Wonky whales: The evolution of cranial asymmetry in cetaceans

🐋 📈

Authors: Ellen J. Coombs, Julien Clavel, Travis Park, Morgan Churchill, Anjali Goswami

To cite the paper:

Coombs EJ, Clavel J, Park T, Churchill M, Goswami A. Wonky whales: The evolution of cranial asymmetry in cetaceans. BMC Biology. 2020.

Available at: https://github.com/EllenJCoombs/Asymmetry-evolution-cetaceans

If using any of this code or data please cite the paper above and this repo

To cite this repo:

Coombs EJ, Clavel J, Park T, Churchill M, Goswami A. Wonky whales: The evolution of cranial asymmetry in cetaceans. BMC Biology. 2020. Github: https://github.com/EllenJCoombs/Asymmetry-evolution-cetaceans plus the Zenodo DOI: https://doi.org/10.5281/zenodo.3893943

Data 📊 📉

.xlsx documents have multiple tabs

.csv documents have single tabs

All data can be converted to .csv for use in R

The data are provided in the Raw data folder

1. Raw radii data - the raw radii data for each specimen (n = 172); split by suborder, with details on ranking (.xlsx)
2. Phylo names and regime data - specimen data; ID, species, family, geological age, echolocation frequency categories (.csv)
3. Landmark radii - all artiodactyls - sum radii data for landmarks 67-123 (.csv)
4. Rostrum removed - data with rostrum removed (.xlsx)
5. Fossils removed - data with fossils removed (.xlsx)

Analysis 📈 🐋

In this repository you will find raw data (.csv and .xlsx files) and code for analyses (code supplied as .R files)

📁

• Raw data

As above

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• Code for analyses

Binary-ASCII-ply.R

Build-phylogeny.R

Clavel-models-shifts-jump.R

Clavel-plotShifts.R

Discrete-trait-models.R

EXCLUDE-tree-Lloyd-and-Slater.R

LandvR-plot.R

LandvR.R

Model-diagnostics.R

Phylo-ANOVAs_Bnejamini-Hochberg.R

Plotting-with-timescales.R

License 📃

This project is licensed under the MIT License - see the LICENSE.md file for details

Session Info 📋

For reproducibility purposes, here is the output of devtools::session_info() used to perform the analyses in the publication.

R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] phangorn_2.5.5          subplex_1.5-4           gtools_3.5.0            spam_2.2-2             
 [5] tidyselect_0.2.5        purrr_0.3.3             lattice_0.20-35         phytools_0.6-99        
 [9] vctrs_0.2.3             colorspace_1.3-2        expm_0.999-4            viridisLite_0.3.0      
[13] yaml_2.2.1              rlang_0.4.4             pillar_1.4.3            glue_1.3.1             
[17] ggfortify_0.4.5         lifecycle_0.1.0         stringr_1.4.0           dotCall64_1.0-0        
[21] munsell_0.5.0           combinat_0.0-8          gtable_0.2.0            coda_0.19-1            
[25] parallel_3.5.0          Rcpp_1.0.1              corpcor_1.6.9           scales_1.0.0           
[29] plotrix_3.7-6           clusterGeneration_1.3.4 scatterplot3d_0.3-41    mvMORPH_1.1.0          
[33] gridExtra_2.3           fastmatch_1.1-0         mnormt_1.5-5            ggplot2_3.2.1          
[37] stringi_1.1.7           ggrepel_0.8.1           animation_2.6           dplyr_0.8.4            
[41] numDeriv_2016.8-1.1     grid_3.5.0              quadprog_1.5-7          tools_3.5.0            
[45] magrittr_1.5            maps_3.3.0              lazyeval_0.2.1          tibble_2.1.3           
[49] tidyr_1.0.2             crayon_1.3.4            ape_5.3                 pkgconfig_2.0.3        
[53] MASS_7.3-49             Matrix_1.2-14           ggConvexHull_0.1.0      viridis_0.5.1          
[57] assertthat_0.2.0        rstudioapi_0.11         R6_2.2.2                glassoFast_1.0         
[61] igraph_1.2.4.1          nlme_3.1-137            compiler_3.5.0