Excluding variables specified in a VIF object
Phisically exclude the collinear variables which are identified using vifcor or vifstep from a set of variables.
exclude(x, vif, ...)
x |
explanatory variables (predictors), defined as a raster object ( |
vif |
an object of class |
... |
additional argument as in |
Before using this function, you should execute one of vifstep or vifcor which detect collinearity based on calculating variance inflation factor (VIF) statistics. If vif is missing, then vifstep is called.
an object of class same as x (i.e. RasterStack or RasterBrick or data.frame or matrix)
Babak Naimi naimi.b@gmail.com
IF you used this method, please cite the following article for which this package is developed:
Naimi, B., Hamm, N.A.S., Groen, T.A., Skidmore, A.K., and Toxopeus, A.G. 2014. Where is positional uncertainty a problem for species distribution modelling?, Ecography 37 (2): 191-203.
## Not run:
file <- system.file("external/spain.grd", package="usdm")
r <- brick(file) # reading a RasterBrick object including 10 raster layers in Spain
r
vif(r) # calculates vif for the variables in r
v1 <- vifcor(r, th=0.9) # identify collinear variables that should be excluded
v1
re1 <- exclude(r,v1) # exclude the collinear variables that were identified in
# the previous step
re1
v2 <- vifstep(r, th=10) # identify collinear variables that should be excluded
v2
re2 <- exclude(r, v2) # exclude the collinear variables that were identified in
# the previous step
re2
re3 <- exclude(r) # first, vifstep is called
re3
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.