@@ -261,21 +261,21 @@ make the structure of your data generally look like this:
-
2024-03-09
+
2024-04-05
abcd
Escherichia coli
S
S
-
2024-03-09
+
2024-04-05
abcd
Escherichia coli
S
R
-
2024-03-09
+
2024-04-05
efgh
Escherichia coli
R
diff --git a/articles/AMR_files/figure-html/unnamed-chunk-10-1.png b/articles/AMR_files/figure-html/unnamed-chunk-10-1.png
index a99e8b43..0142534b 100644
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diff --git a/articles/EUCAST.html b/articles/EUCAST.html
index 48178d7d..09aede96 100644
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@@ -15,8 +15,8 @@
-
-
+
+
@@ -39,7 +39,7 @@
AMR (for R)
- 2.1.1.9015
+ 2.1.1.9016
diff --git a/articles/MDR.html b/articles/MDR.html
index 45088703..d201ef2c 100644
--- a/articles/MDR.html
+++ b/articles/MDR.html
@@ -15,8 +15,8 @@
-
-
+
+
@@ -39,7 +39,7 @@
AMR (for R)
- 2.1.1.9015
+ 2.1.1.9016
@@ -402,19 +402,19 @@ names or codes, this would have worked exactly the same way:
head(my_TB_data)#> rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin
-#> 1 S R I R R R
-#> 2 R I R I I I
-#> 3 S R S R S S
-#> 4 I I I S S I
-#> 5 I I R S S R
-#> 6 I R R I S R
+#> 1 S S S S R S
+#> 2 R I R S R S
+#> 3 S S I I S S
+#> 4 I I I I I I
+#> 5 R S I S I R
+#> 6 I I I I R R#> kanamycin
-#> 1 R
-#> 2 S
+#> 1 S
+#> 2 R#> 3 S
-#> 4 I
-#> 5 R
-#> 6 I
+#> 4 S
+#> 5 S
+#> 6 S
We can now add the interpretation of MDR-TB to our data set. You can
use:
(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support!)
-
A New Milestone: One Health Support (= Human + Veterinary + Environmental)
+
A New Milestone: One Health Support (= Human + Veterinary + Environmental)
This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the University of Prince Edward Island, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.
-
Breaking
+
Breaking
Removed all functions and references that used the deprecated rsi class, which were all replaced with their sir equivalents over a year ago
-
New
+
New
One Health implementation
Function as.sir() now has extensive support for animal breakpoints from CLSI. Use breakpoint_type = "animal" and set the host argument to a variable that contains animal species names.
The clinical_breakpoints data set contains all these breakpoints, and can be downloaded on our download page.
@@ -184,18 +184,19 @@
Function limit_mic_range(), which allows to limit MIC values to a manually set range. This is the powerhouse behind the scale_*_mic() functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.
-
Changed
+
Changed
For MICs:
Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960)
Added new argument keep_operators to as.mic(). This can be "all" (default), "none", or "edges". This argument is also available in the new limit_mic_range() and scale_*_mic() functions.
+
Comparisons of MIC values are now more strict. For example, >32 is higher than (and never equal to) 32. Thus, as.mic(">32") == as.mic(32) now returns FALSE, and as.mic(">32") > as.mic(32) now returns TRUE.
Greatly improved vctrs integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that dplyr::rowwise() and dplyr::c_across() are now supported for e.g. columns of class mic. Despite this, this AMR package is still zero-dependent on any other package, including dplyr and vctrs.
+
Greatly improved vctrs integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that functions such as dplyr’s bind_rows(), rowwise() and c_across() are now supported for e.g. columns of class mic. Despite this, this AMR package is still zero-dependent on any other package, including dplyr and vctrs.
Updated all ATC codes from WHOCC
Updated all antibiotic DDDs from WHOCC
-
Other
+
Other
Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input
diff --git a/pkgdown.yml b/pkgdown.yml
index 1d4a66a5..ac549208 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -11,7 +11,7 @@ articles:
other_pkg: other_pkg.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
-last_built: 2024-03-09T15:50Z
+last_built: 2024-04-05T14:56Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles
diff --git a/reference/AMR-options.html b/reference/AMR-options.html
index b67d0213..3a54ffce 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)
- 2.1.1.9015
+ 2.1.1.9016
diff --git a/reference/AMR.html b/reference/AMR.html
index 8753380e..fc0b850d 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 January 2024) 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 clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. 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 public 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)
- 2.1.1.9015
+ 2.1.1.9016
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diff --git a/reference/WHOCC.html b/reference/WHOCC.html
index b5caeb4a..8e586d20 100644
--- a/reference/WHOCC.html
+++ b/reference/WHOCC.html
@@ -1,5 +1,5 @@
-WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC • AMR (for R)WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC • AMR (for R)
@@ -10,7 +10,7 @@
AMR (for R)
- 2.1.1.9015
+ 2.1.1.9016
diff --git a/reference/WHONET.html b/reference/WHONET.html
index 25b2fbb8..dcb0946b 100644
--- a/reference/WHONET.html
+++ b/reference/WHONET.html
@@ -1,5 +1,5 @@
-Data Set with 500 Isolates - WHONET Example — WHONET • AMR (for R)Data Set with 500 Isolates - WHONET Example — WHONET • AMR (for R)
@@ -10,7 +10,7 @@
AMR (for R)
- 2.1.1.9015
+ 2.1.1.9016
diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html
index 8d4e5420..bbf838f0 100644
--- a/reference/ab_from_text.html
+++ b/reference/ab_from_text.html
@@ -1,5 +1,5 @@
-Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text • AMR (for R)Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text • AMR (for R)
@@ -10,7 +10,7 @@
AMR (for R)
- 2.1.1.9015
+ 2.1.1.9016
diff --git a/reference/ab_property.html b/reference/ab_property.html
index f1d8e39e..8f173b37 100644
--- a/reference/ab_property.html
+++ b/reference/ab_property.html
@@ -1,5 +1,5 @@
-Get Properties of an Antibiotic — ab_property • AMR (for R)Get Properties of an Antibiotic — ab_property • AMR (for R)
@@ -10,7 +10,7 @@
AMR (for R)
- 2.1.1.9015
+ 2.1.1.9016
diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html
index 36265174..897d2a32 100644
--- a/reference/add_custom_antimicrobials.html
+++ b/reference/add_custom_antimicrobials.html
@@ -1,5 +1,5 @@
-Add Custom Antimicrobials — add_custom_antimicrobials • AMR (for R)Add Custom Antimicrobials — add_custom_antimicrobials • AMR (for R)
@@ -10,7 +10,7 @@
AMR (for R)
- 2.1.1.9015
+ 2.1.1.9016
diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html
index 58d11544..ab787649 100644
--- a/reference/add_custom_microorganisms.html
+++ b/reference/add_custom_microorganisms.html
@@ -1,5 +1,5 @@
-Add Custom Microorganisms — add_custom_microorganisms • AMR (for R)Add Custom Microorganisms — add_custom_microorganisms • AMR (for R)
@@ -10,7 +10,7 @@
AMR (for R)
- 2.1.1.9015
+ 2.1.1.9016
diff --git a/reference/age.html b/reference/age.html
index 2be90bf5..315b9f94 100644
--- a/reference/age.html
+++ b/reference/age.html
@@ -1,5 +1,5 @@
-Age in Years of Individuals — age • AMR (for R)Age in Years of Individuals — age • AMR (for R)
@@ -10,7 +10,7 @@
AMR (for R)
- 2.1.1.9015
+ 2.1.1.9016
@@ -222,16 +222,16 @@
df#> birth_date age age_exact age_at_y2k
-#> 1 1965-12-05 58 58.25956 34
-#> 2 1980-03-01 44 44.02186 19
-#> 3 1949-11-01 74 74.35246 50
-#> 4 1947-02-14 77 77.06557 52
-#> 5 1940-02-19 84 84.05191 59
-#> 6 1988-01-10 36 36.16120 11
-#> 7 1997-08-27 26 26.53279 2
-#> 8 1978-01-26 46 46.11749 21
-#> 9 1972-06-17 51 51.72678 27
-#> 10 1986-08-10 37 37.57923 13
+#> 1 1965-12-05 58 58.33333 34
+#> 2 1980-03-01 44 44.09563 19
+#> 3 1949-11-01 74 74.42623 50
+#> 4 1947-02-14 77 77.13934 52
+#> 5 1940-02-19 84 84.12568 59
+#> 6 1988-01-10 36 36.23497 11
+#> 7 1997-08-27 26 26.60656 2
+#> 8 1978-01-26 46 46.19126 21
+#> 9 1972-06-17 51 51.80055 27
+#> 10 1986-08-10 37 37.65301 13