Update post capr demo

[guuswilmink]

This 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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Is it clear how to use this from the Readme (particularly "Getting started with Capr-PHEMS")?

[guuswilmink]

Not sure why the Github actions are failing;
It indicates something is going wrong upon running .Rprofile with the "renv" package installation.
I don't know what is causing it, but this should not be the case locally on any machines.