Final files related to parity paper.
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Data
ExploratoryNotebooks
PAUPExampleFile
PhylogenyMaking
Scripts
TreePL
Trees
.RData
Contents.txt
Dockerfile
Makefile
Makefileheat
README.md

README.md

ParityPaper

Find a blog post on the research here.

Final files related to parity paper. Old repository here, it's very messy. These are only the files used directly to perform analyses described in the paper.

Contents

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 (rgbkrk@gmail.com) that reproduces the R language setup needed to run our code.