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MARSS (version 3.11.3)

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

3.11.3

License

GPL-2

Maintainer

Elizabeth Holmes NOAA Federal

Last Published

October 21st, 2020

Functions in MARSS (3.11.3)

MARSSaic

AIC for MARSS Models
MARSS.dfa

Multivariate Dynamic Factor Analysis
MARSS.marxss

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

Vectorized Multivariate AR-1 State-space Model
MARSSFisherI

Observed Fisher Information Matrix at the MLE
MARSS

Fit a MARSS Model via Maximum-Likelihood Estimation
CSEGtmufigure

Plot Forecast Uncertainty
MARSS.marss

Multivariate AR-1 State-space Model
CSEGriskfigure

Plot Extinction Risk Metrics
MARSS-package

Multivariate Autoregressive State-Space Model Estimation
MARSSinfo

MARSS Error Messages and Warnings
MARSShatyt

Compute Expected Value of Y, YY, and YX
MARSSharveyobsFI

Hessian Matrix via the Harvey (1989) Recursion
MARSSinnovationsboot

Bootstrapped Data using Stoffer and Wall's Algorithm
MARSSkem

EM Algorithm function for MARSS models
MARSSboot

Bootstrap MARSS Parameter Estimates
MARSSapplynames

Names for marssMLE Object Components
MARSShessian

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

Hessian Matrix via Numerical Approximation
MARSSoptim

Parameter estimation for MARSS models using optim
MARSSparamCIs

Standard Errors, Confidence Intervals and Bias for MARSS Parameters
MARSSvectorizeparam

Vectorize or Replace the par List
MARSSsimulate

Simulate Data from a MARSS Model
MARSSkemcheck

Model Checking for MLE objects Passed to MARSSkem
MARSSkf

Kalman Filtering and Smoothing
describe.marssMODEL

Describe a marssMODEL Objects
MARSSresiduals.tt1

MARSS One-Step-Ahead Residuals
MARSSresiduals.tt

MARSS Contemporaneous Residuals
MARSSinits

Initial Values for MLE
checkModelList

Check model List Passed into MARSS Call
checkMARSSInputs

Check inputs to MARSS call
coef.marssMLE

Coefficient function for MARSS MLE objects
allowed

MARSS Function Defaults and Allowed Methods
marss.conversion

Convert Model Objects between Forms
datasets

Example Data Sets
population-count-data

Population Data Sets
glance.marssMLE

Return brief summary information on a MARSS fit
forecast.marssMLE

forecast function for MARSS MLE objects
harborSeal

Harbor Seal Population Count Data (Log counts)
MARSSresiduals

MARSS Residuals
MARSSresiduals.tT

MARSS Smoothed Residuals
fitted.marssMLE

Return fitted values for X(t) and Y(t) in a MARSS model
SalmonSurvCUI

Salmon Survival Indices
marssPredict-class

Class "marssPredict"
ldiag

Return a diagonal list matrix
plot.marssMLE

Plot MARSS MLE objects
is.marssMLE

Tests marssMLE object for completeness
isleRoyal

Isle Royale Wolf and Moose Data
marssMLE-class

Class "marssMLE"
is.marssMODEL

Test Model Objects
predict

predict and forecast MARSS MLE objects
stdInnov

Standardized Innovations
tidy.marssMLE

Return estimated parameters with summary information
plot.marssPredict

Plot MARSS Forecast and Predict objects
toLatex.marssMODEL

Create a LaTeX Version of the Model
marssResiduals-class

Class "marssResiduals"
print.marssMLE

Printing functions for MARSS MLE objects
print.marssMODEL

Printing marssMODEL Objects
accuracy.marssMLE

Return accuracy metrics
print.marssPredict

Printing function for MARSS Predict objects
predict.marssMLE

predict and forecast MARSS MLE objects
marssMODEL-class

Class "marssMODEL"
logLik.marssMLE

logLik method for MARSS MLE objects
sysdata

Palettes
zscore

z-score a vector or matrix
residuals.marssMLE

Model and state fitted values, residuals, and residual sigma
loggerhead

Loggerhead Turtle Tracking Data
utility.functions

Utility Functions
tsSmooth.marssMLE

Smoothed and filtered x and y time series
plankton

Plankton Data Sets
model.frame.marssMODEL

model.frame method for marssMLE and marssMODEL objects