pharmaverse / admiralmetabolic Goto Github PK

Background Information

See #5 to understand what we are looking for. Please put all your discussion there. Don't hold anything back!

Definition of Done

Clear focus areas identified - these could be:

• Metabolic-specific ADaM datasets
• Metabolic-specific derived parameters in standard ADaMs (eg. ADVS)
• Metabolic-specific variables in standard ADaMs (eg. ADSL)

Please select a category the issue is focused on?

Other

Let us know where something needs a refresh or put your idea here!

Website theme currently looks like this:

Which does not match the admiral family theme:

Task is to identify where this is controlled (could it be in __pkgdown.yml?) and update. Might be good to compare files across the various admiral repos.

Base the vignette on the BDS Findings vignette from {admiral} (also uses ADVS – lucky us!) but don't duplicate sections that would be identical. See {admiralpeds} ADVS vignette as an example.​

Suggestion on contest/structure:

• Explain what the common obesity endpoints are.​
• Explain how to add them to ADVS using {admiral} tools.​ Could consider criterion flags - we have a brand-new function in {admiral}, derive_vars_crit_flag(). ​

Background Information

Two possible questionnaire datasets specific to our TA are the UWQoL (Impact of Weight on Quality of Life) and TFEQ (Three-Factor Eating Questionnaire), but there could definitely be others.

Let's use this issue to share our research findings around each of the questionnaires. This could include:

• Licensing (are they free to use)?
• Why these questionnaires are of interest for admiralmetabolic
• When implemented in something like an ADQS, are there any steps that are non-standard or unique to these questionnaires? This could be special computed scores, special processing, etc.

Please share any findings as soon as you have them to not duplicate any work.

Definition of Done

Obtain a detailed understanding of each of the questionnaires, enabling us to set out

• what test data we need to create
• what templates we need to create
• what vingettes we need to create
• why we are doing this, i.e. what is unique to the TA that warrants inclusion into {admiralmetabolic}?

Background Information

See #5 to understand why we need test data. We will likely need to identify the initial focus areas (#7) for the package (#7) before we can understand what test data we need.

Follow the guidance from pharmaversesdtm as eventually we will move our test data out into this repo/package. If unsure of any conventions to follow, @manciniedoardo can advise.

Don't go overboard as this is only for driving the vignettes and templates so likely 5-10 patients should be enough.

Definition of Done

Some starter test data which we can build on over time, which can help address focus areas in #7.

Background Information

This repo has been generated from the admiraltemplate repo. Various placeholder files/images need to be updated with metabolic-specific counterparts.

Definition of Done

Update selected items in the followingg:

• .Rbuildignore
• .lycheeignore
• DESCRIPTION
• README.md
• inst/WORDLIST
• man/figures/logo.png
• vignettes/admiraltemplate.Rmd
• __pkgdown.yml
• tests/testthat.R

Rename:

• R/admiraltemplate-package.R
• project file

Background Information

DEXA data, including:

• Lean Body Mass​
• Visceral Fat Mass​
• Total Fat Mass
  is used as an endpoint in many obesity trials, so it would be good to set up some test data for it.

Definition of Done

• Identify which SDTMv domain the DEXA data should go in
• Identify what data to include

Background Information

Currently, DESCRIPTION file records a dependency on admiral 1.1.0. But this version has a bug, and admiral 1.1.1 is due to release imminently. Once this happens, the DESCRIPTION file should be updated to point to it.

Definition of Done

Update DESCRIPTION file with following line admiral (>= 1.1.1) in place of existing one.

Please select a category the issue is focused on?

No response

Let us know where something needs a refresh or put your idea here!

The License.md file needs to be updated so that the right companies (NN and Roche) are mentioned. See here how it was done in admiralpeds.

Please select a category the issue is focused on?

Other

Let us know where something needs a refresh or put your idea here!

See admiralophtha:

Compared to admiralmetabolic:

Follow the same process as was done for this corresponding issue to update.

Background Information

We need to create an {admiralmetabolic} version of pharmaversesdtm::vs because the patients in the existing vs dataset are not obese.

This dataset will eventually be moved to {pharmaversesdtm}, but for the moment we will create it within {admiralmetabolic}.

Check out pharmaversesdtm repo for inspiration.

Definition of Done

• top-level data_raw folder created to house vs_metabolic, i.e. the script that generates our metabolic version of vs
• vs_metabolic program set up. program should read in vs and dm_metabolic, then keep only patients in the latter and edit all relevant tests (weight, BMI, etc) to make them obese.
• New vs_metabolic dataset documented in data.R

Showcase from start to finish how to create a full obesity ADVS. ​This should include:

• Parameter mappings​
• Endpoint programming​
• Any new computations​
  Start work once #22 is merged.

Use {admiral} ADVS template as a starting point.

Background Information

We need to create an {admiralmetabolic} version of pharmaversesdtm::dm which contains a small subset (5?) of the patients in the full dm dataset, so that we can use the same 5 patients across all of our new test data.

This dataset will eventually be moved to {pharmaversesdtm}, but for the moment we will create it within {admiralmetabolic}.

Check out pharmaversesdtm repo for inspiration.

Definition of Done

• top-level data_raw folder created to house dm_metabolic, i.e. the script that generates our metabolic version of dm
• dm_metabolic program set up. program should read in dm, keep only a few (5?) patients.
• Review all dm_metabolic variables to see if any changes are required.
• New dm_metabolic dataset documented in data.R

Background Information

See here and here.

These changes were erroneously made to admiraltemplate and were live when admiralmetabolic was set up, so we need to undo them.

Definition of Done

• staged_dependencies file added as done here