P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-08-29 09:18:55 +02:00
Code Releases Activity

new eucast breakpoints parsing

Browse Source
This commit is contained in:
Matthijs Berends
2026-08-20 13:28:21 +01:00
parent bd9244206d
commit 2c33297cf6
147 changed files with 13626 additions and 15226 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
.github/prehooks/commit-msg vendored
View File

@@ -14,7 +14,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
.github/prehooks/pre-commit vendored
View File

@@ -14,7 +14,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
.github/workflows/check-current-testthat-dev-versions.yaml vendored
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
.github/workflows/check-current-testthat.yaml vendored
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
.github/workflows/check-old-tinytest.yaml vendored
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
.github/workflows/codecovr.yaml vendored
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
.github/workflows/publish-to-pypi.yml vendored
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
.github/workflows/renew-gpt-training-data.yml vendored
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
.github/workflows/todo-tracker.yml vendored
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
.github/workflows/website.yaml vendored
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

4
DESCRIPTION
View File

@@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 3.0.1.9086 Version: 3.0.1.9087
Date: 2026-08-13 Date: 2026-08-20
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by

23
NEWS.md
View File

@@ -1,9 +1,28 @@
# AMR 3.0.1.9086 # AMR 3.0.1.9087
Planned as v3.1.0, end of June 2026. Planned as v3.1.0, end of September 2026.
### Breaking Changes ### Breaking Changes
* The former *kingdoms* Bacteria and Archaea are now each divided into four kingdoms with new top-level *domains* 'Bacteria' and 'Archaea' (Göker and Oren, 2024, DOI: 10.1099/ijsem.0.006242). Following this, a new `domain` column in the `microorganisms` data set was added, and more importantly, `mo_kingdom()` now returns the formal kingdom (e.g. `"Pseudomonadati"` instead of `"Bacteria"`). Use `mo_domain()` for the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa, etc.), `kingdom` and `domain` are identical. * The former *kingdoms* Bacteria and Archaea are now each divided into four kingdoms with new top-level *domains* 'Bacteria' and 'Archaea' (Göker and Oren, 2024, DOI: 10.1099/ijsem.0.006242). Following this, a new `domain` column in the `microorganisms` data set was added, and more importantly, `mo_kingdom()` now returns the formal kingdom (e.g. `"Pseudomonadati"` instead of `"Bacteria"`). Use `mo_domain()` for the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa, etc.), `kingdom` and `domain` are identical.
| `mo_kingdom()` < 3.1.0 | `mo_kingdom()` now | `mo_domain()` (unchanged) |
|------------------------|---------------------|---------------------------|
| Bacteria | Bacillati | Bacteria |
| | Fusobacteriati | Bacteria |
| | Pseudomonadati | Bacteria |
| | Thermotogati | Bacteria |
| | | |
| Archaea | Methanobacteriati | Archaea |
| | Nanobdellati | Archaea |
| | Promethearchaeati | Archaea |
| | Thermoproteati | Archaea |
| | | |
| Fungi | Fungi | Fungi |
| | | |
| Protozoa | Protozoa | Protozoa |
Thus, `mo_domain()` was previously an alias of `mo_kingdom()`; it is now a distinct function returning the domain. Output of `mo_domain()` is therefore unchanged, while `mo_kingdom()` now returns the formal, new kingdom.
* Faster parallel computing via the `future` package for `as.sir()` and `wisca()`: a non-sequential plan (e.g. `future::plan(future::multisession)`) must be active before using `parallel = TRUE`. * Faster parallel computing via the `future` package for `as.sir()` and `wisca()`: a non-sequential plan (e.g. `future::plan(future::multisession)`) must be active before using `parallel = TRUE`.
### New ### New

2
R/aa_amr-package.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/aa_globals.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/aa_helper_functions.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/aa_helper_pm_functions.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/aa_options.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/ab.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/ab_from_text.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/ab_property.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/age.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/amr_course.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/amr_selectors.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/antibiogram.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/atc_online.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/av.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/av_from_text.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/av_property.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/availability.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/bug_drug_combinations.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/count.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/custom_antimicrobials.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/custom_interpretive_rules.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/custom_mdro_guideline.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/custom_microorganisms.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

11
R/data.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
@@ -312,7 +312,14 @@
#' The default is `"human"`, which can also be set with the package option [`AMR_breakpoint_type`][AMR-options]. Use [`as.sir(..., breakpoint_type = ...)`][as.sir()] to interpret raw data using a specific breakpoint type, e.g. `as.sir(..., breakpoint_type = "ECOFF")` to use ECOFFs. #' The default is `"human"`, which can also be set with the package option [`AMR_breakpoint_type`][AMR-options]. Use [`as.sir(..., breakpoint_type = ...)`][as.sir()] to interpret raw data using a specific breakpoint type, e.g. `as.sir(..., breakpoint_type = "ECOFF")` to use ECOFFs.
#' #'
#' ### Imported From WHONET #' ### Imported From WHONET
#' Clinical breakpoints in this package were validated through and imported from [WHONET](https://whonet.org), a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on [their website](https://whonet.org). The developers of WHONET and this `AMR` package have been in contact about sharing their work. We highly appreciate their great development on the WHONET software. #' Some breakpoints in this package were validated through and imported from [WHONET](https://whonet.org), a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on [their website](https://whonet.org). The developers of WHONET and this `AMR` package have been in contact about sharing their work. We highly appreciate their great development on the WHONET software.
#'
#' From WHONET, imported were:
#'
#' * All CLSI breakpoints, including ECOFF
#' * EUCAST breakpoints between `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))` and 2018
#'
#' EUCAST breakpoints from 2019 onwards, were retrieved directly from <https://www.eucast.org>.
#' #'
#' Our import and reproduction script can be found here: <https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R>. #' Our import and reproduction script can be found here: <https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R>.
#' #'

2
R/disk.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/export_biosample.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/first_isolate.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/g.test.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/get_episode.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/ggplot_pca.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/ggplot_sir.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/guess_ab_col.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/interpretive_rules.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/italicise_taxonomy.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/join_microorganisms.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/key_antimicrobials.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/kurtosis.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/like.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/mdro.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/mean_amr_distance.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/mic.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/mo.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/mo_matching_score.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

10
R/mo_property.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
@@ -44,19 +44,19 @@
#' #'
#' [mo_ref()] returns the abbreviated authority of the nomenclatural act that created the queried name combination. When `keep_synonyms = FALSE` (default), this is the authority of the currently accepted name. When `keep_synonyms = TRUE`, this is the authority under which the queried (possibly outdated) name was published. Emendations (changes to the species description without a name change) are not reflected; only the combination or original description authority is returned. #' [mo_ref()] returns the abbreviated authority of the nomenclatural act that created the queried name combination. When `keep_synonyms = FALSE` (default), this is the authority of the currently accepted name. When `keep_synonyms = TRUE`, this is the authority under which the queried (possibly outdated) name was published. Emendations (changes to the species description without a name change) are not reflected; only the combination or original description authority is returned.
#' #'
#' The short name ([mo_shortname()]) returns the first character of the genus and the full species, such as `"E. coli"`, for species and subspecies. Exceptions are abbreviations of staphylococci (such as *"CoNS"*, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as *"GBS"*, Group B Streptococci). Please bear in mind that e.g. *E. coli* could mean *Escherichia coli* (kingdom of Bacteria) as well as *Entamoeba coli* (kingdom of Protozoa). Returning to the full name will be done using [as.mo()] internally, giving priority to bacteria and human pathogens, i.e. `"E. coli"` will always be considered *Escherichia coli*. As a result, `mo_fullname(mo_shortname("Entamoeba coli"))` returns `"Escherichia coli"`. #' The short name ([mo_shortname()]) returns the first character of the genus and the full species, such as `"E. coli"`, for species and subspecies. Exceptions are abbreviations of staphylococci (such as *"CoNS"*, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as *"GBS"*, Group B Streptococci). Please bear in mind that e.g. *E. coli* could mean *Escherichia coli* (domain of Bacteria) as well as *Entamoeba coli* (domain of Protozoa). Returning to the full name will be done using [as.mo()] internally, giving priority to bacteria and human pathogens, i.e. `"E. coli"` will always be considered *Escherichia coli*. As a result, `mo_fullname(mo_shortname("Entamoeba coli"))` returns `"Escherichia coli"`.
#' #'
#' Following the formal introduction of the new kingdom rank into prokaryotic nomenclature in 2024 (\doi{10.1099/ijsem.0.006242}), [mo_kingdom()] and [mo_domain()] return different results for bacteria and archaea: [mo_kingdom()] returns the new formal kingdom (e.g. "Pseudomonadati", "Bacillati"), while [mo_domain()] returns the new domain (e.g. "Bacteria", "Archaea"). For non-prokaryotic organisms, both functions return identical results. #' Following the formal introduction of the new kingdom rank into prokaryotic nomenclature in 2024 (\doi{10.1099/ijsem.0.006242}), [mo_kingdom()] and [mo_domain()] return different results for bacteria and archaea: [mo_kingdom()] returns the new formal kingdom (e.g. "Pseudomonadati", "Bacillati"), while [mo_domain()] returns the new domain (e.g. "Bacteria", "Archaea"). For non-prokaryotic organisms, both functions return identical results.
#' #'
#' Determination of human pathogenicity ([mo_pathogenicity()]) is strongly based on Bartlett *et al.* (2022, \doi{10.1099/mic.0.001269}). This function returns a [factor] with the levels *Pathogenic*, *Potentially pathogenic*, *Non-pathogenic*, and *Unknown*. #' Determination of human pathogenicity ([mo_pathogenicity()]) is strongly based on Bartlett *et al.* (2022, \doi{10.1099/mic.0.001269}). This function returns a [factor] with the levels *Pathogenic*, *Potentially pathogenic*, *Non-pathogenic*, and *Unknown*.
#' #'
#' Determination of the Gram stain ([mo_gramstain()] is based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318/)), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, [PMID 34694987](https://pubmed.ncbi.nlm.nih.gov/34694987/)). Bacteria in these phyla are considered Gram-positive in this `AMR` package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`. Functions [mo_is_gram_negative()] and [mo_is_gram_positive()] always return `TRUE` or `FALSE` (or `NA` when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria. #' Determination of the Gram stain ([mo_gramstain()] is based on the taxonomic domain and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318/)), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, [PMID 34694987](https://pubmed.ncbi.nlm.nih.gov/34694987/)). Bacteria in these phyla are considered Gram-positive in this `AMR` package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`. Functions [mo_is_gram_negative()] and [mo_is_gram_positive()] always return `TRUE` or `FALSE` (or `NA` when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.
#' #'
#' Determination of yeasts ([mo_is_yeast()]) is based on the taxonomic kingdom and class. *Budding yeasts* are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. *True yeasts* quite specifically refers to yeasts in the underlying order Saccharomycetales (such as *Saccharomyces cerevisiae*). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return `TRUE`. It returns `FALSE` otherwise (or `NA` when the input is `NA` or the MO code is `UNKNOWN`). #' Determination of yeasts ([mo_is_yeast()]) is based on the taxonomic domain and class. *Budding yeasts* are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. *True yeasts* quite specifically refers to yeasts in the underlying order Saccharomycetales (such as *Saccharomyces cerevisiae*). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return `TRUE`. It returns `FALSE` otherwise (or `NA` when the input is `NA` or the MO code is `UNKNOWN`).
#' #'
#' Determination of intrinsic resistance ([mo_is_intrinsic_resistant()]) is based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(names(EUCAST_VERSION_EXPECTED_PHENOTYPES[1]))`. The [mo_is_intrinsic_resistant()] function can be vectorised over both argument `x` (input for microorganisms) and `ab` (input for antimicrobials). #' Determination of intrinsic resistance ([mo_is_intrinsic_resistant()]) is based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(names(EUCAST_VERSION_EXPECTED_PHENOTYPES[1]))`. The [mo_is_intrinsic_resistant()] function can be vectorised over both argument `x` (input for microorganisms) and `ab` (input for antimicrobials).
#' #'
#' Determination of both bacterial oxygen tolerance ([mo_oxygen_tolerance()]) and morphology ([mo_morphology()]) are based on BacDive, see *Source*. The function [mo_is_anaerobic()] only returns `TRUE` if the oxygen tolerance is `"anaerobe"`, indicating an obligate anaerobic species or genus. It always returns `FALSE` for species outside the taxonomic kingdom of Bacteria. #' Determination of both bacterial oxygen tolerance ([mo_oxygen_tolerance()]) and morphology ([mo_morphology()]) are based on BacDive, see *Source*. The function [mo_is_anaerobic()] only returns `TRUE` if the oxygen tolerance is `"anaerobe"`, indicating an obligate anaerobic species or genus. It always returns `FALSE` for species outside the taxonomic domain of Bacteria.
#' #'
#' The function [mo_url()] will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. [This MycoBank URL](`r TAXONOMY_VERSION$MycoBank$url`) is used for fungi wherever available , [this LPSN URL](`r TAXONOMY_VERSION$MycoBank$url`) for bacteria wherever available, and [this GBIF link](`r TAXONOMY_VERSION$GBIF$url`) otherwise. #' The function [mo_url()] will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. [This MycoBank URL](`r TAXONOMY_VERSION$MycoBank$url`) is used for fungi wherever available , [this LPSN URL](`r TAXONOMY_VERSION$MycoBank$url`) for bacteria wherever available, and [this GBIF link](`r TAXONOMY_VERSION$GBIF$url`) otherwise.
#' #'

2
R/mo_source.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/pca.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/plotting.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/proportion.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/random.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/resistance_predict.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/sir.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/sir_calc.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/sir_df.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/skewness.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/top_n_microorganisms.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/translate.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/vctrs.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/whocc.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/zz_deprecated.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
R/zzz.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

4
_pkgdown.yml
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #
@@ -56,7 +56,7 @@ footer:
left: [devtext] left: [devtext]
right: [logo] right: [logo]
components: components:
devtext: '<code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.' devtext: '<code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.'
logo: '<a target="_blank" href="https://www.rug.nl"><img src="https://amr-for-r.org/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl"><img src="https://amr-for-r.org/logo_umcg.svg" style="max-width: 150px;"></a>' logo: '<a target="_blank" href="https://www.rug.nl"><img src="https://amr-for-r.org/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl"><img src="https://amr-for-r.org/logo_umcg.svg" style="max-width: 150px;"></a>'
home: home:

2
codecov.yml
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
data-raw/_generate_python_wrapper.sh
View File

@@ -14,7 +14,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
data-raw/_language_update.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
data-raw/_pre_commit_checks.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
data-raw/_reproduction_scripts/reproduction_of_antimicrobials.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
data-raw/_reproduction_scripts/reproduction_of_antivirals.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

927
data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints_eucast.R
View File

File diff suppressed because it is too large Load Diff

2
data-raw/_reproduction_scripts/reproduction_of_dosage.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
data-raw/_reproduction_scripts/reproduction_of_example_isolates_unclean.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
data-raw/_reproduction_scripts/reproduction_of_intrinsic_resistant.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
data-raw/_reproduction_scripts/reproduction_of_microorganisms.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
data-raw/_reproduction_scripts/reproduction_of_microorganisms.groups.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

27091
data-raw/breakpoints_eucast_raw.csv
View File

File diff suppressed because it is too large Load Diff

BIN
data-raw/breakpoints_eucast_raw.rds
View File

Binary file not shown.

BIN
data-raw/eucast_new_from_xl.rds Normal file
View File

Binary file not shown.

2
data-raw/loinc.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
data-raw/poorman_prepend.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
data-raw/read_EUCAST.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
data-raw/salmonellae.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

BIN
data-raw/v_12.1_Antifungal_Breakpoint_Tables.xlsx Normal file
View File

Binary file not shown.

BIN
data-raw/v_13.0_Breakpoint_Tables.xlsx
View File

Binary file not shown.

BIN
data-raw/v_16.0__BreakpointTables.xlsx
View File

Binary file not shown.

2
pkgdown/extra.css
View File

@@ -13,7 +13,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
pkgdown/extra.js
View File

@@ -13,7 +13,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
tests/testthat.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

2
tests/testthat/helper-functions.R
View File

@@ -12,7 +12,7 @@
# https://doi.org/10.18637/jss.v104.i03 # # https://doi.org/10.18637/jss.v104.i03 #
# # # #
# Developed at the University of Groningen and the University Medical # # Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many # # Center Groningen in the Netherlands, in collaboration with many #
# colleagues from around the world, see our website. # # colleagues from around the world, see our website. #
# # # #
# This R package is free software; you can freely use and distribute # # This R package is free software; you can freely use and distribute #

Some files were not shown because too many files have changed in this diff Show More