@@ -231,21 +231,21 @@ make the structure of your data generally look like this:
-
2022-11-10
+
2022-11-12
abcd
Escherichia coli
S
S
-
2022-11-10
+
2022-11-12
abcd
Escherichia coli
S
R
-
2022-11-10
+
2022-11-12
efgh
Escherichia coli
R
@@ -375,12 +375,12 @@ data set:
-
+
-
+
date
@@ -395,66 +395,66 @@ data set:
-
2014-05-09
-
P10
-
Hospital B
-
Klebsiella pneumoniae
-
S
-
S
-
S
-
S
-
F
-
-
-
2012-12-23
-
H10
-
Hospital D
-
Streptococcus pneumoniae
-
S
-
R
-
S
-
S
-
M
-
-
-
2011-01-22
-
L6
+
2017-08-16
+
S1
Hospital A
Escherichia coli
R
S
S
-
S
-
M
+
R
+
F
-
2013-03-14
-
C1
+
2014-12-04
+
J1
Hospital B
Escherichia coli
-
I
-
S
-
S
-
S
-
M
-
-
-
2012-07-02
-
K8
-
Hospital D
-
Streptococcus pneumoniae
R
S
S
S
M
+
+
2012-07-21
+
R6
+
Hospital C
+
Escherichia coli
+
S
+
S
+
R
+
S
+
F
+
-
2011-02-12
-
U4
-
Hospital B
+
2012-11-26
+
K8
+
Hospital A
Staphylococcus aureus
S
+
R
+
S
+
S
+
M
+
+
+
2011-07-23
+
Z2
+
Hospital B
+
Escherichia coli
+
R
+
R
+
S
+
S
+
F
+
+
+
2016-05-31
+
S7
+
Hospital B
+
Escherichia coli
+
S
S
S
S
@@ -494,16 +494,16 @@ Longest: 1
1
M
-
10,478
-
52.39%
-
10,478
-
52.39%
+
10,563
+
52.82%
+
10,563
+
52.82%
2
F
-
9,522
-
47.61%
+
9,437
+
47.19%
20,000
100.00%
@@ -616,9 +616,9 @@ takes into account the antimicrobial susceptibility test results using
# Basing inclusion on all antimicrobial results, using a points threshold of# 2# Including isolates from ICU.
-# => Found 10,664 'phenotype-based' first isolates (53.3% of total where a
+# => Found 10,633 'phenotype-based' first isolates (53.2% of total where a# microbial ID was available)
-
So only 53.3% is suitable for resistance analysis! We can now filter
+
So only 53.2% is suitable for resistance analysis! We can now filter
on it with the filter() function, also from the
dplyr package:
# base R:plot(disk_values, mo ="E. coli", ab ="cipro")
diff --git a/articles/AMR_files/figure-html/disk_plots-1.png b/articles/AMR_files/figure-html/disk_plots-1.png
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diff --git a/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png b/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png
index f92d006c..1c0127ef 100644
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diff --git a/articles/AMR_files/figure-html/mic_plots-1.png b/articles/AMR_files/figure-html/mic_plots-1.png
index 1903820c..7f991ed1 100644
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diff --git a/articles/AMR_files/figure-html/mic_plots-2.png b/articles/AMR_files/figure-html/mic_plots-2.png
index 25ce22f0..2091a7c6 100644
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diff --git a/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png b/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png
index 82902797..ecf9655d 100644
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diff --git a/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png b/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png
index 724d0d75..72d684bb 100644
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diff --git a/articles/AMR_files/figure-html/plot 1-1.png b/articles/AMR_files/figure-html/plot 1-1.png
index 58c61e05..adf84e62 100644
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diff --git a/articles/AMR_files/figure-html/plot 3-1.png b/articles/AMR_files/figure-html/plot 3-1.png
index c81a4ef0..35e75e45 100644
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diff --git a/articles/AMR_files/figure-html/plot 4-1.png b/articles/AMR_files/figure-html/plot 4-1.png
index e9131fe1..e57911ec 100644
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diff --git a/articles/AMR_files/figure-html/plot 5-1.png b/articles/AMR_files/figure-html/plot 5-1.png
index 18f65174..2e3b546e 100644
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diff --git a/articles/EUCAST.html b/articles/EUCAST.html
index 7ec0280e..46978456 100644
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@@ -38,7 +38,7 @@
AMR (for R)
- 1.8.2.9046
+ 1.8.2.9047
diff --git a/articles/MDR.html b/articles/MDR.html
index 2d6e1d6c..d58edf2f 100644
--- a/articles/MDR.html
+++ b/articles/MDR.html
@@ -38,7 +38,7 @@
AMR (for R)
- 1.8.2.9046
+ 1.8.2.9047
@@ -370,18 +370,18 @@ 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 S I R
-# 2 I I R R I R
-# 3 S R S I I R
-# 4 R S S R S R
-# 5 R S S S S I
-# 6 S R R I S I
+# 1 R S R S R R
+# 2 R I R R R I
+# 3 I R S I S R
+# 4 I I I R I S
+# 5 R R S R I S
+# 6 S S R R R I# kanamycin# 1 I# 2 S
-# 3 R
-# 4 I
-# 5 R
+# 3 S
+# 4 S
+# 5 S# 6 R
We can now add the interpretation of MDR-TB to our data set. You can
use:
This version will eventually become v2.0! We’re happy to reach a new major milestone soon!
-
Breaking
+
Breaking
Removed all species of the taxonomic kingdom Chromista from the package. This was done for multiple reasons:
CRAN allows packages to be around 5 MB maximum, some packages are exempted but this package is not one of them
Chromista are not relevant when it comes to antimicrobial resistance, thus lacking the primary scope of this package
@@ -143,7 +143,7 @@
Removal of interpretation guidelines older than 10 years, the oldest now included guidelines of EUCAST and CLSI are from 2013
-
New
+
New
EUCAST 2022 and CLSI 2022 guidelines have been added for as.rsi(). EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.
Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. We are very grateful for the valuable input by our colleagues from other countries. The AMR package is now available in 16 languages. The automatic language determination will give a note at start-up on systems in supported languages.
All new algorithm for as.mo() (and thus all mo_*() functions) while still following our original set-up as described in our paper (DOI 10.18637/jss.v104.i03).
@@ -176,7 +176,7 @@
-
Changed
+
Changed
Fix for using as.rsi() on certain EUCAST breakpoints for MIC values
Fix for using as.rsi() on NA values (e.g. as.rsi(as.disk(NA), ...))
Fix for using as.rsi() on bug-drug combinations with multiple breakpoints for different body sites
@@ -207,7 +207,7 @@
Fix for mo_shortname() in case of higher taxonomic ranks (order, class, phylum)
-
Other
+
Other
New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions
Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, and Jonas Salm as contributors, to thank them for their valuable input
All R and Rmd files in this project are now styled using the styler package