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articles/AMR_with_tidymodels.md
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@@ -94,8 +94,8 @@ 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 `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'
@@ -144,8 +144,8 @@ 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 `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'
@@ -153,17 +153,28 @@ prep(resistance_recipe)
#> (cefuroxime), 'FOX' (cefoxitin), 'CTX' (cefotaxime), 'CAZ' (ceftazidime),
#> 'CRO' (ceftriaxone), 'IPM' (imipenem), and 'MEM' (meropenem)
#>
#>
#> ── Recipe ──────────────────────────────────────────────────────────────────────
#>
#> ── Inputs
#>
#>
#> ── Inputs
#>
#> Number of variables by role
#>
#> outcome: 1
#> predictor: 20
#>
#> ── Training information
#>
#>
#> ── Training information
#>
#> Training data contained 1968 data points and no incomplete rows.
#>
#> ── Operations
#>
#>
#> ── Operations
#>
#> • Correlation filter on: AMX CTX | Trained
```
@@ -636,9 +647,10 @@ data_time <- example_isolates %>%
.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'
#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ `resistance()` (`?AMR::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
#> (`?AMR::AMR-options`).
#> ℹ This message will be shown once per session.
data_time