Issue 85: Analytical solutions in stan

seabbs commented 3 weeks ago

Description

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

Checklist

[x] My PR is based on a package issue and I have explicitly linked it.
[x] I have included the target issue or issues in the PR title in the for Issue(s) issue-numbers: PR title
[x] I have read the contribution guidelines.
[x] I have tested my changes locally.
[x] I have added or updated unit tests where necessary.
[x] I have updated the documentation if required.
[x] My code follows the established coding standards.
[x] I have added a news item linked to this PR.
[x] I have reviewed CI checks for this PR and addressed them as far as I am able.

github-actions[bot] commented 3 weeks ago

This is how benchmark results would change (along with a 95% confidence interval in relative change) if ee62bb713b6442a4bee7f9d0745f46e521397290 is merged into main:

:exclamation::snail:cmdstan_fit_gamma: 7.65s -> 7.8s [+1.39%, +2.73%]
:rocket:cmdstan_fit_lognormal: 1.63s -> 694ms [-59.91%, -54.8%]
:heavy_check_mark:dprimarycensoreddist_pweibull_expgrowth: 2.26ms -> 2.24ms [-1.88%, +0.11%]
:heavy_check_mark:dprimarycensoreddist_weibull: 2.29ms -> 2.19ms [-11.85%, +3.29%]
:rocket:fitdistdoublecens_gamma_expgrowth: 660ms -> 655ms [-1.16%, -0.48%]
:heavy_check_mark:fitdistdoublecens_normal: 550ms -> 546ms [-1.53%, +0.29%]
:heavy_check_mark:pprimarycensoreddist_lnorm: 1.81ms -> 1.81ms [-2.74%, +2.22%]
:heavy_check_mark:pprimarycensoreddist_plnrom_expgrowth: 45.1ms -> 45.7ms [-1%, +3.43%] Further explanation regarding interpretation and methodology can be found in the documentation of touchstone.

github-actions[bot] commented 3 weeks ago

This is how benchmark results would change (along with a 95% confidence interval in relative change) if ed10c283c9a7b28a2b0388fdd51def9693e4643b is merged into main:

:heavy_check_mark:cmdstan_fit_gamma_expgrowth: 7.62s -> 7.68s [-0.12%, +1.76%]
:rocket:cmdstan_fit_lognormal_unif: 1.64s -> 559ms [-66.31%, -65.69%]
:heavy_check_mark:dprimarycensoreddist_pweibull_expgrowth: 2.21ms -> 2.22ms [-0.62%, +1.5%]
:heavy_check_mark:dprimarycensoreddist_weibull: 2.15ms -> 2.15ms [-0.51%, +0.47%]
:rocket:fitdistdoublecens_gamma_expgrowth: 673ms -> 669ms [-1.01%, -0.07%]
:rocket:fitdistdoublecens_normal: 561ms -> 557ms [-0.96%, -0.37%]
:heavy_check_mark:pprimarycensoreddist_lnorm: 1.76ms -> 1.79ms [-0.95%, +4.85%]
:heavy_check_mark:pprimarycensoreddist_plnrom_expgrowth: 43.5ms -> 43.3ms [-1.13%, +0.43%] Further explanation regarding interpretation and methodology can be found in the documentation of touchstone.

github-actions[bot] commented 3 weeks ago

This is how benchmark results would change (along with a 95% confidence interval in relative change) if 649b0c2249bed432f32498cd957cfbeb55ac937e is merged into main:

:heavy_check_mark:cmdstan_fit_gamma_expgrowth: 7.69s -> 7.71s [-0.43%, +0.9%]
:rocket:cmdstan_fit_lognormal_unif: 1.69s -> 709ms [-58.75%, -57.41%]
:heavy_check_mark:dprimarycensoreddist_pweibull_expgrowth: 2.29ms -> 2.3ms [-1.15%, +1.51%]
:heavy_check_mark:dprimarycensoreddist_weibull: 2.22ms -> 2.25ms [-0.41%, +2.63%]
:heavy_check_mark:fitdistdoublecens_gamma_expgrowth: 660ms -> 663ms [-0.73%, +1.45%]
:heavy_check_mark:fitdistdoublecens_normal: 550ms -> 547ms [-1.23%, +0.19%]
:heavy_check_mark:pprimarycensoreddist_lnorm: 1.82ms -> 1.85ms [-0.18%, +3.72%]
:heavy_check_mark:pprimarycensoreddist_plnrom_expgrowth: 46.2ms -> 45.7ms [-2.59%, +0.54%] Further explanation regarding interpretation and methodology can be found in the documentation of touchstone.

github-actions[bot] commented 3 weeks ago

This is how benchmark results would change (along with a 95% confidence interval in relative change) if cdb4099274d550b7f4d53adbce4ee83d3498d41a is merged into main:

:exclamation::snail:cmdstan_fit_gamma_expgrowth: 7.78s -> 7.91s [+0.8%, +2.42%]
:rocket:cmdstan_fit_lognormal_unif: 1.65s -> 772ms [-54.79%, -51.73%]
:heavy_check_mark:dprimarycensoreddist_pweibull_expgrowth: 2.43ms -> 2.41ms [-2.37%, +0.72%]
:heavy_check_mark:dprimarycensoreddist_weibull: 2.33ms -> 2.34ms [-1.22%, +1.62%]
:heavy_check_mark:fitdistdoublecens_gamma_expgrowth: 667ms -> 673ms [-0.32%, +2.02%]
:heavy_check_mark:fitdistdoublecens_normal: 554ms -> 552ms [-1.09%, +0.34%]
:heavy_check_mark:pprimarycensoreddist_lnorm: 2ms -> 2.03ms [-3.95%, +6.89%]
:heavy_check_mark:pprimarycensoreddist_plnrom_expgrowth: 48.3ms -> 48.1ms [-2.31%, +1.78%] Further explanation regarding interpretation and methodology can be found in the documentation of touchstone.

github-actions[bot] commented 3 weeks ago

This is how benchmark results would change (along with a 95% confidence interval in relative change) if 9f8eb5d465ed5132e88e9288c08ef39a8f35aa98 is merged into main:

:exclamation::snail:cmdstan_fit_gamma_expgrowth: 7.69s -> 7.82s [+0.93%, +2.29%]
:rocket:cmdstan_fit_lognormal_unif: 1.62s -> 756ms [-56.36%, -50.62%]
:heavy_check_mark:dprimarycensoreddist_pweibull_expgrowth: 2.39ms -> 2.41ms [-0.84%, +2.78%]
:heavy_check_mark:dprimarycensoreddist_weibull: 2.33ms -> 2.34ms [-1.77%, +2.46%]
:heavy_check_mark:fitdistdoublecens_gamma_expgrowth: 662ms -> 657ms [-2.02%, +0.53%]
:rocket:fitdistdoublecens_normal: 547ms -> 544ms [-0.99%, -0.03%]
:heavy_check_mark:pprimarycensoreddist_lnorm: 1.98ms -> 1.93ms [-8.61%, +3.83%]
:heavy_check_mark:pprimarycensoreddist_plnrom_expgrowth: 48.3ms -> 48.5ms [-0.95%, +1.6%] Further explanation regarding interpretation and methodology can be found in the documentation of touchstone.

github-actions[bot] commented 3 weeks ago

This is how benchmark results would change (along with a 95% confidence interval in relative change) if 136fa5bd1bc944ec518a5674fdb54e513cb368e3 is merged into main:

:heavy_check_mark:cmdstan_fit_gamma_expgrowth: 7.66s -> 7.63s [-1.09%, +0.24%]
:rocket:cmdstan_fit_lognormal_unif: 1.65s -> 678ms [-59.51%, -58.33%]
:heavy_check_mark:dprimarycensoreddist_pweibull_expgrowth: 2.22ms -> 2.23ms [-0.33%, +1.13%]
:heavy_check_mark:dprimarycensoreddist_weibull: 2.17ms -> 2.17ms [-1.09%, +1.73%]
:heavy_check_mark:fitdistdoublecens_gamma_expgrowth: 651ms -> 649ms [-1.24%, +0.58%]
:heavy_check_mark:fitdistdoublecens_normal: 538ms -> 537ms [-0.7%, +0.28%]
:heavy_check_mark:pprimarycensoreddist_lnorm: 1.78ms -> 1.78ms [-0.72%, +1.21%]
:heavy_check_mark:pprimarycensoreddist_plnrom_expgrowth: 43.8ms -> 44.2ms [-0.49%, +2.39%] Further explanation regarding interpretation and methodology can be found in the documentation of touchstone.

github-actions[bot] commented 3 weeks ago

This is how benchmark results would change (along with a 95% confidence interval in relative change) if f8de87db5e67c18da1e2f1371b0ace05b1c0b400 is merged into main:

:heavy_check_mark:cmdstan_fit_gamma_expgrowth: 7.62s -> 7.66s [-0.12%, +1.02%]
:rocket:cmdstan_fit_lognormal_unif: 1.66s -> 698ms [-59.89%, -56.13%]
:heavy_check_mark:dprimarycensoreddist_pweibull_expgrowth: 2.24ms -> 2.25ms [-1.25%, +1.57%]
:heavy_check_mark:dprimarycensoreddist_weibull: 2.21ms -> 2.18ms [-3.26%, +0.79%]
:heavy_check_mark:fitdistdoublecens_gamma_expgrowth: 660ms -> 657ms [-0.92%, +0.03%]
:rocket:fitdistdoublecens_normal: 547ms -> 544ms [-0.97%, -0.19%]
:heavy_check_mark:pprimarycensoreddist_lnorm: 1.83ms -> 1.81ms [-4.93%, +2.97%]
:heavy_check_mark:pprimarycensoreddist_plnrom_expgrowth: 44.9ms -> 45.5ms [-1.18%, +3.7%] Further explanation regarding interpretation and methodology can be found in the documentation of touchstone.

github-actions[bot] commented 3 weeks ago

This is how benchmark results would change (along with a 95% confidence interval in relative change) if 0c62c3447c8b404f079951f5b6a4ac09cbe4daf8 is merged into main:

:heavy_check_mark:cmdstan_fit_gamma_expgrowth: 7.71s -> 7.77s [-0.39%, +1.86%]
:rocket:cmdstan_fit_lognormal_unif: 1.62s -> 731ms [-57.89%, -51.81%]
:heavy_check_mark:dprimarycensoreddist_pweibull_expgrowth: 2.4ms -> 2.42ms [-0.88%, +2.7%]
:exclamation::snail:dprimarycensoreddist_weibull: 2.31ms -> 2.39ms [+1.27%, +5.59%]
:rocket:fitdistdoublecens_gamma_expgrowth: 662ms -> 659ms [-0.79%, -0.01%]
:heavy_check_mark:fitdistdoublecens_normal: 551ms -> 550ms [-0.48%, +0.35%]
:exclamation::snail:pprimarycensoreddist_lnorm: 1.92ms -> 1.98ms [+1.53%, +4.93%]
:heavy_check_mark:pprimarycensoreddist_plnrom_expgrowth: 48.4ms -> 49ms [-0.05%, +2.37%] Further explanation regarding interpretation and methodology can be found in the documentation of touchstone.

codecov[bot] commented 3 weeks ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

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

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #95 +/- ## ======================================= Coverage 99.76% 99.76% ======================================= Files 10 10 Lines 423 427 +4 ======================================= + Hits 422 426 +4 Misses 1 1 ``` | [Flag](https://app.codecov.io/gh/epinowcast/primarycensoreddist/pull/95/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=epinowcast) | Coverage Δ | | |---|---|---| | [](https://app.codecov.io/gh/epinowcast/primarycensoreddist/pull/95/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=epinowcast) | `99.76% <100.00%> (+<0.01%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=epinowcast#carryforward-flags-in-the-pull-request-comment) to find out more.

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github-actions[bot] commented 3 weeks ago

This is how benchmark results would change (along with a 95% confidence interval in relative change) if aaf7663b377624a05276d95d50e3a9a567c22542 is merged into main:

:heavy_check_mark:cmdstan_fit_gamma_expgrowth: 7.67s -> 7.66s [-0.82%, +0.38%]
:rocket:cmdstan_fit_lognormal_unif: 1.66s -> 751ms [-58.21%, -51.2%]
:exclamation::snail:dprimarycensoreddist_pweibull_expgrowth: 2.37ms -> 2.44ms [+0.27%, +5.3%]
:exclamation::snail:dprimarycensoreddist_weibull: 2.31ms -> 2.37ms [+0.41%, +4.19%]
:heavy_check_mark:fitdistdoublecens_gamma_expgrowth: 663ms -> 662ms [-0.62%, +0.31%]
:heavy_check_mark:fitdistdoublecens_normal: 551ms -> 551ms [-0.26%, +0.24%]
:exclamation::snail:pprimarycensoreddist_lnorm: 1.9ms -> 2ms [+3.41%, +7.32%]
:heavy_check_mark: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.

epinowcast / primarycensored