Remove `simulate_tree()` and `simulate_tree_from_pop()` and replace usage with `simulate_chains()`

epiverse-trace / epichains

Methods for simulating and analysing the sizes and lengths of infectious disease transmission chains from branching process models

https://epiverse-trace.github.io/epichains/

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Remove `simulate_tree()` and `simulate_tree_from_pop()` and replace usage with `simulate_chains()` #182

Closed jamesmbaazam closed 9 months ago

jamesmbaazam commented 9 months ago

This PR closes #181 by:

Unexporting and removing all occurrences of simulate_tree() and simulate_tree_from_pop(),
Replacing their use with simulate_chains() in tests, vignettes, and examples.

Additionally, where necessary, descriptions involving simulate_tree() and simulate_tree_from_pop() have been rephrased. Examples include the README (64015e1e20568ac852cd1f29a25b1b6721ef733a) and Getting Started vignettes (e38453a58306466c2576c47b6558610d4be67072).

github-actions[bot] commented 9 months ago

This pull request:

Adds 0 new dependencies (direct and indirect)
Adds 0 new system dependencies
Removes 2 existing dependencies (direct and indirect)
Removes 1 existing system dependencies

(Note that results may be inacurrate if you branched from an outdated version of the target branch.)

codecov-commenter commented 9 months ago

Codecov Report

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

Comparison is base (26748ba) 99.26% compared to head (bbdb332) 99.41%.

:exclamation: Current head bbdb332 differs from pull request most recent head 173ef46. Consider uploading reports for the commit 173ef46 to get more accurate results

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #182 +/- ## ========================================== + Coverage 99.26% 99.41% +0.15% ========================================== Files 8 8 Lines 682 517 -165 ========================================== - Hits 677 514 -163 + Misses 5 3 -2 ```

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sbfnk commented 9 months ago

Also closes #158

jamesmbaazam commented 9 months ago

Thanks. #158 will be better addressed by #186.

sbfnk commented 9 months ago

Ah sorry yes that makes sense