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))