From e9c6e5e2e96f8bc187f3e1be6f7ea8c814a73dc5 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Sat, 26 Apr 2025 14:42:58 +0000 Subject: [PATCH] Built site for AMR@2.1.1.9255: d166aa2 --- 404.html | 2 +- LICENSE-text.html | 2 +- articles/AMR.html | 8 +- articles/AMR_for_Python.html | 2 +- articles/AMR_with_tidymodels.html | 2 +- articles/EUCAST.html | 2 +- articles/MDR.html | 2 +- articles/PCA.html | 2 +- articles/WHONET.html | 2 +- articles/datasets.html | 10 +- articles/index.html | 2 +- articles/welcome_to_AMR.html | 2 +- authors.html | 2 +- index.html | 4 +- news/index.html | 16 +- pkgdown.yml | 2 +- reference/AMR-deprecated.html | 2 +- reference/AMR-options.html | 2 +- reference/AMR.html | 2 +- reference/WHOCC.html | 2 +- reference/WHONET.html | 2 +- reference/ab_from_text.html | 2 +- reference/ab_property.html | 2 +- reference/add_custom_antimicrobials.html | 4 +- reference/add_custom_microorganisms.html | 2 +- reference/age.html | 2 +- reference/age_groups.html | 2 +- reference/antibiogram.html | 2 +- reference/antimicrobial_selectors.html | 2 +- reference/antimicrobials.html | 2 +- reference/as.ab.html | 4 +- reference/as.av.html | 2 +- reference/as.disk.html | 27 +- reference/as.mic-2.png | Bin 0 -> 34759 bytes reference/as.mic-3.png | Bin 0 -> 52488 bytes reference/as.mic-4.png | Bin 0 -> 50804 bytes reference/as.mic.html | 24 +- reference/as.mo.html | 2 +- reference/as.sir.html | 348 ++++++----------------- reference/atc_online.html | 2 +- reference/av_from_text.html | 2 +- reference/av_property.html | 2 +- reference/availability.html | 2 +- reference/bug_drug_combinations.html | 2 +- reference/clinical_breakpoints.html | 2 +- reference/count.html | 2 +- reference/custom_eucast_rules.html | 2 +- reference/dosage.html | 2 +- reference/eucast_rules.html | 2 +- reference/example_isolates.html | 2 +- reference/example_isolates_unclean.html | 2 +- reference/export_ncbi_biosample.html | 2 +- reference/first_isolate.html | 2 +- reference/g.test.html | 2 +- reference/get_episode.html | 2 +- reference/ggplot_pca.html | 2 +- reference/ggplot_sir.html | 2 +- reference/guess_ab_col.html | 2 +- reference/index.html | 2 +- reference/intrinsic_resistant.html | 2 +- reference/italicise_taxonomy.html | 2 +- reference/join.html | 2 +- reference/key_antimicrobials.html | 2 +- reference/kurtosis.html | 2 +- reference/like.html | 2 +- reference/mdro.html | 2 +- reference/mean_amr_distance.html | 2 +- reference/microorganisms.codes.html | 2 +- reference/microorganisms.groups.html | 2 +- reference/microorganisms.html | 2 +- reference/mo_matching_score.html | 2 +- reference/mo_property.html | 2 +- reference/mo_source.html | 2 +- reference/pca.html | 2 +- reference/plot-10.png | Bin 72304 -> 62433 bytes reference/plot-11.png | Bin 94847 -> 19275 bytes reference/plot-12.png | Bin 90342 -> 72304 bytes reference/plot-13.png | Bin 26557 -> 94847 bytes reference/plot-14.png | Bin 26524 -> 90342 bytes reference/plot-15.png | Bin 27742 -> 26557 bytes reference/plot-16.png | Bin 0 -> 40375 bytes reference/plot-17.png | Bin 0 -> 26524 bytes reference/plot-18.png | Bin 0 -> 40357 bytes reference/plot-19.png | Bin 0 -> 39510 bytes reference/plot-2.png | Bin 24961 -> 59121 bytes reference/plot-20.png | Bin 0 -> 27742 bytes reference/plot-3.png | Bin 27928 -> 54904 bytes reference/plot-4.png | Bin 30774 -> 24961 bytes reference/plot-5.png | Bin 27160 -> 27928 bytes reference/plot-6.png | Bin 33179 -> 30774 bytes reference/plot-7.png | Bin 80570 -> 27160 bytes reference/plot-8.png | Bin 62433 -> 33179 bytes reference/plot-9.png | Bin 19275 -> 80570 bytes reference/plot.html | 47 ++- reference/proportion.html | 2 +- reference/random.html | 2 +- reference/resistance_predict.html | 2 +- reference/skewness.html | 2 +- reference/top_n_microorganisms.html | 2 +- reference/translate.html | 2 +- search.json | 2 +- 101 files changed, 199 insertions(+), 431 deletions(-) create mode 100644 reference/as.mic-2.png create mode 100644 reference/as.mic-3.png create mode 100644 reference/as.mic-4.png create mode 100644 reference/plot-16.png create mode 100644 reference/plot-17.png create mode 100644 reference/plot-18.png create mode 100644 reference/plot-19.png create mode 100644 reference/plot-20.png diff --git a/404.html b/404.html index c35767cbc..9c4740478 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ AMR (for R) - 2.1.1.9253 + 2.1.1.9255
set.seed(123)
mic_values <- random_mic(100)
sir_values <- as.sir(mic_values, mo = "K. pneumoniae", ab = "cipro", guideline = "EUCAST 2024")
-#>
-#> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with
-#> all the details of the breakpoint interpretations.
-#>
-#> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin), EUCAST 2024... NOTE
-#> • Multiple breakpoints available for ciprofloxacin (CIP) in Klebsiella pneumoniae - assuming body site 'Non-meningitis'.
my_data <- tibble(MIC = mic_values, SIR = sir_values)
my_data
diff --git a/articles/AMR_for_Python.html b/articles/AMR_for_Python.html
index 9017c5ae7..605915f50 100644
--- a/articles/AMR_for_Python.html
+++ b/articles/AMR_for_Python.html
@@ -31,7 +31,7 @@
AMR (for R)
- 2.1.1.9253
+ 2.1.1.9255
diff --git a/articles/AMR_with_tidymodels.html b/articles/AMR_with_tidymodels.html
index fd703a5b1..935c3ac58 100644
--- a/articles/AMR_with_tidymodels.html
+++ b/articles/AMR_with_tidymodels.html
@@ -31,7 +31,7 @@
AMR (for R)
- 2.1.1.9253
+ 2.1.1.9255
diff --git a/articles/EUCAST.html b/articles/EUCAST.html
index 23c9926ce..ded798274 100644
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@@ -31,7 +31,7 @@
AMR (for R)
- 2.1.1.9253
+ 2.1.1.9255
diff --git a/articles/MDR.html b/articles/MDR.html
index 65882cd08..2dcb639d4 100644
--- a/articles/MDR.html
+++ b/articles/MDR.html
@@ -31,7 +31,7 @@
AMR (for R)
- 2.1.1.9253
+ 2.1.1.9255
diff --git a/articles/PCA.html b/articles/PCA.html
index 42984956a..e087d425a 100644
--- a/articles/PCA.html
+++ b/articles/PCA.html
@@ -31,7 +31,7 @@
AMR (for R)
- 2.1.1.9253
+ 2.1.1.9255
diff --git a/articles/WHONET.html b/articles/WHONET.html
index d2630370c..f2a59e314 100644
--- a/articles/WHONET.html
+++ b/articles/WHONET.html
@@ -31,7 +31,7 @@
AMR (for R)
- 2.1.1.9253
+ 2.1.1.9255
diff --git a/articles/datasets.html b/articles/datasets.html
index 23c19ccaa..902edfa5b 100644
--- a/articles/datasets.html
+++ b/articles/datasets.html
@@ -31,7 +31,7 @@
AMR (for R)
- 2.1.1.9253
+ 2.1.1.9255
@@ -425,13 +425,13 @@ column names:
ab, cid, name, group, a
iv_ddd, iv_units, and loinc.
This data set is in R available as antimicrobials
, after
you load the AMR
package.
-It was last updated on 20 April 2025 10:55:31 UTC. Find more info
+
It was last updated on 26 April 2025 14:23:14 UTC. Find more info
about the contents, (scientific) source, and structure of this data set
here.
Direct download links:
- Download as original
-R Data Structure (RDS) file (44 kB)
+R Data Structure (RDS) file (43 kB)
- Download as tab-separated
text file (0.1 MB)
@@ -498,7 +498,7 @@ as comma separated values.
Aminoglycoside antibacterials
Other aminoglycosides
ak, ami, amik, …
-amicacin, amikacillin, amikacina, …
+amikacillin, amikacina, amikacine, …
1.0
@@ -547,7 +547,7 @@ inhibitors
Beta-lactam antibacterials, penicillins
Penicillins with extended spectrum
am, amp, ampi
-acillin, adobacillin, alpen, …
+adobacillin, alpen, amblosin, …
2.0
g
6.0
diff --git a/articles/index.html b/articles/index.html
index 1c4b9620c..51d2c3958 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -7,7 +7,7 @@
AMR (for R)
- 2.1.1.9253
+ 2.1.1.9255
diff --git a/articles/welcome_to_AMR.html b/articles/welcome_to_AMR.html
index 6a315ea9e..1b1bab716 100644
--- a/articles/welcome_to_AMR.html
+++ b/articles/welcome_to_AMR.html
@@ -31,7 +31,7 @@
AMR (for R)
- 2.1.1.9253
+ 2.1.1.9255
diff --git a/authors.html b/authors.html
index 400356a31..98e9ecfab 100644
--- a/authors.html
+++ b/authors.html
@@ -7,7 +7,7 @@
AMR (for R)
- 2.1.1.9253
+ 2.1.1.9255
diff --git a/index.html b/index.html
index 8966d76d4..cb3d5713d 100644
--- a/index.html
+++ b/index.html
@@ -34,7 +34,7 @@
AMR (for R)
- 2.1.1.9253
+ 2.1.1.9255
@@ -502,7 +502,7 @@
install.packages("AMR", repos = "beta.amr-for-r.org")
# if this does not work, try to install directly from GitHub using the 'remotes' package:
-remotes::install_github("msberends/AMR")
+remotes::install_github("msberends/AMR")
(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! Install this beta using the instructions here.)
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’s Atlantic Veterinary College, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.
antibiotics
has been renamed to antimicrobials
as the data set contains more than just antibiotics. Using antibiotics
will still work, but now returns a warning.rsi
class, which were all replaced with their sir
equivalents over two years ago.resistance_predict()
and sir_predict()
is now deprecated and will be removed in a future version. Use the tidymodels
framework instead, for which we wrote a basic introduction.as.sir()
now has extensive support for veterinary breakpoints from CLSI. Use breakpoint_type = "animal"
and set the host
argument to a variable that contains animal species names.parallel
package (part of base R). Use as.sir(your_data, parallel = TRUE)
to run SIR interpretation using multiple cores.guideline
, ab
, mo
, and uti
: as.sir(..., ab = "column1", mo = "column2", uti = "column3")
. This greatly improves the flexibility for users.sir
class for Positron.xpt
) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.This changelog only contains changes from AMR v3.0 (March 2025) and later.