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model.matrix troubles with AlgDesign

4 messages · Ulrike Grömping, Heather Turner

Original
Ulrike Grömping
# 
Dear DevelopeRs,

in continuing with my suite of packages on experimental design, I am stuck
with an issue that appears to be related to package AlgDesign - I have tried
to get it solved by Bob Wheeler, but he seems to be stuck as well. 

Whenever AlgDesign is loaded, some of my code does not work any more. For
example, in a fresh R session: 

require(DoE.base)
fac.design(nlevels=c(2,6,2))
require(AlgDesign)
fac.design(nlevels=c(2,6,2))
The reason seems to be that AlgDesign creates a function
model.matrix.formula that only finds variables that are in the global
environment and variables that are in the data frame given with the formula,
but not calculation results from the intermediate calling environment. 

Results from traceback():
9: nrow(aus)
8: eval(expr, envir, enclos)
7: eval(predvars, data, env)
6: model.frame.default(object, data, xlev = xlev)
5: model.frame(object, data, xlev = xlev)
4: model.matrix.default(frml, data, ...)
3: model.matrix.formula(1:nrow(aus) ~ ., data = aus)
2: model.matrix(1:nrow(aus) ~ ., data = aus)
1: fac.design(nlevels = c(2, 6, 2))

If I reset model.matrix.formula to model.matrix.default, the problem
disappears (but AlgDesign's comfort functions for squares etc. do not work
any longer). In this particular case, I can also avoid the issue by
modifying the formula in fac.design, removing the left-hand side. But this
just means to wait for the next place where troubles occur. Between 3 and 4
of the traceback(), AlgDesign's function model.matrix.formula modifies the
formula frml using AlgDesign's function expand.formula:

model.matrix.formula <- function (frml, data = sys.frame(sys.parent()), ...) 
{
    if (!missing(data)) {
        if (!inherits(data, "data.frame")) 
            stop("data must be a data.frame")
        if (!inherits(frml, "formula")) 
            stop("frml must be a formuls")
        frml <- expand.formula(frml, colnames(data))
    }
    model.matrix.default(frml, data, ...)
}


I have looked at expand.formula as well, and I've been wondering whether a
simple fix can be found by adding environment information (which?) within
that function (I believe that the relevant portion of the code is included
below):

expand.formula <- function (frml, varNames, const = TRUE, numerics = NULL) 
{
## omitted quite a bit of code 
##...
    frml <- deparse(frml, width = 500)
    while ((0 != (pos <- findFunction("quad", frml))[1]) || (0 != 
        (pos <- findFunction("cubicS", frml))[1]) || (0 != (pos <-
findFunction("cubic", 
        frml))[1])) {
        prog <- substr(frml, pos[1], pos[2])
        strHead <- substr(frml, 1, pos[1] - 1)
        strTail <- substr(frml, pos[2] + 1, nchar(frml))
        prog <- eval(parse(text = prog))
        frml <- paste(strHead, prog, strTail, sep = "")
    }
    if (0 != (pos <- findDot(".", frml))[1]) {
        strHead <- substr(frml, 1, pos[1] - 1)
        strTail <- substr(frml, pos[2] + 1, nchar(frml))
        prog <- eval(parse(text = "doDot()"))
        frml <- paste(strHead, prog, strTail, sep = "")
    }
    if (!const) 
        frml <- paste(frml, "+0", sep = "")
    frml <- as.formula(frml)
    frml
}

Any help would be greatly appreciated.

Regards, Ulrike
1 day later
Heather Turner
# 
Hi Ulrike,

It looks like 'aus' is created by fac.design(); is there any reason why
you can't add the variable
y <- 1:nrow(aus)
to this data frame and use y as the response in your formula?

Otherwise I think aus needs to be in the environment of frml (or frml
needs to be given the environment of aus).

Heather
Ulrike Groemping wrote:
Ulrike Grömping
# 
Hi Heather, 

thanks, I would be able to add the variable y <- 1:nrow(aus), I would even
be able to omit these. 
What concerns me is the fact that the presence of function
model.matrix.formula in package AlgDesign will stop model.matrix from
working as expected in further situations that I have not spotted yet. 

For the future development of package DoE.wrapper, I would like to include
AlgDesign in the Depends field, and that would mean that the package would
then stop user functions with perfectly valid code from working correctly.
So I would like to find a way to modify model.matrix.formula or
expand.formula from AlgDesign so that AlgDesign stops messing up usages of
model.matrix in other contexts. I think that the solution may perhaps lie in
assigning the right environment to frml in expand.formula, but I am not
familiar enough with assigning environments to know what the right strategy
would be.

Any suggestions ?

Regards, 
Ulrike
Heather Turner wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Heather Turner
    

    

      
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Ah ok, I get the problem now.

I think you just need to modify model.matrix.formula as follows

 model.matrix.formula <- function (frml, data = sys.frame(sys.parent()),
 ...)
 {
     if (!missing(data)) {
         if (!inherits(data, "data.frame"))
             stop("data must be a data.frame")
         if (!inherits(frml, "formula"))
             stop("frml must be a formuls")
         env <- environment(frml)
         frml <- expand.formula(frml, colnames(data))
         environment(frml) <- env
     }
     model.matrix.default(frml, data, ...)
 }

or the equivalent could be done inside expand.formula, which might be
neater actually.

Hope that fixes it,

Heather

        
Ulrike Groemping wrote: