admiralneuro (development version)

Template programs

Added ADLB template scripts ad_adlb.R which creates a Laboratory Analysis Dataset. (#117)

Added Vignette “Creating ADLB”. (#115)
Added a new vignette “Explore ADaM Templates” to the “Get Started” menu. It displays the {admiralneuro} templates. (#126)
A night mode option has been added to the {admiralneuro} website. This can be be toggled using the sun/moon icon in the top right corner of the navigation bar. Tooltips have also been set up for each of the icons on the navigation bar. (#125)

Developer Notes

Creating the website for pull requests was enabled. Add “[create website]” to the pull request title to trigger website creation. (#125)
Fixed links in the vignettes and added the Slack invitation link to .lycheeignore for a successful CI/CD Links/Validate Links workflow run. (#131)
Clickable links to personal websites or GitHub profiles were added in the home page sidebar for every {admiralneuro} author. Up-versioned {admiraldev} to 1.5.0, as the custom {admiral} roclets (i.e., roxygen_*() functions) have now been moved to {admiraldev}. Update to roxygen2 8.0.0. (#135)
Updated ADLB template and vignette to incorporate new parameter TAU181P from updated lb_neuro in pharmaversesdtm. Added links to ADNV and ADLB vignettes in admiralneuro vignettes. (#138)

Improved test coverage in compute_centiloid() function when invalid tracer combination is provided. The function also now only accepts positive SUVR values. (#106)

Developer Notes

Aligned the templates’ save directory with {pharmaverseadam} requirements. (#91)

The function compute_upsit_percentile() calculates percentiles based on age, sex, and UPSIT scores. (# 95)

ADNV template scripts ad_adnv.R which creates a Nervous System Analysis Dataset. (#113)

Moved test SDTM datasets dm_neuro, nv_neuro, suppnv_neuro and ag_neuro from {admiralneuro} to {pharmaversesdtm}. (#92)
Updated the kapa.ai data-modal-search-placeholder to “Ask me a question about {admiralneuro} or the {admiral} ecosystem…” (#119)

Initial package release mainly focused on Alzheimer’s disease specifically for the PET scan analysis.

The function compute_centiloid() computes centiloid values based on Amyloid PET tracer, SUVR value and pipeline, and reference region. (#21)

ADAPET template scripts ad_adapet.R which creates an Amyloid PET Scan Analysis Dataset. (#25)
ADTPET template scripts ad_adtpet.R which creates a Tau PET Scan Analysis Dataset. (#25)