Download as original R Data Structure (RDS) file (3 kB)
@@ -1302,7 +1302,7 @@
A data set with 2,000 rows and 46 columns, containing the following column names:
date, patient, age, gender, ward, mo, PEN, OXA, FLC, AMX, AMC, AMP, TZP, CZO, FEP, CXM, FOX, CTX, CAZ, CRO, GEN, TOB, AMK, KAN, TMP, SXT, NIT, FOS, LNZ, CIP, MFX, VAN, TEC, TCY, TGC, DOX, ERY, CLI, AZM, IPM, MEM, MTR, CHL, COL, MUP and RIF.
This data set is in R available as example_isolates, after you load the AMR package.
-It was last updated on 21 October 2022 13:14:53 UTC. Find more info about the structure of this data set here.
+It was last updated on 21 October 2022 14:26:06 UTC. Find more info about the structure of this data set here.
Source
@@ -1707,7 +1707,7 @@
A data set with 3,000 rows and 8 columns, containing the following column names:
patient_id, hospital, date, bacteria, AMX, AMC, CIP and GEN.
This data set is in R available as example_isolates_unclean, after you load the AMR package.
-
It was last updated on 21 October 2022 13:14:53 UTC. Find more info about the structure of this data set here.
+
It was last updated on 21 October 2022 14:26:06 UTC. Find more info about the structure of this data set here.
Source
diff --git a/articles/index.html b/articles/index.html
index f5ebd4fe..c12ff551 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -10,7 +10,7 @@
AMR (for R)
-
1.8.2.9027
+
1.8.2.9029
-
AMR 1.8.2.9027
+
AMR 1.8.2.9029
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
- Chromista are almost never clinically relevant, thus lacking the secondary scope of this package
@@ -141,7 +141,7 @@
- Argument
combine_IR has been removed from this package (affecting all count_df(), proportion_df() and rsi_all()), since it was replaced with combine_SI three years ago
-
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.
- All new algorithm for
as.mo() (and thus internally all mo_*() functions) while still following our original set-up as described in our paper (DOI 10.18637/jss.v104.i03).- A new argument
keep_synonyms allows to not correct for updated taxonomy, in favour of the now deleted argument allow_uncertain
@@ -158,11 +158,11 @@
- 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.
- Added confidence intervals in AMR calculation. This is now included in
rsi_df() and proportion_df() and manually available as rsi_confidence_interval()
-- Support for using antibiotic selectors in scoped
dplyr verbs (worh or without vars()), such as in: ... %>% summarise_at(aminoglycosides(), resistance)
+ - Support for using antibiotic selectors in scoped
dplyr verbs (with or without vars()), such as in: ... %>% summarise_at(aminoglycosides(), resistance), see resistance()
-
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)
@@ -187,7 +187,7 @@
- Fix for using
as.ab() on NA values
-
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 and Anton Mymrikov as contributors, to thank them for their valuable input
- All R and Rmd files in this project are now styled using the
styler package
diff --git a/pkgdown.yml b/pkgdown.yml
index 129a67fa..08706b2a 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: 2022-10-21T13:16Z
+last_built: 2022-10-21T14:28Z
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 6ddc9c6a..4990677c 100644
--- a/reference/AMR-deprecated.html
+++ b/reference/AMR-deprecated.html
@@ -10,7 +10,7 @@
AMR (for R)
- 1.8.2.9027
+ 1.8.2.9029
diff --git a/reference/ggplot_pca.html b/reference/ggplot_pca.html
index 9a4b8fce..55d92efa 100644
--- a/reference/ggplot_pca.html
+++ b/reference/ggplot_pca.html
@@ -10,7 +10,7 @@
AMR (for R)
- 1.8.2.9027
+ 1.8.2.9029