Re: [R] Venn diagram

2007-05-31 Thread Paul Artes

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 
 as said before! The question has already been asked, but unfortunately 
 there was no answer...
 
  
 
 Thank you a lot,
 
 Nina Hubner
 
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Re: [R] omit y=zero line in histogram

2007-04-28 Thread Paul Artes

Reply to self:
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

2007-04-25 Thread Paul Artes

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)

2007-04-17 Thread Paul Artes

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


Mohammad Ehsanul Karim wrote:
 
 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 
  
 ##
 
 Thank you for your time.
 Thanks in advance.
 
 Mohammad Ehsanul Karim
 wildscop at yahoo dot com
 Institute of Statistical Research and Training
 University of Dhaka
 
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[R] Link

2006-08-22 Thread Paul Artes

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

2006-06-23 Thread Paul Artes

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

2006-06-18 Thread Paul Artes

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
your interest. 

Best wishes

Paul
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