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articles/AMR_with_tidymodels.md
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@@ -94,9 +94,9 @@ data <- example_isolates %>%
mo = as.factor(mo_gramstain(mo))) %>%
# drop NAs - the ones without a Gramstain (fungi, etc.)
drop_na()
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin),
#> AMK (amikacin), and KAN (kanamycin)
#> ℹ For `?betalactams()` using columns PEN (benzylpenicillin), OXA (oxacillin),
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> (amikacin), and KAN (kanamycin)
#> ℹ For `betalactams()` using columns PEN (benzylpenicillin), OXA (oxacillin),
#> FLC (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid),
#> AMP (ampicillin), TZP (piperacillin/tazobactam), CZO (cefazolin), FEP
#> (cefepime), CXM (cefuroxime), FOX (cefoxitin), CTX (cefotaxime), CAZ
@@ -143,9 +143,9 @@ a training set using `prep()`:
``` r
prep(resistance_recipe)
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin),
#> AMK (amikacin), and KAN (kanamycin)
#> ℹ For `?betalactams()` using columns PEN (benzylpenicillin), OXA (oxacillin),
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
#> (amikacin), and KAN (kanamycin)
#> ℹ For `betalactams()` using columns PEN (benzylpenicillin), OXA (oxacillin),
#> FLC (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid),
#> AMP (ampicillin), TZP (piperacillin/tazobactam), CZO (cefazolin), FEP
#> (cefepime), CXM (cefuroxime), FOX (cefoxitin), CTX (cefotaxime), CAZ
@@ -644,10 +644,10 @@ data_time <- example_isolates %>%
.names = "res_{.col}"),
.groups = "drop") %>%
filter(!is.na(res_AMX) & !is.na(res_AMC) & !is.na(res_CIP)) # Drop missing values
#> ℹ Using column 'mo' as input for `col_mo`.
#> ℹ `?resistance()` assumes the EUCAST guideline and thus considers the 'I'
#> ℹ Using column mo as input for `col_mo`.
#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see AMR-options.
#> option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session.
data_time