primarycensored 0.6.0

[seabbs]

This release renames the package to primarycensored from primarycensoredist and also renames many of the functions to remove the dist in their name. This was done to make the package name and the functions more consistent and to remove the need to use the dist suffix. It also aligns it with the new PrimaryCensored.jl package in our Julia ecosystem.

Aside from name changes, this release also adds an analytical solution for the weibull distribution with uniform primary censoring, removes the need to assign functions to the global environment for fitdistdoublecens() by using withr, and adds a check_truncation() function to check if the truncation time is larger than the maximum observed delay. This is used in fitdistdoublecens() and pcd_as_stan_data() to ensure that the truncation time is appropriate to maximise computational efficiency.

Package

• Removed the need to assign functions to the global environment for fitdistdoublecens() by using withr.
• Added a check_truncation() function to check if the truncation time is larger than the maximum observed delay. This is used in fitdistdoublecens() and pcd_as_stan_data() to ensure that the truncation time is appropriate to maximise computational efficiency.
• pcd_as_cmdstan_data() has been renamed to pcd_as_stan_data() to better reflect that it is used for Stan models in general rather than just the CmdStan models.
• The stan code has been refactored into a folder of functions within the current stan folder and the stan model has been moved into the stan folder. All paths to the stan code have been updated to reflect this.
• Added R and stan implementations of the primary censored cdf for the weibull distribution with uniform primary censoring.
• The package has been renamed to primarycensored as have all functions that use "dist" in their name.

Documentation

• Simplified the "Analytic solutions" vignette by removing verbose derivation details.
• Added links between vignettes to make it easier to navigate the documentation.
• Added explicit usage of pdist, dprimary, rdist, and rprimary arguments in the getting started vignette to make it easier to link to mathematical details.
• Fixed error in "Analytic solutions" vignette where the Weibull density was not being treated as zero for negative delays.
• Split "Why it works" vignette into two separate vignettes, "Why it works" and "Analytic solutions for censored delay distributions"

Pull requests

• Update codemeta.json by @github-actions in Update codemeta.json #103
• Issue 72: Split why it works vignette into intro and analytic solutions vignette by @SamuelBrand1 in Issue 72: Split why it works vignette into intro and analytic solutions vignette #106
• Bump JamesIves/github-pages-deploy-action from 4.6.4 to 4.6.8 by @dependabot in Bump JamesIves/github-pages-deploy-action from 4.6.4 to 4.6.8 #110
• Update README by @github-actions in Update README #111
• use local environment for fitdist call by @sbfnk in use local environment for fitdist call #113
• Update codemeta.json by @github-actions in Update codemeta.json #114
• Update README by @github-actions in Update README #115
• Issue Check why it works for maths lines we can do without #84: Prune not helpful to arg flow maths by @seabbs in Issue #84: Prune not helpful to arg flow maths #116
• Issue Link to why it works from getting started #82: Link between vignettes by @seabbs in Issue #82: Link between vignettes #118
• Issue Add heuristics when the relative_obs_time is much bigger than the maximum observed delay #69: Add check_truncation by @seabbs in Issue #69: Add check_truncation #120
• Update README by @github-actions in Update README #121
• Issue 109: Add explicit dist and primary arg usage to getting started by @seabbs in Issue 109: Add explicit dist and primary arg usage to getting started #122
• Issue 70: Restructure stan code by @seabbs in Issue 70: Restructure stan code #123
• Issue 125: Update analytic solutions to deal with possible neg t values by @SamuelBrand1 in Issue 125: Update analytic solutions to deal with possible neg t values #126
• Issue 94: Add R and Stan for analytical Weibull by @seabbs in Issue 94: Add R and Stan for analytical Weibull #109
• Update codemeta.json by @github-actions in Update codemeta.json #128
• Issue primarycensoreddist -> primarycensored #108: Rename from primarycensoreddist to primarycensored by @seabbs in Issue #108: Rename from primarycensoreddist to primarycensored #130
• Update README by @github-actions in Update README #132
• Update codemeta.json by @github-actions in Update codemeta.json #131

New Contributors

• @sbfnk made their first contribution in use local environment for fitdist call #113

Full Changelog: v0.5.0...v0.6.0

---

This discussion was created from the release primarycensored 0.6.0.