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MARSS (version 3.4)

Multivariate Autoregressive State-Space Modeling

Description

The MARSS package provides maximum-likelihood parameter estimation for constrained and unconstrained linear multivariate autoregressive state-space (MARSS) models fit to multivariate time-series data. Fitting is primarily via an Expectation-Maximization (EM) algorithm, although fitting via the BFGS algorithm (using the optim function) is also provided. MARSS models are a class of dynamic linear model (DLM) and vector autoregressive model (VAR) model. Functions are provided for parametric and innovations bootstrapping, Kalman filtering and smoothing, bootstrap model selection criteria (AICb), confidences intervals via the Hessian approximation and via bootstrapping and calculation of auxiliary residuals for detecting outliers and shocks. The user guide shows examples of using MARSS for parameter estimation for a variety of applications, model selection, dynamic factor analysis, outlier and shock detection, and addition of covariates. Type RShowDoc("UserGuide", package="MARSS") at the R command line to open the MARSS user guide. Online workshops (lecture material and labs) at http://faculty.washington.edu/eeholmes/workshops.shtml

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Version

Install

install.packages('MARSS')

Monthly Downloads

750

Version

3.4

License

GPL-2

Maintainer

Elizabeth Holmes NOAA Federal

Last Published

February 18th, 2013

Functions in MARSS (3.4)

MARSShatyt

Compute Expected Value of Y,YY, and YX
MARSSaic

AIC for MARSS models
MARSSapplynames

Names for marssMLE Object Components
MARSS-package

Multivariate Autoregressive State-Space Model Estimation
MARSS.marxss

Multivariate AR-1 State-space Model with Inputs
CSEGriskfigure

Plot Extinction Risk Metrics
MARSS

Interface MARSS Model Specification and Estimation
MARSSinfo

Information for MARSS Error Messages and Warnings
MARSSkem

Maximum Likelihood Estimation for Multivariate Autoregressive State-Space Models
is.marssm

Model Objects
MARSSboot

Bootstrap MARSS Parameter Estimates
checkModelList

Check model list passed into MARSS call
MARSSkemcheck

Model Checking for MLE objects passed to MARSSkem
is.blockdiag

Matrix Utilities
marssm-class

Class "marssm"
stdInnov

Standardized Innovations
allowed

MARSS function defaults and allowed methods
checkMARSSInputs

Check inputs to MARSS call
MARSSinnovationsboot

Bootstrapped Data using Stoffer and Wall's Algorithm
harborSeal

Harbor Seal Population Count Data (Log counts)
MARSSinits

Initial Values for MLE
graywhales

Population Data Sets
MARSSkf

Kalman Filtering and Smoothing for Time-varying MARSS models
CSEGtmufigure

Plot Forecast Uncertainty
parmat

Retrieve Parameter Matrix
MARSSsimulate

Simulate Data from a MARSS Model and Parameter Estimates
loggerhead

Loggerhead Turtle Tracking Data
plankton

Plankton Data Sets
residuals.marssMLE

MARSS standardized residuals
MARSSmcinit

Monte Carlo Initialization
MARSSvectorizeparam

Vectorize or replace the par lists
MARSSoptim

Parameter estimation for MARSS models using optim
MARSShessian

MARSS Parameter Variance-Covariance Matrix from the Hessian Matrix
marssMLE-class

Class "marssMLE"
marssMLE

Maximum Likelihood MARSS Estimation Object
MARSSparamCIs

Standard Errors and Confidence Intervals for MARSS Parameters