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Releases: thehyve/Capr-PHEMS

Capr-PHEMS

20 Sep 11:30
@guuswilmink guuswilmink
v2.0.0
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This release includes the following major updates:

  • Added script under inst/scripts/main.R to be run in its entirety.
    • This is intended to facilitate the results collection process; one click of a button after configuration will generate all requested results
    • This replaces the R Markdown script previously present as the main code. This Rmd script now serves solely to provide examples and can be found under extras/Capr-PHEMS_examples.Rmd and extras/pdf_vignette/Capr-PHEMS_examples.pdf
  • Additional concept sets encompassing all variables per use case as they were provided to the Hyve (i.e. one big concept set per use case)
  • Added isStandardDB function
    • This function checks the standardness of provided concepts by cross-referencing your CDM instance/database's "concept" table. This was added to make the checking of standard concepts much more straightforward and compared to isStandard, and makes isStandard obsolete in the presence of a CDM instance.
  • CaprPHEMS can now be installed as a library.
    • After cloning the repo, run devtools::install_local() from the project folder to install the library (*note; this may be possible using devtools::install_github("thehyve/Capr-PHEMS"). To test after merge.)
    • Functions within CaprPHEMS can be accessed by calling CaprPHEMS::(); for example CaprPHEMS::countOccurences(...)

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Other updates:

  • Changes to result saves:
    • For isStandard and isStandardDB, results are only saved for provided files that contain non-standard concepts.
    • When no non-standard concepts are found for a file (or for a CDM table in the case of isStandardDB), the name of this file (or CDM table) is saved to "isStandard_OnlyStandard.txt" or "isStandardDB_OnlyStandard.txt" respectively. This is done for all files/tables.
  • Predefined conceptSets have been ported to RData format in the "data/" directory and are documented under R/data.R
  • Many files have been moved/removed. This particularly affects files that are/were in "inst/extdata/".
  • requirements.txt added for clarity on libraries and versions.
  • Improved feedback from functions upon errors
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