README.md

Data and analysis from: "Body mass, temperature, and depth shape productivity in sharks and rays"

This repository contains the data and model-fitting process used for the article "Body mass, temperature, and depth shape productivity in sharks and rays", which is currently in press at Ecology and Evolution.

Description of data and file structure

The dataset includes life history information and phylogeny for 63 species of sharks(40 spp), rays (20 spp), and chimaeras (3 spp), and contains three files:

chond-data.csv: Data frame with 63 rows (species) and 11 variables. Some of these variables are based on the same life history trait but are transformed for ease of interpretation and analysis.

The 11 variables are:

• id (int): ordinal variable
• species(chr): scientific name
• maxwt_all (num): maximum weight, in grams
• log_wt (num): natural log of maximum weight
• rmax (num): maximum intrinsic rate of population increase, r_max
• t_median (num): median environmental temperature in Celsius
• t_med_corr (num): median environmental temperature in Celsius, corrected for mesothermic species. This is the temperature used in analyses as it represents median metabolic temperature
• invtemp (num): inverse temperature, calculated as 1/k_BT, where k_B is the Boltzmann constant (8.617 × 10 −5 eV) and T is median corrected temperature in Kelvin
• invtemp_scaled (num): scaled invtemp
• depth_median (num): median depth, in metres
• depth_scaled (num): scaled depth_median

stein-et-al-single.tree: Phylogenetic tree with scaled branch lengths from Stein et al. (2018) used in analyses. These are freely downloadable from http://vertlife.org/sharktree/.

rmax-scaling-analysis.R: R code with minimum working example of how to load data files, fit models phylogenetic linear models using the pgls function in the caper package, run information-theoretic comparisons, and check diagnostics.

Sharing/access Information

These data and analysis can also be found at https://github.com/sebpardo/shark-rmax-scaling.