I have five shapefiles of bordering counties in California that I am trying to combine into one large shapefile and maintain the original borders of the counties. I then want to plot points such as this so the map only needs to be a simple map of county boundaries. Is there a way to do this in R or will I have to use something like ArcGIS?
There is extensive documentation about merging within a shapefile such as here where both shapefiles have the same coordinates. But no documentation on shapefiles that only partially share coordinates.
If you only need to put all the borders into one data set then you can do that with sp/rgdal easily enough, but if you need to actually merge borders geometrically (clip/join/dissolve) and so on the support in R is not that simple.
Roughly the simple option is read each shapefile with readOGR, then spRbind them together. If rgdal presents difficulties for building/installing then there are other options for reading shapefiles in various packages.
btw, "something like ArcGIS" but much closer to "free": www.manifold.net