[Rd] problem using model.frame()

From: Gavin Simpson <gavin.simpson_at_ucl.ac.uk>
Date: Tue 16 Aug 2005 - 15:15:18 GMT


Hi I'm having a problem with model.frame, encapsulated in this example:

y1 <- matrix(c(3,1,0,1,0,1,1,0,0,0,1,0,0,0,1,1,0,1,1,1),

             nrow = 5, byrow = TRUE)
y1 <- as.data.frame(y1)
rownames(y1) <- paste("site", 1:5, sep = "") colnames(y1) <- paste("spp", 1:4, sep = "") y1

model.frame(~ y1)
Error in model.frame(formula, rownames, variables, varnames, extras, extranames, :

        invalid variable type

temp <- as.matrix(y1)
model.frame(~ temp)
  temp.spp1 temp.spp2 temp.spp3 temp.spp4

1         3         1         0         1
2         0         1         1         0
3         0         0         1         0
4         0         0         1         1
5         0         1         1         1

Ideally the above wouldn't have names like temp.var1, temp.var2, but one could deal with that later.

I have tracked down the source of the error message to line 1330 in model.c - here I'm stumped as I don't know any C, but it looks as if the code is looping over the variables in the formula and checking of they are the right "type". So a matrix of variables gets through, but a data.frame doesn't.

It would be good if model.frame could cope with data.frames in formulae, but seeing as I am incapable of providing a patch, is there a way around this problem?

Below is the head of the function I am currently using, including the function for parsing the formula - borrowed and hacked from ordiParseFormula() in package vegan.

I can work out the class of the rhs of the forumla. Is there a way to create a suitable environment for the data argument of parseFormula() such that it contains the rhs dataframe coerced to a matrix, which then should get through model.frame.default without error? How would I go about manipulating/creating such an environment? Any other ideas?

Thanks in advance

Gav

coca.formula <- function(formula, method = c("predictive", "symmetric"),

                         reg.method = c("simpls", "eigen"), weights = NULL,
                         n.axes = NULL, symmetric = FALSE, data)
  {
    parseFormula <- function (formula, data)
      {
        browser()
        Terms <- terms(formula, "Condition", data = data)
        flapart <- fla <- formula <- formula(Terms, width.cutoff = 500)
        specdata <- formula[[2]]
        X <- eval(specdata, data, parent.frame())
        X <- as.matrix(X)
        formula[[2]] <- NULL
        if (formula[[2]] == "1" || formula[[2]] == "0")
          Y <- NULL
        else {
          mf <- model.frame(formula, data, na.action = na.fail)
          Y <- model.matrix(formula, mf)
          if (any(colnames(Y) == "(Intercept)")) {
            xint <- which(colnames(Y) == "(Intercept)")
            Y <- Y[, -xint, drop = FALSE]
          }
        }
        list(X = X, Y = Y)
      }
    if (missing(data))
      data <- parent.frame()

    #browser()
    dat <- parseFormula(formula, data)
-- 

%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565
ENSIS Ltd. & ECRC [E] gavin.simpsonATNOSPAMucl.ac.uk UCL Department of Geography [W] http://www.ucl.ac.uk/~ucfagls/cv/ 26 Bedford Way [W] http://www.ucl.ac.uk/~ucfagls/ London. WC1H 0AP.
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Received on Wed Aug 17 01:20:17 2005

This archive was generated by hypermail 2.1.8 : Mon 20 Feb 2006 - 03:21:16 GMT