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Coefficient function for MARSS MLE objects

coef_marssMLE.Rd

MARSS() outputs marssMLE objects. coef(object), where object is the output from a MARSS() call, will print out the estimated parameters. The default output is a list with values for each parameter, however the output can be altered using the type argument to output a vector of all the estimated values (type="vector") or a list with the full parameter matrix with the estimated and fixed elements (type="matrix"). For a summary of the parameter estimates with CIs from the estimated Hessian, use try tidy(object).

Usage

# S3 method for marssMLE
coef(object, ..., type = "list", form = NULL, what = "par")

Arguments

object

A marssMLE object.

...

Other arguments. Not used.

type

What to output. Default is "list". Options are

"list"

A list of only the estimated values in each matrix. Each model matrix has it's own list element.

"vector"

A vector of all the estimated values in each matrix.

"matrix"

A list of the parameter matrices each parameter with fixed values at their fixed values and the estimated values at their estimated values. Time-varying parameters, including d and c in a marxss form model, are returned as an array with time in the 3rd dimension.

parameter name

Returns the parameter matrix for that parameter with fixed values at their fixed values and the estimated values at their estimated values. Note, time-varying parameters, including d and c in a marxss form model, are returned as an array with time in the 3rd dimension.

form

This argument can be ignored. By default, the model form specified in the call to MARSS() is used to determine how to display the coefficients. This information is in attr(object$model,"form") . The default form is "marxss"; see MARSS.marxss(). However, the internal functions convert this to form "marss"; see MARSS.marss(). The marss form of the model is stored (in object$marss). You can look at the coefficients in marss form by passing in form="marss".

what

By default, coef() shows the parameter estimates. Other options are "par.se", "par.lowCI", "par.upCI", "par.bias", and "start".

Value

A list of the estimated parameters for each model matrix.

Author

Eli Holmes, NOAA, Seattle, USA.

See also

tidy(), print()

Examples

dat <- t(harborSeal)
dat <- dat[c(2, 11), ]
fit <- MARSS(dat)
#> Success! abstol and log-log tests passed at 26 iterations.
#> Alert: conv.test.slope.tol is 0.5.
#> Test with smaller values (<0.1) to ensure convergence.
#> 
#> MARSS fit is
#> Estimation method: kem 
#> Convergence test: conv.test.slope.tol = 0.5, abstol = 0.001
#> Estimation converged in 26 iterations. 
#> Log-likelihood: 11.74016 
#> AIC: -9.480311   AICc: -6.3692   
#>  
#>                                           Estimate
#> R.diag                                      0.0115
#> U.X.CoastalEstuaries                        0.0613
#> U.X.OR.NorthCoast                           0.0510
#> Q.(X.CoastalEstuaries,X.CoastalEstuaries)   0.0147
#> Q.(X.OR.NorthCoast,X.OR.NorthCoast)         0.0122
#> x0.X.CoastalEstuaries                       7.3823
#> x0.X.OR.NorthCoast                          6.2707
#> Initial states (x0) defined at t=0
#> 
#> Standard errors have not been calculated. 
#> Use MARSSparamCIs to compute CIs and bias estimates.
#> 

coef(fit)
#> $Z
#>      [,1]
#> 
#> $A
#>      [,1]
#> 
#> $R
#>            [,1]
#> diag 0.01148472
#> 
#> $B
#>      [,1]
#> 
#> $U
#>                          [,1]
#> X.CoastalEstuaries 0.06134704
#> X.OR.NorthCoast    0.05099574
#> 
#> $Q
#>                                               [,1]
#> (X.CoastalEstuaries,X.CoastalEstuaries) 0.01468309
#> (X.OR.NorthCoast,X.OR.NorthCoast)       0.01218082
#> 
#> $x0
#>                        [,1]
#> X.CoastalEstuaries 7.382266
#> X.OR.NorthCoast    6.270672
#> 
#> $V0
#>      [,1]
#> 
#> $G
#>      [,1]
#> 
#> $H
#>      [,1]
#> 
#> $L
#>      [,1]
#> 
#> $C
#>      [,1]
#> 
#> $D
#>      [,1]
#> 
#> $c
#>      [,1]
#> 
#> $d
#>      [,1]
#> 
coef(fit, type = "vector")
#>                                    R.diag 
#>                                0.01148472 
#>                      U.X.CoastalEstuaries 
#>                                0.06134704 
#>                         U.X.OR.NorthCoast 
#>                                0.05099574 
#> Q.(X.CoastalEstuaries,X.CoastalEstuaries) 
#>                                0.01468309 
#>       Q.(X.OR.NorthCoast,X.OR.NorthCoast) 
#>                                0.01218082 
#>                     x0.X.CoastalEstuaries 
#>                                7.38226633 
#>                        x0.X.OR.NorthCoast 
#>                                6.27067221 
coef(fit, type = "matrix")
#> $Z
#>                  X.CoastalEstuaries X.OR.NorthCoast
#> CoastalEstuaries                  1               0
#> OR.NorthCoast                     0               1
#> 
#> $A
#>                  [,1]
#> CoastalEstuaries    0
#> OR.NorthCoast       0
#> 
#> $R
#>                  CoastalEstuaries OR.NorthCoast
#> CoastalEstuaries       0.01148472    0.00000000
#> OR.NorthCoast          0.00000000    0.01148472
#> 
#> $B
#>                    X.CoastalEstuaries X.OR.NorthCoast
#> X.CoastalEstuaries                  1               0
#> X.OR.NorthCoast                     0               1
#> 
#> $U
#>                          [,1]
#> X.CoastalEstuaries 0.06134704
#> X.OR.NorthCoast    0.05099574
#> 
#> $Q
#>                    X.CoastalEstuaries X.OR.NorthCoast
#> X.CoastalEstuaries         0.01468309      0.00000000
#> X.OR.NorthCoast            0.00000000      0.01218082
#> 
#> $x0
#>                        [,1]
#> X.CoastalEstuaries 7.382266
#> X.OR.NorthCoast    6.270672
#> 
#> $V0
#>                    X.CoastalEstuaries X.OR.NorthCoast
#> X.CoastalEstuaries                  0               0
#> X.OR.NorthCoast                     0               0
#> 
#> $D
#>                  [,1]
#> CoastalEstuaries    0
#> OR.NorthCoast       0
#> 
#> $C
#>                    [,1]
#> X.CoastalEstuaries    0
#> X.OR.NorthCoast       0
#> 
#> $d
#>      [,1]
#> [1,]    0
#> 
#> $c
#>      [,1]
#> [1,]    0
#> 
#> $G
#>      [,1] [,2]
#> [1,]    1    0
#> [2,]    0    1
#> 
#> $H
#>      [,1] [,2]
#> [1,]    1    0
#> [2,]    0    1
#> 
#> $L
#>      [,1] [,2]
#> [1,]    1    0
#> [2,]    0    1
#> 
# to retrieve just the Q matrix
coef(fit, type = "matrix")$Q
#>                    X.CoastalEstuaries X.OR.NorthCoast
#> X.CoastalEstuaries         0.01468309      0.00000000
#> X.OR.NorthCoast            0.00000000      0.01218082