@@ -243,21 +243,21 @@ make the structure of your data generally look like this:
-
2023-04-21
+
2023-05-08
abcd
Escherichia coli
S
S
-
2023-04-21
+
2023-05-08
abcd
Escherichia coli
S
R
-
2023-04-21
+
2023-05-08
efgh
Escherichia coli
R
diff --git a/articles/EUCAST.html b/articles/EUCAST.html
index f2c76a85..518ea109 100644
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@@ -15,7 +15,7 @@
-
+
@@ -38,7 +38,7 @@
AMR (for R)
- 2.0.0.9013
+ 2.0.0.9014
diff --git a/articles/MDR.html b/articles/MDR.html
index e3fc90ea..bf123bd7 100644
--- a/articles/MDR.html
+++ b/articles/MDR.html
@@ -15,7 +15,7 @@
-
+
@@ -38,7 +38,7 @@
AMR (for R)
- 2.0.0.9013
+ 2.0.0.9014
@@ -385,19 +385,19 @@ names or codes, this would have worked exactly the same way:
head(my_TB_data)#> rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin
-#> 1 S I R I S S
-#> 2 I I R I R R
-#> 3 I S S I R R
-#> 4 I R R I I I
-#> 5 I S S R I R
-#> 6 R R I R S I
+#> 1 S R R S R R
+#> 2 S R S I S R
+#> 3 S R I I I S
+#> 4 S I R I R R
+#> 5 R S R R R I
+#> 6 S S S R I R#> kanamycin
-#> 1 S
-#> 2 S
-#> 3 S
-#> 4 R
-#> 5 S
-#> 6 S
+#> 1 I
+#> 2 R
+#> 3 I
+#> 4 S
+#> 5 R
+#> 6 R
We can now add the interpretation of MDR-TB to our data set. You can
use:
@@ -257,7 +257,7 @@ data using a custom made website. The webdesign knowledge needed
R has a huge community.
Many R users just ask questions on websites like StackOverflow.com, the largest
-online community for programmers. At the time of writing, 487 449
+online community for programmers. At the time of writing, 489 114
R-related questions have already been asked on this platform (that
covers questions and answers for any programming language). In my own
experience, most questions are answered within a couple of
diff --git a/articles/WHONET.html b/articles/WHONET.html
index b2dcb1c1..4deddaef 100644
--- a/articles/WHONET.html
+++ b/articles/WHONET.html
@@ -15,7 +15,7 @@
-
+
@@ -38,7 +38,7 @@
AMR (for R)
- 2.0.0.9013
+ 2.0.0.9014
diff --git a/articles/datasets.html b/articles/datasets.html
index dbf96899..2cd07699 100644
--- a/articles/datasets.html
+++ b/articles/datasets.html
@@ -15,7 +15,7 @@
-
+
@@ -38,7 +38,7 @@
AMR (for R)
- 2.0.0.9013
+ 2.0.0.9014
@@ -176,7 +176,7 @@
Fixed some WHONET codes for microorganisms and consequently a couple of entries in clinical_breakpoints
@@ -152,6 +152,7 @@
Added microbial codes for Gram-negative/positive anaerobic bacteria
mo_rank() now returns NA for ‘unknown’ microorganisms (B_ANAER, B_ANAER-NEG, B_ANAER-POS, B_GRAMN, B_GRAMP, F_FUNGUS, F_YEAST, and UNKNOWN)
+
Fixed a bug for as.mo() that led to coercion of NA values when using custom microorganism codes
diff --git a/pkgdown.yml b/pkgdown.yml
index 350533ac..14e4851f 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -11,7 +11,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
-last_built: 2023-04-21T08:12Z
+last_built: 2023-05-08T11:07Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles
diff --git a/reference/AMR-deprecated.html b/reference/AMR-deprecated.html
index 89dd81b4..3f50e63d 100644
--- a/reference/AMR-deprecated.html
+++ b/reference/AMR-deprecated.html
@@ -1,5 +1,5 @@
-Deprecated Functions — AMR-deprecated • AMR (for R)Deprecated Functions — AMR-deprecated • AMR (for R)
@@ -10,7 +10,7 @@
AMR (for R)
- 2.0.0.9013
+ 2.0.0.9014
diff --git a/reference/AMR-options.html b/reference/AMR-options.html
index 585834e4..77f7a6b0 100644
--- a/reference/AMR-options.html
+++ b/reference/AMR-options.html
@@ -1,5 +1,5 @@
-Options for the AMR package — AMR-options • AMR (for R)Options for the AMR package — AMR-options • AMR (for R)
@@ -10,7 +10,7 @@
AMR (for R)
- 2.0.0.9013
+ 2.0.0.9014
diff --git a/reference/AMR.html b/reference/AMR.html
index cf991863..76e2181d 100644
--- a/reference/AMR.html
+++ b/reference/AMR.html
@@ -6,7 +6,7 @@ This work was published in the Journal of Statistical Software (Volume 104(3); d
and doi:10.33612/diss.192486375
).
After installing this package, R knows ~52 000 microorganisms (updated December 2022) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral breakpoint guidelines from CLSI and EUCAST are included from the last 10 years. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
-The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.">The AMR Package — AMR • AMR (for R)The AMR Package — AMR • AMR (for R)AMR (for R)
- 2.0.0.9013
+ 2.0.0.9014
diff --git a/reference/Rplot005.png b/reference/Rplot005.png
index 011ff6db2377542804c2c66fcade544dd0cb2a86..1886ed572cf2ede09c58946e9504c738a6f3e9b8 100644
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