README.md

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.