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2026-03-22 19:55:49 +00:00
parent 3560dfd611
commit c95646d39c
120 changed files with 617 additions and 675 deletions
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28
reference/antibiogram.md
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@@ -598,9 +598,9 @@ example_isolates
antibiogram(example_isolates,
antimicrobials = c(aminoglycosides(), carbapenems())
)
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin),
#> AMK (amikacin), and KAN (kanamycin)
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # An Antibiogram: 10 × 7
#> # Type: Non-WISCA with 95% CI
#> Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem Tobramycin
@@ -623,8 +623,8 @@ antibiogram(example_isolates,
ab_transform = "atc",
mo_transform = "gramstain"
)
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin),
#> AMK (amikacin), and KAN (kanamycin)
#> # An Antibiogram: 2 × 5
#> # Type: Non-WISCA with 95% CI
#> Pathogen J01GB01 J01GB03 J01GB04 J01GB06
@@ -639,7 +639,7 @@ antibiogram(example_isolates,
ab_transform = "name",
mo_transform = "name"
)
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # An Antibiogram: 5 × 3
#> # Type: Non-WISCA with 95% CI
#> Pathogen Imipenem Meropenem
@@ -677,7 +677,7 @@ antibiogram(example_isolates,
antimicrobials = ureidopenicillins() + c("", "GEN", "tobra"),
mo_transform = "gramstain"
)
#> ℹ For `ureidopenicillins()` using column 'TZP' (piperacillin/tazobactam)
#> ℹ For `?ureidopenicillins()` using column TZP (piperacillin/tazobactam)
#> # An Antibiogram: 2 × 4
#> # Type: Non-WISCA with 95% CI
#> Pathogen Piperacillin/tazobac…¹ Piperacillin/tazobac…² Piperacillin/tazobac…³
@@ -714,9 +714,9 @@ antibiogram(example_isolates,
antimicrobials = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward"
)
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin),
#> AMK (amikacin), and KAN (kanamycin)
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # An Antibiogram: 14 × 8
#> # Type: Non-WISCA with 95% CI
#> `Syndromic Group` Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem
@@ -741,7 +741,7 @@ antibiogram(example_isolates,
# now define a data set with only E. coli
ex1 <- example_isolates[which(mo_genus() == "Escherichia"), ]
#> ℹ Using column 'mo' as input for `mo_genus()` (`?AMR::mo_genus()`)
#> ℹ Using column 'mo' as input for `?mo_genus()`
# with a custom language, though this will be determined automatically
# (i.e., this table will be in Spanish on Spanish systems)
@@ -753,8 +753,8 @@ antibiogram(ex1,
),
language = "es"
)
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin),
#> AMK (amikacin), and KAN (kanamycin)
#> # An Antibiogram: 2 × 5
#> # Type: Non-WISCA with 95% CI
#> `Grupo sindrómico` Patógeno Amikacina Gentamicina Tobramicina
@@ -793,7 +793,7 @@ ureido <- antibiogram(example_isolates,
syndromic_group = "ward",
wisca = TRUE
)
#> ℹ For `ureidopenicillins()` using column 'TZP' (piperacillin/tazobactam)
#> ℹ For `?ureidopenicillins()` using column TZP (piperacillin/tazobactam)
# in an Rmd file, you would just need to return `ureido` in a chunk,
# but to be explicit here: