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(v2.1.1.9278) support AMR selectors in custom MDRO guideline
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@ -72,6 +72,11 @@ eucast_rules(df, rules = "custom", custom_rules = y, info = FALSE, overwrite = T
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}\if{html}{\out{</div>}}
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}
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\subsection{Sharing rules among multiple users}{
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The rules set (the \code{y} object in this case) could be exported to a shared file location using \code{\link[=saveRDS]{saveRDS()}} if you collaborate with multiple users. The custom rules set could then be imported using \code{\link[=readRDS]{readRDS()}}.
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}
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\subsection{Usage of multiple antimicrobials and antimicrobial group names}{
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You can define antimicrobial groups instead of single antimicrobials for the rule consequence, which is the part \emph{after} the tilde (~). In the examples above, the antimicrobial group \code{aminopenicillins} includes both ampicillin and amoxicillin.
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167
man/custom_mdro_guideline.Rd
Normal file
167
man/custom_mdro_guideline.Rd
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@ -0,0 +1,167 @@
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/custom_mdro_guideline.R
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\name{custom_mdro_guideline}
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\alias{custom_mdro_guideline}
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\alias{c.custom_mdro_guideline}
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\alias{print.custom_mdro_guideline}
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\title{Define Custom MDRO Guideline}
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\usage{
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custom_mdro_guideline(..., as_factor = TRUE)
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\method{c}{custom_mdro_guideline}(x, ..., as_factor = NULL)
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\method{print}{custom_mdro_guideline}(x, ...)
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}
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\arguments{
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\item{...}{Guideline rules in \link[base:tilde]{formula} notation, see below for instructions, and in \emph{Examples}.}
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\item{as_factor}{A \link{logical} to indicate whether the returned value should be an ordered \link{factor} (\code{TRUE}, default), or otherwise a \link{character} vector.}
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\item{x}{A \link{data.frame} with antimicrobials columns, like \code{AMX} or \code{amox}. Can be left blank for automatic determination.}
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}
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\value{
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A \link{list} containing the custom rules
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}
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\description{
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Define custom a MDRO guideline for your organisation or specific analysis and use the output of this function in \code{\link[=mdro]{mdro()}}.
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}
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\details{
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Using a custom MDRO guideline is of importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.
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}
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\section{How it works}{
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\subsection{Basics}{
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If you are familiar with the \code{\link[dplyr:case_when]{case_when()}} function of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule itself is written \emph{before} the tilde (\code{~}) and the consequence of the rule is written \emph{after} the tilde:
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\if{html}{\out{<div class="sourceCode r">}}\preformatted{custom <- custom_mdro_guideline(CIP == "R" & age > 60 ~ "Elderly Type A",
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ERY == "R" & age > 60 ~ "Elderly Type B")
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}\if{html}{\out{</div>}}
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If a row/an isolate matches the first rule, the value after the first \code{~} (in this case \emph{'Elderly Type A'}) will be set as MDRO value. Otherwise, the second rule will be tried and so on. The number of rules is unlimited.
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You can print the rules set in the console for an overview. Colours will help reading it if your console supports colours.
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\if{html}{\out{<div class="sourceCode r">}}\preformatted{custom
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#> A set of custom MDRO rules:
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#> 1. If CIP is R and age is higher than 60 then: Elderly Type A
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#> 2. If ERY is R and age is higher than 60 then: Elderly Type B
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#> 3. Otherwise: Negative
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#> Unmatched rows will return NA.
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#> Results will be of class 'factor', with ordered levels: Negative < Elderly Type A < Elderly Type B
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}\if{html}{\out{</div>}}
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The outcome of the function can be used for the \code{guideline} argument in the \code{\link[=mdro]{mdro()}} function:
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\if{html}{\out{<div class="sourceCode r">}}\preformatted{x <- mdro(example_isolates, guideline = custom)
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#> Determining MDROs based on custom rules, resulting in factor levels: Negative < Elderly Type A < Elderly Type B.
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#> - Custom MDRO rule 1: CIP == "R" & age > 60 (198 rows matched)
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#> - Custom MDRO rule 2: ERY == "R" & age > 60 (732 rows matched)
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#> => Found 930 custom defined MDROs out of 2000 isolates (46.5\%)
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table(x)
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#> x
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#> Negative Elderly Type A Elderly Type B
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#> 1070 198 732
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}\if{html}{\out{</div>}}
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Rules can also be combined with other custom rules by using \code{\link[=c]{c()}}:
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\if{html}{\out{<div class="sourceCode r">}}\preformatted{x <- mdro(example_isolates,
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guideline = c(custom,
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custom_mdro_guideline(ERY == "R" & age > 50 ~ "Elderly Type C")))
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#> Determining MDROs based on custom rules, resulting in factor levels: Negative < Elderly Type A < Elderly Type B < Elderly Type C.
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#> - Custom MDRO rule 1: CIP == "R" & age > 60 (198 rows matched)
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#> - Custom MDRO rule 2: ERY == "R" & age > 60 (732 rows matched)
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#> - Custom MDRO rule 3: ERY == "R" & age > 50 (109 rows matched)
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#> => Found 1039 custom defined MDROs out of 2000 isolates (52.0\%)
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table(x)
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#> x
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#> Negative Elderly Type A Elderly Type B Elderly Type C
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#> 961 198 732 109
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}\if{html}{\out{</div>}}
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}
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\subsection{Sharing rules among multiple users}{
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The rules set (the \code{custom} object in this case) could be exported to a shared file location using \code{\link[=saveRDS]{saveRDS()}} if you collaborate with multiple users. The custom rules set could then be imported using \code{\link[=readRDS]{readRDS()}}.
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}
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\subsection{Usage of multiple antimicrobials and antimicrobial group names}{
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You can define antimicrobial groups instead of single antimicrobials for the rule itself, which is the part \emph{before} the tilde (~). Use \code{\link[=any]{any()}} or \code{\link[=all]{all()}} to specify the scope of the antimicrobial group:
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\if{html}{\out{<div class="sourceCode r">}}\preformatted{custom_mdro_guideline(
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AMX == "R" ~ "My MDRO #1",
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any(cephalosporins_2nd() == "R") ~ "My MDRO #2",
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all(glycopeptides() == "R") ~ "My MDRO #3"
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)
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}\if{html}{\out{</div>}}
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These 35 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:
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\itemize{
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\item aminoglycosides\cr(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)
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\item aminopenicillins\cr(amoxicillin and ampicillin)
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\item antifungals\cr(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)
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\item antimycobacterials\cr(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)
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\item betalactams\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam)
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\item betalactams_with_inhibitor\cr(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid)
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\item carbapenems\cr(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, and tebipenem)
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\item cephalosporins\cr(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)
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\item cephalosporins_1st\cr(cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, and cephradine)
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\item cephalosporins_2nd\cr(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening test, cefprozil, cefuroxime, cefuroxime axetil, and loracarbef)
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\item cephalosporins_3rd\cr(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, and latamoxef)
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\item cephalosporins_4th\cr(cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetecol, cefoselis, cefozopran, cefpirome, and cefquinome)
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\item cephalosporins_5th\cr(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam)
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\item cephalosporins_except_caz\cr(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)
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\item fluoroquinolones\cr(besifloxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)
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\item glycopeptides\cr(avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, and vancomycin-macromethod)
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\item glycopeptides_except_lipo\cr(avoparcin, bleomycin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, and vancomycin-macromethod)
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\item isoxazolylpenicillins\cr(cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and oxacillin screening test)
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\item lincosamides\cr(clindamycin, lincomycin, and pirlimycin)
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\item lipoglycopeptides\cr(dalbavancin, oritavancin, and telavancin)
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\item macrolides\cr(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, and tylvalosin)
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\item monobactams\cr(aztreonam, aztreonam/avibactam, aztreonam/nacubactam, carumonam, and tigemonam)
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\item nitrofurans\cr(furazidin, furazolidone, nifurtoinol, nitrofurantoin, and nitrofurazone)
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\item oxazolidinones\cr(cadazolid, cycloserine, linezolid, tedizolid, and thiacetazone)
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\item penicillins\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, carbenicillin, carindacillin, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, temocillin, ticarcillin, and ticarcillin/clavulanic acid)
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\item phenicols\cr(chloramphenicol, florfenicol, and thiamphenicol)
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\item polymyxins\cr(colistin, polymyxin B, and polymyxin B/polysorbate 80)
|
||||
\item quinolones\cr(besifloxacin, cinoxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nalidixic acid screening test, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pefloxacin screening test, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)
|
||||
\item rifamycins\cr(rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine)
|
||||
\item streptogramins\cr(pristinamycin and quinupristin/dalfopristin)
|
||||
\item sulfonamides\cr(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadimethoxine, sulfadimidine, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfamoxole, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, and sulfathiourea)
|
||||
\item tetracyclines\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, and tigecycline)
|
||||
\item tetracyclines_except_tgc\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, and tetracycline screening test)
|
||||
\item trimethoprims\cr(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole)
|
||||
\item ureidopenicillins\cr(azlocillin, mezlocillin, piperacillin, and piperacillin/tazobactam)
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
\examples{
|
||||
x <- custom_mdro_guideline(
|
||||
CIP == "R" & age > 60 ~ "Elderly Type A",
|
||||
ERY == "R" & age > 60 ~ "Elderly Type B"
|
||||
)
|
||||
x
|
||||
|
||||
# run the custom rule set (verbose = TRUE will return a logbook instead of the data set):
|
||||
out <- mdro(example_isolates, guideline = x)
|
||||
table(out)
|
||||
|
||||
out <- mdro(example_isolates, guideline = x, verbose = TRUE)
|
||||
head(out)
|
||||
|
||||
# you can create custom guidelines using selectors (see ?antimicrobial_selectors)
|
||||
my_guideline <- custom_mdro_guideline(
|
||||
AMX == "R" ~ "Custom MDRO 1",
|
||||
all(cephalosporins_2nd() == "R") ~ "Custom MDRO 2"
|
||||
)
|
||||
my_guideline
|
||||
|
||||
out <- mdro(example_isolates, guideline = my_guideline)
|
||||
table(out)
|
||||
}
|
||||
86
man/mdro.Rd
86
man/mdro.Rd
@ -8,24 +8,18 @@
|
||||
\alias{BRMO}
|
||||
\alias{3MRGN}
|
||||
\alias{4MRGN}
|
||||
\alias{custom_mdro_guideline}
|
||||
\alias{brmo}
|
||||
\alias{mrgn}
|
||||
\alias{mdr_tb}
|
||||
\alias{mdr_cmi2012}
|
||||
\alias{eucast_exceptional_phenotypes}
|
||||
\title{Determine Multidrug-Resistant Organisms (MDRO)}
|
||||
\source{
|
||||
See the supported guidelines above for the \link{list} of publications used for this function.
|
||||
}
|
||||
\usage{
|
||||
mdro(x = NULL, guideline = "CMI 2012", col_mo = NULL, esbl = NA,
|
||||
carbapenemase = NA, mecA = NA, mecC = NA, vanA = NA, vanB = NA,
|
||||
info = interactive(), pct_required_classes = 0.5, combine_SI = TRUE,
|
||||
verbose = FALSE, only_sir_columns = any(is.sir(x)), ...)
|
||||
|
||||
custom_mdro_guideline(..., as_factor = TRUE)
|
||||
|
||||
brmo(x = NULL, only_sir_columns = any(is.sir(x)), ...)
|
||||
|
||||
mrgn(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...)
|
||||
@ -94,9 +88,9 @@ These functions are context-aware. This means that the \code{x} argument can be
|
||||
For the \code{pct_required_classes} argument, values above 1 will be divided by 100. This is to support both fractions (\code{0.75} or \code{3/4}) and percentages (\code{75}).
|
||||
|
||||
\strong{Note:} Every test that involves the Enterobacteriaceae family, will internally be performed using its newly named \emph{order} Enterobacterales, since the Enterobacteriaceae family has been taxonomically reclassified by Adeolu \emph{et al.} in 2016. Before that, Enterobacteriaceae was the only family under the Enterobacteriales (with an i) order. All species under the old Enterobacteriaceae family are still under the new Enterobacterales (without an i) order, but divided into multiple families. The way tests are performed now by this \code{\link[=mdro]{mdro()}} function makes sure that results from before 2016 and after 2016 are identical.
|
||||
}
|
||||
\section{Supported International / National Guidelines}{
|
||||
\subsection{Supported International / National Guidelines}{
|
||||
|
||||
Please suggest to implement guidelines by \href{https://github.com/msberends/AMR/issues/new?template=2-feature-request.yml&title=Add\%20new\%20MDRO\%20guideline}{letting us know}.
|
||||
|
||||
Currently supported guidelines are (case-insensitive):
|
||||
\itemize{
|
||||
@ -106,12 +100,16 @@ Magiorakos AP, Srinivasan A \emph{et al.} "Multidrug-resistant, extensively drug
|
||||
\item \code{guideline = "EUCAST 3.3"} (or simply \code{guideline = "EUCAST"})
|
||||
|
||||
The European international guideline - EUCAST Expert Rules Version 3.3 "Intrinsic Resistance and Unusual Phenotypes" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf}{link})
|
||||
|
||||
Also:
|
||||
\itemize{
|
||||
\item \code{guideline = "EUCAST 3.2"}
|
||||
|
||||
The European international guideline - EUCAST Expert Rules Version 3.2 "Intrinsic Resistance and Unusual Phenotypes" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf}{link})
|
||||
The former European international guideline - EUCAST Expert Rules Version 3.2 "Intrinsic Resistance and Unusual Phenotypes" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf}{link})
|
||||
\item \code{guideline = "EUCAST 3.1"}
|
||||
|
||||
The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link})
|
||||
The former European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link})
|
||||
}
|
||||
\item \code{guideline = "TB"}
|
||||
|
||||
The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (\href{https://www.who.int/publications/i/item/9789241548809}{link})
|
||||
@ -129,56 +127,15 @@ Also:
|
||||
The former Dutch national guideline - Werkgroep Infectiepreventie (WIP), RIVM, last revision as of 2017: "Bijzonder Resistente Micro-Organismen (BRMO)"
|
||||
}
|
||||
}
|
||||
|
||||
Please suggest to implement guidelines by letting us know: \url{https://github.com/msberends/AMR/issues/new}.
|
||||
}
|
||||
|
||||
\section{Using Custom Guidelines}{
|
||||
\subsection{Using Custom Guidelines}{
|
||||
|
||||
Using a custom MDRO guideline is of importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.
|
||||
|
||||
Custom guidelines can be set with the \code{\link[=custom_mdro_guideline]{custom_mdro_guideline()}} function. This is of great importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.
|
||||
|
||||
If you are familiar with the \code{\link[dplyr:case_when]{case_when()}} function of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule is written \emph{before} the tilde (\code{~}) and the consequence of the rule is written \emph{after} the tilde:
|
||||
|
||||
\if{html}{\out{<div class="sourceCode">}}\preformatted{custom <- custom_mdro_guideline(CIP == "R" & age > 60 ~ "Elderly Type A",
|
||||
ERY == "R" & age > 60 ~ "Elderly Type B")
|
||||
}\if{html}{\out{</div>}}
|
||||
|
||||
If a row/an isolate matches the first rule, the value after the first \code{~} (in this case \emph{'Elderly Type A'}) will be set as MDRO value. Otherwise, the second rule will be tried and so on. The number of rules is unlimited.
|
||||
|
||||
You can print the rules set in the console for an overview. Colours will help reading it if your console supports colours.
|
||||
|
||||
\if{html}{\out{<div class="sourceCode">}}\preformatted{custom
|
||||
#> A set of custom MDRO rules:
|
||||
#> 1. CIP is "R" and age is higher than 60 -> Elderly Type A
|
||||
#> 2. ERY is "R" and age is higher than 60 -> Elderly Type B
|
||||
#> 3. Otherwise -> Negative
|
||||
#>
|
||||
#> Unmatched rows will return NA.
|
||||
}\if{html}{\out{</div>}}
|
||||
|
||||
The outcome of the function can be used for the \code{guideline} argument in the \code{\link[=mdro]{mdro()}} function:
|
||||
|
||||
\if{html}{\out{<div class="sourceCode">}}\preformatted{x <- mdro(example_isolates,
|
||||
guideline = custom)
|
||||
table(x)
|
||||
#> Negative Elderly Type A Elderly Type B
|
||||
#> 1070 198 732
|
||||
}\if{html}{\out{</div>}}
|
||||
|
||||
Rules can also be combined with other custom rules by using \code{\link[=c]{c()}}:
|
||||
|
||||
\if{html}{\out{<div class="sourceCode">}}\preformatted{x <- mdro(example_isolates,
|
||||
guideline = c(custom,
|
||||
custom_mdro_guideline(ERY == "R" & age > 50 ~ "Elderly Type C")))
|
||||
table(x)
|
||||
#> Negative Elderly Type A Elderly Type B Elderly Type C
|
||||
#> 961 198 732 109
|
||||
}\if{html}{\out{</div>}}
|
||||
|
||||
The rules set (the \code{custom} object in this case) could be exported to a shared file location using \code{\link[=saveRDS]{saveRDS()}} if you collaborate with multiple users. The custom rules set could then be imported using \code{\link[=readRDS]{readRDS()}}.
|
||||
Custom guidelines can be set with the \code{\link[=custom_mdro_guideline]{custom_mdro_guideline()}} function.
|
||||
}
|
||||
}
|
||||
|
||||
\section{Antimicrobials}{
|
||||
|
||||
To let the function automatically detect antimicrobial column names, do not provide any named arguments. It will then use \code{\link[=guess_ab_col]{guess_ab_col()}} to find them.
|
||||
@ -194,29 +151,22 @@ This AMR package follows insight; use \code{\link[=susceptibility]{susceptibilit
|
||||
}
|
||||
|
||||
\examples{
|
||||
out <- mdro(example_isolates, guideline = "EUCAST")
|
||||
out <- mdro(example_isolates)
|
||||
str(out)
|
||||
table(out)
|
||||
|
||||
out <- mdro(example_isolates,
|
||||
guideline = custom_mdro_guideline(
|
||||
AMX == "R" ~ "Custom MDRO 1",
|
||||
VAN == "R" ~ "Custom MDRO 2"
|
||||
)
|
||||
)
|
||||
out <- mdro(example_isolates, guideline = "EUCAST 3.3")
|
||||
table(out)
|
||||
|
||||
\donttest{
|
||||
if (require("dplyr")) {
|
||||
example_isolates \%>\%
|
||||
mdro() \%>\%
|
||||
table()
|
||||
|
||||
# no need to define `x` when used inside dplyr verbs:
|
||||
example_isolates \%>\%
|
||||
mutate(MDRO = mdro()) \%>\%
|
||||
pull(MDRO) \%>\%
|
||||
table()
|
||||
count(MDRO)
|
||||
}
|
||||
}
|
||||
}
|
||||
\seealso{
|
||||
\code{\link[=custom_mdro_guideline]{custom_mdro_guideline()}}
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user