R: Masks of seas or lands

seaMask {spaMM}

R Documentation

Masks of seas or lands

Description

These convenient masks can be added to maps of (parts of) the world to mask map information for these areas.

However, many other tools may be available since this documentation was conceived. See e.g. the rnaturalearth package, used to provide a sea mask in an example for filled.mapMM

Usage

data("seaMask")
data("landMask")
# data("worldcountries") # deprecated and removed
# data("oceanmask") # deprecated and removed

Format

seaMask 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.

Details

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://gitlab.mbb.univ-montp2.fr/francois/spamm-ref/-/blob/master/vignettePlus/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.

Examples

## 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")
             }))
}