P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-13 01:51:52 +02:00
Code Releases Activity

(v1.7.1.9051) updated taxonomy, updated git branch name

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-10-06 13:23:57 +02:00
parent 8f5e5a3fc2
commit 37e6e35ec4
139 changed files with 2694 additions and 1862 deletions
Download Patch File Download Diff File Expand all files Collapse all files

13
NEWS.md
View File

@ -1,5 +1,5 @@
# `AMR` 1.7.1.9050
## <small>Last updated: 5 October 2021</small>
# `AMR` 1.7.1.9051
## <small>Last updated: 6 October 2021</small>
### Breaking changes
* Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version
@ -11,6 +11,7 @@
* Support for Danish, and also added missing translations of all antimicrobial drugs in Italian, French and Portuguese
### Changed
* Updated the bacterial taxonomy to 5 October 2021 (according to [LPSN](https://lpsn.dsmz.de)), including all 11 new staphylococcal species named since 1 January last year
* The `antibiotics` data set now contains **all ATC codes** that are available through the [WHOCC website](https://www.whocc.no), regardless of drugs being present in more than one ATC group. This means that:
* Some drugs now contain multiple ATC codes (e.g., metronidazole contains 5)
* `antibiotics$atc` is now a `list` containing `character` vectors, and this `atc` column was moved to the 5th position of the `antibiotics` data set
@ -500,7 +501,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
### New
* Support for the newest [EUCAST Clinical Breakpoint Tables v.10.0](https://www.eucast.org/clinical_breakpoints/), valid from 1 January 2020. This affects translation of MIC and disk zones using `as.rsi()` and inferred resistance and susceptibility using `eucast_rules()`.
* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt>. This **allows for machine reading these guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file [can be found here](https://github.com/msberends/AMR/blob/master/data-raw/read_EUCAST.R).
* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt>. This **allows for machine reading these guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file [can be found here](https://github.com/msberends/AMR/blob/main/data-raw/read_EUCAST.R).
* Support for LOINC and SNOMED codes
* Support for LOINC codes in the `antibiotics` data set. Use `ab_loinc()` to retrieve LOINC codes, or use a LOINC code for input in any `ab_*` function:
```r
@ -817,7 +818,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
* All references to antibiotics in our package now use EARS-Net codes, like `AMX` for amoxicillin
* Functions `atc_certe`, `ab_umcg` and `atc_trivial_nl` have been removed
* All `atc_*` functions are superseded by `ab_*` functions
* All output will be translated by using an included translation file which [can be viewed here](https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv)
* All output will be translated by using an included translation file which [can be viewed here](https://github.com/msberends/AMR/blob/main/data-raw/translations.tsv)
* Improvements to plotting AMR results with `ggplot_rsi()`:
* New argument `colours` to set the bar colours
* New arguments `title`, `subtitle`, `caption`, `x.title` and `y.title` to set titles and axis descriptions
@ -841,7 +842,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
freq(age) %>%
boxplot()
```
* Removed all hardcoded EUCAST rules and replaced them with a new reference file which [can be viewed here](https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv)
* Removed all hardcoded EUCAST rules and replaced them with a new reference file which [can be viewed here](https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv)
* Added ceftazidim intrinsic resistance to *Streptococci*
* Changed default settings for `age_groups()`, to let groups of fives and tens end with 100+ instead of 120+
* Fix for `freq()` for when all values are `NA`
@ -1352,7 +1353,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
* Added [ORCID](https://orcid.org) of authors to DESCRIPTION file
* Added unit testing with the `testthat` package
* Added build tests for Linux and macOS using Travis CI (https://travis-ci.org/msberends/AMR)
* Added line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/master/R)
* Added line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/main/R)
# AMR 0.1.1