tests/testthat/test-filled.mapMM.R

In spaMM: Mixed-Effect Models, with or without Spatial Random Effects

cat(crayon::yellow("\ntest filled.mapMM:"))
# filled.mapMM

data("blackcap")
bfit <- corrHLfit(migStatus ~ means+ Matern(1|longitude+latitude),data=blackcap,
                  HLmethod="ML",
                  ranFix=list(lambda=0.5537,phi=1.376e-05,rho=0.0544740,nu=0.6286311))

## showing add.map
#if (requireNamespace("maps",quietly=TRUE)) { ## required for add.map=TRUE 
  # nloptr and bobyqa perform different smoothings !
  filled.mapMM(bfit,add.map=TRUE,
             plot.title=title(main="Inferred migration propensity of blackcaps",
                              xlab="longitude",ylab="latitude"))
#} else message("package 'maps' not available, a filled.mapMM() test cannot be run")

data("Loaloa")  
lfit <- 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,rho=2.255197,lambda=1.075))   

## longer computation requiring interpolation of 197 points 
#if (requireNamespace("maps",quietly=TRUE)) { ## required for add.map=TRUE 
  filled.mapMM(lfit,add.map=TRUE,
             decorations=quote(points(pred[,coordinates],pch=15,cex=0.3)),
             plot.title=title(main="Inferred prevalence, North Cameroon",
                              xlab="longitude",ylab="latitude"))
#} else message("package 'maps' not available, a filled.mapMM() test cannot be run")
# test of syntax, no expect_ yet

## local maximum issue
# obj <- function(v) {logLik(corrHLfit(formula=migStatus ~ 1 + Matern(1|longitude+latitude),
#                                      HLmethod='ML',data=blackcap,ranFix=as.list(v)))}
# mygrid <- expand.grid(rho=seq(0.2,0.5,0.025),nu=seq(16))
# apply(mygrid,1L,obj) -> blu
# spaMM.filled.contour(x=seq(0.2,0.5,0.025),y=seq(16),z=matrix(blu,ncol=16))