Directory: Data Contains: Original Pyron and Burbrink dataset and the heatmap data used to make Figure 4.
Directory: Exploratory Notebooks Contains: Scripts used at various points in exploratory data analyses. Graphically front-ended via the iPython notebook for exploration.
Directory: PAUPExampleFile Contains: Sample of PAUP file used in Analyses to generate Table 2.
Directory: Scripts Contains: Analysis scripts used for paper. Heatmap_data_gen.R performs the model-fitting used to generate Figure 4. Heatmap.py actually makes the heatmap shown on figure four from the raw data output by Heatmap_data_gen.R. Bisse.R is used to run the BiSSE analysis described in methods, with results shown on Figures 3 and 5.
Directory: TreePL Contains: Configuration file for TreePL dating. Results from 7CalibrationConfig are visualized in the paper.
Directory: Trees Contains: Three sets of trees: raw, uncalibrated trees, time-calibrated trees and time-calibrated trees with BiSSE states annotated to them. Raw and time-scaled trees each contain four trees, as described in the methods section. BiSSE-Annotated contains twelve trees: each of the four trees having been run withe three parameter configurations in BiSSE. Subdirectory 8-calibration contains trees run using the an extra calibration in TreePL, as described in the paper. These trees are mentioned, but not shown, in the paper.
Makefiles: Makefiles reproduce the analyses completed. Makefile will run the BiSSE model-fitting to each of the four time-scaled trees with each of the 3 parameter settings (correcting for sampling bias). This will run a while. Makefileheat will reproduce the heatmap data. This will run for a long while. We have also included a Dockerfile contributed by Kyle R. Kelley (firstname.lastname@example.org) that reproduces the R language setup needed to run our code.