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

[Thomas Lumley]

On Mon, 27 Oct 2003, Gavin Simpson wrote:

>
> 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:

Yes, that's right.

> (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.


You should be able to use
   newdata=predData[n]
which would substitute to
   newdata=predData["Alk1"]
or even just
   newdata=predData

If you actually needed to substitute the tags you would (I think) need to
work with the parsed expression directly, which is possible but icky:

> names(pAsgn[[3]][[2]][[3]])[2]<-"Alk1"
> pAsgn
predList[[i]][[n]] <- try(predict(resList$Y$X, newdata = data.frame(Alk1 = predData$X),
    type = "response", se = TRUE))


	-thomas