Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://doi.org/10.18637/jss.v104.i03.
Incorporate these changes for v2.0.0, expected to hit CRAN in January/February 2023:
[x] Implement new algorithm for microorganisms determination
[x] e.g. #54
[x] Read about stringdist package, maybe include some code to this package (license is compatible, be sure to add attribution)
[x] Translations:
[x] Add more translations (check with Deepl), such as Ukrainian, Turkish, Greek, Japanese, Polish, simplified Chinese
[x] #64
[x] Add instruction to repo documentation
[x] Add new data-raw/_language_update.R workflow
[x] Update antibiotics data set
[x] #62
[x] Update antibiotics data set with new DDDs, etc.
[x] Check WHOCC website for missing antibiotic agents - all of J0 should be present in our data set
[x] Include latest EUCAST and CLSI breakpoints (check with WHONET), and EUCAST Expert Rules (probably 2023 guidelines), also add v12 of expert rules and update intrinsic_resistant
[x] Update the microorganisms data set
[x] Change all references from CoL to GBIF, also on website and internal variables
[x] Update reproduction script to rely on DOI 10.15468/39omei and latest LPSN
[x] Be sure to cite right: GBIF Secretariat (2021). GBIF Backbone Taxonomy. Checklist dataset https://doi.org/10.15468/39omei accessed via GBIF.org on 2022-09-02 (parametrise date with R Markdown)
[x] Include new identifiers: species_id should contain TaxonID from GBIF records, otherwise LPSN record number
[x] Include #51
[x] Remove families without genera, order without families, classes without orders, phyla without classes
[x] Develop new microbial codes that are more reproducible and sustainable, yet still readable + add translation from older versions Won’t do - codes would become too lengthy
[x] Try to increase speed of first_isolate(), get_new_episode()
[x] Get rid of git_development.sh and git_merge.sh workflows (replace with git pre-commit hook)
[x] Write developers guideline to explain how things work in this repo
[x] Update CITATION to include our JSS paper, also put DOI in the description of the DESCRIPTION file + edit Welcome vignette and website index accordingly
[x] Convert all data sets to tibbles, also update unit tests
Incorporate these changes for v2.0.0, expected to hit CRAN in January/February 2023:
stringdistpackage, maybe include some code to this package (license is compatible, be sure to add attribution)data-raw/_language_update.Rworkflowantibioticsdata setantibioticsdata set with new DDDs, etc.intrinsic_resistantmicroorganismsdata setspecies_idshould contain TaxonID from GBIF records, otherwise LPSN record numberDevelop new microbial codes that are more reproducible and sustainable, yet still readable + add translation from older versionsWon’t do - codes would become too lengthyfirst_isolate(),get_new_episode()git_development.shandgit_merge.shworkflows (replace with git pre-commit hook)pkgdown2.0.0 and Bootstrap 5mainbranch using GHACITATIONto include our JSS paper, also put DOI in the description of theDESCRIPTIONfile + edit Welcome vignette and website index accordinglytype_sum()to pillar