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Software

All of my public code is available on GitHub. I also maintain several software projects, including:

If you found my software useful, please consider supporting my work with some cheese ūüßÄ.

I’ve written extensively on software and code on my blog. Several of my published manuscripts also describe software:

(2019) J Chang, DL Rabosky, ME Alfaro. Estimating diversification rates on incompletely sampled phylogenies: theoretical concerns and practical solutions. Systematic Biology 69(3):602-611 doi:10.1093/sysbio/syz081 [link]

(2019) J Chang, DL Rabosky, SA Smith, ME Alfaro. An R package and online resource for macroevolutionary studies using the ray-finned fish tree of life. Methods in Ecology and Evolution 10(7):1118-1124 doi:10.1111/2041-210X.13182

(2018) DL Rabosky, J Chang, PO Title, PF Cowman, L Sallan, M Friedman, K Kaschner, C Garilao, TJ Near, M Coll, ME Alfaro. An inverse latitudinal gradient in speciation rate for marine fishes. Nature 559(7714):392-395 doi:10.1038/s41586-018-0273-1

(2015) J Chang, ME Alfaro. Crowdsourced geometric morphometrics enable rapid large-scale collection and analysis of phenotypic data. Methods in Ecology and Evolution 7(4):472-482 doi:10.1111/2041-210x.12508

(2013) DL Rabosky, F Santini, JM Eastman, SA Smith, BL Sidlauskas, J Chang, ME Alfaro. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nature Communications 4:1958 doi:10.1038/ncomms2958

(2012) BC Faircloth, J Chang, ME Alfaro. TAPIR enables high-throughput estimation and comparison of phylogenetic informativeness incorporating locus-specific substitution models. [arXiv:1202.1215]