R help - Nov 2012 - Partial dependence plot in randomForest package (all flat responses)

Hi,
I'm trying to make a partial plot with package randomForest in R. After I
perform my random forest object I type

partialPlot(data.rforest, pred.data=act2, x.var=centroid, "C") 

where data.rforest is my randomforest object, act2 is the original dataset,
centroid is one of the predictor and C is one of the classes in my response
variable. 
Whatever predictor or response class I try I always get a plot with a
straight line (a completely flat response). Similarly, If I set a
categorical variable as predictor, I get a barplot with all the bar with the
same height. I suppose I'm doing something wrong here because all other
analysis on the same rforest object seem correct (e.g. varImp or MDSplot).
Is it possible it is related to some option set in random forest object? Can
somebody see the problem here?
Thanks for your time



--
View this message in context:
http://r.789695.n4.nabble.com/Partial-dependence-plot-in-randomForest-package-all-flat-responses-tp4650470.html
Sent from the R help mailing list archive at Nabble.com.

Not unless we have more information.  Please read the Posting Guide to see how
to make it easier for people to answer your question.

Best,
Andy

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On Behalf Of Oritteropus
Sent: Thursday, November 22, 2012 2:02 PM
To: r-help at r-project.org
Subject: [R] Partial dependence plot in randomForest package (all flat
responses)

Hi,
I'm trying to make a partial plot with package randomForest in R. After I
perform my random forest object I type

partialPlot(data.rforest, pred.data=act2, x.var=centroid, "C") 

where data.rforest is my randomforest object, act2 is the original dataset,
centroid is one of the predictor and C is one of the classes in my response
variable. 
Whatever predictor or response class I try I always get a plot with a
straight line (a completely flat response). Similarly, If I set a
categorical variable as predictor, I get a barplot with all the bar with the
same height. I suppose I'm doing something wrong here because all other
analysis on the same rforest object seem correct (e.g. varImp or MDSplot).
Is it possible it is related to some option set in random forest object? Can
somebody see the problem here?
Thanks for your time



--
View this message in context:
http://r.789695.n4.nabble.com/Partial-dependence-plot-in-randomForest-package-all-flat-responses-tp4650470.html
Sent from the R help mailing list archive at Nabble.com.

______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Notice:  This e-mail message, together with any attachme...{{dropped:11}}