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Issue 85: Analytical solutions in stan #95

Merged
merged 16 commits into from
Sep 21, 2024
Merged

Issue 85: Analytical solutions in stan #95

merged 16 commits into from
Sep 21, 2024

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seabbs
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@seabbs seabbs commented Sep 20, 2024

Description

This PR closes #85 by adding analytical solutions in stan and tests to compare them to R side solutions.

Checklist

  • My PR is based on a package issue and I have explicitly linked it.
  • I have included the target issue or issues in the PR title in the for Issue(s) issue-numbers: PR title
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  • I have tested my changes locally.
  • I have added or updated unit tests where necessary.
  • I have updated the documentation if required.
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@seabbs seabbs marked this pull request as ready for review September 21, 2024 22:22
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codecov bot commented Sep 21, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.76%. Comparing base (345e95b) to head (aaf7663).
Report is 1 commits behind head on main.

Additional details and impacted files
@@           Coverage Diff           @@
##             main      #95   +/-   ##
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  Coverage   99.76%   99.76%           
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  Files          10       10           
  Lines         423      427    +4     
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+ Hits          422      426    +4     
  Misses          1        1           
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99.76% <100.00%> (+<0.01%) ⬆️

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LGTM (self-review)

@seabbs seabbs merged commit 24da423 into main Sep 21, 2024
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@seabbs seabbs deleted the stan-analytical branch September 21, 2024 22:42
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This is how benchmark results would change (along with a 95% confidence interval in relative change) if aaf7663 is merged into main:

  • ✔️cmdstan_fit_gamma_expgrowth: 7.67s -> 7.66s [-0.82%, +0.38%]
  • 🚀cmdstan_fit_lognormal_unif: 1.66s -> 751ms [-58.21%, -51.2%]
  • ❗🐌dprimarycensoreddist_pweibull_expgrowth: 2.37ms -> 2.44ms [+0.27%, +5.3%]
  • ❗🐌dprimarycensoreddist_weibull: 2.31ms -> 2.37ms [+0.41%, +4.19%]
  • ✔️fitdistdoublecens_gamma_expgrowth: 663ms -> 662ms [-0.62%, +0.31%]
  • ✔️fitdistdoublecens_normal: 551ms -> 551ms [-0.26%, +0.24%]
  • ❗🐌pprimarycensoreddist_lnorm: 1.9ms -> 2ms [+3.41%, +7.32%]
  • ✔️pprimarycensoreddist_plnrom_expgrowth: 48.1ms -> 48.4ms [-1.07%, +2.03%]
    Further explanation regarding interpretation and methodology can be found in the documentation of touchstone.

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Implement analytical solutions in R and stan
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