TreeTools
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ms609
Create, modify and analyse phylogenetic trees in R
[Exact and efficient phylodynamic simulation from arbitrarily large populations](https://arxiv.org/html/2402.17153v1)
Hi, I am trying to measure distances between two trees, and getting this error message: `> TreeDistance(t1, t2) Error: This many leaves cannot be supported. Please contact the TreeTools maintainer...
- [x] Create templates for bespoke actions at ms609/actions. - [ ] List on [GitHub marketplace](https://docs.github.com/en/developers/github-marketplace)
Included at present as alias for `%in%.Splits()`. - [x] Replace in 'Quartet' on CRAN - [x] Update code - [x] Release on CRAN - [ ] Deprecate - [x] Add...
- [x] Move `edge` parameter after parent & child in `DescendantEdges` call [breaking change?] - [x] If `edge = NULL`, in `DescendantEdges()`, call `AllDescendantEdges()` - [x] Make `AllDescendantEdges()` internal -...
- [x] Add the Robust, Universal Tree Balance Index of doi:[10.1093/sysbio/syac027](https://dx.doi.org/10.1093/sysbio/syac027), implemented for data.frames in R in https://github.com/robjohnnoble/RUtreebalance/blob/v1.0/RUtreebalance.R (with opportunities to improve) - [ ] Add other metrics from https://arxiv.org/pdf/2109.12281.pdf
[Haag _et al._](https://www.biorxiv.org/content/10.1101/2022.06.20.496790v1) measure the ruggedness of a tree landscape by training a regression model (trained on molecular datasets, [implemented in C](https://github.com/tschuelia/CPythia)) based on: - Unique topologies after 100 parsimony...
- [ ] Rewrite in C++ - [ ] Retain order of original tree (at least if in preorder)