisms` data set
|
||||
@ -140,7 +140,7 @@ septic_patients \%>\%
|
||||
ggplot_rsi(x = "Antibiotic",
|
||||
facet = "mo") +
|
||||
labs(title = "AMR of Top Two Microorganisms In Blood Culture Isolates",
|
||||
subtitle = "Only First Isolates, CoNS grouped according to Becker et al.",
|
||||
subtitle = "Only First Isolates, CoNS grouped according to Becker et al. (2014)",
|
||||
x = "Microorganisms")
|
||||
}
|
||||
}
|
||||
|
||||
14
man/join.Rd
14
man/join.Rd
@ -11,22 +11,22 @@
|
||||
\alias{anti_join_microorganisms}
|
||||
\title{Join a table with \code{microorganisms}}
|
||||
\usage{
|
||||
inner_join_microorganisms(x, by = "bactid", suffix = c("2", ""), ...)
|
||||
inner_join_microorganisms(x, by = "mo", suffix = c("2", ""), ...)
|
||||
|
||||
left_join_microorganisms(x, by = "bactid", suffix = c("2", ""), ...)
|
||||
left_join_microorganisms(x, by = "mo", suffix = c("2", ""), ...)
|
||||
|
||||
right_join_microorganisms(x, by = "bactid", suffix = c("2", ""), ...)
|
||||
right_join_microorganisms(x, by = "mo", suffix = c("2", ""), ...)
|
||||
|
||||
full_join_microorganisms(x, by = "bactid", suffix = c("2", ""), ...)
|
||||
full_join_microorganisms(x, by = "mo", suffix = c("2", ""), ...)
|
||||
|
||||
semi_join_microorganisms(x, by = "bactid", ...)
|
||||
semi_join_microorganisms(x, by = "mo", ...)
|
||||
|
||||
anti_join_microorganisms(x, by = "bactid", ...)
|
||||
anti_join_microorganisms(x, by = "mo", ...)
|
||||
}
|
||||
\arguments{
|
||||
\item{x}{existing table to join, also supports character vectors}
|
||||
|
||||
\item{by}{a variable to join by - could be a column name of \code{x} with values that exist in \code{microorganisms$bactid} (like \code{by = "bacteria_id"}), or another column in \code{\link{microorganisms}} (but then it should be named, like \code{by = c("my_genus_species" = "fullname")})}
|
||||
\item{by}{a variable to join by - could be a column name of \code{x} with values that exist in \code{microorganisms$mo} (like \code{by = "bacteria_id"}), or another column in \code{\link{microorganisms}} (but then it should be named, like \code{by = c("my_genus_species" = "fullname")})}
|
||||
|
||||
\item{suffix}{if there are non-joined duplicate variables in \code{x} and \code{y}, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.}
|
||||
|
||||
|
||||
@ -5,13 +5,14 @@
|
||||
\alias{key_antibiotics_equal}
|
||||
\title{Key antibiotics for first \emph{weighted} isolates}
|
||||
\usage{
|
||||
key_antibiotics(tbl, col_bactid = "bactid", universal_1 = "amox",
|
||||
key_antibiotics(tbl, col_mo = "mo", universal_1 = "amox",
|
||||
universal_2 = "amcl", universal_3 = "cfur", universal_4 = "pita",
|
||||
universal_5 = "cipr", universal_6 = "trsu", GramPos_1 = "vanc",
|
||||
GramPos_2 = "teic", GramPos_3 = "tetr", GramPos_4 = "eryt",
|
||||
GramPos_5 = "oxac", GramPos_6 = "rifa", GramNeg_1 = "gent",
|
||||
GramNeg_2 = "tobr", GramNeg_3 = "coli", GramNeg_4 = "cfot",
|
||||
GramNeg_5 = "cfta", GramNeg_6 = "mero", warnings = TRUE)
|
||||
GramNeg_5 = "cfta", GramNeg_6 = "mero", warnings = TRUE,
|
||||
col_bactid = "bactid")
|
||||
|
||||
key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"),
|
||||
ignore_I = TRUE, points_threshold = 2, info = FALSE)
|
||||
@ -19,7 +20,7 @@ key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"),
|
||||
\arguments{
|
||||
\item{tbl}{table with antibiotics coloms, like \code{amox} and \code{amcl}.}
|
||||
|
||||
\item{col_bactid}{column name of the unique IDs of the microorganisms: \code{bactid}'s. If this column has another class than \code{"bactid"}, values will be coerced using \code{\link{as.bactid}}.}
|
||||
\item{col_mo}{column name of the unique IDs of the microorganisms, see \code{\link{mo}}. If this column has another class than \code{"mo"}, values will be coerced using \code{\link{as.mo}}.}
|
||||
|
||||
\item{universal_1, universal_2, universal_3, universal_4, universal_5, universal_6}{column names of \strong{broad-spectrum} antibiotics, case-insensitive}
|
||||
|
||||
@ -29,6 +30,8 @@ key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"),
|
||||
|
||||
\item{warnings}{give warning about missing antibiotic columns, they will anyway be ignored}
|
||||
|
||||
\item{col_bactid}{(deprecated, use \code{col_mo} instead)}
|
||||
|
||||
\item{x, y}{characters to compare}
|
||||
|
||||
\item{type}{type to determine weighed isolates; can be \code{"keyantibiotics"} or \code{"points"}, see Details}
|
||||
@ -76,9 +79,9 @@ my_patients <- my_patients \%>\%
|
||||
mutate(keyab = key_antibiotics(.)) \%>\%
|
||||
mutate(
|
||||
# now calculate first isolates
|
||||
first_regular = first_isolate(., "date", "patient_id", "bactid"),
|
||||
first_regular = first_isolate(., "date", "patient_id", "mo"),
|
||||
# and first WEIGHTED isolates
|
||||
first_weighted = first_isolate(., "date", "patient_id", "bactid",
|
||||
first_weighted = first_isolate(., "date", "patient_id", "mo",
|
||||
col_keyantibiotics = "keyab")
|
||||
)
|
||||
|
||||
|
||||
@ -6,7 +6,7 @@
|
||||
\title{Dataset with ~2650 microorganisms}
|
||||
\format{A data.frame with 2,646 observations and 12 variables:
|
||||
\describe{
|
||||
\item{\code{bactid}}{ID of microorganism}
|
||||
\item{\code{mo}}{ID of microorganism}
|
||||
\item{\code{bactsys}}{Bactsyscode of microorganism}
|
||||
\item{\code{family}}{Family name of microorganism}
|
||||
\item{\code{genus}}{Genus name of microorganism, like \code{"Echerichia"}}
|
||||
@ -26,6 +26,6 @@ microorganisms
|
||||
A dataset containing 2,646 microorganisms. MO codes of the UMCG can be looked up using \code{\link{microorganisms.umcg}}.
|
||||
}
|
||||
\seealso{
|
||||
\code{\link{guess_bactid}} \code{\link{antibiotics}} \code{\link{microorganisms.umcg}}
|
||||
\code{\link{guess_mo}} \code{\link{antibiotics}} \code{\link{microorganisms.umcg}}
|
||||
}
|
||||
\keyword{datasets}
|
||||
|
||||
@ -6,16 +6,16 @@
|
||||
\title{Translation table for UMCG with ~1100 microorganisms}
|
||||
\format{A data.frame with 1090 observations and 2 variables:
|
||||
\describe{
|
||||
\item{\code{mocode}}{Code of microorganism according to UMCG MMB}
|
||||
\item{\code{bactid}}{Code of microorganism in \code{\link{microorganisms}}}
|
||||
\item{\code{umcg}}{Code of microorganism according to UMCG MMB}
|
||||
\item{\code{mo}}{Code of microorganism in \code{\link{microorganisms}}}
|
||||
}}
|
||||
\usage{
|
||||
microorganisms.umcg
|
||||
}
|
||||
\description{
|
||||
A dataset containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$bactid} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{bactid}'s with \code{\link{guess_bactid}}.
|
||||
A dataset containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$mo} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{mo}'s with \code{\link{guess_mo}}.
|
||||
}
|
||||
\seealso{
|
||||
\code{\link{guess_bactid}} \code{\link{microorganisms}}
|
||||
\code{\link{guess_mo}} \code{\link{microorganisms}}
|
||||
}
|
||||
\keyword{datasets}
|
||||
|
||||
@ -37,12 +37,12 @@ mo_type_nl(x)
|
||||
mo_gramstain_nl(x)
|
||||
}
|
||||
\arguments{
|
||||
\item{x}{a (vector of a) valid \code{\link{bactid}} or any text that can be coerced to a valid bactid with \code{\link{as.bactid}}}
|
||||
\item{x}{a (vector of a) valid \code{\link{mo}} or any text that can be coerced to a valid microorganism code with \code{\link{as.mo}}}
|
||||
|
||||
\item{property}{one of the column names of one of the \code{\link{microorganisms}} data set, like \code{"bactid"}, \code{"bactsys"}, \code{"family"}, \code{"genus"}, \code{"species"}, \code{"fullname"}, \code{"gramstain"} and \code{"aerobic"}}
|
||||
\item{property}{one of the column names of one of the \code{\link{microorganisms}} data set, like \code{"mo"}, \code{"bactsys"}, \code{"family"}, \code{"genus"}, \code{"species"}, \code{"fullname"}, \code{"gramstain"} and \code{"aerobic"}}
|
||||
}
|
||||
\description{
|
||||
Use these functions to return a specific property of a microorganism from the \code{\link{microorganisms}} data set, based on their \code{bactid}. Get such an ID with \code{\link{as.bactid}}.
|
||||
Use these functions to return a specific property of a microorganism from the \code{\link{microorganisms}} data set, based on their \code{mo}. Get such an ID with \code{\link{as.mo}}.
|
||||
}
|
||||
\examples{
|
||||
# All properties
|
||||
|
||||
@ -71,13 +71,13 @@ tbl \%>\%
|
||||
library(dplyr)
|
||||
septic_patients \%>\%
|
||||
# get bacteria properties like genus and species
|
||||
left_join_microorganisms("bactid") \%>\%
|
||||
left_join_microorganisms("mo") \%>\%
|
||||
# calculate first isolates
|
||||
mutate(first_isolate =
|
||||
first_isolate(.,
|
||||
"date",
|
||||
"patient_id",
|
||||
"bactid",
|
||||
"mo",
|
||||
col_specimen = NA,
|
||||
col_icu = NA)) \%>\%
|
||||
# filter on first E. coli isolates
|
||||
@ -95,7 +95,7 @@ septic_patients \%>\%
|
||||
if (!require(ggplot2)) {
|
||||
|
||||
data <- septic_patients \%>\%
|
||||
filter(bactid == "ESCCOL") \%>\%
|
||||
filter(mo == "ESCCOL") \%>\%
|
||||
resistance_predict(col_ab = "amox",
|
||||
col_date = "date",
|
||||
info = FALSE,
|
||||
|
||||
@ -14,7 +14,7 @@
|
||||
\item{\code{age}}{age of the patient}
|
||||
\item{\code{sex}}{sex of the patient}
|
||||
\item{\code{patient_id}}{ID of the patient, first 10 characters of an SHA hash containing irretrievable information}
|
||||
\item{\code{bactid}}{ID of microorganism, see \code{\link{microorganisms}}}
|
||||
\item{\code{mo}}{ID of microorganism, see \code{\link{microorganisms}}}
|
||||
\item{\code{peni:rifa}}{40 different antibiotics with class \code{rsi} (see \code{\link{as.rsi}}); these column names occur in \code{\link{antibiotics}} data set and can be translated with \code{\link{abname}}}
|
||||
}}
|
||||
\usage{
|
||||
@ -36,7 +36,7 @@ library(dplyr)
|
||||
|
||||
# Add first isolates to our dataset:
|
||||
my_data <- my_data \%>\%
|
||||
mutate(first_isolates = first_isolate(my_data, "date", "patient_id", "bactid"))
|
||||
mutate(first_isolates = first_isolate(my_data, "date", "patient_id", "mo"))
|
||||
|
||||
# -------- #
|
||||
# ANALYSIS #
|
||||
@ -46,7 +46,7 @@ my_data <- my_data \%>\%
|
||||
# and numbers (n) of E. coli, divided by hospital:
|
||||
|
||||
my_data \%>\%
|
||||
filter(bactid == guess_bactid("E. coli"),
|
||||
filter(mo == guess_mo("E. coli"),
|
||||
first_isolates == TRUE) \%>\%
|
||||
group_by(hospital_id) \%>\%
|
||||
summarise(n = n_rsi(amox),
|
||||
@ -57,7 +57,7 @@ my_data \%>\%
|
||||
# percentages of E. coli, trend over the years:
|
||||
|
||||
my_data \%>\%
|
||||
filter(bactid == guess_bactid("E. coli"),
|
||||
filter(mo == guess_mo("E. coli"),
|
||||
first_isolates == TRUE) \%>\%
|
||||
group_by(year = format(date, "\%Y")) \%>\%
|
||||
summarise(n = n_rsi(amcl),
|
||||
|
||||
Reference in New Issue
Block a user