This repository includes R scripts for statistical analysis and is a complement to an article published in Scientific Reports. The permanent doi is here
There are three data files:
| Content | File name |
|---|---|
| Main dataframe | "Eardata.csv" |
| Phylogeny | "JZ tree Prum merged hackett.tree" |
| Dive depth data | "Depth list.csv" |
The column names of the main dataframe are described in "columnnames.csv"
The "Set up data.R". script loads the dataframes with auditory measurements, the phylogeny, and the dive depth dataset. The last section of the script sets up the data for aquatic-only analyses. The script calls other script files:
| File name | Purpose |
|---|---|
| "SW_HW_.R" | Computes the regression to interpolate head mass for a few species of unknown head mass |
| "load phylogeny and make CDO.R" | Loads the phylogeny and make a 'comparative data object' |
| "add_dive_depth_data.R" | Joins the dive data into the main dataframe |
The "Run phyPCA.R" script run the pPCAs and "Plot PCA.R" plots the pPCA results. "Run phyPCA.R" calls "Extract pgls residuals.R" to get the residuals used as input for the pPCA.
The "run PGLS and AIC.R" script runs the pgls functions for ear measures and computes the AICc. This script calls separate PGLS scripts, one for each model being compared:
| Model | File name |
|---|---|
| Head mass the only predictor | "pgls_HM.R" |
| (Head mass ecology | "pgls_HM_plus_ecol.R" |
| Head mass x ecology | "pgls_HM_times_ecol.R" |
| Head mass dive score (aquatic-only analysis) | "pgls_HM_plus_divescore.R" |
| Head mass x dive score (aquatic-only analysis) | "pgls_HM_times_divescore.R" |
| Head mass x dive score | "Depth list.csv" |
This runs the analysis involving the connectivity of cranial air cavities. There is a separate script for the interaural canal (IAC) and the interbullar passage (IBP).
"brms IAC models.R"
"brms IBP models.R"
This script computes the correlation coefficient for measurement repeatability
"All ICC.csv" - data file containing repeated measurements
"ICC_.R" - runs and plots the ICC
"plot ecology on circular phylogeny.R" - plot ecological groupings on circular phylogeny (Fig 2), and sampling by phylogeny (Fig S2)
"Residualphylogplots_a panel top.R - plot the residual plot (Fig 3)