@@ -1315,14 +1315,14 @@ values for Klebsiella pneumoniae and ciprofloxacin:
#> 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
+#> 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_for_Python.html b/articles/AMR_for_Python.html
index dabc6e894..4a8a179a3 100644
--- a/articles/AMR_for_Python.html
+++ b/articles/AMR_for_Python.html
@@ -30,7 +30,7 @@
AMR (for R)
- 3.0.0.9033
+ 3.0.0.9034
#> # 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'
+#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
-#> ℹ For `betalactams()` using columns 'PEN' (benzylpenicillin), 'OXA'
+#> 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'
@@ -227,9 +227,9 @@ 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'
+#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
-#> ℹ For `betalactams()` using columns 'PEN' (benzylpenicillin), 'OXA'
+#> 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'
@@ -494,7 +494,7 @@ 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 Using column 'mo' as input for `col_mo`.
data_time
#> # A tibble: 32 × 5
diff --git a/articles/EUCAST.html b/articles/EUCAST.html
index aa959c6cc..611e9a7cf 100644
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@@ -30,7 +30,7 @@
AMR (for R)
- 3.0.0.9033
+ 3.0.0.9034
A more convenient function is
mo_is_intrinsic_resistant() that uses the same guideline,
diff --git a/articles/PCA.html b/articles/PCA.html
index 08c1df420..0295ca341 100644
--- a/articles/PCA.html
+++ b/articles/PCA.html
@@ -30,7 +30,7 @@
AMR (for R)
- 3.0.0.9033
+ 3.0.0.9034