Time series

MARSS R package containing a suite of univariate and multivariate state space time series models (MARSS, DLMs, DFA, etc) using the Kalman Filter / EM algorithm

atsa R package containing a collection of univariate time series models, primarily for teaching at UW
tvvarss R package containing multivariate state space models with time-varying interactions

bayesdfa R package for performing Bayesian Dynamic Factor Analysis (DFA)

Spatiotemporal stuff

nwfscDeltaGLM R package for index standardization at the NWFSC using Bayesian models in JAGS

nwfscSurvey R package for getting NWFSC trawl survey data (west coast bottom trawl survey WCBTS)

sdmTMB R package created by DFO to do spatiotemporal modeling with R-INLA and TMB

glmmfields R package for fitting Bayesian spatiotemporal Gaussian predictive process models

vista R package for making diagnostic / residual plots for spatiotemporal models

Protected species

bycatch R package for using Bayesian GLMs and time series models to estimate total bycatch for fisheries that are only partially observed

srkw-status R package for summarizing / documenting Southern Resident killer whale births, deaths, and demographic rates.


MixSIAR R package for performing Bayesian estimation of stable isotope (or fatty acid) data with mixing models

salmix R package for fitting models to phenology data, e.g. daily fish counts collected over multiple years, with the goal of estimating phenological shifts

getAIS R package for scraping AIS data from the US Coast Guard

shellfish-genetic-risks R package (with Python) for simulating genetic individual based model for shellfish aquaculture to conduct MSEs