From rgentlem at fhcrc.org  Sun Apr  8 09:52:26 2007
From: rgentlem at fhcrc.org (Robert Gentleman)
Date: Sun, 08 Apr 2007 00:52:26 -0700
Subject: [Rd] buglet in terms calculations
Message-ID: <46189F3A.3080702@fhcrc.org>

Hi,
   Vince and I have noticed a problem with non-syntactic names in data 
frames and some modeling code (but not all modeling code).

   The following, while almost surely as documented could be a bit more 
helpful:

  m = matrix(rnorm(100), nc=10)
  colnames(m) = paste(1:10, letters[1:10], sep="_")

  d = data.frame(m, check.names=FALSE)

  f = formula(`1_a` ~ ., data=d)

  tm = terms(f, data=d)

  ##failure here, as somehow back-ticks have become part of the name
  ##not a quoting mechanism
  d[attr(tm, "term.labels")]

   The variable attribute, in the terms object, keeps them as quotes, so 
modeling code that uses that attribute seems fine, but code that uses 
the term.labels fails. In particular, it seems (of those tested) that 
glm, lda, randomForest seem to work fine, while nnet, rpart can't
handle nonsyntactic names in formulae as such

   In particlar, rpart contains this code:

  lapply(m[attr(Terms, "term.labels")], tfun)

   which fails for the reasons given.


  One way to get around this, might be to modify the do_termsform code,
right now we have:
    PROTECT(varnames = allocVector(STRSXP, nvar));
     for (v = CDR(varlist), i = 0; v != R_NilValue; v = CDR(v))
         SET_STRING_ELT(varnames, i++, STRING_ELT(deparse1line(CAR(v), 
     0), 0));

  and then for term.labels, we copy over the varnames (with :, as 
needed) and perhaps we need to save the unquoted names somewhere?

  Or is there some other approach that will get us there? Certainly 
cleaning up the names via
   cleanTick = function(x) gsub("`", "", x)

  works, but it seems a bit ugly, and it might be better if the modeling 
code was modified.

   best wishes



-- 

Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org



[Rd] buglet in terms calculations
Robert Gentleman