From hb at biostat.ucsf.edu  Mon Jan 27 02:42:03 2014
From: hb at biostat.ucsf.edu (Henrik Bengtsson)
Date: Sun, 26 Jan 2014 17:42:03 -0800
Subject: [Rd] package NAMESPACE question
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On Sun, Jan 26, 2014 at 6:34 AM, Axel Urbiz <axel.urbiz at gmail.com> wrote:
> Hi Duncan,
>
> My most sincere apologies. It's really not my intention to waste anyones
> time. More the opposite...for some reason I thought that the problem had to
> do with my call to options() and thought that would be enough. Here's
> something reproducible:
>
> I built a foo package based on the code under the "----" below. In the
> namespace file, I've only exported: trt and cmt (not contr.none and
> contr.diff). Notice that cmt calls contr.none and contr.diff by default.

As a start, try to export everything, particularly 'contr.none' and
'contr.diff' and see if that works.  Just a guess, but worth trying
out.

My $.02

/Henrik

>
> Then in R, I run this code and I get this error message:
>
> library(foo)
> set.seed(1)
> dd <- data.frame(y = rbinom(100, 1, 0.5), treat = rbinom(100, 1, 0.5), x =
> rnorm(100),
>                          f = gl(4, 250, labels = c("A", "B", "C", "D")))
> dd2 <- cmt(y ~ x + f + trt(treat), data =dd)
>> Error in get(ctr, mode = "function", envir = parent.frame()) :
>    object 'contr.none' of mode 'function' was not found
>
> Thanks,
> Axel.
>
> --------------------------------------------
>
> trt <- function(x) x
>
> cmt <- function(formula, data, subset, na.action = na.pass, cts = TRUE)  {
>
>   if (!inherits(formula, "formula"))
>     stop("Method is only for formula objects.")
>   mf <- match.call(expand.dots = FALSE)
>   args <- match(c("formula", "data", "subset", "na.action"),
>                 names(mf), 0)
>   mf <- mf[c(1, args)]
>   mf$drop.unused.levels <- TRUE
>   mf[[1]] <- as.name("model.frame")
>   special <- "trt"
>   mt <- if(missing(data)) terms(formula, special) else terms(formula,
> special, data = data)
>   mf$formula <- mt
>   mf <- eval.parent(mf)
>   Terms <- attr(mf, "terms")
>   attr(Terms, "intercept") <- 0
>   trt.var <- attr(Terms, "specials")$trt
>   ct <- mf[, trt.var]
>   y <- model.response(mf, "numeric")
>   var_names <- attributes(Terms)$term.labels[-(trt.var-1)]
>   treat.names <- levels(as.factor(ct))
>   oldcontrasts <- unlist(options("contrasts"))
>   if (cts)
>     options(contrasts = c(unordered = "contr.none", ordered = "contr.diff"))
>   x <- model.matrix(terms(reformulate(var_names)),
>                     mf, contrasts)
>   options(contrasts = oldcontrasts)
>   intercept <- which(colnames(x) == "(Intercept)")
>   if (length(intercept > 0)) x <- x[, -intercept]
>   return(x)
>   }
>
> #######################################
> # An alternative contrasts function for unordered factors
> # Ensures symmetric treatment of all levels of a factor
> #######################################
> contr.none <- function(n, contrasts) {
>   if (length(n) == 1)
>     contr.treatment(n, contrasts = n<=2)
>   else
>     contr.treatment(n, contrasts = length(unique(n))<=2)
> }
>
> #######################################
> # An alternative contrasts function for ordered factors
> # Ensures use of a difference penalty for such factors
> #######################################
> contr.diff <- function (n, contrasts = TRUE)
> {
>   if (is.numeric(n) && length(n) == 1) {
>     if (n > 1)
>       levs <- 1:n
>     else stop("not enough degrees of freedom to define contrasts")
>   }
>   else {
>     levs <- n
>     n <- length(n)
>   }
>   contr <- array(0, c(n, n), list(levs, paste(">=", levs, sep="")))
>   contr[outer(1:n,1:n, ">=")] <- 1
>   if (n < 2)
>     stop(gettextf("contrasts not defined for %d degrees of freedom",
>                   n - 1), domain = NA)
>   if (contrasts)
>     contr <- contr[, -1, drop = FALSE]
>   contr
> }
>
>
>
> On Sun, Jan 26, 2014 at 1:21 PM, Duncan Murdoch <murdoch.duncan at gmail.com>wrote:
>
>> On 14-01-25 6:05 PM, Axel Urbiz wrote:
>>
>>> Thanks again all. Essentially, this is the section of the code that is
>>> causing trouble. This is part of the (exported) function which calls
>>> contr.none (not exported). As mentioned, when I call the exported function
>>> it complains with the error described before.
>>>
>>>
>>>    oldcontrasts <- unlist(options("contrasts"))
>>>      if (cts)
>>>          options(contrasts = c(unordered = "contr.none", ordered =
>>> "contr.diff"))
>>>      x <- model.matrix(terms(reformulate(var_names)), mf, contrasts)
>>>      options(contrasts = oldcontrasts)
>>>
>>
>> This is hugely incomplete.  Please stop wasting everyone's time, and post
>> something reproducible.
>>
>> Duncan Murdoch
>>
>>
>
>         [[alternative HTML version deleted]]
>
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[Rd] package NAMESPACE question
Henrik Bengtsson