Data and code for "Downsized: Gray whales using an alternative foraging ground have smaller morphology"

Overview

This project compares length-at-age growth, as well as skull and fluke size, between ENP and PCFG gray whales.

Code

1. growth_model_v4.R – to run growth model 

2. model_outputs_v4.Rmd – uses outputs from growth_model_v4.R to create summary data frames and figures in manuscript.

Data description

enp_Agbayani_etal_2020.csv = dataset compiled and used by Agbayani et al., 2020 to analyze ENP length-at-age growth from data comprised of standings, whaling, and aerial photogrammetry between 1926 and 1997. Contact Selina Agbayani for further details: [e-mail].  Agbayani S, Fortune SME, Trites AW. 2020. Growth and development of North Pacific gray whales (Eschrichtius robustus). J Mammal 101, 742–754. (doi:10.1093/jmammal/gyaa028). https://doi.org/10.1093/jmammal/gyaa028

enp_length&age.csv = scientific whaling data on ENP gray whales collected by Rice and Wolman (1971). Contains total length (TL), sex, and age data for individuals.

enp_morphological_data.csv = scientific whaling data on ENP gray whales collected by Rice and Wolman (1971). Contains total length (TL), snout-blowhole (SnB), and fluke span (FS) measurements, as well as metadata such as sex, age, demographic info, and date of specimen collection.

pcfg_data_growth_model.csv = morphometric and age data for PCFG gray whales collected via drone-based photogrammetry and photo-ID history. Contains total length (TL), snout-blowhole (SnB), and fluke span (FS) measurements, as well as metadata such as sex and age, 

Most columns are self explanatory. Below are descriptions of columns that are less obvious that may be in each or some of the .csv files.

whale_ID: ID of whale
AID: whale_ID + date (YYYYMMDD)
population: ENP or PCFG
Age: age of whale in years
AgeType: 0 = “known age”, 1 = ‘min age’ for PCFG. For ENP, earplugs are considered known age.
TL.mean: mean of posterior distribution for TL for that individual
TL.lower: lower bound of 95% highest posterior density interval (HPDI)
TL.upper: upper bound of 95% HPDI
TL.cv: coefficient of variation (%) of posterior distribution for TL for that individual
TL.var: variance of posterior distribution for TL for that individual
TL.sd: standard deviation of posterior distribution for TL for that individual 
SnB.std: snout-blowhole measurement standardized by TL. Same suffixes apply (i.e, SnB.std.mean = the mean of the posterior distribution for SnB for that individual)
Fs.std: fluke span measurement standardized by TL. Same suffixes apply (i.e, Fs.std.mean = the mean of the posterior distribution for Fs for that individual)
suffix “.HPDwidth”: the width of the HPDI (.upper - .lower)