On Tue, 2005-08-16 at 12:35 -0400, Gabor Grothendieck wrote: > On 8/16/05, Gavin Simpson <[EMAIL PROTECTED]> wrote: > > On Tue, 2005-08-16 at 11:25 -0400, Gabor Grothendieck wrote: > > > It can handle data frames like this: > > > > > > model.frame(y1) > > > or > > > model.frame(~., y1) > > > > Thanks Gabor, > > > > Yes, I know that works, but I want the function coca.formula to accept a > > formula like this y2 ~ y1, with both y1 and y2 being data frames. It is > > The expressions I gave work generally (i.e. lm, glm, ...), not just in > model.matrix, so would it be ok if the user just does this? > > yourfunction(y2 ~., y1)
Thanks again Gabor for your comments, I'd prefer the y1 ~ y2 as data frames - as this is the most natural way of doing things. I'd like to have (y2 ~., y1) as well, and (y2 ~ spp1 + spp2 + spp3, y1) also work - silently without any trouble. > If it really is important to do it the way you describe, are the data > frames necessarily numeric? If so you could preprocess your formula > by placing as.matrix around all the variables representing data frames > using something like this: > > https://www.stat.math.ethz.ch/pipermail/r-help/2004-December/061485.html Yes, they are numeric matrices (as data frames). I've looked at this, but I'd prefer to not have to do too much messing with the formula. > Of course, if they are necessarily numeric maybe they can be matrices in > the first place? Because read.table etc. produce data.frames and this is the natural way to work with data in R. Following your suggestions, I altered my code to evaluate the rhs of the formula and check if it was of class "data.frame". If it is then I stop processing and return it as a data.frame as this point. If not, it eventually gets passed on to model.frame() for it to deal with it. So far - limited testing - it seems to do what I wanted all along. I'm sure there's a gotcha in there somewhere but at least the code runs so I can check for problems against my examples. Right, back to writing documentation... G > > more intuitive, to my mind at least for this particular example and > > analysis, to specify the formula with a data frame on the rhs. > > > > model.frame doesn't work with the formula "~ y1" if the object y1, in > > the environment when model.frame evaluates the formula, is a data.frame. > > It works if y1 is a matrix, however. I'd like to work around this > > problem, say by creating an environment in which y1 is modified to be a > > matrix, if possible. Can this be done? > > > > At the moment I have something working by grabbing the bits of the > > formula and then using get() to grab the named object. Of course, this > > won't work if someone wants to use R's formula interface with the > > following formula y2 ~ var1 + var2 + var3, data = y1, or to use the > > subset argument common to many formula implementations. I'd like to have > > the function work in as general a manner as possible, so I'm fishing > > around for potential solutions. > > > > All the best, > > > > Gav > > > > > > > > On 8/16/05, Gavin Simpson <[EMAIL PROTECTED]> wrote: > > > > 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 > > > > > > -- > > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > > 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. > > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > > > > > > -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% 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
