Well, I still can not get Prof. Harrell's lrm() work for my ordinal data.
I am not sure what went wrong. I emailed Dr Harrell 3 days ago. I guess
he is out of town, since I have not been able to reach him. I would
highly appreciate it very much if any of you can point out what mistake I
made in my S code. I really feel so helpless here. I chceked his help
library of lrm, but was not able to locate the data set he illustrates
there. So for simplicity, let us see the cheese data (see the bottom of
this message or page 175 of McCullagha and Nelder)
My understanding to Prof Harrell's message is to create 2 variables as
follows:
> response
[1] 1 2 3 4 4 4 4 4 4 4 5 5 5 5 5 5 5 5 6 6 6 6 6 6 6 6 7 7 7 7 7 7 7 7 7
7 7
[38] 7 7 7 7 7 7 7 7 8 8 8 8 8 8 8 8 9 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 3 3
3 3 3
[75] 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 4 4 4 5 5 5 5 5 5 5 6 6 6 6 6 6 7 8 9
1 2 3
[112] 3 3 3 3 3 4 4 4 4 4 4 4 4 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
5 5 6
[149] 6 6 6 6 6 6 7 7 7 7 7 8 9 1 2 3 4 5 5 5 6 6 6 6 6 6 6 7 7 7 7 7 7 7
7 7 7
[186] 7 7 7 7 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 9 9 9 9 9 9 9 9 9 9 9
> cheese
[1] "A" "A" "A" "A" "A" "A" "A" "A" "A" "B" "B" "B" "B" "B" "B" "B" "B"
"B"
[19] "C" "C" "C" "C" "C" "C" "C" "C" "C" "D" "D" "D" "D" "D" "D" "D" "D"
"D"
[37] "A" "A" "A" "A" "A" "A" "A" "A" "A" "B" "B" "B" "B" "B" "B" "B" "B"
"B"
[55] "C" "C" "C" "C" "C" "C" "C" "C" "C" "D" "D" "D" "D" "D" "D" "D" "D"
"D"
[73] "A" "A" "A" "A" "A" "A" "A" "A" "A" "B" "B" "B" "B" "B" "B" "B" "B"
"B"
[91] "C" "C" "C" "C" "C" "C" "C" "C" "C" "D" "D" "D" "D" "D" "D" "D" "D"
"D"
[109] "A" "A" "A" "A" "A" "A" "A" "A" "A" "B" "B" "B" "B" "B" "B" "B" "B"
"B"
[127] "C" "C" "C" "C" "C" "C" "C" "C" "C" "D" "D" "D" "D" "D" "D" "D" "D"
"D"
[145] "A" "A" "A" "A" "A" "A" "A" "A" "A" "B" "B" "B" "B" "B" "B" "B" "B"
"B"
[163] "C" "C" "C" "C" "C" "C" "C" "C" "C" "D" "D" "D" "D" "D" "D" "D" "D"
"D"
[181] "A" "A" "A" "A" "A" "A" "A" "A" "A" "B" "B" "B" "B" "B" "B" "B" "B"
"B"
[199] "C" "C" "C" "C" "C" "C" "C" "C" "C" "D" "D" "D" "D" "D" "D" "D" "D"
"D"
> lrm(response~as.factor(cheese))
Error in dim<-: Invalid value for dimension 1: dim=c(0, ..)
Dumped
Well, something wrong here, but I cannot figure out what.
With a lot of thanks...
On Mon, 23 Mar 1998, Frank E Harrell Jr wrote:
> Dear Hui-Lin,
>
> S-news asks subscribers to try contacting the author of the add-on
> library first. -Thanks
>
> lrm does not accept a frequency weight at present.
> Be sure to give modeling functions the basic categorical predictors instead
> of deriving dummy variables yourself. So the answer to your question is
> to build a data frame that repeats each row of your data up to the needed
> frequency, then do lrm(response ~ cheese, data=newdataframe). I'll leave
> it to someone else to devise an elegant way to expand the data frame
> by the frequency variable. Something along the lines of
>
> newdataframe <- original.data.frame[s,]
>
> will do it once a very long vector s is created (using rep) that has duplicate
> row
> numbers. The length of s will equal the sum of the frequencies.
>
> lrm does not handle frequency weights because all of my datasets have at least
> one continuous variable in them.
>
> -Frank Harrell
>
>
> -----Original Message-----
> From: Hui-Lin Hu <huilin@u.washington.edu>
> To: s-news@wubios.wustl.edu <s-news@wubios.wustl.edu>
> Date: Monday, March 23, 1998 9:19 PM
> Subject: [S] ordinal outcomes
>
>
> >
> >
> >Hi there,
> >
> >This should be easy for those who has ever used Harrell's lrm function.
> >It is the first time for me to use this function, but I have not been able
> >to make it work. I am not sure what went wrong. Could any of you help me?
> >What exactly should be written in () of lrm()?
> >
> >Here is the cheese data from page 175 of McCullagha and Nelder.
> >How to use lrm() to get the logistic treatment effects on page 176 of this
> >book?
> >
> >col 1 (x1) = 1 if Cheese = A
> >col 2 (x2) = 1 if Cheese = B
> >col 3 (x3) = 1 if Cheese = C
> >col 4 (y) : Response category
> >col 5 (wt) : Count in each cell of the crosstable "Cheese * Categorical
> > Response"
> >
> > 1 0 0 1 0
> > 1 0 0 2 0
> > 1 0 0 3 1
> > 1 0 0 4 7
> > 1 0 0 5 8
> > 1 0 0 6 8
> > 1 0 0 7 19
> > 1 0 0 8 8
> > 1 0 0 9 1
> > 0 1 0 1 6
> > 0 1 0 2 9
> > 0 1 0 3 12
> > 0 1 0 4 11
> > 0 1 0 5 7
> > 0 1 0 6 6
> > 0 1 0 7 1
> > 0 1 0 8 0
> > 0 1 0 9 0
> > 0 0 1 1 1
> > 0 0 1 2 1
> > 0 0 1 3 6
> > 0 0 1 4 8
> > 0 0 1 5 23
> > 0 0 1 6 7
> > 0 0 1 7 5
> > 0 0 1 8 1
> > 0 0 1 9 0
> > 0 0 0 1 0
> > 0 0 0 2 0
> > 0 0 0 3 0
> > 0 0 0 4 1
> > 0 0 0 5 3
> > 0 0 0 6 7
> > 0 0 0 7 14
> > 0 0 0 8 16
> > 0 0 0 9 11
> >
> >
> >
> >
> >
> >
> >
> >-----------------------------------------------------------------------
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