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

[Gavin Simpson]

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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