Hi Manuel,
raster[] will give you a vector of the raster values so 

#create a new raster of the same red and extent as cob_r
forest_raster<-cob_r

# assuming forest pixels have a value of 1
forest_raster[forest_raster[]!=1]<-0
plot(forest_raster)

Does that work?

Date: Tue, 15 Oct 2013 10:49:50 -0600
From: mspinol...@gmail.com
To: r-sig-geo@r-project.org
Subject: [R-sig-Geo] Selecting cells in a raster

Dear list members,
 
I have a raster with land use data (with values from 1 to 9).  I want to
select the cells with value 1 wich belong to forest.  How can I do that?  I
was trying:
 
forest <- cob_r ==1
plot(forest)
 
but it didn´t work
 
> cob_r
class       : RasterLayer
dimensions  : 314, 236, 74104  (nrow, ncol, ncell)
resolution  : 300, 300  (x, y)
extent      : 447181, 517981, 1121851, 1216051  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=tmerc +lat_0=0 +lon_0=-84 +k=0.9999 +x_0=500000 +y_0=0
+datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0
data source : in memory
names       : layer
values      : 1, 9  (min, max)
 
-- 
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin...@una.ac.cr
mspinol...@gmail.com
Teléfono: (506) 2277-3598
Fax: (506) 2237-7036
Personal website: Lobito de río <https://sites.google.com/site/lobitoderio/>
Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
 
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