gfcondition: Annual indices of average groundfish body condition

This repository contains code used to generate sex and maturity specific indices of average body condition and associated density distributions for species frequently sampled by Canadian Pacific bottom trawl surveys. Common trends in body condition indices were then identified using a Bayesian Dynamic Factor Analysis implemented with the bayesdfa R package (https://fate-ewi.github.io/bayesdfa/) and compared with environmental indices available in the PACEA R package (https://github.com/pbs-assess/pacea).

These analyses are described in:

English, P.A., Anderson, S.C., and Forrest, R.E. (2026) Body Condition as a Shared Response to Environment in a Commercially Important Demersal Fish Assemblage. Fish and Fisheries. https://doi.org/10.1111/faf.70053

• This repository is structured as an R package.
• All data retrieval, processing, and analysis scripts are found in the analysis folder and are numbered in the order that they must be run.
• Scripts load the R package with devtools::load_all(".") where necessary.
• Scripts starting with 00- are for data preparation and are provided for reference, but do not need to be run on their own. These files are either sourced by other files, or contain the original data retrieval and processing steps used to generate the data files provided.
• Scripts without numbers (x-) are for plotting, supplementary tests, or summary statistic, and may need to be run after the main analysis is complete.
• Script 05-dfa.R can be run repeatedly for each sex and maturity class (e.g., set_group <- "mature males") and with and without using condition indices where the estimated effects of density-dependence have been removed from the estimated annual averages (e.g., adjusted_for_density <- TRUE).