R help - Aug 2011 - randomForest partial dependence plot variable names

Hello,

I am running randomForest models on a number of species.  I would like to be
able to automate the printing of dependence plots for the most important
variables in each model, but I am unable to figure out how to enter the
variable names into my code.  I had originally thought to extract them from
the $importance matrix after sorting by metric (e.g. %IncMSE), but the
importance matrix is n by 2 - containing only the data for each metric
(%IncMSE and IncNodePurity).  It is clearly linked to the variable names,
but I am unsure how to extract those names for use in scripting.  Any
assistance would be greatly appreciated as I am currently typing the
variable names into each partialPlot call for every model I run.....and that
is taking a LONG time.

Thanks!

	[[alternative HTML version deleted]]

See if the following is close to what you're looking for.  If not, please
give more detail on what you want to do.

data(airquality)
airquality <- na.omit(airquality)
set.seed(131)
ozone.rf <- randomForest(Ozone ~ ., airquality, importance=TRUE)
imp <- importance(ozone.rf)  # get the importance measures
impvar <- rownames(imp)[order(imp[, 1], decreasing=TRUE)]  # get the sorted
names
op <- par(mfrow=c(2, 3))
for (i in seq_along(impvar)) {
    partialPlot(ozone.rf, airquality, impvar[i], xlab=impvar[i],
                main=paste("Partial Dependence on", impvar[i]),
ylim=c(30, 70))
}
par(op)

Andy 
> -----Original Message-----
> From: r-help-bounces at r-project.org 
> [mailto:r-help-bounces at r-project.org] On Behalf Of Katharine Miller
> Sent: Thursday, August 04, 2011 4:38 PM
> To: r-help at r-project.org
> Subject: [R] randomForest partial dependence plot variable names
> 
> Hello,
> 
> I am running randomForest models on a number of species.  I 
> would like to be
> able to automate the printing of dependence plots for the 
> most important
> variables in each model, but I am unable to figure out how to 
> enter the
> variable names into my code.  I had originally thought to 
> extract them from
> the $importance matrix after sorting by metric (e.g. %IncMSE), but the
> importance matrix is n by 2 - containing only the data for each metric
> (%IncMSE and IncNodePurity).  It is clearly linked to the 
> variable names,
> but I am unsure how to extract those names for use in scripting.  Any
> assistance would be greatly appreciated as I am currently typing the
> variable names into each partialPlot call for every model I 
> run.....and that
> is taking a LONG time.
> 
> Thanks!
> 
> 	[[alternative HTML version deleted]]
> 
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