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Add §"Working with phylogenetic data" #34

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Add §"Working with phylogenetic data"
ms609 Sep 1, 2025
182997e
Correct grammar
ms609 Sep 2, 2025
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10 changes: 9 additions & 1 deletion Phylogenetics.md
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Expand Up @@ -104,6 +104,15 @@ Packages within the task view fall within one or more of the following task cate
- `r github("Leonardini/treeCentrality")` can compute several statistics inspired from network science.


## Working with phylogenetic data in R
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@willgearty willgearty Sep 2, 2025

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Should this be a ### heading? The table of contents near the top lists the first ## heading as follows:
Working with trees in R: packages dedicated to the handling, manipulation, and visualization of phylogenetic data
It seems to me that this new category would fall under that?

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@willgearty willgearty Sep 2, 2025

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In fact, I wonder if the top heading should be changed to "Working with phylogenetic data in R", and then this new subcategory could be changed to e.g., "Working with other phylogenetic data in R"?

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@ms609 ms609 Sep 2, 2025

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Hmm, good point; I usually use "phylogenetic data" to refer to the observations from which phylogenies are reconstructed, but in the ToC it is almost used as though the trees themselves are the phylogenetic data.

In my view the new content represents a step before reconstructing trees, so fits logically before tree reconstruction in the current structure. On this view, perhaps we ought to move the current "working with trees in R" section after "Building trees in R" (you can't work with trees if you haven't (re)constructed them yet!).

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@willgearty willgearty Sep 2, 2025 •
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Ah yes, that makes a lot more sense. I could see this new category then remaining a separate category (the first category?), followed by the current second category and then the current first category? (perhaps with some editing of the ToC?)


- `r pkg("phangorn")`, `r pkg("TreeTools")` and `r pkg("TreeSearch")` contain functions for reading phylogenetic datasets into R and manipulating the resulting objects.
- `r github("uyedaj/rphenoscate")` allows character matrices to be synthesized from semantic phenotype data, and facilitates analysis of "inapplicable" characters – such as morphological characters that are dependent on a parent trait – by constructing formal character hierarchies and the corresponding rate matrices (Tarasov 2023).
- `r pkg("phenex")` facilitates the annotation of character matrices files with ontology terminology.
- `r pkg("Claddis")` and `r pkg("EvoPhylo")` generate distance matrices from phylogenetic data, with functions to identify clusters and plot the corresponding morphospaces from these matrices.
- `r pkg("geiger")` and `r pkg("phangorn")` contain functions to simulate phylogenetic data from phylogenetic trees.


## Tree building in R

### Phylogenetic inference
Expand All @@ -115,7 +124,6 @@ Packages within the task view fall within one or more of the following task cate
- `r github("helixcn/phylotools")` can build supermatrices for analyses in other software.
- `r pkg("EvoPhylo")` can be used to perform automated morphological character partitioning for bayesian phylogenetic analyses that are performed with [MrBayes](http://nbisweden.github.io/MrBayes/) and [BEAST2](https://www.beast2.org/). It can also be used to analyze the macroevolutionary parameter outputs from such analyses.
- `r bioc("fastreeR")` can be used to calculate distances, build phylogenetic trees, or perform hierarchical clustering between the samples of a VCF or FASTA file.
- `r github("uyedaj/rphenoscate")` facilitates analysis of "inapplicable" characters – such as morphological characters that are dependent on a parent trait – by constructing formal character hierarchies and the corresponding rate matrices (Tarasov 2023).

### Divergence times

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