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MARSS (version 3.10.12)

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 (lectures and computer labs) at See the NEWS file for update information.

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Version

Install

install.packages('MARSS')

Monthly Downloads

750

Version

3.10.12

License

GPL-2

Maintainer

Elizabeth Holmes NOAA Federal

Last Published

February 4th, 2020

Functions in MARSS (3.10.12)

MARSSaic

AIC for MARSS Models
MARSS

Fit a MARSS Model via Maximum-Likelihood Estimation
MARSSFisherI

Observed Fisher Information Matrix at the MLE
MARSS-package

Multivariate Autoregressive State-Space Model Estimation
MARSS.marxss

Multivariate AR-1 State-space Model with Inputs
MARSS.vectorized

Vectorized Multivariate AR-1 State-space Model
CSEGriskfigure

Plot Extinction Risk Metrics
CSEGtmufigure

Plot Forecast Uncertainty
MARSS.dfa

Multivariate Dynamic Factor Analysis
MARSS.marss

Multivariate AR-1 State-space Model
MARSSharveyobsFI

Hessian Matrix via the Harvey (1989) Recursion
MARSSinits

Initial Values for MLE
MARSSinfo

MARSS Error Messages and Warnings
MARSSinnovationsboot

Bootstrapped Data using Stoffer and Wall's Algorithm
MARSSkem

EM Algorithm function for MARSS models
MARSShessian

Parameter Variance-Covariance Matrix from the Hessian Matrix
MARSShessian.numerical

Hessian Matrix via Numerical Approximation
MARSShatyt

Compute Expected Value of Y, YY, and YX
MARSSboot

Bootstrap MARSS Parameter Estimates
MARSSapplynames

Names for marssMLE Object Components
SalmonSurvCUI

Salmon Survial Indices
MARSSresiduals.tT

MARSS Smoothed Residuals
MARSSsimulate

Simulate Data from a MARSS Model
MARSSoptim

Parameter estimation for MARSS models using optim
MARSSparamCIs

Standard Errors, Confidence Intervals and Bias for MARSS Parameters
MARSSresiduals.tt1

MARSS One-Step-Ahead Residuals
MARSSkemcheck

Model Checking for MLE objects Passed to MARSSkem
allowed

MARSS Function Defaults and Allowed Methods
marss.conversion

Convert Model Objects between Forms
coef.marssMLE

Coefficient function for MARSS MLE objects
MARSSvectorizeparam

Vectorize or Replace the par List
datasets

Example Data Sets
fitted.marssMLE

fitted function for MARSS MLE objects
checkMARSSInputs

Check inputs to MARSS call
marssMODEL-class

Class "marssMODEL"
augment.marssMLE

Return the model and state fitted values, residuals, and residual sigma
checkModelList

Check model List Passed into MARSS Call
is.marssMODEL

Test Model Objects
marssMLE-class

Class "marssMLE"
print.marssMODEL

Printing marssMODEL Objects
describe.marssMODEL

Describe a marssMODEL Objects
plot.marssMLE

Plot MARSS MLE objects
residuals.marssMLE

MARSS Residuals
harborSeal

Harbor Seal Population Count Data (Log counts)
logLik.marssMLE

logLik method for MARSS MLE objects
isleRoyal

Isle Royale Wolf and Moose Data
is.marssMLE

Tests marssMLE object for completeness
tidy.marssMLE

Return estimated parameters, expected value of X(t) and Y(t) with summary information
zscore

z-score a vector or matrix
loggerhead

Loggerhead Turtle Tracking Data
print.marssMLE

Printing functions for MARSS MLE objects
MARSSkf

Kalman Filtering and Smoothing
stdInnov

Standardized Innovations
glance.marssMLE

Return brief summary information on a MARSS fit
model.frame.marssMODEL

model.frame method for marssMLE and marssMODEL objects
plankton

Plankton Data Sets
toLatex.marssMODEL

Create a LaTeX Version of the Model
population-count-data

Population Data Sets
utility.functions

Matrix Utilities