As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (proportion_R(), equal to resistance()) and susceptibility as the proportion of S and I (proportion_SI(), equal to susceptibility()). These functions can be used on their own:
# base R:plot(disk_values, mo ="E. coli", ab ="cipro")
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diff --git a/articles/EUCAST.html b/articles/EUCAST.html
index 547771eb..1cef80df 100644
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@@ -38,7 +38,7 @@
AMR (for R)
- 1.8.1.9046
+ 1.8.1.9047
diff --git a/articles/MDR.html b/articles/MDR.html
index 54b8fa41..98362445 100644
--- a/articles/MDR.html
+++ b/articles/MDR.html
@@ -38,7 +38,7 @@
AMR (for R)
- 1.8.1.9046
+ 1.8.1.9047
@@ -314,19 +314,19 @@ Unique: 2
head(my_TB_data)# rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin
-# 1 S R R I I I
-# 2 R R I I R R
-# 3 I R S I I S
-# 4 I R S I I R
-# 5 I I S R I I
-# 6 S R S S R S
+# 1 R S I R R R
+# 2 S R R R I S
+# 3 R S I S I S
+# 4 R S R R I S
+# 5 I I R I S I
+# 6 R S R S I R# kanamycin# 1 I
-# 2 S
-# 3 I
+# 2 R
+# 3 S# 4 S
-# 5 S
-# 6 S
+# 5 I
+# 6 I
We can now add the interpretation of MDR-TB to our data set. You can use:
A data set with 70,764 rows and 16 columns, containing the following column names: mo, fullname, kingdom, phylum, class, order, family, genus, species, subspecies, rank, ref, species_id, source, prevalence and snomed.
This data set is in R available as microorganisms, after you load the AMR package.
-
It was last updated on 29 August 2022 07:59:26 UTC. Find more info about the structure of this data set here.
+
It was last updated on 30 August 2022 20:17:48 UTC. Find more info about the structure of this data set here.
A data set with 14,338 rows and 4 columns, containing the following column names: fullname, fullname_new, ref and prevalence.
Note: remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column ‘fullname’. For the scientific reference of the new names, i.e. of column ‘fullname_new’, see the microorganisms data set.
This data set is in R available as microorganisms.old, after you load the AMR package.
-
It was last updated on 29 August 2022 07:59:26 UTC. Find more info about the structure of this data set here.
+
It was last updated on 30 August 2022 20:17:48 UTC. Find more info about the structure of this data set here.
A data set with 464 rows and 14 columns, containing the following column names: ab, cid, name, group, atc, atc_group1, atc_group2, abbreviations, synonyms, oral_ddd, oral_units, iv_ddd, iv_units and loinc.
This data set is in R available as antibiotics, after you load the AMR package.
-
It was last updated on 29 August 2022 07:59:26 UTC. Find more info about the structure of this data set here.
+
It was last updated on 30 August 2022 20:17:48 UTC. Find more info about the structure of this data set here.
A data set with 102 rows and 9 columns, containing the following column names: atc, cid, name, atc_group, synonyms, oral_ddd, oral_units, iv_ddd and iv_units.
This data set is in R available as antivirals, after you load the AMR package.
-
It was last updated on 29 August 2022 07:59:26 UTC. Find more info about the structure of this data set here.
+
It was last updated on 30 August 2022 20:17:48 UTC. Find more info about the structure of this data set here.
A data set with 20,369 rows and 11 columns, containing the following column names: guideline, method, site, mo, rank_index, ab, ref_tbl, disk_dose, breakpoint_S, breakpoint_R and uti.
This data set is in R available as rsi_translation, after you load the AMR package.
-
It was last updated on 29 August 2022 07:59:26 UTC. Find more info about the structure of this data set here.
+
It was last updated on 30 August 2022 20:17:48 UTC. Find more info about the structure of this data set here.
A data set with 169 rows and 9 columns, containing the following column names: ab, name, type, dose, dose_times, administration, notes, original_txt and eucast_version.
This data set is in R available as dosage, after you load the AMR package.
-
It was last updated on 29 August 2022 07:59:26 UTC. Find more info about the structure of this data set here.
+
It was last updated on 30 August 2022 20:17:48 UTC. Find more info about the structure of this data set here.
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.
+
Function to calculate the mean AMR distance: mean_amr_distance(). The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand.
Support for data.frame-enhancing R packages, more specifically: data.table, tibble, and tsibble. AMR package functions that have a data set as output (such as rsi_df() and bug_drug_combinations()), will now return the same data type as the input. Furthermore, all our data sets are now in tibble format.
Our data sets are now also continually exported to Apache Feather and Apache Parquet formats. You can find more info in this article on our website.
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.
-
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), ...))
Removed as.integer() for MIC values, since MIC are not integer values and running table() on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally as.integer() on factors work)
New website to make use of the new Bootstrap 5 and pkgdown v2.0. 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 and Anton Mymrikov as contributors, to thank them for their valuable input
Set up Git Large File Storage (Git LFS) for the large SAS and SPSS file formats
diff --git a/reference/resistance_predict.html b/reference/resistance_predict.html
index 1f7d71ad..3ffab093 100644
--- a/reference/resistance_predict.html
+++ b/reference/resistance_predict.html
@@ -10,7 +10,7 @@
AMR (for R)
- 1.8.1.9046
+ 1.8.1.9047
diff --git a/reference/rsi_translation.html b/reference/rsi_translation.html
index 65d99d6f..70a95906 100644
--- a/reference/rsi_translation.html
+++ b/reference/rsi_translation.html
@@ -10,7 +10,7 @@
AMR (for R)
- 1.8.1.9046
+ 1.8.1.9047
diff --git a/reference/skewness.html b/reference/skewness.html
index 529236dd..7b3b15b0 100644
--- a/reference/skewness.html
+++ b/reference/skewness.html
@@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
AMR (for R)
- 1.8.1.9046
+ 1.8.1.9047
@@ -166,7 +166,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu