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reference/custom_mdro_guideline.md
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@@ -413,24 +413,31 @@ All 38 antimicrobial selectors are supported for use in the rules:
- [`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
isoniazid/sulfamethoxazole/trimethoprim/pyridoxine,
ormetroprim/sulfamethoxazole, sulfachlorpyridazine, sulfadiazine,
sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine,
sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole,
sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine,
sulfamerazine/trimethoprim, sulfamethazine, sulfamethizole,
sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine,
sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole,
sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole,
sulfapyridine, sulfasuccinamide, sulfathiazole, sulfathiourea,
sulfisoxazole, sulfonamide, and trimethoprim/sulfamethoxazole
- [`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
sarecycline, tetracycline, tetracycline screening test,
tetracycline/oleandomycin, and tigecycline
- [`trimethoprims()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
can select:
brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim,
brodimoprim, iclaprim,
isoniazid/sulfamethoxazole/trimethoprim/pyridoxine,
ormetroprim/sulfamethoxazole, sulfadiazine, sulfadiazine/tetroxoprim,
sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine,
sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine,
sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim,
@@ -506,14 +513,6 @@ my_guideline
#> 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