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reference/custom_mdro_guideline.md
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reference/custom_mdro_guideline.md
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# Define Custom MDRO Guideline
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Define custom a MDRO guideline for your organisation or specific
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analysis and use the output of this function in
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[`mdro()`](https://amr-for-r.org/reference/mdro.md).
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## Usage
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``` r
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custom_mdro_guideline(..., as_factor = TRUE)
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# S3 method for class 'custom_mdro_guideline'
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c(x, ..., as_factor = NULL)
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```
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## Arguments
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- ...:
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Guideline rules in [formula](https://rdrr.io/r/base/tilde.html)
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notation, see below for instructions, and in *Examples*.
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- as_factor:
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A [logical](https://rdrr.io/r/base/logical.html) to indicate whether
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the returned value should be an ordered
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[factor](https://rdrr.io/r/base/factor.html) (`TRUE`, default), or
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otherwise a [character](https://rdrr.io/r/base/character.html) vector.
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For combining rules sets (using
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[`c()`](https://rdrr.io/r/base/c.html)) this value will be inherited
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from the first set at default.
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- x:
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Existing custom MDRO rules
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## Value
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A [list](https://rdrr.io/r/base/list.html) containing the custom rules
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## Details
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Using a custom MDRO guideline is of importance if you have custom rules
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to determine MDROs in your hospital, e.g., rules that are dependent on
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ward, state of contact isolation or other variables in your data.
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### Basics
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If you are familiar with the
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[`case_when()`](https://dplyr.tidyverse.org/reference/case_when.html)
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function of the `dplyr` package, you will recognise the input method to
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set your own rules. Rules must be set using what R considers to be the
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'formula notation'. The rule itself is written *before* the tilde (`~`)
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and the consequence of the rule is written *after* the tilde:
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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 a row/an isolate matches the first rule, the value after the first
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`~` (in this case *'Elderly Type A'*) will be set as MDRO value.
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Otherwise, the second rule will be tried and so on. The number of rules
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is unlimited.
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You can print the rules set in the console for an overview. Colours will
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help reading it if your console supports colours.
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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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The outcome of the function can be used for the `guideline` argument in
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the [`mdro()`](https://amr-for-r.org/reference/mdro.md) function:
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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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Rules can also be combined with other custom rules by using
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[`c()`](https://rdrr.io/r/base/c.html):
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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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### Sharing rules among multiple users
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The rules set (the `custom` object in this case) could be exported to a
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shared file location using
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[`saveRDS()`](https://rdrr.io/r/base/readRDS.html) if you collaborate
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with multiple users. The custom rules set could then be imported using
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[`readRDS()`](https://rdrr.io/r/base/readRDS.html).
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### Usage of multiple antimicrobials and antimicrobial group names
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You can define antimicrobial groups instead of single antimicrobials for
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the rule itself, which is the part *before* the tilde (~). Use
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[`any()`](https://rdrr.io/r/base/any.html) or
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[`all()`](https://rdrr.io/r/base/all.html) to specify the scope of the
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antimicrobial group:
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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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All 35 antimicrobial selectors are supported for use in the rules:
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- [`aminoglycosides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
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can select:
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amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin,
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bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high,
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habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high,
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kanamycin/cephalexin, micronomicin, neomycin, netilmicin,
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pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin,
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streptoduocin, streptomycin, streptomycin-high, tobramycin, and
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tobramycin-high
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- [`aminopenicillins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
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can select:
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amoxicillin and ampicillin
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- [`antifungals()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
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can select:
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amorolfine, amphotericin B, amphotericin B-high, anidulafungin,
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butoconazole, caspofungin, ciclopirox, clotrimazole, econazole,
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fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin,
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ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole,
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manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin,
|
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posaconazole, rezafungin, ribociclib, sulconazole, terbinafine,
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terconazole, and voriconazole
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- [`antimycobacterials()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
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can select:
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4-aminosalicylic acid, calcium aminosalicylate, capreomycin,
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clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid,
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||||
ethionamide, isoniazid,
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isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide,
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||||
p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide,
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||||
rifabutin, rifampicin, rifampicin/ethambutol/isoniazid,
|
||||
rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid,
|
||||
rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, sodium
|
||||
aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone,
|
||||
thioacetazone/isoniazid, tiocarlide, and viomycin
|
||||
|
||||
- [`betalactams()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
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can select:
|
||||
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/taniborbactam, 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, taniborbactam, tebipenem, temocillin, ticarcillin,
|
||||
ticarcillin/clavulanic acid, and tigemonam
|
||||
|
||||
- [`betalactams_with_inhibitor()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
amoxicillin/clavulanic acid, amoxicillin/sulbactam,
|
||||
ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam,
|
||||
cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam,
|
||||
cefepime/nacubactam, cefepime/taniborbactam, 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
|
||||
|
||||
- [`carbapenems()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA,
|
||||
imipenem/relebactam, meropenem, meropenem/nacubactam,
|
||||
meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem
|
||||
acoxil, taniborbactam, and tebipenem
|
||||
|
||||
- [`cephalosporins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
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/taniborbactam, 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
|
||||
|
||||
- [`cephalosporins_1st()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin,
|
||||
cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole,
|
||||
and cephradine
|
||||
|
||||
- [`cephalosporins_2nd()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan,
|
||||
cefotiam, cefoxitin, cefoxitin screening test, cefprozil, cefuroxime,
|
||||
cefuroxime axetil, and loracarbef
|
||||
|
||||
- [`cephalosporins_3rd()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
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
|
||||
|
||||
- [`cephalosporins_4th()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
cefepime, cefepime/amikacin, cefepime/clavulanic acid,
|
||||
cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam,
|
||||
cefepime/tazobactam, cefepime/zidebactam, cefetecol, cefoselis,
|
||||
cefozopran, cefpirome, and cefquinome
|
||||
|
||||
- [`cephalosporins_5th()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole
|
||||
medocaril, and ceftolozane/tazobactam
|
||||
|
||||
- [`fluoroquinolones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
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
|
||||
|
||||
- [`glycopeptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin,
|
||||
ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin,
|
||||
vancomycin, and vancomycin-macromethod
|
||||
|
||||
- [`isoxazolylpenicillins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and
|
||||
oxacillin screening test
|
||||
|
||||
- [`lincosamides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
clindamycin, lincomycin, and pirlimycin
|
||||
|
||||
- [`lipoglycopeptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
dalbavancin, oritavancin, and telavancin
|
||||
|
||||
- [`macrolides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
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
|
||||
|
||||
- [`monobactams()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
aztreonam, aztreonam/avibactam, aztreonam/nacubactam, carumonam, and
|
||||
tigemonam
|
||||
|
||||
- [`nitrofurans()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
furazidin, furazolidone, nifurtoinol, nitrofurantoin, and
|
||||
nitrofurazone
|
||||
|
||||
- [`oxazolidinones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
cadazolid, cycloserine, linezolid, tedizolid, and thiacetazone
|
||||
|
||||
- [`penicillins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
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
|
||||
|
||||
- [`phenicols()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
chloramphenicol, florfenicol, and thiamphenicol
|
||||
|
||||
- [`polymyxins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
colistin, polymyxin B, and polymyxin B/polysorbate 80
|
||||
|
||||
- [`quinolones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
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
|
||||
|
||||
- [`rifamycins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
rifabutin, rifampicin, rifampicin/ethambutol/isoniazid,
|
||||
rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid,
|
||||
rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine
|
||||
|
||||
- [`streptogramins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
pristinamycin and quinupristin/dalfopristin
|
||||
|
||||
- [`sulfonamides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadimethoxine,
|
||||
sulfadimidine, sulfafurazole, sulfaisodimidine, sulfalene,
|
||||
sulfamazone, sulfamerazine, sulfamethizole, sulfamethoxazole,
|
||||
sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine,
|
||||
sulfamoxole, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine,
|
||||
sulfathiazole, and sulfathiourea
|
||||
|
||||
- [`tetracyclines()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
cetocycline, chlortetracycline, clomocycline, demeclocycline,
|
||||
doxycycline, eravacycline, lymecycline, metacycline, minocycline,
|
||||
omadacycline, oxytetracycline, penimepicycline, rolitetracycline,
|
||||
sarecycline, tetracycline, tetracycline screening test, and
|
||||
tigecycline
|
||||
|
||||
- [`trimethoprims()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
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
|
||||
|
||||
- [`ureidopenicillins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
|
||||
can select:
|
||||
azlocillin, mezlocillin, piperacillin, and piperacillin/tazobactam
|
||||
|
||||
## Examples
|
||||
|
||||
``` r
|
||||
x <- custom_mdro_guideline(
|
||||
CIP == "R" & age > 60 ~ "Elderly Type A",
|
||||
ERY == "R" & age > 60 ~ "Elderly Type B"
|
||||
)
|
||||
x
|
||||
#> A set of custom MDRO rules:
|
||||
#> 1. If CIP is R and age is higher than 60 then: Elderly Type A
|
||||
#> 2. If ERY is R and age is higher than 60 then: Elderly Type B
|
||||
#> 3. Otherwise: Negative
|
||||
#>
|
||||
#> Unmatched rows will return NA.
|
||||
#> Results will be of class 'factor', with ordered levels: Negative < Elderly Type A < Elderly Type B
|
||||
|
||||
# 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
|
||||
#> Negative Elderly Type A Elderly Type B
|
||||
#> 1070 198 732
|
||||
|
||||
out <- mdro(example_isolates, guideline = x, verbose = TRUE)
|
||||
head(out)
|
||||
#> row_number microorganism MDRO
|
||||
#> V1 1 <NA> Elderly Type B
|
||||
#> V2 2 <NA> Elderly Type B
|
||||
#> V3 3 <NA> Negative
|
||||
#> V4 4 <NA> Negative
|
||||
#> V5 5 <NA> Negative
|
||||
#> V6 6 <NA> Negative
|
||||
#> reason
|
||||
#> V1 matched rule 2: ERY == "R" & age > 60
|
||||
#> V2 matched rule 2: ERY == "R" & age > 60
|
||||
#> V3 no rules matched
|
||||
#> V4 no rules matched
|
||||
#> V5 no rules matched
|
||||
#> V6 no rules matched
|
||||
#> all_nonsusceptible_columns guideline
|
||||
#> V1 PEN, TMP, SXT, LNZ, VAN, TEC, TCY, ERY, CLI, AZM, RIF Custom guideline
|
||||
#> V2 PEN, TMP, SXT, LNZ, VAN, TEC, TCY, ERY, CLI, AZM, RIF Custom guideline
|
||||
#> V3 PEN, FLC, CXM, CAZ, ERY, AZM, COL Custom guideline
|
||||
#> V4 PEN, FLC, CXM, CAZ, ERY, AZM, COL Custom guideline
|
||||
#> V5 PEN, FLC, CXM, CAZ, TMP, ERY, AZM, COL Custom guideline
|
||||
#> V6 PEN, FLC, CXM, CAZ, TMP, ERY, CLI, AZM, COL Custom guideline
|
||||
|
||||
# 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
|
||||
#> A set of custom MDRO rules:
|
||||
#> 1. If AMX is R then: Custom MDRO 1
|
||||
#> 2. If all of cephalosporins_2nd() is R then: Custom MDRO 2
|
||||
#> 3. Otherwise: Negative
|
||||
#>
|
||||
#> Unmatched rows will return NA.
|
||||
#> Results will be of class 'factor', with ordered levels: Negative < Custom MDRO 1 < Custom MDRO 2
|
||||
|
||||
out <- mdro(example_isolates, guideline = my_guideline)
|
||||
#> ℹ Column 'esbl' is SIR eligible (despite only having empty values), since
|
||||
#> it seems to be tazobactam (TAZ)
|
||||
#> ℹ Column 'mecC' is SIR eligible (despite only having empty values), since
|
||||
#> it seems to be mecillinam (MEC)
|
||||
#> ℹ Column 'vanA' is SIR eligible (despite only having empty values), since
|
||||
#> it seems to be lenampicillin (LEN)
|
||||
#> ℹ Column 'vanB' is SIR eligible (despite only having empty values), since
|
||||
#> it seems to be metronidazole (MTR)
|
||||
#> ℹ For `cephalosporins_2nd()` using columns 'CXM' (cefuroxime) and 'FOX'
|
||||
#> (cefoxitin)
|
||||
#> ℹ Assuming a filter on all 2 cephalosporins_2nd. Wrap around `all()` or
|
||||
#> `any()` to prevent this note.
|
||||
table(out)
|
||||
#> out
|
||||
#> Negative Custom MDRO 1 Custom MDRO 2
|
||||
#> 1144 804 52
|
||||
```
|
||||
Reference in New Issue
Block a user