All of my public code is available on GitHub. I also help maintain and serve on the Project Leadership Committee for the Homebrew package manager, and also contribute to the unaffiliated Brewsci project. I also maintain the Fish Tree of Life website.
I’ve written extensively on software and code on my blog. Several of my published manuscripts also describe software:
(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 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
(2015) PS Gilbert, J Chang, E Sobel, JS Sinsheimer, BC Faircloth, ME Alfaro. Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers for the fish series Percomorpha. Molecular Phylogenetics and Evolution 92:140-146 doi:10.1016/j.ympev.2015.05.027
(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