use cases of convert_blanks_to_na()

Hi Dinakar, @cicdguy

Any chance you could help me set up a devel version of the blog site. Or point me in the right direction/hold some hands while I fumble around in the daark ????

Write out assumption, strategy and scope for blog in the Wiki

There are several working groups that stemmed from {admiral}, create a blog that highlights their purpose and scope.

          A value level validation use case, where `admiral` is used to validate a small chunk of the data:

• validate a parameter by using admiral::derive_param_computed.
• Derivation text: derive new parameter/records for ADEX.PARAMCD = ADPCYMG (Actual Dose per Cycle) based on existing parameters - Actual Dose per Cycle (ADPCYMG) = Total Amount of Dose (TOTDOSE) / Number of Cycles (NUMCYC);
• admiral::derive_param_computed can add a parameter computed from the analysis value of other parameters.
  In this example, ADEX.AVAL (where ADEX.PARAPMCD = ADPCYMG)
= ADEX.AVAL (where ADEX.PARAPMCD = TOTDOSE) / ADEX.AVAL (where ADEX.PARAPMCD = NUMCYC)

# read in data
path_ads <- "xxxx"
adex <- haven::read_sas(paste0(path_ads, "adex.sas7bdat")) %>% 
  select(USUBJID, PARAM, PARAMCD, AVAL)

# subset input data to PARAMCD = "TOTDOSE", "NUMCYC"
adex_TOTDOSE_NUMCYC <- adex %>% filter(PARAMCD %in% c("TOTDOSE", "NUMCYC"))
# admiral::derive_param_computed()
val <- 
  derive_param_computed(
  adex_TOTDOSE_NUMCYC,
  by_vars = exprs(USUBJID),
  parameters = c("TOTDOSE", "NUMCYC"),
  analysis_value = AVAL.TOTDOSE / AVAL.NUMCYC,
  set_values_to = exprs(
    PARAMCD = "ADPCYMG",
    PARAM = "Actual Dose per Cycle (mg)"
  )
) 

# compare with primary
diffdf::diffdf(adex %>% filter(PARAMCD == "ADPCYMG"), 
               val %>% filter(PARAMCD == "ADPCYMG"), 
               keys = c("USUBJID", "PARAMCD"))

Originally posted by @kaz462 in #2 (comment)

In this blog post, we will describe the process of reproducing the R Submissions Pilot 2 App using our in-house developed framework. We will share our stories learned, a short introduction to Rhino and how we added value by using pkglite.

We should write a blogpost comparing the approaches chosen by tidyverse vs admiral.
I have specifically in mind the use of exprs() when selecting multiple variables compared to vars() in tidyverse.

We can think about mentioning why we diverge from the tidyverse standards (need for reliability) and that we may switch to the tidyverse standard in the future.

There may be other decisions where we diverge from tidyverse standards worth mentioning but they really should have an impact on the end user (in my opinion).

Discussion point:

I would like to change the name of the repo to better represent what we do here.
This is relevant because the name is featured in all URL's.

github.com/pharmaverse/blog/ would not be bad.
However, that somewhat depends on the scope: is it going to be THE pharmaverse blog?
What about the thing NEST is planning?

What do you think, @pharmaverse/commswg

Possible breakage of the derive_param_computed blog post when updated

Set up Google Analytics

Reference issue below
pharmaverse/admiral#1827 (comment)

Create a blog about the use of derive_summary_records()

I was thinking of writing a post about what is admiral, its birth (with screenshots), how was and how is the situation in terms of contributors, its extensions, and what is the modularized framework.
Most of those information came from Ross Farrugia presentation on R/Pharma 2022 and were the base of the slides that were shared with the Council.

What's on the website/brief tour

• Version on website and what they mean?
• templates versus vignettes
• families and keywords
• function documentation strategy
• ?

@pharmaverse/commswg - hi all

I noticed when clicking around the different posts that we don't have a button to get back to the home page.

Can anyone look into this?

• What is purpose/scope of site (Ben)
• derive_summary_records (Ben)
• derive_param_computed
• convert_blanks_to_na (Sadchla)
• Bayer validation post (Kangjie)
• Differences between derive and compute
• Extension packages and use_ad_template (Ben)
• Version on website and what they mean? (Sadchla)

Maybe we can come up with a temporary tags that people can chose from to avoid too many tags.

Upcoming

• convert_blanks_na() - July 11th
• rounding differences - July 25th

Proposed

• @StefanThoma blog post on UseR Conference (July 21st) - making cross-company package
• [ ]

Ideation

• Advice on how to choose image for post (most likely hex sticker)
• Functions that have low probability of being changed/deprecated

Wondering if we can have a blog post for {falcon} on the pharmaver/blog site? The post has been shared on LinkedIn.

https://www.linkedin.com/pulse/harmonizing-clinical-reporting-through-falcon-initiative-vincent-shen

https://github.com/pharmaverse/admiral/tree/main/.github/ISSUE_TEMPLATE

Want to get the image to be the pharmaverse in the tab.

• Styler Checker
• Link Checker
• Other Quarto Workflows?
• Fine tune the quarto publish

See: https://github.com/r-lib/actions

Newcomers and using admiral and collaboration cross company

Long term Strategy for Images for Posts

• Gets boring with same hex sticker
• How to differentiate between same high-level subject: functions, process, extension packages.

I was thinking of writing a post about what is pharmaverse, why we should choose it, where we can find its packages, and list some useful links.
Most of those information came from Ross Farrugia presentation on R/Pharma 2022 and were the base of the slides that were shared with the Council.

In quarto, emails are written in the format:
Person
In markdown, it is:
Person

This is an issue for the link checker, because when converting from quarto to markdown I simply change the extension.

Solution:
In R file responsible for changing extension also delete the "."

Note on handy tools in R/CICD.R

So it create a link to the source code for the file above the citation.

When we get a little more stable - we should start setting up the renv.lock as this will link to R environment.

Originally posted by @bms63 in #56 (comment)

R-Script to run which creates a blogpost draft for new blogposts.

End result here is not a finished template, but just to set something up for now that can be adjusted later.

          > @pharmaverse/commswg

We have to discuss the front images and corresponding tags. The function I created here copies default images for specific tags / image parameter. We should also discuss the tags we want to use. In my opinion, writers should use as many of the predefined tags as possible. Should they be able to create their own?

No I don't think people should make their own tags - we should provide a set and create news one if needed.

Originally posted by @bms63 in #40 (comment)

Remove CICD spelling post

Clean out old freeze, etc files that are no longer tracked

Highlight the package argument in use_ad_template()

https://stefanthoma.github.io/quarto-blog/posts/2023-03-14_shiny_script_upload/

I'm wondering if we have admiral loaded with admiraldev if we can just use our assertions rather than checkmate. once less depenedency.

Originally posted by @bms63 in #49 (comment)

There is additional information on creating posts in Readme that is not in the Scope post.

This should be aligned and re-published.

• Identify Categories that should be used for posts