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Analysis
Data
Functions
Manuscript
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README.md
README.txt

README.md

Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses

Thomas Guillerme and Natalie Cooper.

This repository contains all the code and data used in the manuscript.

Paper published in Biology Letters.

Data

All the raw data (cladistic matrices) and transformed data (cladistic matrices with corrected taxonomy entries) are abailable in the data folder on this repository. The raw data are also avaialble on figshare.

Analysis

All the individual functions for this analysis (and their testing) are avaiable in the function folder.

The analysis is divided into three steps

  1. Extracting the living taxa from the matrices
  2. Analysing data availability and distribution per order
  3. Summarising the results

Note that the first steps take some time (several hours on your usual ~2GHz clock speed machine's CPU) so the results from this steps is made directly available here.

1. Extracting the living taxa from the matrices

This step sorts all the OTUS from all the matrices into either living or fossil taxa in order to have the list of all the available mammals with discrtete morphological data. The code for this step is available here.

2. Analysing data availability and distribution per order

The second step analysis the data availability within each mammalian order. It calculates the proportion of living mammals with avaiable cladistic data as well as the distribution of this data accross the phylogeny. The code for this step is available here.

3. Summarising the results

Finally, the third step summarises the results of the analysis in step 2 and generates the manuscript figure/table (fable!) containing all the information of the availability and distribution of living mammals cladistic data. The code for this step is available here. Note that the output is a table in LaTeX format (longtable).

Supplementary analysis

The code for each supplementary analysis is available in the following links: