Masks of seas or lands
These convenient masks can be added to maps of (parts of) the world to mask map information for these areas.
data("seaMask")
data("landMask")
# data("worldcountries") # deprecated and removed
# data("oceanmask") # deprecated and removedseaMask and landMask are data frames with two variables, x and y for longitude and latitude.
Its contents are suitable for use with polypath: they define different polygones, each separated by a row of NAs.
worldcountries and oceanmask were sp::SpatialPolygonsDataFrame objects previously included in spaMM (see Details for replacement). Such objects were useful for creating land masks for different geographical projections.
The removed objects worldcountries and oceanmask were suitable for plots involving geographical projections not available through map, and more generally for raster plots. A land mask could be produced out of worldcountries by filling the countries, as by fill="black" in the code for country.layer in the Examples in https://kimura.univ-montp2.fr/~rousset/spaMM/example_raster.html. These objects may now be available through the same web page, but a better place to look for the same functionality is the IsoriX package (objects CountryBorders and OceanMask).
seaMask and landMask were created from the world map in the maps package.
polypath requires polygons, while map(interior=FALSE,plot=FALSE) returns small segments. landMask is the result of reconnecting the segments into full coastlines of all land blocks.
https://kimura.univ-montp2.fr/~rousset/spaMM/example_raster.html for access to, and use of worldcountries and oceanmask; https://cran.r-project.org/package=IsoriX for replacement CountryBorders and OceanMask for these objects.
## Predicting behaviour for a land bird: simplified fit for illustration
data("blackcap")
bfit <- fitme(migStatus ~ means+ Matern(1|longitude+latitude),data=blackcap,
fixed=list(lambda=0.5537,phi=1.376e-05,rho=0.0544740,nu=0.6286311))
## the plot itself, with a sea mask,
## and an ad hoc 'pointmask' to see better the predictions on small islands
#
def_pointmask <- function(xy,r=1,npts=12) {
theta <- 2*pi/npts *seq(npts)
hexas <- lapply(seq(nrow(xy)), function(li){
p <- as.numeric(xy[li,])
hexa <- cbind(x=p[1]+r*cos(theta),y=p[2]+r*sin(theta))
rbind(rep(NA,2),hexa) ## initial NA before each polygon
})
do.call(rbind,hexas)
}
ll <- blackcap[,c("longitude","latitude")]
pointmask <- def_pointmask(ll[c(2,4,5,6,7),],r=0.8) ## small islands only
#
if (spaMM.getOption("example_maxtime")>1) {
data("seaMask")
filled.mapMM(bfit,add.map=TRUE,
plot.title=title(main="Inferred migration propensity of blackcaps",
xlab="longitude",ylab="latitude"),
decorations=quote(points(pred[,coordinates],cex=1,pch="+")),
plot.axes=quote({axis(1);axis(2);
polypath(rbind(seaMask,pointmask),border=FALSE,
col="grey", rule="evenodd")
}))
}Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.