stjohn/hsj

Repo for HSJ disparity metric and optimality criteria for phylogenetic trees

HSJ

^{Silhouettes modified from phylopic.org (Scutigerella immaculata by Janssen, Prpic, Damen, & Keesey; Lithobius forficatus by B. Lang).}

Includes code, examples and some data files for computing a scalable disparity metric for datasets with hierarchical characters and scoring phylogenetic trees under the optimality criteria for phylogenetic trees.

What's here:

The repo is organized into 3 folders, corresponding to code, illustrative examples, and the data files used in Hopkins and St. John, 2021.

To cite:

If you use the disparity metric code, please reference:

• Hopkins, M. J. and K. St. John. 2018. A new family of dissimilarity metrics for discrete character matrices that include inapplicable characters and its importance for disparity studies. Proceedings of the Royal Society B 285:20181784.

and the Claddis R package:

• Lloyd, G. 2016. Estimating morphological diversity and tempo with discrete character-taxon matrices: implementation, challenges, progress, and future directions. Biological Journal of the Linnean Society 118:131–151.
• Lloyd, G. T. 2018. Journeys through discrete-character morphospace: synthesizing phylogeny, tempo, and disparity. Palaeontology 61:637–645.

If you use the tree scoring code, please reference:

• Hopkins, M.J. and K. St. John. 2021. Incorporating Hierarchical Characters into Phylogenetic Analysis. Systematic Biology, 70(6):1163-1180.

It is built on the extendible framework of Brazeau et al. 2019 and uses the R packages Claddis, TreeTools, Phangorn, TreeSearch and R scripts for the HSJ approach:

• Brazeau, M. D., T. Guillerme, and M. R. Smith. 2019. An algorithm for Morphological Phylogenetic Analysis with Inapplicable Data. Systematic Biology, 68:619–631.
• Brazeau, M. D., M. R. Smith, and T. Guillerme. 2017. MorphyLib: a library for phylogenetic analysis of categorical trait data with inapplicability. Version 0.0.1-alpha (http://www.morphyproject.org/)
• Hopkins, M. J. and K. St. John. 2018. A new family of dissimilarity metrics for discrete character matrices that include inapplicable characters and its importance for disparity studies. Proceedings of the Royal Society B, 285:20181784.
• Lloyd, G. 2016. Estimating morphological diversity and tempo with discrete character-taxon matrices: implementation, challenges, progress, and future directions. Biological Journal of the Linnean Society, 118:131–151.
• Lloyd, G. T. 2018. Journeys through discrete-character morphospace: synthesizing phylogeny, tempo, and disparity. Palaeontology, 61:637–645.
• Schliep K.P. 2011. phangorn: phylogenetic analysis in R. Bioinformatics, 27(4) 592-593. R package version 2.5.5.
• Smith, M. R. 2018. TreeSearch: phylogenetic tree search using custom optimality criteria. R package version 0.4.0.

hsj's Issues

Updated functions for updated Claddis

Hello Dr. St. John,

I'm trying to run your example codes for morphological data sets with missing data to infer phylogenies using the HSJ distance metric, but it seems that the functions are out of date because of the recent updates on the Claddis package. The function names in Claddis have changed and this seems to be affecting your hsjTS function. When I run it using your provided examples, I get the following:

hsjTS(t1, phy4.3, mor4.3, typ4.3, alpha = 0.5)
Error in newClad$Matrix_1$Matrix[c1, j] : subscript out of bounds
Called from: initialInternalLabels(tree, clad, nTaxa, numNodes)

Do you have an updated code for your functions?

Best regards,

Tiago