Kuskokwim_Chinook Run Reconstruction

This repository contains Kuskokwim River Chinook salmon run reconstruction and SR analyses.

Folder Structure

Folder is created by year that contains several subfolders: Data, Model, and Outputs. Note numbers and names of folders and sub folders may differ among years to reflect changes in methodologies and data

Year folder: Contains each year's data, model, and outputs

Data folder: contains data files used.

	* Kusko_Chinook_data_lookup.csv  : This file lists abbrabiations usde data file and definition
	* Kusko_Chinook_RR_Input_yyyy.csv : This file contains harvest, escapement data used for the model 
	* Kusko_Chinook_RR_Age_yyyy.csv  : This file contains Harvest and Escapement scale age data 

Model folder: contains models used.

• R_functions: Contains r functions to process

  • ADMBtoR.R : Set of functions reading and writing list data to text data

  • Create_age_data.R: Read Age data

  • Outputs folder: contains model results

How to update the model

• Step 1: Copy and paste ENTIRE previous year's folder and rename to current year
• Step 2: Update Data *.csv file
• Outputs folder: contains model results

How to update the repository

1. Copy the repository via RStudio
2. Pull to Update your project folder to mach the repository
3. Commit After updating your files and folders
4. Push to update the repository

How to run the model

TMB (Template Model Builder)

Required packages: Rtool, TMB, RTMB, Reshape2.
Rtool, TMB, RTMB: Needed to run TMB model Reshape2: Used to transpose (long to wide, wide to long) data.