Closes #98 - minor word changes in README.md

[jimrothstein]

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[jimrothstein]

@manciniedoardo

DRAFT
Added only a few comments, just to start.
README.md is very good; you are correct.

[jimrothstein]

Not right approach. I have another idea ....

[jimrothstein]

I think this is closer to useful but not in form of code comments

• line 164, find path to ADaM templates for the installed pkg (~/R/86_64...library/4.4/admiral/templates)
• line 166, collect names of all these templates (ad_xxxx.R)
• line 168, find path to Rdata files for installed pkg (~/R/86_64...library/4.4/admiral/data)
• line 178, apply run_template() function to templates (ad_xxxx.R)
  
  Better approach?

[jimrothstein]

• 87 cmd is of the form "Rscript" and the R template file to run
• 88 actually runs the template file using Rscript
• 93 finds path to local cache directory
• 95 rda_file is of the form ad_xxxx.rda
• 97 data is actual ADaM as a tibble. The function load_rda() loads the tibble in its execution environment and returns the tibble.
• 113 saves this ADaM tibble in the source for this package, pharmaverseadam/data
  

[jimrothstein]

@manciniedoardo

Not ready for true review.

• Goal: document script that creates ADaM files.
  Idea was to add comments. But for my own understanding, I find annotating lines -- see above -- to be clearest. Also, several directories are involved.

• So what I'd like to do is explain the big picture first in 2-3 sentences and list the directories to be used.
  Then code comments might be easier to follow.

If OK, I'll go ahead and do this.

[jimrothstein]

@manciniedoardo
Appreciate if you take a look, but I DO NEED to go through comments again.
So asking what you think so far.
(Some comments are not mine, some comments need to cleaned, need to redo the introduction).

[manciniedoardo]

Thanks @jimrothstein! Left some comments

[manciniedoardo]

Suggested change

	# save file to pharmaverseadam data dir (pharmaverseadam/data/adae.rda)
	# save file to pharmaverseadam data dir (pharmaverseadam/data/<adamname>.rda)

[jimrothstein]

I will adopt your notation ( pharmaverseadam/data/<adamname>.rda)

[manciniedoardo]

i think we can keep this because it's useful for logging purposes

[jimrothstein]

@manciniedoardo
Made your changes ... thanks!

A few more changes/comments will make the code clearer, I think.

• improve notation for files/directories.
• a few more clarifying comments.
• some prior comments are not helpful to me.

But first, do you feel it is worth the effort?

[manciniedoardo]

@manciniedoardo Made your changes ... thanks!

A few more changes/comments will make the code clearer, I think.

• improve notation for files/directories.
• a few more clarifying comments.
• some prior comments are not helpful to me.

But first, do you feel it is worth the effort?

thanks @jimrothstein! absolutely, feel free to take it as far as you deem necessary.

[jimrothstein]

@manciniedoardo UPDATE

An issue in admiral is to verify templates are working. (pharmaverse/admiral#2662)
This PR pharamaverseadam uses same templates to generate ADaMs.

Working with @StefanThoma on admiral issue.

Where the two scripts overlap, I hope to make variables, functions consistent .

Not there yet. When admiral script is more stable, will ask for your advice and suggestions.

[manciniedoardo]

@jimrothstein we just merged a small update to the documentation process that will have created a conflict, please merge main into this branch and accept the changes from main

[manciniedoardo]

@jimrothstein @StefanThoma maybe it would be good for us to meet at some point soon and discuss how this is going/next steps?

[jimrothstein]

Yes, discussion would be good.
(Also, having github problem; trying to resolve.)

@jimrothstein @StefanThoma maybe it would be good for us to meet at some point soon and discuss how this is going/next steps?

[shajoezhu]

can we please update this branch from main, and run a reverse dependency check before approving this
thanks

[manciniedoardo]

can we please update this branch from main, and run a reverse dependency check before approving this thanks

sure, but at the same time I'm not sure of the status of this PR anyway as create_adams_data.R file has been edited other times and for parallel efforts anyway.

[Fanny-Gautier]

Closed without merging. Many of these updates were implemented in other PRs. Thanks a lot Jim for your comments and updates, they were very helpful to understand the workflow.