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 -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. & ECRC [E] [EMAIL PROTECTED] 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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