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gdrplatform / gDRcore

R package to process dose-response curve data with the GR methods
https://gdrplatform.github.io/gDRcore
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Gdr 2419 #140

Closed gladkia closed 4 months ago

gladkia commented 4 months ago

Description

Improve pkgdown site

What changed?

Logistic checklist

Screenshots (optional)

gladkia commented 4 months ago

Could you maybe rethink group for functions?

  1. IMO not all function in "Combination helpers" is used only for combination data.
  2. "Mappping" seems to be list of function supporting "Pipeline"
  3. "Utils" and "Preparing input" are both "Preparing input for pipline"? As also "Identifying keys", right?
  4. etc.

Please, consider also

  1. update or "gDRcore.Rmd" vignette - "Drug processing section" section where due to lack of empty line list of steps disappeared;
  2. update the gDRcore architecture diagram in READMA.md as it is no longer readable on the pkgdown site.

PS: And fot is the reasone for function from constant.R file?

1st section

  1. Thanks. Fixed.
  2. Yes. Please note that runDrugResponseProcessingPipeline() is the top-level function for running the whole pipeline, dependent on multiple functions from gDRcore.
  3. Prepare input refers to the S3 methods called 'prepare_input' for data.table and MAE as well as their dependencies (internal helper functions). The utils comprises a broader, less specific category I've moved a single function from 'Identifying keys' to the utils category.

2nd section

  1. Done.
  2. Adrian suggested getting rid of this diagram from README.md. I'll try to prepare an analogous diagram with plantuml. It will be added to the vignette instead of the README.md.
  3. 'constants.R' - there are no functions there - only three constant objects: drugNameRegex, untreated_tag_patterns, and untreatedDrugNameRegex.
gladkia commented 4 months ago

I've just added pipeline diagrams to Rmd. See https://github.com/gdrplatform/gDRcore/pull/140/commits/4b6f3d7ce4165e00708cecd76ac31039e48caf4f and https://github.com/gdrplatform/gDRcore/pull/140/commits/0c74a0371bb5ec998dd4cdd0d8e8d99dfb050324. @bczech , @j-smola FYI.