spaMM (version 1.4.1)

Loaloa: Loa loa prevalence in North Cameroon, 1991-2001

Description

This data set describes prevalence of infection by the nematode Loa loa in North Cameroon, 1991-2001. This is a superset of the data discussed by Diggle and Ribeiro (2007) and Diggle et al. (2007). The study investigated the relationship between altitude, vegetation indices, and prevalence of the parasite.

Usage

data(Loaloa)

source

The data were last retrieved on March 1, 2013 from P.J. Ribeiro's web resources at www.leg.ufpr.br/doku.php/pessoais:paulojus:mbgbook:datasets.

References

Diggle, P., and Ribeiro, P. 2007. Model-based geostatistics, Springer series in statistics, Springer, New York. Diggle, P. J., Thomson, M. C., Christensen, O. F., Rowlingson, B., Obsomer, V., Gardon, J., Wanji, S., Takougang, I., Enyong, P., Kamgno, J., Remme, J. H., Boussinesq, M., and Molyneux, D. H. 2007. Spatial modelling and the prediction of Loa loa risk: decision making under uncertainty, Ann. Trop. Med. Parasitol. 101, 499-509.

Examples

data(Loaloa)
## Variations on the model fit by Diggle et al. on a subset of these data

## With HLmethod=HL(0,1), this takes ~35s on a recent laptop

corrHLfit(cbind(npos,ntot-npos)~elev1+elev2+elev3+elev4+maxNDVI1+seNDVI
                   +Matern(1|longitude+latitude),HLmethod="HL(0,1)",
                 data=Loaloa,family=binomial(),ranFix=list(nu=0.5)) 
## nu=0.5 is the exponential correlation     

## the following fits take ~ 1 -- 5 minutes each.

corrHLfit(cbind(npos,ntot-npos)~elev1+elev2+elev3+elev4+maxNDVI1+seNDVI
            +Matern(1|longitude+latitude),
              data=Loaloa,family=binomial(),ranFix=list(nu=0.5)) 

## Diggle and Ribeiro (2007) assumed (in this package notation) Nugget=2/7:
corrHLfit(cbind(npos,ntot-npos)~elev1+elev2+elev3+elev4+maxNDVI1+seNDVI
           +Matern(1|longitude+latitude),
             data=Loaloa,family=binomial(),ranFix=list(nu=0.5,Nugget=2/7))

## with nugget estimation:
corrHLfit(cbind(npos,ntot-npos)~elev1+elev2+elev3+elev4+maxNDVI1+seNDVI
           +Matern(1|longitude+latitude),
             data=Loaloa,family=binomial(),
             init.corrHLfit=list(Nugget=0.1),ranFix=list(nu=0.5))