[R-sig-eco] Model specification with RPy/vegan integration

[Gregory, Matthew]

Hi all,

(This might be a bit tangetial and technical question for this
listserve.  Please advise if there is a more appropriate venue.)

I'm trying to call vegan 'cca' from Python using Rpy.  I read my species
and environmental data into R data frames without an issue and can even
run the 'full' cca model without a problem, e.g. 

  from rpy import *
  set_default_mode(NO_CONVERSION)

  # Import the vegan library
  r.library('vegan')

  # Open up the data files and read into data frames
  spp_file = r.read_csv('spp.csv', header=r.TRUE)
  env_file = r.read_csv('env.csv', header=r.TRUE)
  spp = r.data_frame(spp_file, row_names='FCID')
  env = r.data_frame(env_file, row_names='FCID')

  # Squareroot transform the species matrix
  spp = r.sqrt(spp)

  # Create the vegan CCA
  out_cca = r.cca(spp, env)

However, when I try to specify the model to only include a subset of the
environmental variables, e.g.

  # Create the vegan CCA
  model = r("spp ~ ANNPRE + ANNTMP + DEM + SLPPCT")
  out_cca = r.cca(model, env)

I get the error "Error in eval(expr, envir, enclos) : object "spp" not
found".  Note that running the subsetted model in the R console works
correctly as expected.  Furthermore, I can run example code from the RPy
pages which uses the '~' notation to specify models and it works
correctly as well.  I'm sure I have a silly little syntax error, but I'm
just not seeing it.

Thanks for help,
matt