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Issue 35 and 36: Package CmdStan model #67

Merged
merged 13 commits into from
Sep 16, 2024
Merged

Issue 35 and 36: Package CmdStan model #67

merged 13 commits into from
Sep 16, 2024

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seabbs
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@seabbs seabbs commented Sep 14, 2024

Description

This PR introduces tools to help address #35 and #36 and makes the cmdstan support match the fitdistrplus support. It also closes #35 by adding parameter recovery testing using the new stan package model.

It adds

  • A efficient delay estimation model that generalises the manually written approach in the fitting to stan vignette
  • Adds helper functions to load this model and to parse data into the list format it requires.
  • Adds the use of this model to fitting with stan vignette.

Before this PR is ready to review I need to:

  • Add a news item
  • Add tests of the new functionality (this may close Add parameter recovery using stan to tests #35)
  • Open issues to consider the structure of the stan code and to add heuristics when the relative_obs_time is much bigger than the maximum observed delay.

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
  • I have read the contribution guidelines.
  • I have tested my changes locally.
  • I have added or updated unit tests where necessary.
  • I have updated the documentation if required.
  • My code follows the established coding standards.
  • I have added a news item linked to this PR.
  • I have reviewed CI checks for this PR and addressed them as far as I am able.

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codecov bot commented Sep 14, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.67%. Comparing base (1c4e6f1) to head (2fc8f8a).
Report is 1 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main      #67      +/-   ##
==========================================
+ Coverage   99.62%   99.67%   +0.05%     
==========================================
  Files           7        8       +1     
  Lines         268      310      +42     
==========================================
+ Hits          267      309      +42     
  Misses          1        1              

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LGTM (self-review)

@seabbs seabbs merged commit 852d291 into main Sep 16, 2024
11 checks passed
@seabbs seabbs deleted the add-stan-model branch September 16, 2024 15:23
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Add parameter recovery using stan to tests
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