Gdr 2419

[gladkia]

Description

Improve pkgdown site

What changed?

• updated news and added reference sections
• Related JIRA issue: GDR-2419
• pkgdown site link: https://gdrplatform.github.io/gDRcore/

Logistic checklist

• Package version bumped
• Changelog updated

Screenshots (optional)

[j-smola]

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?

[gladkia]

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]

I've just added pipeline diagrams to Rmd. See 4b6f3d7 and 0c74a03.
@bczech , @j-smola FYI.