Re: [R] Trellis Conditional contourplot
Finally I got the unreasonable contour plotted.
http://www.geocities.com/useebi/data/kdecontour.jpeg
The codes to get the plot,
cdplot2d(survived ~ age + sibsp, data = titanic3)
are in http://www.geocities.com/useebi/data/cdplot2d.txt
One step that I couldn't accomplish as in cdplot is to eliminate those
undefined conditional densities outside the ranges of the two covariates. The
plot dosen't make sense for areas with no x and y observation. Probably, this
is why the goal did not sound like anything reasonable.
Anyway, I guess the naked eyes are pretty good to estimate the conditional
density from the color coded scatterplot if nothing else works!
marco
Deepayan Sarkar [EMAIL PROTECTED] wrote:
On 10/25/06, Marco LO wrote:
OK!
# The R codes to generate the Trellis plot are from the R help archive by
Karl Ove Hufthammer
panel.estcontplot - function(x, y, ..., pretty=TRUE, region=FALSE)
{
cest.gr=kde2d(x, y)
cest.gr.lat=con2tr(cest.gr)
panel.contourplot(cest.gr.lat$x, cest.gr.lat$y, cest.gr.lat$z,
subscripts = seq(nrow(cest.gr.lat)),
pretty=pretty, region=region, contour=TRUE, ...)
}
# The titanic3 dataset is from
http://biostat.mc.vanderbilt.edu/twiki/pub/Main/DataSets/titanic3.xls
with missing value imputations according to the book
library(Hmisc)
set.seed(17)
xtrans - transcan(~ I(age) + pclass + sex + sibsp + parch + survived, data
= titanic3,
n.impute=5, pl=F, trantab=T, imputed=T, transformed=TRUE)
titanic3[ ,'age'] - xtrans$transformed[ ,'age']
titanic3[ ,'survived'] - as.factor(titanic[ ,'survived'])
library(lattice)
xyplot(age ~ sibsp | survived, data = titanic3, panel=panel.estcontplot)
Anyway, I realized that Trellis could only be conditional on the categorical
variable while what I really want is conditional density plot of survived on
the two covariates.
That goal does not sound like anything reasonable to me, but I don't
know much about categorical data analysis, so I'll let someone else
answer. However, based on your first post where you implied that you
expected 'densities' to 'add up to 1', I _will_ suggest this: if the
phrase counting measure does not mean anything to you, you should
seriously consider consulting a local statistician to whom it does.
-Deepayan
-
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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.
Re: [R] Trellis Conditional contourplot
Finally I got the unreasonable contour plotted. http://www.geocities.com/useebi/data/kdecontour.jpeg The codes to get the plot, cdplot2d(survived ~ age + sibsp, data = titanic3) are in http://www.geocities.com/useebi/data/cdplot2d.txt One step that I couldn't accomplish as in cdplot is to eliminate those undefined conditional densities outside the ranges of the two covariates. The plot dosen't make sense for areas with no x and y observation. Probably, this is why the goal did not sound like anything reasonable. You can do something pretty similar with ggplot: qplot(age, sibsp, . ~ survived, data=titanic3, type=c(jitter,2density)) (except clearly the density calculation is very different) Hadley __ R-help@stat.math.ethz.ch 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.
Re: [R] Trellis Conditional contourplot
OK!
# The R codes to generate the Trellis plot are from the R help archive by
Karl Ove Hufthammer
panel.estcontplot - function(x, y, ..., pretty=TRUE, region=FALSE)
{
cest.gr=kde2d(x, y)
cest.gr.lat=con2tr(cest.gr)
panel.contourplot(cest.gr.lat$x, cest.gr.lat$y, cest.gr.lat$z,
subscripts = seq(nrow(cest.gr.lat)),
pretty=pretty, region=region, contour=TRUE, ...)
}
# The titanic3 dataset is from
http://biostat.mc.vanderbilt.edu/twiki/pub/Main/DataSets/titanic3.xls with
missing value imputations according to the book
library(Hmisc)
set.seed(17)
xtrans - transcan(~ I(age) + pclass + sex + sibsp + parch + survived, data =
titanic3,
n.impute=5, pl=F, trantab=T, imputed=T, transformed=TRUE)
titanic3[ ,'age'] - xtrans$transformed[ ,'age']
titanic3[ ,'survived'] - as.factor(titanic[ ,'survived'])
library(lattice)
xyplot(age ~ sibsp | survived, data = titanic3, panel=panel.estcontplot)
Anyway, I realized that Trellis could only be conditional on the categorical
variable while what I really want is conditional density plot of survived on
the two covariates. Thus I tried to twist cdplot with kde2d to substitute
density.
http://www.geocities.com/useebi/data/cdplot2d.txt
However, I still have no success. Would anyone help, please!
Thanks
marco
Deepayan Sarkar [EMAIL PROTECTED] wrote:
On 10/24/06, Marco LO wrote:
Hello All,
I've problems to interpret the contourplot for a binary response dependent
variable. For example, I ploted the survived probability for the titanic3
dataset,
http://www.geocities.com/useebi/data/CondenContour.jpeg
Trellis displayed two panels of contour, one for dead and one for alive.
However,
the contours between the two panels didn't conform to the rule of prob(dead) =
1 - prob(alive). How I should read the contours? What I did wrongly?
Hard to say, since we have no idea what you actually did. As the
footer of every r-help message says:
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
-Deepayan
Is there an example that I could follow?
Thanks!
marco
-
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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.
Re: [R] Trellis Conditional contourplot
On 10/25/06, Marco LO [EMAIL PROTECTED] wrote:
OK!
# The R codes to generate the Trellis plot are from the R help archive by
Karl Ove Hufthammer
panel.estcontplot - function(x, y, ..., pretty=TRUE, region=FALSE)
{
cest.gr=kde2d(x, y)
cest.gr.lat=con2tr(cest.gr)
panel.contourplot(cest.gr.lat$x, cest.gr.lat$y, cest.gr.lat$z,
subscripts = seq(nrow(cest.gr.lat)),
pretty=pretty, region=region, contour=TRUE, ...)
}
# The titanic3 dataset is from
http://biostat.mc.vanderbilt.edu/twiki/pub/Main/DataSets/titanic3.xls
with missing value imputations according to the book
library(Hmisc)
set.seed(17)
xtrans - transcan(~ I(age) + pclass + sex + sibsp + parch + survived, data
= titanic3,
n.impute=5, pl=F, trantab=T, imputed=T, transformed=TRUE)
titanic3[ ,'age'] - xtrans$transformed[ ,'age']
titanic3[ ,'survived'] - as.factor(titanic[ ,'survived'])
library(lattice)
xyplot(age ~ sibsp | survived, data = titanic3, panel=panel.estcontplot)
Anyway, I realized that Trellis could only be conditional on the categorical
variable while what I really want is conditional density plot of survived on
the two covariates.
That goal does not sound like anything reasonable to me, but I don't
know much about categorical data analysis, so I'll let someone else
answer. However, based on your first post where you implied that you
expected 'densities' to 'add up to 1', I _will_ suggest this: if the
phrase counting measure does not mean anything to you, you should
seriously consider consulting a local statistician to whom it does.
-Deepayan
__
R-help@stat.math.ethz.ch 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.
[R] Trellis Conditional contourplot
Hello All, I've problems to interpret the contourplot for a binary response dependent variable. For example, I ploted the survived probability for the titanic3 dataset, http://www.geocities.com/useebi/data/CondenContour.jpeg Trellis displayed two panels of contour, one for dead and one for alive. However, the contours between the two panels didn't conform to the rule of prob(dead) = 1 - prob(alive). How I should read the contours? What I did wrongly? Is there an example that I could follow? Thanks! marco - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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.
Re: [R] Trellis Conditional contourplot
On 10/24/06, Marco LO [EMAIL PROTECTED] wrote: Hello All, I've problems to interpret the contourplot for a binary response dependent variable. For example, I ploted the survived probability for the titanic3 dataset, http://www.geocities.com/useebi/data/CondenContour.jpeg Trellis displayed two panels of contour, one for dead and one for alive. However, the contours between the two panels didn't conform to the rule of prob(dead) = 1 - prob(alive). How I should read the contours? What I did wrongly? Hard to say, since we have no idea what you actually did. As the footer of every r-help message says: PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -Deepayan Is there an example that I could follow? Thanks! marco __ R-help@stat.math.ethz.ch 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.
