cesrf-minijack-rates

This repository houses the code and data for conducting the minijack rate analyses found in the manuscript titled: Precocious maturation of hatchery-raised spring Chinook Salmon as age-2 minijacks is not detectably affected by sire age by P. F. Galbreath, H. M. Nuetzel, B. A. Staton, C. A. Stockton, C. M. Knudsen, L. R. Medeiros, I. J. Koch, W. J. Bosch, and A. L. Pierce published in Transactions of the American Fisheries Society.

File structure

• 00-packages.R: loads all R packages used by the code in this repo
• 01-data-prep.R: processes the data file minijack-data.csv for analysis
• 02-functions.R: contains a handful of custom functions to facilitate parametric bootstrapping
• 03-main-analysis.R: fits models and performs bootstrapping. Saves .rds files that are read in by subsequent scripts -- these output files are not tracked by this Git repo. To execute other files in this repo, you will need to run this file -- it takes several hours under the pre-populated settings.
• 04-ms-output.R: creates files for the table and figure output found in the main text of the manuscript
• minijack-data.csv: contains the raw experimental data (variables described in table below)
• power-analysis/power-simulation.R: conducts the power analysis calculations and saves output files that are processed by code in the supplemental Rmd file
• supplemental-material.Rmd: source code to create the supplemental material document.

Dependencies

All analyses were conducted in R version 4.0.2 with these package versions:

Package	Version	Used For
glmmTMB	1.0.2.1	Primary fitting of GLMMs
DHARMa	0.3.3.0	Residual diagnostics for GLMMs
stringr	1.4.0	Misc. string manipulations
lme4	1.1.23	Methods for parametric bootstrap
boot	1.3.25	Methods for summarizing bootstrap
scales	1.1.1	Transparent colors on graphics
snow	0.4.3	Parallel computing
rlecuyer	0.3.5	Setting random seeds in parallel computing

Variables in Data

The file minijack-data.csv contains all of the raw data for the analysis. Each row is an individual progeny with variables shown in the table below:

Variable	Description
year	The year the cross was made
dam_id	A unique identifier for the dam (female parent)
dam_age	The total age of the dam (winters after the dam was spawned)
dam_FL	The fork length of the dam (cm)
dam_POH	The dam post-orbital hypural length (cm)
dam_wt	The weight of the dam (kg)
egg_wt	The average weight of each of the dam's eggs (g)
sire_id	A unique identifier for the sire (male parent)
sire_age	The total age of the sire (winters after the sire was spawned)
sire_FL	The sire fork length (cm)
sire_POH	The sire post-orbital hypural length (cm)
sire_wt	The weight of the sire (kg)
spawn_date	The date of spawning (M/D/YYYY)
spawn_doy	The day of the year of spawning
cross_type	dam_age x sire_age
progeny_mat_status	The maturation status of the progeny; "Minijack" or "Non-maturing"
progeny_length	The total length of the progeny (mm)
progeny_wt	The weight of the progeny (g)