Re: [R] How to add lines to lattice plot produced by rms::bplot
Once you guys figure all this out, I'm glad to modify bplot to pass
more arguments lattice if needed.
Frank E Harrell Jr Professor and ChairmanSchool of Medicine
Department of Biostatistics Vanderbilt University
On Fri, 13 Aug 2010, David Winsemius wrote:
On Aug 13, 2010, at 11:25 PM, Duncan Mackay wrote:
Hi David
I do not know if you have done something like this.
I had tried a few efforts like that, starting with an examination of
str(bp.plot) as you demonstrate.
I tried str(bp.plot) which gave the section about the regions (for
colours) as:
$ panel.args.common:List of 8
..$ x : num [1:2500] 27 28 29 29.9 30.9 ...
..$ y : num [1:2500] 141 141 141 141 141 ...
..$ z : num [1:2500] -1.43 -1.41 -1.39 -1.36 -1.34 ...
..$ at : num [1:10] -2 -1.5 -1 -0.5 0 0.5 1 1.5 2 2.5
..$ region : logi FALSE
..$ zlab :List of 3
.. ..$ label: chr log odds
.. ..$ rot : num 90
.. ..$ cex : num 1
..$ labels : logi TRUE
..$ contour: logi TRUE
I tried (with a bplot object named bldLT40):
bldLT40$legend$right$args$key$at - c(-0.233, seq(.50, 2.25, by=0.25),
seq(2.5, 5.0, by=0.5), 6:10)
... and then tried
bldLT40$panel.args$at - c(-0.233, seq(.50, 2.25, by=0.25), seq(2.5,
5.0, by=0.5), 6:10)
Neither of these efforts changed the boundaries beteen colors in the
plot area. The first effort changed the legend scal,e but that just
created a misalignment of the colors of plot area and the legend. I
would be interested in either a strategy that lets one alter the color
level changes of the z variable (which in bplot-created objects is
zhat, or lets one specify the values at which contour lines are
drawn in contourplot.
Thanks for your efforts.
--
David.
I added the col.region and colours from a plot levelplot that I had
done to see what would occur to the trellis parameters. No colours
were produced when plotted.
bp.plot - bplot(p, lfun=contourplot, color.key = TRUE, col.regions
=
c
(#FF
,#00,#A9E2FF,#8080FF,#FF,#FFD18F,#FF) )
$ panel.args.common:List of 10
..$ x : num [1:2500] 27 28 29 29.9 30.9 ...
..$ y : num [1:2500] 141 141 141 141 141 ...
..$ z : num [1:2500] -1.43 -1.41 -1.39 -1.36 -1.34 ...
..$ at : num [1:10] -2 -1.5 -1 -0.5 0 0.5 1 1.5 2 2.5
..$ region : logi FALSE
..$ color.key : logi TRUE
..$ zlab :List of 3
.. ..$ label: chr log odds
.. ..$ rot : num 90
.. ..$ cex : num 1
..$ labels : logi TRUE
..$ contour: logi TRUE
..$ col.regions: chr [1:7] #FF #00 #A9E2FF
#8080FF ...
So it has been added to the panel.args.common, whether you can
access these are another matter.
I then tried
bp.plot - bplot(p, lfun=contourplot, par.settings = list(axis.text
= list(cex = 0.65)), color.key = TRUE, col.regions =
c
(#FF
,#00,#A9E2FF,#8080FF,#FF,#FFD18F,#FF) )
which changed the size of the axis text so it may be the case of
having to add the col.regions etc to the appropriate list in
par.settings
I'll leave you to amend and access the colours.
You may have to add values for the wireframe/levelplot arguments
like at etc. and col.regions (I think that is the function) to
produce an appropriate colour range of your choice
It is a while since I have delved into these sorts of plots.
Need some sustenance.
Regards
Duncan
Duncan Mackay
Department of Agronomy and Soil Science
University of New England
ARMIDALE NSW 2351
Email home: mac...@northnet.com.au
At 10:33 14/08/2010, you wrote:
I have a plot produced by function bplot (package = rms) that is
really a lattice plot (class=trellis). It is similar to this plot
produced by a very minor modification of the first example on the
bplot help page:
require(rms)
n - 1000# define sample size
set.seed(17) # so can reproduce the results
age- rnorm(n, 50, 10)
blood.pressure - rnorm(n, 120, 15)
cholesterol- rnorm(n, 200, 25)
sex- factor(sample(c('female','male'), n,TRUE))
label(age)- 'Age' # label is in Hmisc
label(cholesterol)- 'Total Cholesterol'
label(blood.pressure) - 'Systolic Blood Pressure'
label(sex)- 'Sex'
units(cholesterol)- 'mg/dl' # uses units.default in Hmisc
units(blood.pressure) - 'mmHg'
# Specify population model for log odds that Y=1
L - .4*(sex=='male') + .045*(age-50) +
(log(cholesterol - 10)-5.2)*(-2*(sex=='female') + 2*(sex=='male'))
# Simulate binary y to have Prob(y=1) = 1/[1+exp(-L)]
y - ifelse(runif(n) plogis(L), 1, 0)
ddist - datadist(age, blood.pressure, cholesterol, sex)
options(datadist='ddist')
fit - lrm(y ~ blood.pressure + sex * (age + rcs(cholesterol,4)),
x=TRUE, y=TRUE)
p - Predict(fit, age, cholesterol, sex='male', np=50) # vary sex
last
bp.plot - bplot(p, lfun=contourplot)
bp.plot
I have tried a variety of efforts at using update (which I assume
is a
lattice function although I can find no help page for it. It does
appear in some of the lattice hep pages and my
Re: [R] How to add lines to lattice plot produced by rms::bplot
On Aug 14, 2010, at 9:59 AM, Frank Harrell wrote:
Once you guys figure all this out, I'm glad to modify bplot to pass
more arguments lattice if needed.
As always, Frank, I appreciate your support. In this case I think it's
not needed. What seems to be needed is simply the correct use of the
at argument. (I thought I had tried this before but apparently
mucked it up somehow.) This gives the desired color levels separation
and labeling of the default levelplot version of bplot output:
bldLT40 - bplot(mdl.pred , perim=boundaries, at=c(-0.233, seq(.50,
2.25, by=0.25), seq(2.5, 5.0, by=0.5), 6:10) )
bldLT40
And this produces the expected output with its contouplot version:
bldLT40c - bplot(mdl.pred , perim=boundaries, lfun=contourplot,
at=c(-0.233, seq(.50, 2.25, by=0.25), seq(2.5, 5.0, by=0.5), 6:10) )
bldLT40c
My only quibble with that last one was that the labels had three
digits to the right of the decimal pt but that happily went away when
I changed the low end to 0.25. All is good here.
--
David.
Frank E Harrell Jr Professor and ChairmanSchool of Medicine
Department of Biostatistics Vanderbilt
University
On Fri, 13 Aug 2010, David Winsemius wrote:
On Aug 13, 2010, at 11:25 PM, Duncan Mackay wrote:
Hi David
I do not know if you have done something like this.
I had tried a few efforts like that, starting with an examination of
str(bp.plot) as you demonstrate.
I tried str(bp.plot) which gave the section about the regions (for
colours) as:
$ panel.args.common:List of 8
..$ x : num [1:2500] 27 28 29 29.9 30.9 ...
..$ y : num [1:2500] 141 141 141 141 141 ...
..$ z : num [1:2500] -1.43 -1.41 -1.39 -1.36 -1.34 ...
..$ at : num [1:10] -2 -1.5 -1 -0.5 0 0.5 1 1.5 2 2.5
..$ region : logi FALSE
..$ zlab :List of 3
.. ..$ label: chr log odds
.. ..$ rot : num 90
.. ..$ cex : num 1
..$ labels : logi TRUE
..$ contour: logi TRUE
I tried (with a bplot object named bldLT40):
bldLT40$legend$right$args$key$at - c(-0.233, seq(.50, 2.25,
by=0.25),
seq(2.5, 5.0, by=0.5), 6:10)
... and then tried
bldLT40$panel.args$at - c(-0.233, seq(.50, 2.25, by=0.25), seq(2.5,
5.0, by=0.5), 6:10)
Neither of these efforts changed the boundaries beteen colors in the
plot area. The first effort changed the legend scal,e but that just
created a misalignment of the colors of plot area and the legend. I
would be interested in either a strategy that lets one alter the
color
level changes of the z variable (which in bplot-created objects is
zhat, or lets one specify the values at which contour lines are
drawn in contourplot.
Thanks for your efforts.
--
David.
I added the col.region and colours from a plot levelplot that I had
done to see what would occur to the trellis parameters. No colours
were produced when plotted.
bp.plot - bplot(p, lfun=contourplot, color.key = TRUE, col.regions
=
c
(#FF
,#00,#A9E2FF,#8080FF,#FF,#FFD18F,#FF) )
$ panel.args.common:List of 10
..$ x : num [1:2500] 27 28 29 29.9 30.9 ...
..$ y : num [1:2500] 141 141 141 141 141 ...
..$ z : num [1:2500] -1.43 -1.41 -1.39 -1.36 -1.34 ...
..$ at : num [1:10] -2 -1.5 -1 -0.5 0 0.5 1 1.5 2 2.5
..$ region : logi FALSE
..$ color.key : logi TRUE
..$ zlab :List of 3
.. ..$ label: chr log odds
.. ..$ rot : num 90
.. ..$ cex : num 1
..$ labels : logi TRUE
..$ contour: logi TRUE
..$ col.regions: chr [1:7] #FF #00 #A9E2FF
#8080FF ...
So it has been added to the panel.args.common, whether you can
access these are another matter.
I then tried
bp.plot - bplot(p, lfun=contourplot, par.settings = list(axis.text
= list(cex = 0.65)), color.key = TRUE, col.regions =
c
(#FF
,#00,#A9E2FF,#8080FF,#FF,#FFD18F,#FF) )
which changed the size of the axis text so it may be the case of
having to add the col.regions etc to the appropriate list in
par.settings
I'll leave you to amend and access the colours.
You may have to add values for the wireframe/levelplot arguments
like at etc. and col.regions (I think that is the function) to
produce an appropriate colour range of your choice
It is a while since I have delved into these sorts of plots.
Need some sustenance.
Regards
Duncan
Duncan Mackay
Department of Agronomy and Soil Science
University of New England
ARMIDALE NSW 2351
Email home: mac...@northnet.com.au
At 10:33 14/08/2010, you wrote:
I have a plot produced by function bplot (package = rms) that is
really a lattice plot (class=trellis). It is similar to this plot
produced by a very minor modification of the first example on the
bplot help page:
require(rms)
n - 1000# define sample size
set.seed(17) # so can reproduce the results
age- rnorm(n, 50, 10)
blood.pressure - rnorm(n, 120, 15)
cholesterol- rnorm(n, 200, 25)
sex- factor(sample(c('female','male'), n,TRUE))
label(age)- 'Age' # label is in Hmisc
label(cholesterol)-
Re: [R] How to add lines to lattice plot produced by rms::bplot
Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University On Sat, 14 Aug 2010, David Winsemius wrote: On Aug 14, 2010, at 9:59 AM, Frank Harrell wrote: Once you guys figure all this out, I'm glad to modify bplot to pass more arguments lattice if needed. As always, Frank, I appreciate your support. In this case I think it's not needed. What seems to be needed is simply the correct use of the at argument. (I thought I had tried this before but apparently mucked it up somehow.) This gives the desired color levels separation and labeling of the default levelplot version of bplot output: bldLT40 - bplot(mdl.pred , perim=boundaries, at=c(-0.233, seq(.50, 2.25, by=0.25), seq(2.5, 5.0, by=0.5), 6:10) ) bldLT40 And this produces the expected output with its contouplot version: bldLT40c - bplot(mdl.pred , perim=boundaries, lfun=contourplot, at=c(-0.233, seq(.50, 2.25, by=0.25), seq(2.5, 5.0, by=0.5), 6:10) ) bldLT40c My only quibble with that last one was that the labels had three digits to the right of the decimal pt but that happily went away when I changed the low end to 0.25. All is good here. -- David. Excellent. Thanks David. If you think of anything that would be a good addition to the examples or other parts of the help file, shoot me a few lines and I'll paste them in. Frank Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University On Fri, 13 Aug 2010, David Winsemius wrote: On Aug 13, 2010, at 11:25 PM, Duncan Mackay wrote: Hi David I do not know if you have done something like this. I had tried a few efforts like that, starting with an examination of str(bp.plot) as you demonstrate. I tried str(bp.plot) which gave the section about the regions (for colours) as: $ panel.args.common:List of 8 ..$ x : num [1:2500] 27 28 29 29.9 30.9 ... ..$ y : num [1:2500] 141 141 141 141 141 ... ..$ z : num [1:2500] -1.43 -1.41 -1.39 -1.36 -1.34 ... ..$ at : num [1:10] -2 -1.5 -1 -0.5 0 0.5 1 1.5 2 2.5 ..$ region : logi FALSE ..$ zlab :List of 3 .. ..$ label: chr log odds .. ..$ rot : num 90 .. ..$ cex : num 1 ..$ labels : logi TRUE ..$ contour: logi TRUE I tried (with a bplot object named bldLT40): bldLT40$legend$right$args$key$at - c(-0.233, seq(.50, 2.25, by=0.25), seq(2.5, 5.0, by=0.5), 6:10) ... and then tried bldLT40$panel.args$at - c(-0.233, seq(.50, 2.25, by=0.25), seq(2.5, 5.0, by=0.5), 6:10) Neither of these efforts changed the boundaries beteen colors in the plot area. The first effort changed the legend scal,e but that just created a misalignment of the colors of plot area and the legend. I would be interested in either a strategy that lets one alter the color level changes of the z variable (which in bplot-created objects is zhat, or lets one specify the values at which contour lines are drawn in contourplot. Thanks for your efforts. -- David. I added the col.region and colours from a plot levelplot that I had done to see what would occur to the trellis parameters. No colours were produced when plotted. bp.plot - bplot(p, lfun=contourplot, color.key = TRUE, col.regions = c (#FF ,#00,#A9E2FF,#8080FF,#FF,#FFD18F,#FF) ) $ panel.args.common:List of 10 ..$ x : num [1:2500] 27 28 29 29.9 30.9 ... ..$ y : num [1:2500] 141 141 141 141 141 ... ..$ z : num [1:2500] -1.43 -1.41 -1.39 -1.36 -1.34 ... ..$ at : num [1:10] -2 -1.5 -1 -0.5 0 0.5 1 1.5 2 2.5 ..$ region : logi FALSE ..$ color.key : logi TRUE ..$ zlab :List of 3 .. ..$ label: chr log odds .. ..$ rot : num 90 .. ..$ cex : num 1 ..$ labels : logi TRUE ..$ contour: logi TRUE ..$ col.regions: chr [1:7] #FF #00 #A9E2FF #8080FF ... So it has been added to the panel.args.common, whether you can access these are another matter. I then tried bp.plot - bplot(p, lfun=contourplot, par.settings = list(axis.text = list(cex = 0.65)), color.key = TRUE, col.regions = c (#FF ,#00,#A9E2FF,#8080FF,#FF,#FFD18F,#FF) ) which changed the size of the axis text so it may be the case of having to add the col.regions etc to the appropriate list in par.settings I'll leave you to amend and access the colours. You may have to add values for the wireframe/levelplot arguments like at etc. and col.regions (I think that is the function) to produce an appropriate colour range of your choice It is a while since I have delved into these sorts of plots. Need some sustenance. Regards Duncan Duncan Mackay Department of Agronomy and Soil Science University of New England ARMIDALE NSW 2351 Email home: mac...@northnet.com.au At 10:33 14/08/2010, you wrote: I have a plot produced by function bplot (package = rms) that is really a lattice plot (class=trellis). It is similar to this plot produced by a very minor modification of the first example on the
Re: [R] How to add lines to lattice plot produced by rms::bplot
Hi David
I do not know if you have done something like this.
I tried str(bp.plot) which gave the section about the regions (for colours) as:
$ panel.args.common:List of 8
..$ x : num [1:2500] 27 28 29 29.9 30.9 ...
..$ y : num [1:2500] 141 141 141 141 141 ...
..$ z : num [1:2500] -1.43 -1.41 -1.39 -1.36 -1.34 ...
..$ at : num [1:10] -2 -1.5 -1 -0.5 0 0.5 1 1.5 2 2.5
..$ region : logi FALSE
..$ zlab :List of 3
.. ..$ label: chr log odds
.. ..$ rot : num 90
.. ..$ cex : num 1
..$ labels : logi TRUE
..$ contour: logi TRUE
I added the col.region and colours from a plot levelplot that I had done to
see what would occur to the trellis parameters. No colours were produced
when plotted.
bp.plot - bplot(p, lfun=contourplot, color.key = TRUE, col.regions =
c(#FF,#00,#A9E2FF,#8080FF,#FF,#FFD18F,#FF) )
$ panel.args.common:List of 10
..$ x : num [1:2500] 27 28 29 29.9 30.9 ...
..$ y : num [1:2500] 141 141 141 141 141 ...
..$ z : num [1:2500] -1.43 -1.41 -1.39 -1.36 -1.34 ...
..$ at : num [1:10] -2 -1.5 -1 -0.5 0 0.5 1 1.5 2 2.5
..$ region : logi FALSE
..$ color.key : logi TRUE
..$ zlab :List of 3
.. ..$ label: chr log odds
.. ..$ rot : num 90
.. ..$ cex : num 1
..$ labels : logi TRUE
..$ contour: logi TRUE
..$ col.regions: chr [1:7] #FF #00 #A9E2FF #8080FF ...
So it has been added to the panel.args.common, whether you can access these
are another matter.
I then tried
bp.plot - bplot(p, lfun=contourplot, par.settings = list(axis.text =
list(cex = 0.65)), color.key = TRUE, col.regions =
c(#FF,#00,#A9E2FF,#8080FF,#FF,#FFD18F,#FF) )
which changed the size of the axis text so it may be the case of having to
add the col.regions etc to the appropriate list in par.settings
I'll leave you to amend and access the colours.
You may have to add values for the wireframe/levelplot arguments like
at etc. and col.regions (I think that is the function) to produce an
appropriate colour range of your choice
It is a while since I have delved into these sorts of plots.
Need some sustenance.
Regards
Duncan
Duncan Mackay
Department of Agronomy and Soil Science
University of New England
ARMIDALE NSW 2351
Email home: mac...@northnet.com.au
At 10:33 14/08/2010, you wrote:
I have a plot produced by function bplot (package = rms) that is
really a lattice plot (class=trellis). It is similar to this plot
produced by a very minor modification of the first example on the
bplot help page:
require(rms)
n - 1000# define sample size
set.seed(17) # so can reproduce the results
age- rnorm(n, 50, 10)
blood.pressure - rnorm(n, 120, 15)
cholesterol- rnorm(n, 200, 25)
sex- factor(sample(c('female','male'), n,TRUE))
label(age)- 'Age' # label is in Hmisc
label(cholesterol)- 'Total Cholesterol'
label(blood.pressure) - 'Systolic Blood Pressure'
label(sex)- 'Sex'
units(cholesterol)- 'mg/dl' # uses units.default in Hmisc
units(blood.pressure) - 'mmHg'
# Specify population model for log odds that Y=1
L - .4*(sex=='male') + .045*(age-50) +
(log(cholesterol - 10)-5.2)*(-2*(sex=='female') + 2*(sex=='male'))
# Simulate binary y to have Prob(y=1) = 1/[1+exp(-L)]
y - ifelse(runif(n) plogis(L), 1, 0)
ddist - datadist(age, blood.pressure, cholesterol, sex)
options(datadist='ddist')
fit - lrm(y ~ blood.pressure + sex * (age + rcs(cholesterol,4)),
x=TRUE, y=TRUE)
p - Predict(fit, age, cholesterol, sex='male', np=50) # vary sex last
bp.plot - bplot(p, lfun=contourplot)
bp.plot
I have tried a variety of efforts at using update (which I assume is a
lattice function although I can find no help page for it. It does
appear in some of the lattice hep pages and my understanding is that
it pushes objects onto the list structure of a plot object. I've also
tried adding to it with llines()
#-
Oh, never mind. I recovered a memory that I had seen a solution on
rhelp and had saved it. Turns out it was from Peter Ehlers, to whom I
offer thanks. I was trying to add a step function: ht and weight from
a dataframe, bld:
trellis.focus(panel, 1, 1)
panel.lines(x=bld$inches, y=bld$BMI28, type='s')
trellis.unfocus()
Success!
Now... how do I control the color levels in levelplot or contourplot???
David Winsemius, MD
West Hartford, CT
__
R-help@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.
__
R-help@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.
Re: [R] How to add lines to lattice plot produced by rms::bplot
On Aug 13, 2010, at 11:25 PM, Duncan Mackay wrote:
Hi David
I do not know if you have done something like this.
I had tried a few efforts like that, starting with an examination of
str(bp.plot) as you demonstrate.
I tried str(bp.plot) which gave the section about the regions (for
colours) as:
$ panel.args.common:List of 8
..$ x : num [1:2500] 27 28 29 29.9 30.9 ...
..$ y : num [1:2500] 141 141 141 141 141 ...
..$ z : num [1:2500] -1.43 -1.41 -1.39 -1.36 -1.34 ...
..$ at : num [1:10] -2 -1.5 -1 -0.5 0 0.5 1 1.5 2 2.5
..$ region : logi FALSE
..$ zlab :List of 3
.. ..$ label: chr log odds
.. ..$ rot : num 90
.. ..$ cex : num 1
..$ labels : logi TRUE
..$ contour: logi TRUE
I tried (with a bplot object named bldLT40):
bldLT40$legend$right$args$key$at - c(-0.233, seq(.50, 2.25, by=0.25),
seq(2.5, 5.0, by=0.5), 6:10)
... and then tried
bldLT40$panel.args$at - c(-0.233, seq(.50, 2.25, by=0.25), seq(2.5,
5.0, by=0.5), 6:10)
Neither of these efforts changed the boundaries beteen colors in the
plot area. The first effort changed the legend scal,e but that just
created a misalignment of the colors of plot area and the legend. I
would be interested in either a strategy that lets one alter the color
level changes of the z variable (which in bplot-created objects is
zhat, or lets one specify the values at which contour lines are
drawn in contourplot.
Thanks for your efforts.
--
David.
I added the col.region and colours from a plot levelplot that I had
done to see what would occur to the trellis parameters. No colours
were produced when plotted.
bp.plot - bplot(p, lfun=contourplot, color.key = TRUE, col.regions
=
c
(#FF
,#00,#A9E2FF,#8080FF,#FF,#FFD18F,#FF) )
$ panel.args.common:List of 10
..$ x : num [1:2500] 27 28 29 29.9 30.9 ...
..$ y : num [1:2500] 141 141 141 141 141 ...
..$ z : num [1:2500] -1.43 -1.41 -1.39 -1.36 -1.34 ...
..$ at : num [1:10] -2 -1.5 -1 -0.5 0 0.5 1 1.5 2 2.5
..$ region : logi FALSE
..$ color.key : logi TRUE
..$ zlab :List of 3
.. ..$ label: chr log odds
.. ..$ rot : num 90
.. ..$ cex : num 1
..$ labels : logi TRUE
..$ contour: logi TRUE
..$ col.regions: chr [1:7] #FF #00 #A9E2FF
#8080FF ...
So it has been added to the panel.args.common, whether you can
access these are another matter.
I then tried
bp.plot - bplot(p, lfun=contourplot, par.settings = list(axis.text
= list(cex = 0.65)), color.key = TRUE, col.regions =
c
(#FF
,#00,#A9E2FF,#8080FF,#FF,#FFD18F,#FF) )
which changed the size of the axis text so it may be the case of
having to add the col.regions etc to the appropriate list in
par.settings
I'll leave you to amend and access the colours.
You may have to add values for the wireframe/levelplot arguments
like at etc. and col.regions (I think that is the function) to
produce an appropriate colour range of your choice
It is a while since I have delved into these sorts of plots.
Need some sustenance.
Regards
Duncan
Duncan Mackay
Department of Agronomy and Soil Science
University of New England
ARMIDALE NSW 2351
Email home: mac...@northnet.com.au
At 10:33 14/08/2010, you wrote:
I have a plot produced by function bplot (package = rms) that is
really a lattice plot (class=trellis). It is similar to this plot
produced by a very minor modification of the first example on the
bplot help page:
require(rms)
n - 1000# define sample size
set.seed(17) # so can reproduce the results
age- rnorm(n, 50, 10)
blood.pressure - rnorm(n, 120, 15)
cholesterol- rnorm(n, 200, 25)
sex- factor(sample(c('female','male'), n,TRUE))
label(age)- 'Age' # label is in Hmisc
label(cholesterol)- 'Total Cholesterol'
label(blood.pressure) - 'Systolic Blood Pressure'
label(sex)- 'Sex'
units(cholesterol)- 'mg/dl' # uses units.default in Hmisc
units(blood.pressure) - 'mmHg'
# Specify population model for log odds that Y=1
L - .4*(sex=='male') + .045*(age-50) +
(log(cholesterol - 10)-5.2)*(-2*(sex=='female') + 2*(sex=='male'))
# Simulate binary y to have Prob(y=1) = 1/[1+exp(-L)]
y - ifelse(runif(n) plogis(L), 1, 0)
ddist - datadist(age, blood.pressure, cholesterol, sex)
options(datadist='ddist')
fit - lrm(y ~ blood.pressure + sex * (age + rcs(cholesterol,4)),
x=TRUE, y=TRUE)
p - Predict(fit, age, cholesterol, sex='male', np=50) # vary sex
last
bp.plot - bplot(p, lfun=contourplot)
bp.plot
I have tried a variety of efforts at using update (which I assume
is a
lattice function although I can find no help page for it. It does
appear in some of the lattice hep pages and my understanding is that
it pushes objects onto the list structure of a plot object. I've also
tried adding to it with llines()
#-
Oh, never mind. I recovered a memory that I had seen a solution on
rhelp and had saved it. Turns out
