Clipping rasters in R

Question

I am building a map for the northeastern U.S.A. The map background needs to be either an altitude map or a mean annual temperature map. I have two rasters from Worldclim.org which give me these variables but I need to clip them to the extent of the states I am interested in. Any suggestions on how to do this. This is what I have so far:

   #load libraries
library (sp)
library (rgdal)
library (raster)
library (maps)
library (mapproj)


#load data
state<- data (stateMapEnv)
elevation<-raster("alt.bil")
meantemp<-raster ("bio_1.asc")

#build the raw map
nestates<- c("maine", "vermont", "massachusetts", "new hampshire" ,"connecticut",
  "rhode island","new york","pennsylvania", "new jersey",
  "maryland", "delaware", "virginia", "west virginia")

map(database="state", regions = nestates, interior=T,  lwd=2)
map.axes()

#add site localities
sites<-read.csv("sites.csv", header=T)
lat<-sites$Latitude
lon<-sites$Longitude

map(database="state", regions = nestates, interior=T, lwd=2)
points (x=lon, y=lat, pch=17, cex=1.5, col="black")
map.axes()
library(maps)                                                                  #Add axes to  main map
map.scale(x=-73,y=38, relwidth=0.15, metric=T,  ratio=F)

#create an inset map

 # Next, we create a new graphics space in the lower-right hand corner.  The numbers are proportional distances within the graphics window (xmin,xmax,ymin,ymax) on a scale of 0 to 1.
  # "plt" is the key parameter to adjust
    par(plt = c(0.1, 0.53, 0.57, 0.90), new = TRUE)

  # I think this is the key command from http://www.stat.auckland.ac.nz/~paul/RGraphics/examples-map.R
    plot.window(xlim=c(-127, -66),ylim=c(23,53))

  # fill the box with white
    polygon(c(0,360,360,0),c(0,0,90,90),col="white")

  # draw the map
    map(database="state", interior=T, add=TRUE, fill=FALSE)
    map(database="state", regions=nestates, interior=TRUE, add=TRUE, fill=TRUE, col="grey")

The elevation and meantemp objects are the ones that need to be clipped to the area extent of the nestates object. Any input would help

Answer 1

The function crop in the raster package allows you to use an Extent object or an object for which an Extent can be calculated to cut(subset) another object. The package example:

r <- raster(nrow=45, ncol=90)
r[] <- 1:ncell(r)
e <- extent(-160, 10, 30, 60)
rc <- crop(r, e)

If you wanted to cut in a more detailed manner maybe you could use a SHP of the states and the over function in the sp package.