merrillrudd Goto Github PK

2016_spatio-temporal_models

FSH 507 "Spatio-temporal models for ecologists" in Spring quarter 2016 at University of Washington

admb_course

ADMB course taught at the Alaska Department of Fish and Game, March 13-16, 2018

alaskaherring

Age-structured Assessment Model for Alaska Herring Stocks

bioensembles

Stacking algorithm for integrating uncertainty in life history parameter values for length-based, data-limited fisheries stock assessment

caribbean_assessments

Length-based stock assessments in the Caribbean region

catch_misreporting_sim

Code to run the simulation and analyses associated with my first thesis chapter, the publication of which is in review/resubmission stages.

catchmsy

Integrated Catch MSY method for data poor stock assessment.

catchmsy_test

Self-testing and simulation-testing of integrated CatchMSY method

cr_snapper

Costa Rican spotted snapper stock assessment, conducted for Conservation International

datamoderate

Stock assessment for catch and length data

fishing_recruitment_tradeoff

Module demonstrating the confounding effects of fishing mortality and recruitment on the length distribution in a population.

fishstatsutils

Shared resources for spatio-temporal models

gulf_sturgeon_telemetry

Updated code for Multi-state mark-recapture model to estimate mortality and movement rates of Gulf sturgeon.

gulf_sturgeon_telemetry_cjfas2014

Multi-state mark-recapture model to estimate Gulf sturgeon movement and mortality rates in the Gulf of Mexico.

lbspr

Length Based Spawning Potential Ratio R Package

lime

Length-based integrated mixed effects model

lime_application

Example application of the length-based integrated mixed-effects model. See LIME repo for R package.

lime_demo

lime_shiny

Shiny app for running LIME assessment method

lime_sim

Simulation study to test the length-based integrated mixed effects (LIME) method

or_coho

Spatiotemporal models of Oregon coastal coho salmon densities

per_recruit

razor_clam_pop

Population modeling of razor clams to explore impacts to the social-ecological system with future threats.

ruddr

R functions that I use frequently

simple_fishery_demo

Demonstrating the relationship between maturity, selectivity, length composition of the catch, and abundance-at-age for teaching purposes.

sraplus

ss3sim

An R package for stock-assessment simulation with Stock Synthesis

sss

Simple Stock Synthesis code and examples

status_priors

Using RAM Legacy data and life history to develop priors on stock status for unassessed stocks

streamutils

R package to supplement FishStatsUtils to run stream networks as a spatial model in VAST