From: Frank Harrell <f.harrell_at_vanderbilt.edu>

Date: Tue, 17 May 2011 20:26:26 -0700 (PDT)

>> Dear R-users,

*>>
*

*>> I am using R 2.13.0 and rms 3.3-0 , but can not reproduce figure 7.8 of
*

*>> the
*

*>> handouts *Regression Modeling Strategies* (
*

*>> http://biostat.mc.vanderbilt.edu/wiki/pub/Main/RmS/course2.pdf) by the
*

*>> following code. Could any one help me figure out how to solve this?
*

*>>
*

*>>
*

*>> setwd('C:/Rharrell')
*

*>> require(rms)
*

*>> load('data/counties.sav')
*

*>>
*

*>> older <- counties$age6574 + counties$age75
*

*>> label(older) <- '% age >= 65, 1990'
*

*>> pdensity <- logb(counties$pop.density+1, 10)
*

*>> label(pdensity) <- 'log 10 of 1992 pop per 1990 miles^2'
*

*>> counties <- cbind(counties, older, pdensity) # add 2 vars. not in data
*

*>> frame
*

*>> dd <- datadist(counties)
*

*>> options(datadist='dd')
*

*>>
*

*>> f <- ols(democrat ~ rcs(pdensity,4) + rcs(pop.change,3) +
*

*>> rcs(older,3) + crime + rcs(college,5) + rcs(income,4) +
*

*>> rcs(college,5) %ia% rcs(income,4) +
*

*>> rcs(farm,3) + rcs(white,5) + rcs(turnout,3), data=counties)
*

*>>
*

*>> incomes <- seq(22900, 32800, length=4)
*

*>> show.pts <- function(college.pts, income.pt)
*

*>> {
*

*>> s <- abs(income - income.pt) < 1650
*

*>> # Compute 10th smallest and 10th
*

*>> largest % college
*

*>> # educated in counties with
*

*>> median
*

*>> family income within
*

*>> # $1650 of the target income
*

*>> x <- college[s]
*

*>> x <- sort(x[!is.na(x)])
*

*>> n <- length(x)
*

*>> low <- x[10]; high <- x[n-9]
*

*>> college.pts >= low & college.pts <= high
*

*>> }
*

*>> windows()
*

*>> plot(Predict(f, college, income=incomes, conf.int=FALSE),
*

*>> xlim=c(0,35), ylim=c(30,55), lty=1, lwd=c(.25,1.5,3.5,6),
*

*>> col=c(1,1,2,2), perim=show.pts)
*

*>>
*

*>>
*

*>>
*

*>>
*

*>> Thanks
*

*>>
*

*>>
*

*>>
*

Frank Harrell

Department of Biostatistics, Vanderbilt University

Date: Tue, 17 May 2011 20:26:26 -0700 (PDT)

I converted code using the Design package to be what rms expects but hadn't bothered to re-run the code. For the first note you sent, you can attach(counties) (or better: use with(counties) inside the show.pts function. But I'm getting a warning I'll need to track down before it works 100%:

Warning messages:

1: In income - income.pt :

longer object length is not a multiple of shorter object length
2: In income - income.pt :

longer object length is not a multiple of shorter object length
3: In income - income.pt :

longer object length is not a multiple of shorter object length
4: In income - income.pt :

longer object length is not a multiple of shorter object length

For the nomogram call that needs to be re-worked. The documentation to
nomogram in rms is pretty clear how to proceed. Sorry about the problems.
Note that you don't need windows().

Frank

John Smith-89 wrote:

> > Also I can not reproduce figure 7.11 by > > f <- Newlabels(f, list(turnout='voter turnout (%)')) > windows() > nomogram(f, interact=list(income=incomes), turnout=seq(30,100,by=10), > lplabel='estimated % voting Democratic', cex.var=.8, > cex.axis=.75) > > > > On Tue, May 17, 2011 at 4:04 PM, John Smith <zmring_at_gmail.com> > wrote: >

>> Dear R-users,

> > [[alternative HTML version deleted]] > > ______________________________________________ > 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. >

Frank Harrell

Department of Biostatistics, Vanderbilt University

-- View this message in context: http://r.789695.n4.nabble.com/can-not-use-plot-Predict-rms-reproduce-figure-7-8-from-Regression-Modeling-Strategies-http-biostat-m-tp3530561p3531488.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.Received on Wed 18 May 2011 - 03:33:09 GMT

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