This is the GitHub repository for the cetacean metatree project (authors Graeme Lloyd and Graham Slater), code-named Project Blackfish.
The below explains the file structure of the repository.
(Hidden) Folder of PDFs of papers that could not be included in the metatree as they lack accessible character-taxon matrices.
Folder containing the R scripts for the fossilBAMM diversification analyses and the following subfolders:
Subfolder containing the results for the Dangerous fossilBAMM analyses.
Subfolder containing the results for the Risky fossilBAMM analyses.
Subfolder containing the results for the Safe fossilBAMM analyses.
Folder containing the following subfolders:
Matrix Representations with Parsimony (MRPs) obtained by re-analysing each input data set under parsimony and retaining only unique biparitions until all such biparitions have been sampled.
The original character-taxon matrices for each input data set.
(Hidden) PDFs of the published articles for each input data set.
A series of the same folders as Input data containing any input data sets formatted ready for use, but only recently discoevered so not included in the current metatree iteration. Typically these will correspond to very recent publications.
XML files that record important metadata about each input data set, particularly data set dependence and taxonomic reconciliation.
The license under which this repository can be used.
Folder containing the metatree data organised in the following subfolders:
Folder containing the molecular analysis used as constraint topologies for the extant taxa.
Folder containing the metatree data organised in the following subfolders:
The metatree files for the "dangerous" (full taxonomic coverage) metatree.
The full metatree MPT samples (post safe taxonomic reinsertion).
The metatree files for the "risky" (middle taxonomic coverage) metatree.
The metatree files for the "safe" (lowest taxonomic coverage) metatree.
The strict consensus trees used as inputs for the timetree analyses.
The safe taxonmic reduction trees returned from TNT analysis of the safe, risky and dangerous metatree matrices.
This file.
The set of R scripts used to: 1. populate the repository, 2. generate the metatree files, and 3. process the metree output.
The timetrees (empty).
Folder containing the R scripts and temporal data used to build the timetrees as well as the following subfolders:
Subfolder containing the results for the Dangerous timetree analyses.
Subfolder containing the results for the Risky timetree analyses.
Subfolder containing the results for the Safe timetree analyses.