spaMM (version 1.4.1)

corMatern: Matern Correlation Structure as a corSpatial object

Description

This implements the Matérn correlation structure for use with lme or glmmPQL. Usage is as for others corSpatial objects such as corGaus or corExp, except that the Matérn family has an additional parameter. This function was defined for comparing results obtained with corrHLfit to those produced by lme and glmmmPQL. There are problems in fitting (G)LMMs in the latter way, so it is not a recommended practice.

Usage

corMatern(value = c(1, 0.5), form = ~1, nugget = FALSE, nuScaled = FALSE, 
          metric = c("euclidean", "maximum", "manhattan"), fixed = FALSE)

Arguments

value

An optional vector of parameter values, with serves as initial values or as fixed values depending on the fixed argument. It has either two or three elements, depending on the nugget argument. If nugget is

form

(Pasted from corSpatial) a one sided formula of the form ~ S1+...+Sp, or ~ S1+...+Sp | g, specifying spatial covariates S1 through Sp and, optionally, a grouping factor g. When

nugget

an optional logical value indicating whether a nugget effect is present. Defaults to FALSE.

nuScaled

If nuScaled is set to TRUE the "range" parameter $\rho$ is divided by $2 \sqrt\nu$. With this option and for large values of $\nu$, corMatern reproduces the calculation of corGaus. Default

metric

(Pasted from corSpatial) an optional character string specifying the distance metric to be used. The currently available options are "euclidean" for the root sum-of-squares of distances; "maximum" for the maximum diff

fixed

an optional logical value indicating whether the coefficients should be allowed to vary in the optimization, or kept fixed at their initial value. Defaults to FALSE, in which case the coefficients are allowed to vary.

Value

• an object of class corMatern, also inheriting from class corSpatial, representing a Matérn spatial correlation structure.

Details

This function is a constructor for the corMatern class, representing a Matérn spatial correlation structure. See Matern.corr for details on the Matérn family.

References

Mixed-Effects Models in S and S-PLUS, José C. Pinheiro and Douglas M. Bates, Statistics and Computing Series, Springer-Verlag, New York, NY, 2000.

See Also

glmmPQL, lme

Examples

## LMM
data(blackcap)
blackcapD <-cbind(blackcap,dummy=1) ## obscure, isn't it? 
require(nlme)
## With method= 'ML' in lme, The correlated random effect is described 
##  as a correlated residual error and no extra residual variance is fitted:
lme(fixed = migStatus ~ means, data = blackcapD, random = ~ 1 | dummy, 
    correlation = corMatern(form = ~ longitude+latitude  | dummy), 
    method = "ML")

## Binomial GLMM
## ~54s. on a laptop
data(Loaloa)
LoaloaD <-cbind(Loaloa,dummy=1) 
require(MASS)
glmmPQL(fixed =cbind(npos,ntot-npos)~elev1+elev2+elev3+elev4+maxNDVI1+seNDVI, 
        data = LoaloaD, random = ~ 1 | dummy,family=binomial, 
        correlation = corMatern(form = ~ longitude+latitude | dummy))