@@ -227,14 +226,13 @@ we have with step_corr(), the necessary parameters can be
estimated from a training set using prep():
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), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
-#> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP'
-#> (piperacillin/tazobactam), 'CZO' (cefazolin), 'FEP' (cefepime), 'CXM'
-#> (cefuroxime), 'FOX' (cefoxitin), 'CTX' (cefotaxime), 'CAZ' (ceftazidime),
-#> 'CRO' (ceftriaxone), 'IPM' (imipenem), and 'MEM' (meropenem)
+#> 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
+#> (ceftazidime), CRO (ceftriaxone), IPM (imipenem), and MEM (meropenem)
#>
#>
#> ── Recipe ──────────────────────────────────────────────────────────────────────
@@ -749,10 +747,9 @@ into a structured time-series format.
.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()` (`?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 `?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 This message will be shown once per session.
data_time
diff --git a/articles/AMR_with_tidymodels.md b/articles/AMR_with_tidymodels.md
index 528c273b0..7cc6ce75a 100644
--- a/articles/AMR_with_tidymodels.md
+++ b/articles/AMR_with_tidymodels.md
@@ -94,14 +94,13 @@ 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), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
-#> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP'
-#> (piperacillin/tazobactam), 'CZO' (cefazolin), 'FEP' (cefepime), 'CXM'
-#> (cefuroxime), 'FOX' (cefoxitin), 'CTX' (cefotaxime), 'CAZ' (ceftazidime),
-#> 'CRO' (ceftriaxone), 'IPM' (imipenem), and 'MEM' (meropenem)
+#> 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
+#> (ceftazidime), CRO (ceftriaxone), IPM (imipenem), and MEM (meropenem)
```
**Explanation:**
@@ -144,14 +143,13 @@ 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), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
-#> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP'
-#> (piperacillin/tazobactam), 'CZO' (cefazolin), 'FEP' (cefepime), 'CXM'
-#> (cefuroxime), 'FOX' (cefoxitin), 'CTX' (cefotaxime), 'CAZ' (ceftazidime),
-#> 'CRO' (ceftriaxone), 'IPM' (imipenem), and 'MEM' (meropenem)
+#> 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
+#> (ceftazidime), CRO (ceftriaxone), IPM (imipenem), and MEM (meropenem)
#>
#>
#> ── Recipe ──────────────────────────────────────────────────────────────────────
@@ -647,10 +645,9 @@ 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()` (`?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 `?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 This message will be shown once per session.
data_time
diff --git a/articles/EUCAST.html b/articles/EUCAST.html
index 4ff52c71b..19eceec07 100644
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@@ -30,7 +30,7 @@
AMR (for R)
- 3.0.1.9036
+ 3.0.1.9037
Frequency table
Class: factor > ordered > sir (numeric)
diff --git a/articles/WHONET.md b/articles/WHONET.md
index a69d9c2a2..6508986ef 100644
--- a/articles/WHONET.md
+++ b/articles/WHONET.md
@@ -101,10 +101,9 @@ Longest: 40
# our transformed antibiotic columns
# amoxicillin/clavulanic acid (J01CR02) as an example
data %>% freq(AMC_ND2)
-#> ℹ `susceptibility()` (`?AMR::susceptibility()`) 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 `?susceptibility()` 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 This message will be shown once per session.
```
diff --git a/articles/WISCA.html b/articles/WISCA.html
index 8807ee537..d342fb403 100644
--- a/articles/WISCA.html
+++ b/articles/WISCA.html
@@ -30,7 +30,7 @@
AMR (for R)
- 3.0.1.9036
+ 3.0.1.9037