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improvement for forecasting resistance
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101
man/EUCAST.Rd
101
man/EUCAST.Rd
@ -15,20 +15,20 @@ EUCAST Expert Rules Version 2.0: \cr
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\usage{
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EUCAST_rules(tbl, col_bactid = "bactid", info = TRUE, amcl = "amcl",
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amik = "amik", amox = "amox", ampi = "ampi", azit = "azit",
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aztr = "aztr", cefa = "cefa", cfra = "cfra", cfep = "cfep",
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cfot = "cfot", cfox = "cfox", cfta = "cfta", cftr = "cftr",
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cfur = "cfur", chlo = "chlo", cipr = "cipr", clar = "clar",
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clin = "clin", clox = "clox", coli = "coli", czol = "czol",
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dapt = "dapt", doxy = "doxy", erta = "erta", eryt = "eryt",
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fosf = "fosf", fusi = "fusi", gent = "gent", imip = "imip",
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kana = "kana", levo = "levo", linc = "linc", line = "line",
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mero = "mero", mino = "mino", moxi = "moxi", nali = "nali",
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neom = "neom", neti = "neti", nitr = "nitr", novo = "novo",
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norf = "norf", oflo = "oflo", peni = "peni", pita = "pita",
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poly = "poly", qida = "qida", rifa = "rifa", roxi = "roxi",
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siso = "siso", teic = "teic", tetr = "tetr", tica = "tica",
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tige = "tige", tobr = "tobr", trim = "trim", trsu = "trsu",
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vanc = "vanc")
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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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cftr = "cftr", cfur = "cfur", chlo = "chlo", cipr = "cipr",
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clar = "clar", clin = "clin", clox = "clox", coli = "coli",
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czol = "czol", dapt = "dapt", doxy = "doxy", erta = "erta",
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eryt = "eryt", fosf = "fosf", fusi = "fusi", gent = "gent",
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imip = "imip", kana = "kana", levo = "levo", linc = "linc",
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line = "line", mero = "mero", mezl = "mezl", mino = "mino",
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moxi = "moxi", nali = "nali", neom = "neom", neti = "neti",
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nitr = "nitr", norf = "norf", novo = "novo", oflo = "oflo",
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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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interpretive_reading(...)
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}
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@ -39,7 +39,7 @@ interpretive_reading(...)
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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, 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. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing column will be skipped.}
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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{...}{parameters that are passed on to \code{EUCAST_rules}}
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}
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@ -49,6 +49,73 @@ 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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Abbrevations of the column containing antibiotics:
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\strong{amcl}: amoxicillin and beta-lactamase inhibitor (\emph{J01CR02}),
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\strong{amik}: amikacin (\emph{J01GB06}),
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\strong{amox}: amoxicillin (\emph{J01CA04}),
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\strong{ampi}: ampicillin (\emph{J01CA01}),
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\strong{azit}: azithromycin (\emph{J01FA10}),
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\strong{azlo}: azlocillin (\emph{J01CA09}),
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\strong{aztr}: aztreonam (\emph{J01DF01}),
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\strong{cefa}: cefaloridine (\emph{J01DB02}),
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\strong{cfep}: cefepime (\emph{J01DE01}),
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\strong{cfot}: cefotaxime (\emph{J01DD01}),
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\strong{cfox}: cefoxitin (\emph{J01DC01}),
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\strong{cfra}: cefradine (\emph{J01DB09}),
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\strong{cfta}: ceftazidime (\emph{J01DD02}),
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\strong{cftr}: ceftriaxone (\emph{J01DD04}),
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\strong{cfur}: cefuroxime (\emph{J01DC02}),
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\strong{chlo}: chloramphenicol (\emph{J01BA01}),
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\strong{cipr}: ciprofloxacin (\emph{J01MA02}),
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\strong{clar}: clarithromycin (\emph{J01FA09}),
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\strong{clin}: clindamycin (\emph{J01FF01}),
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\strong{clox}: flucloxacillin (\emph{J01CF05}),
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\strong{coli}: colistin (\emph{J01XB01}),
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\strong{czol}: cefazolin (\emph{J01DB04}),
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\strong{dapt}: daptomycin (\emph{J01XX09}),
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\strong{doxy}: doxycycline (\emph{J01AA02}),
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\strong{erta}: ertapenem (\emph{J01DH03}),
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\strong{eryt}: erythromycin (\emph{J01FA01}),
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\strong{fosf}: fosfomycin (\emph{J01XX01}),
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\strong{fusi}: fusidic acid (\emph{J01XC01}),
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\strong{gent}: gentamicin (\emph{J01GB03}),
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\strong{imip}: imipenem and cilastatin (\emph{J01DH51}),
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\strong{kana}: kanamycin (\emph{J01GB04}),
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\strong{levo}: levofloxacin (\emph{J01MA12}),
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\strong{linc}: lincomycin (\emph{J01FF02}),
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\strong{line}: linezolid (\emph{J01XX08}),
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\strong{mero}: meropenem (\emph{J01DH02}),
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\strong{mezl}: mezlocillin (\emph{J01CA10}),
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\strong{mino}: minocycline (\emph{J01AA08}),
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\strong{moxi}: moxifloxacin (\emph{J01MA14}),
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\strong{nali}: nalidixic acid (\emph{J01MB02}),
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\strong{neom}: neomycin (\emph{J01GB05}),
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\strong{neti}: netilmicin (\emph{J01GB07}),
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\strong{nitr}: nitrofurantoin (\emph{J01XE01}),
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\strong{norf}: norfloxacin (\emph{J01MA06}),
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\strong{novo}: novobiocin (an ATCvet code: \emph{QJ01XX95}),
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\strong{oflo}: ofloxacin (\emph{J01MA01}),
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\strong{peni}: penicillins, combinations with other antibacterials (\emph{J01RA01}),
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\strong{pita}: piperacillin and beta-lactamase inhibitor (\emph{J01CR05}),
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\strong{poly}: polymyxin B (\emph{J01XB02}),
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\strong{pris}: pristinamycin (\emph{J01FG01}),
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\strong{qida}: quinupristin/dalfopristin (\emph{J01FG02}),
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\strong{rifa}: rifampicin (\emph{J04AB02}),
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\strong{roxi}: roxithromycin (\emph{J01FA06}),
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\strong{siso}: sisomicin (\emph{J01GB08}),
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\strong{teic}: teicoplanin (\emph{J01XA02}),
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\strong{tetr}: tetracycline (\emph{J01AA07}),
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\strong{tica}: ticarcillin (\emph{J01CA13}),
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\strong{tige}: tigecycline (\emph{J01AA12}),
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\strong{tobr}: tobramycin (\emph{J01GB01}),
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\strong{trim}: trimethoprim (\emph{J01EA01}),
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\strong{trsu}: sulfamethoxazole and trimethoprim (\emph{J01EE01}),
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\strong{vanc}: vancomycin (\emph{J01XA01}).
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}
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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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@ -67,3 +134,7 @@ a
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b <- EUCAST_rules(a)
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b
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}
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\keyword{eucast}
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\keyword{interpretive}
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\keyword{reading}
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\keyword{resistance}
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@ -92,13 +92,13 @@ A <- my_patients \%>\%
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resistance = resistance(gent))
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B <- my_patients \%>\%
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filter(first_isolate == TRUE) \%>\%
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filter(first_isolate == TRUE) \%>\% # the 1st isolate filter
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group_by(hospital_id) \%>\%
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summarise(count = n_rsi(gent), # gentamicin
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summarise(count = n_rsi(gent),
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resistance = resistance(gent))
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# Have a look at A and B. B is more reliable because every isolate is
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# counted once. Gentamicin resitance in hospital D seems to be 5\%
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# counted once. Gentamicin resitance in hospital D appears to be 5\%
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# higher than originally thought.
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## OTHER EXAMPLES:
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@ -5,53 +5,64 @@
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\alias{rsi_predict}
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\title{Predict antimicrobial resistance}
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\usage{
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resistance_predict(tbl, col_ab, col_date,
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year_max = as.integer(format(as.Date(Sys.Date()), "\%Y")) + 15,
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year_every = 1, model = "binomial", I_as_R = TRUE,
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resistance_predict(tbl, col_ab, col_date, year_min = NULL, year_max = NULL,
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year_every = 1, minimum = 30, model = "binomial", I_as_R = TRUE,
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preserve_measurements = TRUE, info = TRUE)
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rsi_predict(tbl, col_ab, col_date,
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year_max = as.integer(format(as.Date(Sys.Date()), "\%Y")) + 15,
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year_every = 1, model = "binomial", I_as_R = TRUE,
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rsi_predict(tbl, col_ab, col_date, year_min = NULL, year_max = NULL,
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year_every = 1, minimum = 30, model = "binomial", I_as_R = TRUE,
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preserve_measurements = TRUE, info = TRUE)
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}
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\arguments{
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\item{tbl}{table that contains columns \code{col_ab} and \code{col_date}}
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\item{tbl}{a \code{data.frame} containing isolates.}
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\item{col_ab}{column name of \code{tbl} with antimicrobial interpretations (\code{R}, \code{I} and \code{S}), supports tidyverse-like quotation}
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\item{col_ab}{column name of \code{tbl} with antimicrobial interpretations (\code{R}, \code{I} and \code{S})}
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\item{col_date}{column name of the date, will be used to calculate years if this column doesn't consist of years already, supports tidyverse-like quotation}
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\item{col_date}{column name of the date, will be used to calculate years if this column doesn't consist of years already}
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\item{year_max}{highest year to use in the prediction model, deafults to 15 years after today}
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\item{year_min}{lowest year to use in the prediction model, dafaults the lowest year in \code{col_date}}
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\item{year_max}{highest year to use in the prediction model, defaults to 15 years after today}
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\item{year_every}{unit of sequence between lowest year found in the data and \code{year_max}}
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\item{minimum}{minimal amount of available isolates per year to include. Years containing less observations will be estimated by the model.}
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\item{model}{the statistical model of choice. Valid values are \code{"binomial"} (or \code{"binom"} or \code{"logit"}) or \code{"loglin"} or \code{"linear"} (or \code{"lin"}).}
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\item{I_as_R}{treat \code{I} as \code{R}}
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\item{preserve_measurements}{overwrite predictions of years that are actually available in the data, with the original data. The standard errors of those years will be \code{NA}.}
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\item{preserve_measurements}{logical to indicate whether predictions of years that are actually available in the data should be overwritten with the original data. The standard errors of those years will be \code{NA}.}
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\item{info}{print textual analysis with the name and \code{\link{summary}} of the model.}
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}
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\value{
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\code{data.frame} with columns \code{year}, \code{probR}, \code{se_min} and \code{se_max}.
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\code{data.frame} with columns:
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\itemize{
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\item{\code{year}}
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\item{\code{resistance}, the same as \code{estimated} when \code{preserve_measurements = FALSE}, and a combination of \code{observed} and \code{estimated} otherwise}
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\item{\code{se_min}, the lower bound of the standard error with a minimum of \code{0}}
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\item{\code{se_max} the upper bound of the standard error with a maximum of \code{1}}
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\item{\code{observations}, the total number of observations, i.e. S + I + R}
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\item{\code{observed}, the original observed values}
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\item{\code{estimated}, the estimated values, calculated by the model}
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}
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}
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\description{
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Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns \code{se_min} and \code{se_max}. See Examples for a real live example.
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}
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\examples{
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\dontrun{
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# use it directly:
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rsi_predict(tbl = tbl[which(first_isolate == TRUE & genus == "Haemophilus"),],
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col_ab = "amcl", col_date = "date")
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# use it with base R:
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resistance_predict(tbl = tbl[which(first_isolate == TRUE & genus == "Haemophilus"),],
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col_ab = "amcl", col_date = "date")
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# or with dplyr so you can actually read it:
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# or use dplyr so you can actually read it:
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library(dplyr)
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tbl \%>\%
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filter(first_isolate == TRUE,
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genus == "Haemophilus") \%>\%
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rsi_predict(amcl, date)
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resistance_predict(amcl, date)
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}
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@ -73,11 +84,38 @@ septic_patients \%>\%
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species == "coli",
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first_isolate == TRUE) \%>\%
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# predict resistance of cefotaxime for next years
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rsi_predict(col_ab = "cfot",
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col_date = "date",
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year_max = 2025,
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preserve_measurements = FALSE)
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resistance_predict(col_ab = "cfot",
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col_date = "date",
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year_max = 2025,
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preserve_measurements = TRUE,
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minimum = 0)
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# create nice plots with ggplot
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if (!require(ggplot2)) {
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data <- septic_patients \%>\%
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filter(bactid == "ESCCOL") \%>\%
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resistance_predict(col_ab = "amox",
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col_date = "date",
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info = FALSE,
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minimum = 15)
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ggplot(data,
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aes(x = year)) +
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geom_col(aes(y = resistance),
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fill = "grey75") +
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geom_errorbar(aes(ymin = se_min,
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ymax = se_max),
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colour = "grey50") +
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scale_y_continuous(limits = c(0, 1),
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breaks = seq(0, 1, 0.1),
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labels = paste0(seq(0, 100, 10), "\%")) +
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labs(title = expression(paste("Forecast of amoxicillin resistance in ",
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italic("E. coli"))),
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y = "\%IR",
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x = "Year") +
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theme_minimal(base_size = 13)
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}
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}
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\seealso{
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\code{\link{resistance}} \cr \code{\link{lm}} \code{\link{glm}}
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