[R] problem using do.call and substitute for predict.glm using poly()

[Gavin Simpson]

Dear List,

I think I have found the source of my problem in a reply from Thomas 
Lumley to a previous question on R-Help: 
http://www.r-project.org/nocvs/mail/r-help/2002/0586.html

My code is not working because substitute() does not substitute formal 
arguments to functions, and I guess the first X in data.frame(X = 
predData$X) is a formal argument to data.frame().

The recommended options are to use formals() or parse(deparse()) to 
achieve the required effect, but here I get a somewhat stuck.

I was wondering if anyone on the list could show my how to modify my 
existing code:

pAsgn <- paste("predList[[i]][[n]] <- try(predict(resList$Y$X, newdata 
= 	data.frame(X = predData$X), type = 'response', se = TRUE))")
pAsgn <- parse(text = pAsgn)[[1]]
for (i in namY) {
     for (n in namX) {
         TAsgn <- do.call("substitute", list(pAsgn, list(n = n, i = i, X
		= as.name(n), Y = as.name(i))))
         eval(TAsgn)
     }
}

so that data.frame(X = predData$X) is replaced with the value of X such 
that the output from do.call in the loop is something like:

predList[["Acr.harp"]][["Alk1"]] <- try(predict(resList$Acr.harp$Alk1,
     newdata = data.frame(Alk1 = predData$Alk1), type = "response",
     se = TRUE))

If anyone could point me in the right direction it would be most 
appreciated.

All the best

Gav

Gavin Simpson wrote:

> Hi
> 
> I am having a particular problem with some glm models I am running. I 
> have been adapting code from Bill Venables 'Programmers niche' in RNews 
> Vol 2/2 to fit ca. 1000 glm models to a combination of species 0/1 data 
> (as Y) and related physicochemical data (X), to automate the process of 
> fitting this many models. I have successfully managed to fit all the 
> models and have stored the results in a list, each list has 47 main 
> 'branches' (one for each species) and each branch has 23 'leaves' that 
> each contain a glm object
> 
> But R throws up the following error:
> 
> Error in poly(Alk1, degree = 2, coefs = structure(list(alpha = 
> c(37.7515662650602,  :
>         Object "Alk1" not found
> 
> When trying to evaluate the following code:
> 
> pAsgn <- paste("predList[[i]][[n]] <- try(predict(resList$Y$X, newdata 
> =     data.frame(X = predData$X), type = 'response', se = TRUE))")
> pAsgn <- parse(text = pAsgn)[[1]]
> for (i in namY) {
>     for (n in namX) {
>         TAsgn <- do.call("substitute", list(pAsgn, list(n = n, i = i, 
> X             = as.name(n), Y = as.name(i))))
>         eval(TAsgn)
>     }
> }
> 
> Alk1 is used above as an example, all 23 predictors are 'not found' 
> depending on which part of the loop I'm in. Investigation of the 
> predList object after this has run shows for example:
> 
> $Unk.nown$NCR
> [1] "Error in poly(NCR, degree = 2, coefs = structure(list(alpha = 
> c(218.156626506024,  : \n    Object \"NCR\" not found\n"
> attr(,"class")
> [1] "try-error"
> 
> pAsgn contains a parsed R expression:
> 
> predList[[i]][[n]] <- try(predict(resList$Y$X, newdata = data.frame(X 
> =         predData$X), type = "response", se = TRUE))
> 
> I think I have narrowed the problem down to the fact that the first X in 
> newdata = data.frame(X = predData$X)... is not being substitute with the 
> variable in question, where as all the other X and Y's are being 
> substituted:
> (n and i would be supplied by for loops (see above) so I have 
> substituted  two values below as if they had been in the loop)
> 
>  > do.call("substitute", list(pAsgn, list(n = namX[1], i = namY[1], X 
> =             as.name(n), Y = as.name(i))))
> predList[["Acr.harp"]][["Alk1"]] <- try(predict(resList$Unk.nown$NCR,
>     newdata = data.frame(X = predData$NCR), type = "response",
>     se = TRUE))        ^^^^^^ problem here
> 
> If i supply the values I want for one of the runs, such as:
> 
>  > predList[[1]][[1]] <- try(predict(resList$Acr.harp$Alk1, newdata = 
> data.frame(Alk1 = predData$Alk1), type = "response", se = TRUE))
> 
> Then this works, so the question is, how to I get X to be substituted in 
> the above call? Perhaps this is not the cause of the error, so if anyone 
> else has other suggestions.
> 
> Thank you for help.
> 
> Gav
> 
> ps: version
> platform i386-pc-mingw32
> arch     i386
> os       mingw32
> system   i386, mingw32
> status
> major    1
> minor    8.0
> year     2003
> month    10
> day      08
> language R

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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.simpson at ucl.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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