Alexandre,

Atualizei seu CMR, adicionando as últimas linhas para realizar o recorte com um polígono irregular.

### <code r>

require(sp); require(rgdal); require(raster)

## Raster-----------------------------------------------------------

set.seed(20131226)

r <- raster(nc=100, nr=100)

r <- setValues(r, round(runif(ncell(r))* 255))

image(r,col=gray(seq(0,1,0.025)))

## Borda -----------------------------------------------------------

x<-c(-125,-100,0,100,-125)

y<-c(-49,25,0,-50,-49)

limite<-cbind(x,y)

lines(limite, col="yellow")

##

## Converte borda para SpatialPolygon

spt.borda <- SpatialPolygons(list(Polygons(list(Polygon(limite)), "1")))

### Recorte do raster contido no interior da borda

r.crop <- crop(r, spt.borda, snap='out')

image(r.crop, asp=1)

### Recorte com polígono irregular! 

r.masked <- mask(r.crop, spt.borda)

image(r.masked, asp=1)

### </code>

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