# Multivariate Autoregressive State-Space Modeling

## Documentation for package ‘MARSS’ version 3.9

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D F G H I K L M N O P R S T U V W

MARSS-package | Multivariate Autoregressive State-Space Model Estimation

## -- A --

all.equal.vector | Matrix Utilities
alldefaults | MARSS Function Defaults and Allowed Methods
allowed.methods | MARSS Function Defaults and Allowed Methods

## -- C --

checkMARSSInputs | Check inputs to MARSS call
checkModelList | Check model List Passed into MARSS Call
coef | Coefficient function for MARSS MLE objects
coef-method | Class "marssMLE"
coef.MARSS | Coefficient function for MARSS MLE objects
coef.marss | Coefficient function for MARSS MLE objects
coef.marssMLE | Coefficient function for MARSS MLE objects
convert.model.mat | Matrix Utilities
CSEGriskfigure | Plot Extinction Risk Metrics
CSEGtmufigure | Plot Forecast Uncertainty

## -- D --

describe.marssMODEL | Printing marssMODEL Objects

## -- F --

fixed.free.to.formula | Matrix Utilities

## -- G --

graywhales | Population Data Sets
grouse | Population Data Sets

## -- H --

harborSeal | Harbor Seal Population Count Data (Log counts)
harborSealWA | Harbor Seal Population Count Data (Log counts)

## -- I --

Imat | Matrix Utilities
is.blockdiag | Matrix Utilities
is.design | Matrix Utilities
is.diagonal | Matrix Utilities
is.equaltri | Matrix Utilities
is.fixed | Matrix Utilities
is.identity | Matrix Utilities
is.marssMLE | Maximum Likelihood MARSS Estimation Object
is.marssMODEL | Test Model Objects
is.marssMODEL_dfa | Test Model Objects
is.marssMODEL_marss | Test Model Objects
is.marssMODEL_marxss | Test Model Objects
is.solvable | Matrix Utilities
is.validvarcov | Matrix Utilities
is.wholenumber | Matrix Utilities
is.zero | Matrix Utilities
isleRoyal | Isle Royale Wolf and Moose Data
ivesDataByWeek | Plankton Data Sets
ivesDataLP | Plankton Data Sets

## -- K --

kem.methods | MARSS Function Defaults and Allowed Methods
kestrel | Population Data Sets

## -- L --

lakeWAplankton | Plankton Data Sets
lakeWAplanktonRaw | Plankton Data Sets
lakeWAplanktonTrans | Plankton Data Sets
loggerhead | Loggerhead Turtle Tracking Data
loggerheadNoisy | Loggerhead Turtle Tracking Data

## -- M --

makediag | Matrix Utilities
MARSS | MARSS Model Specification and Estimation
MARSS.dfa | Multivariate Dynamic Factor Analysis
MARSS.marxss | Multivariate AR-1 State-space Model with Inputs
MARSSaic | AIC for MARSS Models
MARSSapplynames | Names for marssMLE Object Components
MARSSboot | Bootstrap MARSS Parameter Estimates
MARSShatyt | Compute Expected Value of Y,YY, and YX
MARSShessian | MARSS Parameter Variance-Covariance Matrix from the Hessian Matrix
MARSShessian.backtrans | MARSS Parameter Variance-Covariance Matrix from the Hessian Matrix
MARSSinfo | Information for MARSS Error Messages and Warnings
MARSSinits | Initial Values for MLE
MARSSinits_dlm | Initial Values for MLE
MARSSinits_marss | Initial Values for MLE
MARSSinits_marxss | Initial Values for MLE
MARSSinnovationsboot | Bootstrapped Data using Stoffer and Wall's Algorithm
MARSSkem | Maximum Likelihood Estimation for Multivariate Autoregressive State-Space Models
MARSSkemcheck | Model Checking for MLE objects Passed to MARSSkem
MARSSkf | Kalman Filtering and Smoothing for Time-varying MARSS models
MARSSkfas | Kalman Filtering and Smoothing for Time-varying MARSS models
MARSSkfss | Kalman Filtering and Smoothing for Time-varying MARSS models
MARSSmcinit | Monte Carlo Initialization
marssMLE | Maximum Likelihood MARSS Estimation Object
marssMLE-class | Class "marssMLE"
marssMODEL | Class "marssMODEL"
MARSSoptim | Parameter estimation for MARSS models using optim
MARSSparamCIs | Standard Errors, Confidence Intervals and Bias for MARSS Parameters
MARSSsettings | MARSS Model Specification and Estimation
MARSSsimulate | Simulate Data from a MARSS Model
MARSSvectorizeparam | Vectorize or Replace the par List
marss_to_marxss | Convert Model Objects between Forms
marxss_to_marss | Convert Model Objects between Forms
matrix.power | Matrix Utilities
mystrsplit | Matrix Utilities

## -- N --

neglogLik | Parameter estimation for MARSS models using optim

## -- O --

okanaganRedds | Population Data Sets
optim.methods | MARSS Function Defaults and Allowed Methods

## -- P --

parmat | Matrix Utilities
pcholinv | Matrix Utilities
pinv | Matrix Utilities
prairiechicken | Population Data Sets
predict | Compute the Prediction Intervals, Expected Values, and Standard Errors for States (X) and Observation (Y) from MARSS fits
predict-method | Class "marssMLE"
predict.MARSS | Compute the Prediction Intervals, Expected Values, and Standard Errors for States (X) and Observation (Y) from MARSS fits
predict.marssMLE | Compute the Prediction Intervals, Expected Values, and Standard Errors for States (X) and Observation (Y) from MARSS fits
print | Printing functions for MARSS MLE objects
print-method | Class "marssMLE"
print-method | Class "marssMODEL"
print.MARSS | Printing functions for MARSS MLE objects
print.marssMLE | Printing functions for MARSS MLE objects
print.marssMODEL | Printing marssMODEL Objects

## -- R --

redstart | Population Data Sets
residuals | MARSS Standardized Residuals
residuals-method | Class "marssMLE"
residuals.MARSS | MARSS Standardized Residuals
residuals.marss | MARSS Standardized Residuals
residuals.marssMLE | MARSS Standardized Residuals
rockfish | Population Data Sets
rwishart | Matrix Utilities

## -- S --

SalmonSurvCUI | Salmon Survial Indices
simulate-method | Class "marssMLE"
simulate.marssMLE | Simulate Data from a MARSS Model
stdInnov | Standardized Innovations
sub3D | Matrix Utilities
summary-method | Class "marssMLE"
summary-method | Class "marssMODEL"

## -- T --

takediag | Matrix Utilities

## -- U --

unvec | Matrix Utilities

## -- V --

vec | Matrix Utilities

## -- W --

wilddogs | Population Data Sets