@@ -1281,9 +1281,9 @@ I (proportion_SI(), equa
own:
our_data_1st %>% resistance(AMX)
-#> ℹ `?resistance()` assumes the EUCAST guideline and thus considers the 'I'
+#> 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.
#> [1] 0.4203377
Or can be used in conjunction with group_by() and
@@ -1316,15 +1316,15 @@ values for Klebsiella pneumoniae and ciprofloxacin:
#> # A tibble: 100 × 2
#> MIC SIR
#> <mic> <sir>
-#> 1 <=0.0001 S
-#> 2 0.0160 S
-#> 3 >=8.0000 R
-#> 4 0.0320 S
-#> 5 0.0080 S
-#> 6 64.0000 R
-#> 7 0.0080 S
-#> 8 0.1250 S
-#> 9 0.0320 S
+#> 1 <=0.0001 S
+#> 2 0.0160 S
+#> 3 >=8.0000 R
+#> 4 0.0320 S
+#> 5 0.0080 S
+#> 6 64.0000 R
+#> 7 0.0080 S
+#> 8 0.1250 S
+#> 9 0.0320 S
#> 10 0.0002 S
#> # ℹ 90 more rows
This allows direct interpretation according to EUCAST or CLSI
diff --git a/articles/AMR.md b/articles/AMR.md
index 5304a52c4..d73d32c2f 100644
--- a/articles/AMR.md
+++ b/articles/AMR.md
@@ -3,7 +3,7 @@
**Note:** values on this page will change with every website update
since they are based on randomly created values and the page was written
in [R Markdown](https://rmarkdown.rstudio.com/). However, the
-methodology remains unchanged. This page was generated on 22 March 2026.
+methodology remains unchanged. This page was generated on 24 March 2026.
## Introduction
@@ -51,9 +51,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:|
-| 2026-03-22 | abcd | Escherichia coli | S | S |
-| 2026-03-22 | abcd | Escherichia coli | S | R |
-| 2026-03-22 | efgh | Escherichia coli | R | S |
+| 2026-03-24 | abcd | Escherichia coli | S | S |
+| 2026-03-24 | abcd | Escherichia coli | S | R |
+| 2026-03-24 | efgh | Escherichia coli | R | S |
### Needed R packages
@@ -169,8 +169,8 @@ our_data$bacteria <- as.mo(our_data$bacteria, info = TRUE)
#> ℹ Retrieved values from the `microorganisms.codes` data set for "ESCCOL",
#> "KLEPNE", "STAAUR", and "STRPNE".
#> ℹ Microorganism translation was uncertain for four microorganisms. Run
-#> `?mo_uncertainties()` to review these uncertainties, or use
-#> `?add_custom_microorganisms()` to add custom entries.
+#> `mo_uncertainties()` to review these uncertainties, or use
+#> `add_custom_microorganisms()` to add custom entries.
```
Apparently, there was some uncertainty about the translation to
@@ -179,7 +179,7 @@ taxonomic codes. Let’s check this:
``` r
mo_uncertainties()
#> Matching scores are based on the resemblance between the input and the full
-#> taxonomic name, and the pathogenicity in humans. See `?mo_matching_score()`.
+#> taxonomic name, and the pathogenicity in humans. See `mo_matching_score()`.
#> Colour keys: 0.000-0.549 0.550-0.649 0.650-0.749 0.750-1.000
#> -------------------------------------------------------------------------------
#> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688)
@@ -212,8 +212,8 @@ mo_uncertainties()
#> Streptococcus gallolyticus pasteurianus (0.526), Salmonella Portanigra (0.524),
#> and Streptococcus periodonticum (0.519)
#> ℹ Only the first 10 other matches of each record are shown. Run ``
-#> ?`print(mo_uncertainties(), n = ...)` `` to view more entries, or save
-#> `?mo_uncertainties()` to an object.
+#> `print(mo_uncertainties(), n = ...)` `` to view more entries, or save
+#> `mo_uncertainties()` to an object.
```
That’s all good.
@@ -311,11 +311,11 @@ The outcome of the function can easily be added to our data:
our_data <- our_data %>%
mutate(first = first_isolate(info = TRUE))
#> ℹ Determining first isolates using an episode length of 365 days
-#> ℹ Using column 'bacteria' as input for `col_mo`.
-#> ℹ Column 'first' is SIR eligible (despite only having empty values), since it
+#> ℹ Using column bacteria as input for `col_mo`.
+#> ℹ Column first is SIR eligible (despite only having empty values), since it
#> seems to be cefozopran (ZOP)
-#> ℹ Using column 'date' as input for `col_date`.
-#> ℹ Using column 'patient_id' as input for `col_patient_id`.
+#> ℹ Using column date as input for `col_date`.
+#> ℹ Using column patient_id as input for `col_patient_id`.
#> ℹ Basing inclusion on all antimicrobial results, using a points threshold of 2
#> => Found 2,724 'phenotype-based' first isolates (90.8% of total where a
#> microbial ID was available)
@@ -447,7 +447,7 @@ in:
``` r
our_data_1st %>%
select(date, aminoglycosides())
-#> ℹ For `?aminoglycosides()` using column GEN
+#> ℹ For `aminoglycosides()` using column GEN
#> (gentamicin)
#> # A tibble: 2,724 × 2
#> date GEN
@@ -466,7 +466,7 @@ our_data_1st %>%
our_data_1st %>%
select(bacteria, betalactams())
-#> ℹ For `?betalactams()` using columns AMX (amoxicillin) and AMC
+#> ℹ For `betalactams()` using columns AMX (amoxicillin) and AMC
#> (amoxicillin/clavulanic acid)
#> # A tibble: 2,724 × 3
#> bacteria AMX AMC
@@ -503,7 +503,7 @@ our_data_1st %>%
# filtering using AB selectors is also possible:
our_data_1st %>%
filter(any(aminoglycosides() == "R"))
-#> ℹ For `?aminoglycosides()` using column GEN
+#> ℹ For `aminoglycosides()` using column GEN
#> (gentamicin)
#> # A tibble: 981 × 9
#> patient_id hospital date bacteria AMX AMC CIP GEN first
@@ -522,7 +522,7 @@ our_data_1st %>%
our_data_1st %>%
filter(all(betalactams() == "R"))
-#> ℹ For `?betalactams()` using columns AMX (amoxicillin) and AMC
+#> ℹ For `betalactams()` using columns AMX (amoxicillin) and AMC
#> (amoxicillin/clavulanic acid)
#> # A tibble: 462 × 9
#> patient_id hospital date bacteria AMX AMC CIP GEN first
@@ -541,7 +541,7 @@ our_data_1st %>%
# even works in base R (since R 3.0):
our_data_1st[all(betalactams() == "R"), ]
-#> ℹ For `?betalactams()` using columns AMX (amoxicillin) and AMC
+#> ℹ For `betalactams()` using columns AMX (amoxicillin) and AMC
#> (amoxicillin/clavulanic acid)
#> # A tibble: 462 × 9
#> patient_id hospital date bacteria AMX AMC CIP GEN first
@@ -624,9 +624,9 @@ antibiotic class selectors:
``` r
antibiogram(example_isolates,
antibiotics = 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)
```
| Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin |
@@ -663,8 +663,8 @@ antibiogram(example_isolates,
antibiotics = aminoglycosides(),
ab_transform = "name",
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)
```
| Patógeno | Amikacina | Gentamicina | Kanamicina | Tobramicina |
@@ -707,9 +707,9 @@ on certain columns:
antibiogram(example_isolates,
antibiotics = 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)
```
| Syndromic Group | Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin |
@@ -840,9 +840,9 @@ These functions can be used on their own:
``` r
our_data_1st %>% resistance(AMX)
-#> ℹ `?resistance()` assumes the EUCAST guideline and thus considers the 'I'
+#> 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.
#> [1] 0.4203377
```
diff --git a/articles/AMR_for_Python.html b/articles/AMR_for_Python.html
index f307b7656..89119e6dd 100644
--- a/articles/AMR_for_Python.html
+++ b/articles/AMR_for_Python.html
@@ -30,7 +30,7 @@
AMR (for R)
- 3.0.1.9038
+ 3.0.1.9040
#> # A tibble: 2,000 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
-#> 1 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA
-#> 2 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA
-#> 3 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA
-#> 4 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA
-#> 5 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA
-#> 6 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA
-#> 7 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R
-#> 8 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R
-#> 9 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA
-#> 10 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA
+#> 1 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA
+#> 2 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA
+#> 3 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA
+#> 4 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA
+#> 5 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA
+#> 6 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA
+#> 7 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R
+#> 8 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R
+#> 9 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA
+#> 10 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA
#> # ℹ 1,990 more rows
#> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,
#> # CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,
@@ -179,9 +179,9 @@ package.
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
@@ -226,9 +226,9 @@ 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),
+#> 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
@@ -482,16 +482,16 @@ package.
#> # A tibble: 500 × 19
#> esbl genus AMC AMP TZP CXM FOX CTX CAZ GEN TOB TMP SXT
#> <lgl> <chr> <mic> <mic> <mic> <mic> <mic> <mic> <mic> <mic> <mic> <mic> <mic>
-#> 1 FALSE Esch… 32 32 4 64 64 8.00 8.00 1 1 16.0 20
-#> 2 FALSE Esch… 32 32 4 64 64 4.00 8.00 1 1 16.0 320
-#> 3 FALSE Esch… 4 2 64 8 4 8.00 0.12 16 16 0.5 20
-#> 4 FALSE Kleb… 32 32 16 64 64 8.00 8.00 1 1 0.5 20
-#> 5 FALSE Esch… 32 32 4 4 4 0.25 2.00 1 1 16.0 320
-#> 6 FALSE Citr… 32 32 16 64 64 64.00 32.00 1 1 0.5 20
-#> 7 FALSE Morg… 32 32 4 64 64 16.00 2.00 1 1 0.5 20
-#> 8 FALSE Prot… 16 32 4 1 4 8.00 0.12 1 1 16.0 320
-#> 9 FALSE Ente… 32 32 8 64 64 32.00 4.00 1 1 0.5 20
-#> 10 FALSE Citr… 32 32 32 64 64 8.00 64.00 1 1 16.0 320
+#> 1 FALSE Esch… 32 32 4 64 64 8.00 8.00 1 1 16.0 20
+#> 2 FALSE Esch… 32 32 4 64 64 4.00 8.00 1 1 16.0 320
+#> 3 FALSE Esch… 4 2 64 8 4 8.00 0.12 16 16 0.5 20
+#> 4 FALSE Kleb… 32 32 16 64 64 8.00 8.00 1 1 0.5 20
+#> 5 FALSE Esch… 32 32 4 4 4 0.25 2.00 1 1 16.0 320
+#> 6 FALSE Citr… 32 32 16 64 64 64.00 32.00 1 1 0.5 20
+#> 7 FALSE Morg… 32 32 4 64 64 16.00 2.00 1 1 0.5 20
+#> 8 FALSE Prot… 16 32 4 1 4 8.00 0.12 1 1 16.0 320
+#> 9 FALSE Ente… 32 32 8 64 64 32.00 4.00 1 1 0.5 20
+#> 10 FALSE Citr… 32 32 32 64 64 8.00 64.00 1 1 16.0 320
#> # ℹ 490 more rows
#> # ℹ 6 more variables: NIT <mic>, FOS <mic>, CIP <mic>, IPM <mic>, MEM <mic>,
#> # COL <mic>
@@ -746,10 +746,10 @@ into a structured time-series format.
.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
diff --git a/articles/AMR_with_tidymodels.md b/articles/AMR_with_tidymodels.md
index 7cc6ce75a..2808eb205 100644
--- a/articles/AMR_with_tidymodels.md
+++ b/articles/AMR_with_tidymodels.md
@@ -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
diff --git a/articles/EUCAST.html b/articles/EUCAST.html
index a5d207d47..3bcd3939a 100644
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@@ -30,7 +30,7 @@
AMR (for R)
- 3.0.1.9038
+ 3.0.1.9040
Frequency table
Class: factor > ordered > sir (numeric)
diff --git a/articles/WHONET.md b/articles/WHONET.md
index 6508986ef..be56ef42d 100644
--- a/articles/WHONET.md
+++ b/articles/WHONET.md
@@ -101,9 +101,9 @@ Longest: 40
# our transformed antibiotic columns
# amoxicillin/clavulanic acid (J01CR02) as an example
data %>% freq(AMC_ND2)
-#> ℹ `?susceptibility()` assumes the EUCAST guideline and thus considers the 'I'
+#> 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.
+#> 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 b0e107deb..f43125fde 100644
--- a/articles/WISCA.html
+++ b/articles/WISCA.html
@@ -30,7 +30,7 @@
AMR (for R)
- 3.0.1.9038
+ 3.0.1.9040