From gavin.simpson at ucl.ac.uk  Tue Aug 16 17:15:18 2005
From: gavin.simpson at ucl.ac.uk (Gavin Simpson)
Date: Tue, 16 Aug 2005 16:15:18 +0100
Subject: [Rd] problem using model.frame()
Message-ID: <1124205318.8689.45.camel@gsimpson.geog.ucl.ac.uk>

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)

-- 
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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.
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[Rd] problem using model.frame()
Gavin Simpson