Atlantic cod

To help identify ecosystem and climate influences on Atlantic cod recruitment, distribution, and growth, generalized additive models (GAMs) were used to examine associations between Atlantic cod population dynamics and environmental variables in the Northwest Atlantic region.

Included in this Repository is the following:

1. "Figures" folder containing .png images of supplemental figures not included in technical report:

2. "Code" folder containing R code used:

File	Description
changepoint.R	Chanepoint analysis run on recruitment and growth data using EnvCpt package
cod_distribution.R	.R file used for to achieve distribution GAM results
cod_growth.R	.R file used for to achieve growth GAM results
cod_recruitment_NEFSC.R	.R file used for to achieve recruitment GAM results using NEFSC data
DisMAP_vs_adultjuv_raw.R	.R used to explore possible differences between DisMAP data and NEFSC distribution data disaggregated by adults and juveniles to explore potential environmental effects by maturity stage
Env_data_by_stock.R	.R file used to pull relevant environmental data from ecodata package in R, and wrangle data into consistent format to be read in other .r files. Originally used but later replaced by "Environmental_data2.R" file
Environmental_data2.R	New environmental data with updated lags and bottom temperature data. This was used to wrangle final environmental datasets used in models
Envdata2_MADMF.R	Environmental data wrangling used in MADMF models in the "WGOM_R_MADMF.R" script
GAM_forloop.R	.R file containing functions used to to fun multiple GAM ieterations in effort to streamline best model selection.
Gam_data_exploration.R	.R file containing functions used to check data assumptions and explore data distributions
get_WAA_anomalies.R	.R file used for to get weight at age (WAA) anomaly data used in growth analyses
get_depth_lat.R	.R file used get mean depth and latitude data, disaggregated by adults and juvenile groups Data generated were used in the "DisMAP_vs_adultjuv_raw.R" exploratory analyses
Recruitment_other_data.R	exploratory .R file testing GAM recruitment relationships using MENH and DFO data indstead of NEFSC This was done due to speculation that NEFSC data may not represent age 1 data as well as other surveys
SSB_estimates.R	.R file estimating SSB using WAA and NAA data form NEFSC trawl survey
SSB_estimates_other.R	exploratory .R file estimating SSB using WAA from NEFSC and NAA data form MENH and DFO surveys. *lacks overlap
WGOM_R_MADMF.R	.R file used to run models using age 0 MADMF recruitment data in the WGOM to compare with results from NEFSC age 1 recruitment data.

3. "Final_Data_for_Modelers.zip" zip folder containing data that went into GAM analyses:

• The environmental data can also be used by modelers working within the assessment. However, PLEASE note the environmental data have ALREADY BEEN LAGGED

Any further questions can be directed to Jamie Behan: jbehan@gmri.org