[R] partialPlot within a function

Micha Silver t@vib@r @ending from gm@il@com
Sat Sep 1 22:32:26 CEST 2018

I am running randomForest regressions in a loop, passing a different 
data.frame each time, and trying to plot importance and partial 
dependency plots for all variables in the data.frame. The commands all 
run OK when typed at the prompt, but when I wrap them into a function, 
the partialPlot function fails with:
  Error in eval(x.var) : object 'impvar' not found

It seems that the x.var parameter is getting the variable name 
(impvar[i] in this case) rather than the value of the variable.
What am I missing here?

The easiest way to see this is using the example right from the 
partialPlot help page, but wrapped into a function:

## Looping over variables ranked by importance:
do_pdp <- function(dta) {
         dta <- na.omit(dta)
         ozone.rf <- randomForest(Ozone ~ ., dta, importance=TRUE)
         imp <- importance(ozone.rf)
         impvar <- rownames(imp)[order(imp[, 1], decreasing=TRUE)]
         op <- par(mfrow=c(2, 3))
         for (i in seq_along(impvar)) {
              partialPlot(ozone.rf, dta, impvar[i], xlab=impvar[i],
                      main=paste("Partial Dependence on", impvar[i]),
                      ylim=c(30, 70))

Fails with the above message above for me. Running the commands 
directly, without the "do_pdp" function works fine, of course.

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 19

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods base

other attached packages:
[1] randomForest_4.6-14

loaded via a namespace (and not attached):
[1] compiler_3.5.1 tools_3.5.1


Micha Silver
Ben Gurion Univ.
Sde Boker, Remote Sensing Lab
cell: +972-523-665918

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