Hello,
This is a re-submittal of question I submitted last week, but haven't
rec'd
any responses.
I need to extract the probabilities used to construct the barplots
displayed as part of the graph produced by plot("ctree").
For example,
library(party)
iris.ct <- ctree(Species ~ . , data = iris)
plot(iris.ct)
Instead of a simple example with only 4 terminal nodes, my analysis
produces 55 terminal nodes, so unless someone is really interested I'm only
using the iris data as an example.
This is the model I am sending to ctree. The graph produced is very
informative, but I need the information from the plot(Marshct)
Marshct <- ctree(Physiogomy ~ meanAnnualDepthAve + meanAnnualDepthWetAve +
medAnnualDepthAve + medianAnnualDepthWetAve + medianAnnualDepthDryAve +
continHydroWetAve + DCHperiodAverage + DCHydroDryAve +
threeDayWaterDepthMinAve + threeDayWaterDepthMaxAve + sevenDayDryFreqAve +
sevenDayWaterDepthMaxAve + sevenDayWaterDepthMinAve +
seventeenDayWaterDepMaxAve + seventeenDayWaterDepMinAve +
thirtyoneDayWaterDepthMaxAve + wetIntensityAve + BulkDensity + LOI + TP +
TN + TC + Total_Mg, data = Marsh)
plot(Marshct)
Working in Windows XP with R2.11.1 (2010-05-31)
Thanks
Steve
Steve Friedman Ph. D.
Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034
Steve_Friedman at nps.gov
Office (305) 224 - 4282
Fax (305) 224 - 4147
On Mon, 21 Jun 2010, Steve_Friedman at nps.gov wrote:> > Hello, > > This is a re-submittal of question I submitted last week, but haven't rec'd > any responses. > > I need to extract the probabilities used to construct the barplots > displayed as part of the graph produced by plot("ctree"). > > For example, > > library(party) > > iris.ct <- ctree(Species ~ . , data = iris) > plot(iris.ct)You can compute the information from where(iris.ct) ## terminal node ids treeresponse(iris.ct) ## associated predicted probabilities So, you could do tapply(treeresponse(iris.ct), where(iris.ct), unique) hth, Z> Instead of a simple example with only 4 terminal nodes, my analysis > produces 55 terminal nodes, so unless someone is really interested I'm only > using the iris data as an example. > > This is the model I am sending to ctree. The graph produced is very > informative, but I need the information from the plot(Marshct) > > Marshct <- ctree(Physiogomy ~ meanAnnualDepthAve + meanAnnualDepthWetAve + > medAnnualDepthAve + medianAnnualDepthWetAve + medianAnnualDepthDryAve + > continHydroWetAve + DCHperiodAverage + DCHydroDryAve + > threeDayWaterDepthMinAve + threeDayWaterDepthMaxAve + sevenDayDryFreqAve + > sevenDayWaterDepthMaxAve + sevenDayWaterDepthMinAve + > seventeenDayWaterDepMaxAve + seventeenDayWaterDepMinAve + > thirtyoneDayWaterDepthMaxAve + wetIntensityAve + BulkDensity + LOI + TP + > TN + TC + Total_Mg, data = Marsh) > > plot(Marshct) > > > Working in Windows XP with R2.11.1 (2010-05-31) > > Thanks > Steve > > Steve Friedman Ph. D. > Spatial Statistical Analyst > Everglades and Dry Tortugas National Park > 950 N Krome Ave (3rd Floor) > Homestead, Florida 33034 > > Steve_Friedman at nps.gov > Office (305) 224 - 4282 > Fax (305) 224 - 4147 > > ______________________________________________ > 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. >
You can't get them out of the plot function, but you can calculate
them from the fit. This code returns a matrix with the appropriate
rownames and colnames.
x1 <- treeresponse(iris.ct)
p <- matrix(
unlist(unique(x1)),
ncol=3,
byrow=T
)
colnames(p) <- levels(iris$Species)
rownames(p) <- unique(where(iris.ct))
p
On Mon, Jun 21, 2010 at 3:28 PM, <Steve_Friedman at nps.gov>
wrote:>
> Hello,
>
> This is a re-submittal of question I submitted last week, but haven't
rec'd
> any responses.
>
> I need to extract the probabilities used to construct the barplots
> displayed as part of the graph produced by plot("ctree").
>
> For example,
>
> library(party)
>
> iris.ct <- ctree(Species ~ . , data = iris)
> plot(iris.ct)
>
> Instead of a simple example with only 4 terminal nodes, my analysis
> produces 55 terminal nodes, so unless someone is really interested I'm
only
> using the iris data as an example.
>
> This is the model I am sending to ctree. The graph produced is very
> informative, but I need the information from the plot(Marshct)
>
> Marshct <- ctree(Physiogomy ~ meanAnnualDepthAve + meanAnnualDepthWetAve
+
> medAnnualDepthAve + medianAnnualDepthWetAve + medianAnnualDepthDryAve +
> continHydroWetAve + DCHperiodAverage + DCHydroDryAve +
> threeDayWaterDepthMinAve + threeDayWaterDepthMaxAve + sevenDayDryFreqAve +
> sevenDayWaterDepthMaxAve + sevenDayWaterDepthMinAve +
> seventeenDayWaterDepMaxAve + seventeenDayWaterDepMinAve +
> thirtyoneDayWaterDepthMaxAve + wetIntensityAve + BulkDensity + LOI + TP +
> TN + TC + Total_Mg, data = Marsh)
>
> plot(Marshct)
>
>
> Working in Windows XP with R2.11.1 (2010-05-31)
>
> Thanks
> Steve
>
> Steve Friedman Ph. D.
> Spatial Statistical Analyst
> Everglades and Dry Tortugas National Park
> 950 N Krome Ave (3rd Floor)
> Homestead, Florida 33034
>
> Steve_Friedman at nps.gov
> Office (305) 224 - 4282
> Fax ? ? (305) 224 - 4147
>
> ______________________________________________
> 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.
>
--
Joris Meys
Statistical consultant
Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control
tel : +32 9 264 59 87
Joris.Meys at Ugent.be
-------------------------------
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