# Multivariate Autoregressive State-Space Modeling

## Documentation for package ‘MARSS’ version 2.7

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

MARSS-package | Multivariate Autoregressive State-Space Model Estimation
alldefaults | MARSS function defaults and allowed methods
allowed | MARSS function defaults and allowed methods
allowed.methods | MARSS function defaults and allowed methods
as.design | Matrix Utilities
as.marssm | Model Objects
checkPopWrap | Check Arguments to popWrap()
CSEGriskfigure | Plot Extinction Risk Metrics
CSEGtmufigure | Plot Forecast Uncertainty
describe.marssm | MARSS function defaults and allowed methods
graywhales | Population Data Sets
grouse | Population Data Sets
harborSeal | Harbor Seal Population Count Data (Log counts)
harborSealnomiss | Harbor Seal Population Count Data (Log counts)
harborSealWA | Harbor Seal Population Count Data (Log counts)
Imat | Matrix Utilities
is.blockdiag | Matrix Utilities
is.blockequaltri | Matrix Utilities
is.blockunconst | Matrix Utilities
is.design | Matrix Utilities
is.diagonal | Matrix Utilities
is.equaltri | Matrix Utilities
is.fixed | Matrix Utilities
is.identity | Matrix Utilities
is.marssm | Model Objects
is.marssMLE | Maximum Likelihood MARSS Estimation Object
is.wholenumber | Matrix Utilities
isleRoyal | Population Data Sets
ivesDataByWeek | Plankton Data Sets
ivesDataLP | Plankton Data Sets
kem.methods | MARSS function defaults and allowed methods
kestrel | Population Data Sets
lakeWAplankton | Plankton Data Sets
loggerhead | Loggerhead Turtle Tracking Data
loggerheadNoisy | Loggerhead Turtle Tracking Data
makediag | Matrix Utilities
MARSS | Interface MARSS Model Specification and Estimation
MARSSaic | AIC for MARSS models
MARSSapplynames | Names for marssMLE Object Components
MARSSboot | Bootstrap MARSS Parameter Estimates
MARSScheckdims | MARSS Utilities
MARSScheckpar | MARSS Utilities
MARSShatyt | Compute Expected Value of Y,YY, and YX
MARSShessian | MARSS Parameter Variance-Covariance Matrix from the Hessian Matrix
MARSSinits | 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
MARSSkfas | Kalman Filtering and Smoothing
MARSSLLprofile | Log-likelihood profiles for MARSS Parameters
marssm | Model Objects
marssm-class | Class "marssm"
MARSSmcinit | Monte Carlo Initialization
marssMLE | Maximum Likelihood MARSS Estimation Object
marssMLE-class | Class "marssMLE"
MARSSoptim | Parameter estimation for MARSS models using optim
MARSSoptions | Change MARSS Defaults Utility
MARSSparamCIs | Confidence Intervals for MARSS Parameters
MARSSresids | MARSS standardized residuals
MARSSsettings | Interface MARSS Model Specification and Estimation
MARSSsimulate | Simulate Data from a MARSS Model and Parameter Estimates
MARSSvectorizeparam | Vector to Parameter Matrix Conversion
model.elem | MARSS function defaults and allowed methods
model.elem.w.V0 | MARSS function defaults and allowed methods
neglogLik | Parameter estimation for MARSS models using optim
okanaganRedds | Population Data Sets
optim.methods | MARSS function defaults and allowed methods
popWrap | Wrapper Objects
popWrap-class | Class "popWrap"
prairiechicken | Population Data Sets
print-method | Class "marssMLE"
print-method | Class "marssm"
rockfish | Population Data Sets
stdInnov | Standardized Innovations
summary-method | Class "marssMLE"
summary-method | Class "marssm"
takediag | Matrix Utilities
unvec | Matrix Utilities
vec | Matrix Utilities
wilddogs | Population Data Sets