### Re: [R] Venn diagram

```
I'm really glad to see this topic come up. Area-proportional Venn diagrams
are a phantastic way to visualize agreement. For the 2-rater scenario this
is straightforward; here are two examples from my own work that were done in
R. (I'm far too embarrassed to enclose the code).

http://myweb.dal.ca/partes/venn_example.jpg

For 3 (or more!) variables, it becomes tricky, but Chow and Ruskey have
solved this recently (see link below).

http://www.cs.uvic.ca/~ruskey/Publications/VennArea/VennArea.html
I think there is even a Java applet for demonstration purposes.

It would be phantastic to have a good R-implementation of this...
Unfortunately my own skills are several log units below what's required. I
have written to Chow and Ruskey before but unfortunately not heard anything.
Anyone up for the job??

Best wishes

Paul

Nina Hubner wrote:

Hello,

I am a total beginner with “R” and found a package “venn” to
create a venn diagram.

The problem is, I cannot create the vectors required for the diagram.

The manual say:
R venn(accession, libname, main = All samples)
where accession was a vector containing the codes identifying
the RNA sequences, and libname was a vector containing the codes
identifying the tissue sample (library).

The structure of my data is as follows:

R   structure(list(cyto = c(A, “B”, “C”, “D”), nuc = c(“A”, “B”, “E”,
“”),
chrom = c(“B”, “F”, “”, “”)),.Names = c(cyto, Nuc, chrom))

accession should be A, B, and libname schould be cyto,
nuc and chrom as I understand it...

Could you help me?

Sorry, that might be a very simple question, but I am a total beginner

Thank you a lot,

Nina Hubner

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### Re: [R] omit y=zero line in histogram

```
set border=NA, stupid.

Paul Artes wrote:

Dear all,

hist ( ) plots a horizontal line at y=0 when the respective bin is empty.
I can deal with this by modifying the hist object before plotting it
(x\$density[x\$density == 0] - NA), but I'm sure I've seen a more elegant
way. Perhaps this was in truehist (MASS). I have looked but can't find it.
Does anyone know?

Best wishes

Paul

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### [R] omit y=zero line in histogram

```
Dear all,

hist ( ) plots a horizontal line at y=0 when the respective bin is empty. I
can deal with this by modifying the hist object before plotting it
(x\$density[x\$density == 0] - NA), but I'm sure I've seen a more elegant
way. Perhaps this was in truehist (MASS). I have looked but can't find it.
Does anyone know?

Best wishes

Paul
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### Re: [R] Extracting approximate Wald test (Chisq) from coxph(..frailty)

```
Assign the output of coxph to some object, and use the \$ extractor function
to obtain what you need.

ie:
rtfm - coxph(formula = Surv(time, status) ~ age + sex +  disease +
frailty(id, dist = gauss), data = kidney)
Age - coef(rtfm)[age]
OR
Sex - rtfm\$coef[sex]

Hope this helps.

Paul

Dear List,

How do I extract the approximate Wald test for the
frailty (in the following example 17.89 value)?

What about the P-values, other Chisq, DF, se(coef) and
se2? How can they be extracted?

##
kfitm1
Call:
coxph(formula = Surv(time, status) ~ age + sex +
disease + frailty(id,
dist = gauss), data = kidney)

coef se(coef)
age0.00489 0.0150
sex   -1.69703 0.4609
diseaseGN  0.17980 0.5447
diseaseAN  0.39283 0.5447
diseasePKD-1.13630 0.8250
frailty(id, dist = gauss
se2Chisq DF
age   0.0106  0.11  1.0
sex   0.3617 13.56  1.0
diseaseGN 0.3927  0.11  1.0
diseaseAN 0.3982  0.52  1.0
diseasePKD0.6173  1.90  1.0
frailty(id, dist = gauss17.89 12.1
p
age   0.74000
sex   0.00023
diseaseGN 0.74000
diseaseAN 0.47000
diseasePKD0.17000
frailty(id, dist = gauss 0.12000

Iterations: 6 outer, 30 Newton-Raphson
Variance of random effect= 0.493
Degrees of freedom for terms=  0.5  0.6  1.7 12.1
Likelihood ratio test=47.5  on 14.9 df, p=2.82e-05  n=
76

##

wildscop at yahoo dot com
Institute of Statistical Research and Training
University of Dhaka

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```
Its a very nice document. Here is the link:

http://cran.r-project.org/doc/contrib/Owen-TheRGuide.pdf

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### Re: [R] PowerPoint

```
Most useful: the Ungroup command in ppt lets you take apart the graph when
you insert it as wmf.
I often resort to that when I want to change labels / fonts / colours etc.
Very flexible.
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### Re: [R] Books

```
Dear Anderson,

I'd highly recommend Modern Applied Statistics with S (4th Ed., by WN
Venables  BD Ripley). This has lots and lots of material on the topics of

Best wishes

Paul
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