/NATRICINE-traits

Primary LanguageRMIT LicenseMIT

NATRICINE-traits

Code for Natricine traits paper from V.Deepak's NATRICINE MSCA project.

Author(s): V.Deepak, Gustavo Burin and Natalie Cooper.

This repository contains the R code and data used in the manuscript Multilocus phylogeny, natural-history traits, and classification of natricine (Serpentes: Natricinae) snakes Link to final published pdf will be here. Analyses done using other packages are not included here.

To cite the paper:

DEEPAK, V., NATALIE COOPER, NIKOLAY A. POYARKOV, FRED KRAUS, ABHIJIT DAS, SURYA NARAYANAN, JEFFERY W. STREICHER, GUSTAVO BURIN, SARAH-JANE SMITH and DAVID J. GOWER. Multilocus phylogeny, natural-history traits, and classification of natricine (Serpentes: Natricinae) snakes. 2021. Zoological Journal of the Linnaean Society. In press.

To cite this repo:

DEEPAK, V., GUSTAVO BURIN, and NATALIE COOPER. NATRICINE-traits. Code for the paper. DOI: 10.5281/zenodo.5524558.

DOI

Figure 6

Data

Data required to run the analyses is included in the data/ folder. The full dataset and sets of trees from the paper are available on the NHM Data Portal here. If you use these data please cite the data portal:

Deepak V, Cooper N, Gower DJ. 2020. Dataset: NATRICINE. Natural History Museum Data Portal (data.nhm.ac.uk). https://doi.org/10.5519/0070625.

Analyses

All code used to run R analyses and make figures is included in the analyses/ folder. Before starting remember to open an RStudio project from that folder. Note that analyses using something other than R are not included here. BioGeoBEARS analyses were written by V.Deepak. BAMM analyses were written by Gustavo Burin. Remaining code was written by V Deepak, and tidied by Natalie Cooper.

  • 01-BioGeoBEARS. BioGeoBEARS code and data [Deepak]. Runs biogeography analyses, results in Table 4, and Figure 3.
  • 02-summary_bamm.Rmd. [Gustavo] Runs the BAMM analyses and trait transition analyses. Figures 4 and 5, supplementary Figure S2. Results in Table 5, supplementary Tables S5 and S6.
  • 03-four-trait-tree-figures.R. Creates Figure 6.
  • 04-ancestral-state-estimation.R. Runs ancestral state estimations for natural history traits and creates supplementary Figure S3
  • 05-plot-phylogeny-node-support.R. Code for adding support values to branches of phylogenies.

Other folders

  • /outputs contains the figures created in R. Figure 1 used PhotoShop. Figure 2 used FigTree and PhotoShop.