+
ggplot(data_time, aes(x = year, y = res_AMX, color = gramstain)) +
geom_line() +
labs(title = "AMX Resistance Trends",
diff --git a/articles/EUCAST.html b/articles/EUCAST.html
index b8adc4aec..ea9bfa18d 100644
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@@ -31,7 +31,7 @@
AMR (for R)
- 2.1.1.9232
+ 2.1.1.9233
-
AMR 2.1.1.9232
+
AMR 2.1.1.9233
(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.)
-
A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)
+
A New Milestone: AMR v3.0 with 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’s Atlantic Veterinary College, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.
-
Breaking
+
Breaking
- Dataset
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.
- Removed all functions and references that used the deprecated
rsi class, which were all replaced with their sir equivalents over two years ago.
- Function
resistance_predict() is now deprecated and will be removed in a future version. Use the tidymodels framework instead, for which we wrote a basic introduction.
-
New
+
New
-
One Health implementation
- Function
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.
@@ -116,7 +116,7 @@
-
Changed
+
Changed
- SIR interpretation
- It is now possible to use column names for argument
ab, mo, and uti: as.sir(..., ab = "column1", mo = "column2", uti = "column3"). This greatly improves the flexibility for users.
- Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.
@@ -195,7 +195,7 @@
- Added console colours support of
sir class for Positron
-
Other
+
Other
- Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way
- Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations
- Added Prof. Kat Holt, Dr. Jane Hawkey, and Dr. Natacha Couto as contributors for their many suggestions, ideas and bugfixes
@@ -204,7 +204,7 @@
- Stopped support for SAS (
.xpt) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.
-
Older Versions
+
Older Versions
This changelog only contains changes from AMR v3.0 (March 2025) and later.
- For prior v2 versions, please see our v2 archive.
- For prior v1 versions, please see our v1 archive.
diff --git a/pkgdown.yml b/pkgdown.yml
index bd4f8aa8e..5ccc91a26 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -11,7 +11,7 @@ articles:
PCA: PCA.html
welcome_to_AMR: welcome_to_AMR.html
WHONET: WHONET.html
-last_built: 2025-03-31T08:57Z
+last_built: 2025-03-31T13:00Z
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 bd810dd1f..afe68d8dd 100644
--- a/reference/AMR-deprecated.html
+++ b/reference/AMR-deprecated.html
@@ -7,7 +7,7 @@
AMR (for R)
- 2.1.1.9232
+ 2.1.1.9233
diff --git a/reference/ab_property.html b/reference/ab_property.html
index 40776e6be..e6a2b0f43 100644
--- a/reference/ab_property.html
+++ b/reference/ab_property.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html
index 7d290a472..c068f2bb7 100644
--- a/reference/add_custom_antimicrobials.html
+++ b/reference/add_custom_antimicrobials.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html
index ad257d794..7816c2d6e 100644
--- a/reference/add_custom_microorganisms.html
+++ b/reference/add_custom_microorganisms.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/age.html b/reference/age.html
index e9179287f..0f0be2a02 100644
--- a/reference/age.html
+++ b/reference/age.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/age_groups.html b/reference/age_groups.html
index ea07369c9..f8b4c6532 100644
--- a/reference/age_groups.html
+++ b/reference/age_groups.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/antibiogram.html b/reference/antibiogram.html
index 67c94381f..d7425af9b 100644
--- a/reference/antibiogram.html
+++ b/reference/antibiogram.html
@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/antimicrobial_selectors.html b/reference/antimicrobial_selectors.html
index 9a953e21f..c17b471ce 100644
--- a/reference/antimicrobial_selectors.html
+++ b/reference/antimicrobial_selectors.html
@@ -17,7 +17,7 @@ my_data_with_all_these_columns %>%
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/as.av.html b/reference/as.av.html
index 4370e135b..1d785ccc1 100644
--- a/reference/as.av.html
+++ b/reference/as.av.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/as.disk.html b/reference/as.disk.html
index 722bbdfc3..22b4d4b17 100644
--- a/reference/as.disk.html
+++ b/reference/as.disk.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/as.mic.html b/reference/as.mic.html
index 69472c63d..8d7044a7b 100644
--- a/reference/as.mic.html
+++ b/reference/as.mic.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/as.mo.html b/reference/as.mo.html
index b6270e74e..502f60618 100644
--- a/reference/as.mo.html
+++ b/reference/as.mo.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/as.sir.html b/reference/as.sir.html
index 1a8e9f67d..8c91d071d 100644
--- a/reference/as.sir.html
+++ b/reference/as.sir.html
@@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
@@ -820,16 +820,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
#> # A tibble: 65 × 16
#> datetime index ab_given mo_given host_given ab mo
#> <dttm> <int> <chr> <chr> <chr> <ab> <mo>
-
#> 1 2025-03-31 08:58:25 1 ampicillin Strep p… human AMP B_STRPT_PNMN
-
#> 2 2025-03-31 08:58:25 1 AMP Escheri… human AMP B_[ORD]_ENTRBC…
-
#> 3 2025-03-31 08:58:25 1 AMP Escheri… human AMP B_[ORD]_ENTRBC…
+
#> 1 2025-03-31 13:01:25 1 ampicillin Strep p… human AMP B_STRPT_PNMN
+
#> 2 2025-03-31 13:01:25 1 AMP Escheri… human AMP B_[ORD]_ENTRBC…
+
#> 3 2025-03-31 13:01:25 1 AMP Escheri… human AMP B_[ORD]_ENTRBC…
#> 4 NA NA NA NA NA NA NA
-
#> 5 2025-03-31 08:58:26 1 GEN Escheri… human GEN B_[ORD]_ENTRBC…
-
#> 6 2025-03-31 08:58:26 1 TOB Escheri… human TOB B_[ORD]_ENTRBC…
-
#> 7 2025-03-31 08:58:27 1 AMX B_STRPT… human AMX B_STRPT_PNMN
-
#> 8 2025-03-31 08:58:27 1 AMX B_STRPT… human AMX B_STRPT_PNMN
-
#> 9 2025-03-31 08:58:27 2 AMX B_STRPT… human AMX B_STRPT_PNMN
-
#> 10 2025-03-31 08:58:27 3 AMX B_STRPT… human AMX B_STRPT_PNMN
+
#> 5 2025-03-31 13:01:25 1 GEN Escheri… human GEN B_[ORD]_ENTRBC…
+
#> 6 2025-03-31 13:01:26 1 TOB Escheri… human TOB B_[ORD]_ENTRBC…
+
#> 7 2025-03-31 13:01:26 1 AMX B_STRPT… human AMX B_STRPT_PNMN
+
#> 8 2025-03-31 13:01:26 1 AMX B_STRPT… human AMX B_STRPT_PNMN
+
#> 9 2025-03-31 13:01:26 2 AMX B_STRPT… human AMX B_STRPT_PNMN
+
#> 10 2025-03-31 13:01:26 3 AMX B_STRPT… human AMX B_STRPT_PNMN
#> # ℹ 55 more rows
#> # ℹ 9 more variables: host <chr>, method <chr>, input <chr>, outcome <sir>,
#> # notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
diff --git a/reference/atc_online.html b/reference/atc_online.html
index 8cc3b572d..1832268a1 100644
--- a/reference/atc_online.html
+++ b/reference/atc_online.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/av_from_text.html b/reference/av_from_text.html
index a2ebe497e..a15d98f34 100644
--- a/reference/av_from_text.html
+++ b/reference/av_from_text.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/av_property.html b/reference/av_property.html
index eebdfe687..4ad231e97 100644
--- a/reference/av_property.html
+++ b/reference/av_property.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/bug_drug_combinations.html b/reference/bug_drug_combinations.html
index 277ef8b30..fb1c80250 100644
--- a/reference/bug_drug_combinations.html
+++ b/reference/bug_drug_combinations.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/custom_eucast_rules.html b/reference/custom_eucast_rules.html
index 92e4d7fdd..91929a900 100644
--- a/reference/custom_eucast_rules.html
+++ b/reference/custom_eucast_rules.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/dosage.html b/reference/dosage.html
index badc742a1..faf084e41 100644
--- a/reference/dosage.html
+++ b/reference/dosage.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/example_isolates.html b/reference/example_isolates.html
index 916371abf..8ae4ab0fa 100644
--- a/reference/example_isolates.html
+++ b/reference/example_isolates.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/first_isolate.html b/reference/first_isolate.html
index 41ec5cf5c..92f596f24 100644
--- a/reference/first_isolate.html
+++ b/reference/first_isolate.html
@@ -9,7 +9,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/g.test.html b/reference/g.test.html
index 1d920ff05..278bdfc64 100644
--- a/reference/g.test.html
+++ b/reference/g.test.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/ggplot_pca.html b/reference/ggplot_pca.html
index 631d11469..005c6af66 100644
--- a/reference/ggplot_pca.html
+++ b/reference/ggplot_pca.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/ggplot_sir.html b/reference/ggplot_sir.html
index a76407f68..e6c4a17ac 100644
--- a/reference/ggplot_sir.html
+++ b/reference/ggplot_sir.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/index.html b/reference/index.html
index 1900eb615..00b9b6b75 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/join.html b/reference/join.html
index 813c7a980..eae9598d7 100644
--- a/reference/join.html
+++ b/reference/join.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/key_antimicrobials.html b/reference/key_antimicrobials.html
index c741a3d07..154366664 100644
--- a/reference/key_antimicrobials.html
+++ b/reference/key_antimicrobials.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/kurtosis.html b/reference/kurtosis.html
index 16d1359b4..0e54a9169 100644
--- a/reference/kurtosis.html
+++ b/reference/kurtosis.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/mean_amr_distance.html b/reference/mean_amr_distance.html
index 3ca7c263c..df843cba1 100644
--- a/reference/mean_amr_distance.html
+++ b/reference/mean_amr_distance.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/microorganisms.codes.html b/reference/microorganisms.codes.html
index 68dc2387e..be89758b8 100644
--- a/reference/microorganisms.codes.html
+++ b/reference/microorganisms.codes.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/mo_property.html b/reference/mo_property.html
index a977310a0..baa13786f 100644
--- a/reference/mo_property.html
+++ b/reference/mo_property.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233
diff --git a/reference/mo_source.html b/reference/mo_source.html
index 1d1bcd74a..be7c61e1d 100644
--- a/reference/mo_source.html
+++ b/reference/mo_source.html
@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
AMR (for R)
-
2.1.1.9232
+
2.1.1.9233