date:20050411

François Pinard [EMAIL PROTECTED] writes:

 Hi, R people.
 
 I'm shy reporting this, as a bug in this area sounds very unlikely.  Did
 I make my tests wrongly?  I'm still flaky at all this.  Let me dare
 nevertheless, who knows, just in case...  Please don't kill me! :-)
 
 Not so long ago, I wrote to this list:
 
  (For now, [the library code] works only for me when I do _not_ use `-l
  MY/OWN/LIBDIR' at `R CMD INSTALL' time, I surely made a simple blunder
  somewhere.  Hopefully, I'll figure it out.)
 
 Now using this line within `~/.Renviron':
 
R_LIBS=/home/pinard/etc/R
 
 my tiny package is correctly found by R.  However, R does not seem to
 see any library within that directory if I rather use either of:
 
R_LIBS=$HOME/etc/R
R_LIBS=$HOME/etc/R
 
 The last writing (I mean, something similar) is suggested somewhere in
 the R manuals (but I do not have the manual with me right now to give
 the exact reference, I'm in another town).

?Startup gets you there soon enough (and help.search(Renviron) points
you at Startup):

 Lines in a site or user environment file should be either comment
 lines starting with '#', or lines of the form 'name=value'. The
 latter sets the environmental variable 'name' to 'value',
 overriding an existing value.  If 'value' is of the form
 '${foo-bar}', the value is that of the environmental variable
 'foo' if that exists and is set to a non-empty value, otherwise
 'bar'.  This construction can be nested, so 'bar' can be of the
 same form (as in '${foo-${bar-blah}}').

so R_LIBS=${HOME}/etc/R is what should work. Notice that this is
processed by R internally, not by the shell, so syntax may differ from
the command-line equivalent.


-- 
   O__   Peter Dalgaard Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics 2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark  Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907

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Re: [R] writing to an Excel file

On Mon, 11 Apr 2005, Petr Pikal wrote:
Hi Laura
Pretty common question. You could find an answer going through
archives.
To copy to Excel through clipboard:
write.excel-function(tab, ...) write.table( tab, clipboard,
sep=\t, row.names=F)
write.excel(your.data.frame)
open Excel and press ctrl-C
Well, that is essentially
`writing to a regular data file and importing into Excel',
it just stores the data file on the clipboard.
Another way is to use RDCOM and Rexcel and drive this from Excel.  But 
that needs additional software installed.

Cheers
Petr
On 10 Apr 2005 at 19:56, Laura Holt wrote:
Hi R!
Is there a special function that writes data to an Excel file, please?
I found read.spss and so on in the foreign library, but nothing to
write.
Of course, writing to a regular data file and importing into Excel
works fine, but I thought that there might be another way.
Thanks in advance.
Sincerely,
Laura Holt
mailto: [EMAIL PROTECTED]
R Version 2.0.1 Windows
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--
Brian D. Ripley,  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595
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Re: [R] extracting correlations from nlme

Simon Blomberg [EMAIL PROTECTED] writes:

 I would like to know how (if) I can extract some of the information from
 the summary of my nlme.
 
 This is R. There is no if. Only how.

I think Simon Yoda Blomberg just entered the fortune package 

-- 
   O__   Peter Dalgaard Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics 2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark  Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907

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Re: [R] Building R packages under Windows.

I presume you got this error message:
Error: environment variable Tmpdir not set (or set to unusable value) 
and not default available.
   at ...\perl/R/Utils.pm line 67

The simplest thing to do is to create a folder named Temp in your C 
drive.

I hope it helps.
Best,
Dimitris

Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/16/336899
Fax: +32/16/337015
Web: http://www.med.kuleuven.ac.be/biostat/
http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm
- Original Message - 
From: Duncan Golicher [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Sent: Monday, April 11, 2005 8:58 AM
Subject: [R] Building R packages under Windows.


Hello,
My question is the following. Has anyone put together an idiots 
checklist of the steps needed to build a (small personal) package 
under Windows, or documented their own experiences of building 
packages under Windows?

I ask this as last week there were some very interesting comments 
regarding the advantages of putting personally written functions 
together as a package rather than sourcing them in at the start of a 
session using .Rprofile. They inspired me to try to build my own 
package for a few functions I use in teaching on my laptop running 
Windows XP . I read and reread Writing R extensions I  installed 
Pearl and tried build on a modified package.skeleton. I fairly 
quickly worked out I needed to do things like setting Tmpdir as an 
environment variable, but then I got stuck and frustrated and gave 
up. I'm sure that with more time I would get things working, but I 
don't have more time. Could the process be made smoother through 
better documentation? This may sound like laziness, but I do guess 
that there are others are in the same position who find that the 
initiial hassles of building a package (under Windows) leads to a 
negative cost benefit balance over less elegant  solutions.

Thanks,
Duncan Golicher
--
Dr Duncan Golicher
Ecologia y Sistematica Terrestre
Conservación de la Biodiversidad
El Colegio de la Frontera Sur
San Cristobal de Las Casas, Chiapas, Mexico
Tel. 967 1883 ext 1310
Celular 044 9671041021
[EMAIL PROTECTED]
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[R] gcmrec -- new package for recurrent events

2005-04-11 Thread Gonzalez Ruiz, Juan Ramon


 Dear R-Users,
 
 We would like to announce a new package called gcmrec. This package fits 
 the parameters for the general semiparametric model for recurrent events 
 proposed by Peña and Hollander (2004). This class of models  incorporates an 
 effective age function which encodes the changes that occur after each event 
 occurrence such as the impact of an intervention, it allows for the modeling 
 of the impact of accumulating  event occurrences on the unit, it admits a 
 link function in which the effect of possibly  time-dependent covariates are 
 incorporated, and it allows the incorporation of unobservable  frailty 
 components which induce dependencies among the inter-event times for each 
 unit. 
 
 Future versions will include functions for estimating this model using 
 Penalized approach. 
 
 Regards,
 
 Juan R Gonzalez
 Cancer Prevention and Control Unit
 Catalan Institute of Oncology, Barcelona (Spain)
 
 

[[alternative HTML version deleted]]

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Re: [R] R_LIBS difficulty ?

On Sun, 10 Apr 2005, François Pinard wrote:
Hi, R people.
I'm shy reporting this, as a bug in this area sounds very unlikely.  Did
I make my tests wrongly?  I'm still flaky at all this.  Let me dare
nevertheless, who knows, just in case...  Please don't kill me! :-)
Not so long ago, I wrote to this list:
(For now, [the library code] works only for me when I do _not_ use `-l
MY/OWN/LIBDIR' at `R CMD INSTALL' time, I surely made a simple blunder
somewhere.  Hopefully, I'll figure it out.)
Now using this line within `~/.Renviron':
  R_LIBS=/home/pinard/etc/R
my tiny package is correctly found by R.  However, R does not seem to
see any library within that directory if I rather use either of:
  R_LIBS=$HOME/etc/R
  R_LIBS=$HOME/etc/R
Correct, and as documented.
See the description in ?Startup, which says things like ${foo-bar} are 
allowed but not $HOME, and not ${HOME}/bah or even ${HOME}.

But R_LIBS=~/etc/R will work in .Renviron since ~ is intepreted by R in 
paths.

The last writing (I mean, something similar) is suggested somewhere in
the R manuals (but I do not have the manual with me right now to give
the exact reference, I'm in another town).
It is not mentioned in an R manual, but it is mentioned in the FAQ.
R_LIBS=$HOME/etc/R will work in a shell (and R_LIBS=~/etc/R may not).
Another hint that it could be expected to work is that the same
`~/.Renviron' once contained the line:
  R_BROWSER=$HOME/bin/links
which apparently worked as expected.  (This `links' script launches the
real program with `-g' appended whenever `DISPLAY' is defined.)
Yes, but that was not interpreted by R, rather a shell script called by R.
--
Brian D. Ripley,  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595__
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Re: [R] multi-class modeling

All of this is addressed in the reference for multinom(): it is support 
software for a book.

(You are likely to get a more sympathetic response if you use a real name 
and a signature giving your true affiliation.)

On Sun, 10 Apr 2005, 'array chip' wrote:
Just wonder if someone could comment on using linear
discriminant analysis (LDA) vs. multinomial logistic
regression in multi-class classification/prediction
(nomial dependent variable, not ordinal)? What kind of
difference in results can I expect from the 2 methods,
which is better or more appropriate, or under what
condiditon should I used one instead of the other? And
is there other methods I can try?

On another note, if I want to use logistic regression
using multinom() in package nnet, how can I address
the problem that each class of the dependent variable
has an unequal prevalence? In lda(), I can do this by
using prior argument, but there is no similar argument
in multinom().
Depends what you think the `problem' is.  In lda(), you usually do not
adjust by the 'prior' argument.  Is the problem that your training set is 
a biased sample?  If so, see my PRNN book.

--
Brian D. Ripley,  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595
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Re: [R] R_LIBS difficulty ?

Prof Brian Ripley [EMAIL PROTECTED] writes:

 See the description in ?Startup, which says things like ${foo-bar} are
 allowed but not $HOME, and not ${HOME}/bah or even ${HOME}.

Argh, Brian is right (again!) and I was extrapolating beyond what
actually works.

-- 
   O__   Peter Dalgaard Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics 2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark  Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907

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Re: [R] Building R packages under Windows.

2005-04-11 Thread Uwe Ligges

Duncan Golicher wrote:
Hello,
My question is the following. Has anyone put together an idiots 
checklist of the steps needed to build a (small personal) package under 
Windows, or documented their own experiences of building packages under 
Windows?

I ask this as last week there were some very interesting comments 
regarding the advantages of putting personally written functions 
together as a package rather than sourcing them in at the start of a 
session using .Rprofile. They inspired me to try to build my own package 
for a few functions I use in teaching on my laptop running Windows XP . 
I read and reread Writing R extensions I  installed Pearl and tried 
build on a modified package.skeleton. I fairly quickly worked out I 
needed to do things like setting Tmpdir as an environment variable, but 
then I got stuck and frustrated and gave up. I'm sure that with more 
time I would get things working, but I don't have more time. Could the 
process be made smoother through better documentation? This may sound 
like laziness, but I do guess that there are others are in the same 
position who find that the initiial hassles of building a package (under 
Windows) leads to a negative cost benefit balance over less elegant  
solutions.
The docs are already very condensed for this topic and you need to read 
each line (sometimes each word!). Do you want more text to read through 
that contains the same information?

Telling us what your problem is would be much better. I do not know what 
is missing in the docs - it's just working for me.

Uwe Ligges

Thanks,
Duncan Golicher
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Re: [R] Building R packages under Windows.

2005-04-11 Thread Duncan Murdoch

Duncan Golicher wrote:
Hello,
My question is the following. Has anyone put together an idiots 
checklist of the steps needed to build a (small personal) package 
under Windows, or documented their own experiences of building 
packages under Windows?

I ask this as last week there were some very interesting comments 
regarding the advantages of putting personally written functions 
together as a package rather than sourcing them in at the start of a 
session using .Rprofile. They inspired me to try to build my own 
package for a few functions I use in teaching on my laptop running 
Windows XP . I read and reread Writing R extensions I  installed 
Pearl and tried build on a modified package.skeleton. I fairly quickly 
worked out I needed to do things like setting Tmpdir as an environment 
variable, but then I got stuck and frustrated and gave up. I'm sure 
that with more time I would get things working, but I don't have more 
time. Could the process be made smoother through better documentation? 
This may sound like laziness, but I do guess that there are others are 
in the same position who find that the initiial hassles of building a 
package (under Windows) leads to a negative cost benefit balance over 
less elegant  solutions. 

In versions up to 2.0.1, the description is a little spread out, but the 
main file you want to look at is readme.packages.  I have tried to collect
all the information into one place in the 2.1.0 release (and put it in 
the R Admin manual).  As far as I recall there are no important 
differences between the instructions, so if you download the beta 
version of that manual and try those instructions, I would be very happy 
to hear from you about anything that is unclear or incorrect.  You can 
get the Windows beta build from 
http://cran.r-project.org/bin/windows/base/rdevel.html.  I do not 
think the beta manuals are online anywhere separate from the full release.

Duncan Murdoch
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Re: [R] Building R packages under Windows.

2005-04-11 Thread Uwe Ligges

Duncan Murdoch wrote:
Duncan Golicher wrote:
Hello,
My question is the following. Has anyone put together an idiots 
checklist of the steps needed to build a (small personal) package 
under Windows, or documented their own experiences of building 
packages under Windows?

I ask this as last week there were some very interesting comments 
regarding the advantages of putting personally written functions 
together as a package rather than sourcing them in at the start of a 
session using .Rprofile. They inspired me to try to build my own 
package for a few functions I use in teaching on my laptop running 
Windows XP . I read and reread Writing R extensions I  installed 
Pearl and tried build on a modified package.skeleton. I fairly quickly 
worked out I needed to do things like setting Tmpdir as an environment 
variable, but then I got stuck and frustrated and gave up. I'm sure 
that with more time I would get things working, but I don't have more 
time. Could the process be made smoother through better documentation? 
This may sound like laziness, but I do guess that there are others are 
in the same position who find that the initiial hassles of building a 
package (under Windows) leads to a negative cost benefit balance over 
less elegant  solutions. 

In versions up to 2.0.1, the description is a little spread out, but the 
main file you want to look at is readme.packages.  I have tried to collect
all the information into one place in the 2.1.0 release (and put it in 
the R Admin manual).  As far as I recall there are no important 
differences between the instructions, so if you download the beta 
version of that manual and try those instructions, I would be very happy 
to hear from you about anything that is unclear or incorrect.  You can 
get the Windows beta build from 
http://cran.r-project.org/bin/windows/base/rdevel.html.  I do not 
think the beta manuals are online anywhere separate from the full release.
They are available from
http://stat.ethz.ch/R-manual/R-devel/doc/manual/R-admin.html
Uwe

Duncan Murdoch
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RE: [R] How to search an element in matrix ?

Actually, you will need to use arr.ind=TRUE which is not the default
option. You will get the results in form [i, j] indicating the i^{th}
row and j^{th} column of the element that passes the criteria.

 m - matrix( rnorm(6), nc=3 )
 m
   [,1] [,2]   [,3]
[1,]  0.5066194 0.786876 -1.2848658
[2,] -0.2018563 2.007892  0.4581891

which( m  0.5, arr.ind=T )
 row col
[1,]   1   1
[2,]   1   2
[3,]   2   2

Regards, Adai


On Sun, 2005-04-10 at 21:51 -0700, Vadim Ogranovich wrote:
 A matrix is a vector as well (it is stored by columns), so it has two
 ways of indexing [i,j] and [i]. It may be easier for you to use the
 latter, thus
 which(x == 1) returns all indexes where the matrix x is equal to 1.
 
  -Original Message-
  From: [EMAIL PROTECTED] 
  [mailto:[EMAIL PROTECTED] On Behalf Of tong wang
  Sent: Sunday, April 10, 2005 9:37 PM
  To: r-help@stat.math.ethz.ch
  Subject: [R] How to search an element in matrix ?
  
  Hi you guys,
   I know this might be too simple a question to post, but 
  i searched a lot still couldn't find it.
  Just want to find an element in matrix and return its 
  index , i think there should be some matrix version of 
  match which only works for vector to me.
   thanks in advance for your help.
  
  best,
  tong
  
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Re: [R] Princomp$Scores

2005-04-11 Thread miguel manese

The scores can be manually computed as 

center(your.matrix,scale=F) %*% eigen(cov(your.matrix))$vector  # or cor()

i.e. a linear combination of your mean-corrected data. negative
coefficients does not imply anything, because computation of the signs
of eigenvectors is arbitrary. Absolute value of
princomp(your.matrix)$load indicates which variable influences a
principal component most (this is closer to the correlate thing you
are thinking of, I guess).

On Apr 9, 2005 1:09 AM, Ken Termiso [EMAIL PROTECTED] wrote:
 Hi all,
 
 I was hoping that someone could verify this for me-
 
 when I run princomp() on a matrix, it is my understanding that the scores
 slot of the output is a measure of how well each row correlates (for lack of
 a better word) with each principal component.
 
 i.e. say I have a 300x6 log2 scaled matrix, and I run princomp(). I would
 get back a $scores slot that is also 300x6, where each value can be negative
 or positive. I'd assume that the negative values correspond to rows that are
 negatively correlated with that particular PC, and vice-versa for positives.
 
 Thanks in advance for the help,
 Ken
 
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[R] How to change letters after space into capital letters

2005-04-11 Thread Wolfram Fischer

What is the easiest way to change within vector of strings
each letter after a space into a capital letter?

E.g.:
  c( this is an element of the vector of strings, second element )
becomes:
  c( This Is An Element Of The Vector Of Strings, Second Element )

My reason to try to do this is to get more readable abbreviations.
(A suggestion would be to add an option to abbreviate() which changes
letters after space to uppercase letters before executing the abbreviation
algorithm.)

Thanks - Wolfram

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[R] dealing with multicollinearity

2005-04-11 Thread Manuel Gutierrez


I have a linear model y~x1+x2 of some data where the
coefficient for
x1 is higher than I would have expected from theory
(0.7 vs 0.88)
I wondered whether this would be an artifact due to x1
and x2 being correlated despite that the variance
inflation factor is not too high (1.065):
I used perturbation analysis to evaluate collinearity
library(perturb)
P-perturb(A,pvars=c(x1,x2),prange=c(1,1))
 summary(P)
Perturb variables:
x1   normal(0,1) 
x2   normal(0,1) 

Impact of perturbations on coefficients:
mean s.d. min  max 
(Intercept)  -26.0670.270  -27.235  -25.481
x1 0.7260.0250.6720.882
x2 0.0600.0110.0370.082

I get a mean for x1 of 0.726 which is closer to what
is expected.
I am not an statistical expert so I'd like to know if
my evaluation of the effects of collinearity is
correct and in that case any solutions to obtain a
reliable linear model.
Thanks,
Manuel

Some more detailed information:

 A-lm(y~x1+x2)
 summary(A)

Call:
lm(formula = y ~ x1 + x2)

Residuals:
  Min1QMedian3Q   Max 
-4.221946 -0.484055 -0.004762  0.397508  2.542769 

Coefficients:
 Estimate Std. Error t value Pr(|t|)
(Intercept) -27.234720.27996 -97.282   2e-16 ***
x10.882020.02475  35.639   2e-16 ***
x20.081800.01239   6.604 2.53e-10 ***
---
Signif. codes:  0 `***' 0.001 `**' 0.01 `*' 0.05 `.'
0.1 ` ' 1 

Residual standard error: 0.823 on 241 degrees of
freedom
Multiple R-Squared: 0.8411, Adjusted R-squared: 0.8398

F-statistic: 637.8 on 2 and 241 DF,  p-value: 
2.2e-16 

 cor.test(x1,x2)

Pearson's product-moment correlation

data:  x1 and x2 
t = -3.9924, df = 242, p-value = 8.678e-05
alternative hypothesis: true correlation is not equal
to 0 
95 percent confidence interval:
 -0.3628424 -0.1269618 
sample estimates:
  cor 
-0.248584

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[R] About importing CSV file

2005-04-11 Thread Silvia Bachetti

I have a problem for reading a data from excel (.csv) to R, because the 
numeric variables ( float) are separeted by comma (,) and not by point (.). 
And all the variables are separated by comma (,). The string variables are 
between (). So importing to R the numeric variable (float) are reading as 
integer, and not with decimal part.
Is there a way to solve this problem?

The data set is like this:
CODE,A1,A2,A3,A4,A5,A6,A7,A8,A9,A10,A11,A12,NOTE1,A13,A14,A15,NOTE2,A16,A17,A18,A19,A20,A21,NOTE3,A22,A23,A24,A25,A26,A27,A28,NOTE4,CONCLUSION 

991,1,14,17,TM 
LUNG,19,CARCINOMA,17,,,14,14,14,15,57,2,17,17,17,3,8,14,14,14,17,13,4,4,14,17,14,14,14,17,15,15,24 

992,1,17,17,BPCO,17,TM 
LUNG,17,,,17,17,17,17,2,17,17,17,3,17,17,17,17,17,17,4,17,17,17,14,17,17,16,5,16,88 

993,1,17,17,TM 
LUNG,17,BPCO,17,,,17,17,17,17,2,17,17,17,3,14,17,17,17,17,16,4,4,17,17,17,17,14,17,16,5,16,73 

994,1,14,14,NN,17,NN,17,NN,17,14,17,17,15,88,2,14,14,14,3,14,17,14,17,14,15,2,4,14,8,17,14,14,14,13,5,14,64 

I use this command in R: read.csv(file=prova.csv , header=TRUE , sep=, 
, dec=, , fill=TRUE).
But for example in the first record with code 991: the last part is 
recorded in three integer variable 15 - 15 - 24 and not in two float 
variable as 15 - 15.24
In the second record with code 992: the last part is recorded in four 
integer variable 16 - 5 - 16 - 88 and not in two float variable as 16.5 - 16.88
In the third record with code 993: the middle part is recorded in two 
integer variable 16 - 4 and not in one float variable as 16.4. And the last 
part is recorded in four integer variable 16 - 5 - 16 - 73 and not in two 
float variable as 16.5 - 16.73
And so on.

I there a solution?
Thanks.
Silvia
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[R] R: function code

2005-04-11 Thread Clark Allan

HI

sorry to be a nuisance to all!!!

how can i see the code of a particular function?

e.g. nnet just as an example__
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Re: [R] About importing CSV file

So you expect R to do the following :

 convert  15,15,24to  15.00, 15.24  AND
 convert  16,5,16,88  to  16.50, 16.88

The second conversion should be fairly easy BUT how do you expect R to
know that the first conversion should produce 15.00, 15.24 and not
15.15, 24.00 ?

Without knowing which is which, it would be dangerous and hard to write
any sort of automated script for this.

The best thing would be for you to go back and change your inputs
manually. You can either use 15,,15,24 for consistency or better yet
simply use 15.0, 15.24.

Regards, Adai



On Mon, 2005-04-11 at 12:23 +0200, Silvia Bachetti wrote:
 I have a problem for reading a data from excel (.csv) to R, because the 
 numeric variables ( float) are separeted by comma (,) and not by point (.). 
 And all the variables are separated by comma (,). The string variables are 
 between (). So importing to R the numeric variable (float) are reading as 
 integer, and not with decimal part.
 Is there a way to solve this problem?
 
 The data set is like this:
 
 CODE,A1,A2,A3,A4,A5,A6,A7,A8,A9,A10,A11,A12,NOTE1,A13,A14,A15,NOTE2,A16,A17,A18,A19,A20,A21,NOTE3,A22,A23,A24,A25,A26,A27,A28,NOTE4,CONCLUSION
  
 
 991,1,14,17,TM 
 LUNG,19,CARCINOMA,17,,,14,14,14,15,57,2,17,17,17,3,8,14,14,14,17,13,4,4,14,17,14,14,14,17,15,15,24
  
 
 992,1,17,17,BPCO,17,TM 
 LUNG,17,,,17,17,17,17,2,17,17,17,3,17,17,17,17,17,17,4,17,17,17,14,17,17,16,5,16,88
  
 
 993,1,17,17,TM 
 LUNG,17,BPCO,17,,,17,17,17,17,2,17,17,17,3,14,17,17,17,17,16,4,4,17,17,17,17,14,17,16,5,16,73
  
 
 994,1,14,14,NN,17,NN,17,NN,17,14,17,17,15,88,2,14,14,14,3,14,17,14,17,14,15,2,4,14,8,17,14,14,14,13,5,14,64
  
 
 
 I use this command in R: read.csv(file=prova.csv , header=TRUE , sep=, 
 , dec=, , fill=TRUE).
 But for example in the first record with code 991: the last part is 
 recorded in three integer variable 15 - 15 - 24 and not in two float 
 variable as 15 - 15.24
 In the second record with code 992: the last part is recorded in four 
 integer variable 16 - 5 - 16 - 88 and not in two float variable as 16.5 - 
 16.88
 In the third record with code 993: the middle part is recorded in two 
 integer variable 16 - 4 and not in one float variable as 16.4. And the last 
 part is recorded in four integer variable 16 - 5 - 16 - 73 and not in two 
 float variable as 16.5 - 16.73
 And so on.
 
 I there a solution?
 
 Thanks.
 
 Silvia
 
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[R] DSE package: estVARXls Method

2005-04-11 Thread Reckers, Thomas

I am trying to use the estVARXls in the DSE1 Package method to run a VAR.
However i keep on receiving the following message Error in
periodsOutput(data) : no applicable method for periodsOutput  . Can
anyone help with me this? I am sorry if this question sounds really stupid
but i havent got a lot of experience with R.

Thank you very much
Thomas



The information contained herein is confidential and is inte...{{dropped}}

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Re: [R] R: function code

2005-04-11 Thread Uwe Ligges

Clark Allan wrote:
HI
sorry to be a nuisance to all!!!
how can i see the code of a particular function?
e.g. nnet just as an example
Most easily by downloading the package sources and looking in the R 
directory.

Or in the console:
 library(nnet)
 nnet
 methods(nnet)
 nnet.formula
 nnet.default
 nnet:::predict.nnet
and so on ...
Uwe Ligges


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Re: [R] R: function code

# In your specific case :

 library(nnet)
 methods(nnet)
[1] nnet.default nnet.formula

 nnet.default

 function (x, y, weights, size, Wts, mask = rep(TRUE, length(wts)),
 linout = FALSE, entropy = FALSE, softmax = FALSE, censored = FALSE,
 skip = FALSE, rang = 0.7, decay = 0, maxit = 100, Hess = FALSE,
 trace = TRUE, MaxNWts = 1000, abstol = 1e-04, reltol = 1e-08,
 ...)
 {
SNIP


# More generally 

1) Download http://www.cran.r-project.org/src/contrib/VR_7.2-12.tar.gz
(nnet is part of VR bundle)
2) Uncompress it
3) All the R codes should be VR/nnet/R directory and C codes in
VR/nnet/src directory


Regards, Adai



On Mon, 2005-04-11 at 12:52 +0200, Clark Allan wrote:
 HI
 
 sorry to be a nuisance to all!!!
 
 how can i see the code of a particular function?
 
 e.g. nnet just as an example

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Re: [R] R: function code

2005-04-11 Thread Federico Calboli

On Mon, 2005-04-11 at 12:52 +0200, Clark Allan wrote:
 HI
 
 sorry to be a nuisance to all!!!
 
 how can i see the code of a particular function?
 
 e.g. nnet just as an example

for some function just type the function name  and you get the code:

 ls
function (name, pos = -1, envir = as.environment(pos), all.names =
FALSE,
pattern)
{
if (!missing(name)) {
nameValue - try(name)
if (identical(class(nameValue), try-error)) {
name - substitute(name)
if (!is.character(name))
name - deparse(name)
pos - name
}
else pos - nameValue
}
all.names - .Internal(ls(envir, all.names))
if (!missing(pattern)) {
if ((ll - length(grep([, pattern, fixed = TRUE))) 
0  ll != length(grep(], pattern, fixed = TRUE))) {
if (pattern == [) {
pattern - \\[
warning(paste(replaced regular expression pattern,
  sQuote([), by, sQuote([)))
}
else if (length(grep([^]\\[-, pattern)  0)) {
pattern - sub(\\[-, \\[-, pattern)
warning(paste(replaced, sQuote([-), by,
  sQuote([-), in regular expression pattern))
}
}
grep(pattern, all.names, value = TRUE)
}
else all.names
}
environment: namespace:base


or check out the source code itself.


HTH

F
-- 
Federico C. F. Calboli
Department of Epidemiology and Public Health
Imperial College, St Mary's Campus
Norfolk Place, London W2 1PG

Tel  +44 (0)20 7594 1602 Fax (+44) 020 7594 3193

f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com

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Re: [R] How to change letters after space into capital letters

2005-04-11 Thread Renaud Lancelot

Wolfram Fischer a écrit :
What is the easiest way to change within vector of strings
each letter after a space into a capital letter?
E.g.:
  c( this is an element of the vector of strings, second element )
becomes:
  c( This Is An Element Of The Vector Of Strings, Second Element )
My reason to try to do this is to get more readable abbreviations.
(A suggestion would be to add an option to abbreviate() which changes
letters after space to uppercase letters before executing the abbreviation
algorithm.)
Thanks - Wolfram
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cap.leading - function (string) {
  fn - function(x) {
  v - unlist(strsplit(x, split =  ))
  u - sapply(v, function(x) {
  x - tolower(x)
  substring(x, 1, 1) - toupper(substring(x, 1, 1))
  x
  })
paste(u, collapse =  )
}
  unname(sapply(string, fn))
  }
 cap.leading(c( this is an element of the vector of strings, second 
element ))
[1] This Is An Element Of The Vector Of Strings Second Element

Best,
Renaud
--
Dr Renaud Lancelot, vétérinaire
C/0 Ambassade de France - SCAC
BP 834 Antananarivo 101 - Madagascar
e-mail: [EMAIL PROTECTED]
tel.:   +261 32 40 165 53 (cell)
+261 20 22 665 36 ext. 225 (work)
+261 20 22 494 37 (home)
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Re: [R] R: function code

check these:
library(nnet)
methods(nnet)
nnet.default
nnet.formula
print.nnet
nnet:::print.nnet
I hope it helps.
Best,
Dimitris

Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/16/336899
Fax: +32/16/337015
Web: http://www.med.kuleuven.ac.be/biostat/
http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm
- Original Message - 
From: Clark Allan [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Sent: Monday, April 11, 2005 12:52 PM
Subject: [R] R: function code


HI
sorry to be a nuisance to all!!!
how can i see the code of a particular function?
e.g. nnet just as an example



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Re: [R] How to change letters after space into capital letters

2005-04-11 Thread Barry Rowlingson

Wolfram Fischer wrote:
What is the easiest way to change within vector of strings
each letter after a space into a capital letter?
This perl code seems to work:
#!/usr/bin/perl
$s1=this is a lower-cased string;
$s1=~s/ ([a-z])/ \u\1/g;
print $s1.\n;
 producing:
this Is A Lower-cased String
 but sticking it in a gsub in R doesn't work, even with perl=TRUE:
 s1
[1] this is a lowercased string
 gsub( ([a-z]), \\u\\1,s1,perl=TRUE)
[1] this uis ua ulowercased ustrin
 But ?gsub does warn you that perl REs may vary depending on the phase 
of the moon and the PCRE lib on your system.

 I've just noticed the missing 'g' on the end. Anyone know where that 
went?

 Its looking like a bug in the regex processing:
 gsub( ([a-z]),  \\1,s1,perl=TRUE)
[1] this  is  a  lowercased  strin
 gsub( ([a-z]), \\1,s1,perl=TRUE)
[1] this is a lowercased st
 Anyway, back on topic:
My reason to try to do this is to get more readable abbreviations.
(A suggestion would be to add an option to abbreviate() which changes
letters after space to uppercase letters before executing the abbreviation
algorithm.)
 I think this is what's known as 'Camel Case', because the pattern of 
upper and lower case looks like humps:

http://en.wikipedia.org/wiki/Camel_case
Baz
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[R] Sweave and abbreviating output from R

2005-04-11 Thread Gavin Simpson

Dear List,
I'm using Sweave to produce a series of class handouts for a course I am 
running. The students in previous years have commented about wanting 
output within the handouts so they can see what to expect the output to 
look like. So Sweave is a godsend for producing this type of handout - 
with one exception: Is there a way to suppress some rows of printed 
output so as to save space in the printed documentation? E.g

rnorm(100)
produces about 20 lines of output (depending on options(width)). I'd 
prefer something like:

rnorm(100)
  [1]  0.527739021  0.185551107 -1.239195562  0.020991608 -1.225632520
  [6] -1.000243373 -0.020180393  2.552180776 -1.719061533 -0.195024625
...
  [96] -0.744916379  0.863733400 -0.186667848  1.378236663 -0.499201046
The actual application would be printing of output from summary() 
methods. Ideally it would be nice to ask for line 1-10, 30-40, 100-102, 
for example, so you could print the first few lines of several sections 
of output. I'd like to automate this so I don't need to keep copying and 
pasting into the final tex source or forget to do it if I alter some 
previous part of the Sweave source.

Has anyone tried to do this? Does anyone know of an automatic way of 
achieving the simple abbreviation or the more complicated version I 
described?

Any thoughts on this?
Thanks in advance,
Gav
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Gavin Simpson [T] +44 (0)20 7679 5522
ENSIS Research Fellow [F] +44 (0)20 7679 7565
ENSIS Ltd.  ECRC [E] gavin.simpsonATNOSPAMucl.ac.uk
UCL Department of Geography   [W] http://www.ucl.ac.uk/~ucfagls/cv/
26 Bedford Way[W] http://www.ucl.ac.uk/~ucfagls/
London.  WC1H 0AP.
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
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Re: [R] How to change letters after space into capital letters

On Apr 11, 2005 6:22 AM, Wolfram Fischer [EMAIL PROTECTED] wrote:
 What is the easiest way to change within vector of strings
 each letter after a space into a capital letter?
 
 E.g.:
  c( this is an element of the vector of strings, second element )
 becomes:
  c( This Is An Element Of The Vector Of Strings, Second Element )
 
 My reason to try to do this is to get more readable abbreviations.
 (A suggestion would be to add an option to abbreviate() which changes
 letters after space to uppercase letters before executing the abbreviation
 algorithm.)
 

Look for the thread titled

  String manipulation---mixed case

in the r-help archives.

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Re: [R] Sweave and abbreviating output from R

On Apr 11, 2005 7:22 AM, Gavin Simpson [EMAIL PROTECTED] wrote:
 Dear List,
 
 I'm using Sweave to produce a series of class handouts for a course I am
 running. The students in previous years have commented about wanting
 output within the handouts so they can see what to expect the output to
 look like. So Sweave is a godsend for producing this type of handout -
 with one exception: Is there a way to suppress some rows of printed
 output so as to save space in the printed documentation? E.g
 
 rnorm(100)
 
 produces about 20 lines of output (depending on options(width)). I'd
 prefer something like:
 
 rnorm(100)
   [1]  0.527739021  0.185551107 -1.239195562  0.020991608 -1.225632520
   [6] -1.000243373 -0.020180393  2.552180776 -1.719061533 -0.195024625
 ...
   [96] -0.744916379  0.863733400 -0.186667848  1.378236663 -0.499201046
 
 The actual application would be printing of output from summary()
 methods. Ideally it would be nice to ask for line 1-10, 30-40, 100-102,
 for example, so you could print the first few lines of several sections
 of output. I'd like to automate this so I don't need to keep copying and
 pasting into the final tex source or forget to do it if I alter some
 previous part of the Sweave source.
 
 Has anyone tried to do this? Does anyone know of an automatic way of
 achieving the simple abbreviation or the more complicated version I
 described?
 
 Any thoughts on this?
 

Maybe you could use head(rnorm(100)) instead.  Check ?head
for other arguments.

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[R] ??

2005-04-11 Thread Sec.FACEA

R people,
I'd like to know how can I make inequations with are, specially work 
with lineal programming.
Thanks for your unvaluable help
Adrián
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Re: [R] Sweave and abbreviating output from R

2005-04-11 Thread Roger Bivand

On Mon, 11 Apr 2005, Gavin Simpson wrote:

 Dear List,
 
 I'm using Sweave to produce a series of class handouts for a course I am 
 running. The students in previous years have commented about wanting 
 output within the handouts so they can see what to expect the output to 
 look like. So Sweave is a godsend for producing this type of handout - 
 with one exception: Is there a way to suppress some rows of printed 
 output so as to save space in the printed documentation? E.g
 
 rnorm(100)
 
 produces about 20 lines of output (depending on options(width)). I'd 
 prefer something like:
 
 rnorm(100)
[1]  0.527739021  0.185551107 -1.239195562  0.020991608 -1.225632520
[6] -1.000243373 -0.020180393  2.552180776 -1.719061533 -0.195024625
 ...
[96] -0.744916379  0.863733400 -0.186667848  1.378236663 -0.499201046
 
 The actual application would be printing of output from summary() 
 methods. Ideally it would be nice to ask for line 1-10, 30-40, 100-102, 
 for example, so you could print the first few lines of several sections 
 of output. I'd like to automate this so I don't need to keep copying and 
 pasting into the final tex source or forget to do it if I alter some 
 previous part of the Sweave source.
 
 Has anyone tried to do this? Does anyone know of an automatic way of 
 achieving the simple abbreviation or the more complicated version I 
 described?

Semi-automatic is:

 res - capture.output(rnorm(100))
 cat(res[1:2], ..., res[length(res)], sep=\n)

but I've found that 1) it needs masking from the users, and 2) it is 
difficult to automate when the numbers of output lines generated by print 
methods vary with input data (like in print.htest()). But capture.output 
is very useful.

Roger

 
 Any thoughts on this?
 
 Thanks in advance,
 
 Gav
 

-- 
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: [EMAIL PROTECTED]

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Re: [R] About importing CSV file

Adaikalavan Ramasamy [EMAIL PROTECTED] writes:

So you expect R to do the following :

convert 15,15,24to 15.00, 15.24 AND
convert 16,5,16,88 to 16.50, 16.88

The second conversion should be fairly easy BUT how do you expect R to
know that the first conversion should produce 15.00, 15.24 and not
15.15, 24.00 ?

Without knowing which is which, it would be dangerous and hard to write
any sort of automated script for this.

The best thing would be for you to go back and change your inputs
manually. You can either use 15,,15,24 for consistency or better yet
simply use 15.0, 15.24.

Regards, Adai

Also, if Excel is really generating this format, something is
seriously wrong with Excel or your locale settings. Normally, locales
with comma as decimal point also use semicolon as the field separator
in CSV files, which is the format that read.csv2() handles. Or, just
export as text (TAB delimited) and use read.delim2().

On Mon, 2005-04-11 at 12:23 +0200, Silvia Bachetti wrote:
I have a problem for reading a data from excel (.csv) to R, because the
numeric variables ( float) are separeted by comma (,) and not by point (.).
And all the variables are separated by comma (,). The string variables are
between (). So importing to R the numeric variable (float) are reading as
integer, and not with decimal part.
Is there a way to solve this problem?

The data set is like this:

CODE,A1,A2,A3,A4,A5,A6,A7,A8,A9,A10,A11,A12,NOTE1,A13,A14,A15,NOTE2,A16,A17,A18,A19,A20,A21,NOTE3,A22,A23,A24,A25,A26,A27,A28,NOTE4,CONCLUSION

991,1,14,17,TM
LUNG,19,CARCINOMA,17,,,14,14,14,15,57,2,17,17,17,3,8,14,14,14,17,13,4,4,14,17,14,14,14,17,15,15,24

992,1,17,17,BPCO,17,TM
LUNG,17,,,17,17,17,17,2,17,17,17,3,17,17,17,17,17,17,4,17,17,17,14,17,17,16,5,16,88

993,1,17,17,TM
LUNG,17,BPCO,17,,,17,17,17,17,2,17,17,17,3,14,17,17,17,17,16,4,4,17,17,17,17,14,17,16,5,16,73

994,1,14,14,NN,17,NN,17,NN,17,14,17,17,15,88,2,14,14,14,3,14,17,14,17,14,15,2,4,14,8,17,14,14,14,13,5,14,64

I use this command in R: read.csv(file=prova.csv , header=TRUE , sep=,
, dec=, , fill=TRUE).
But for example in the first record with code 991: the last part is
recorded in three integer variable 15 - 15 - 24 and not in two float
variable as 15 - 15.24
In the second record with code 992: the last part is recorded in four
integer variable 16 - 5 - 16 - 88 and not in two float variable as 16.5 -
16.88
In the third record with code 993: the middle part is recorded in two
integer variable 16 - 4 and not in one float variable as 16.4. And the last
part is recorded in four integer variable 16 - 5 - 16 - 73 and not in two
float variable as 16.5 - 16.73
And so on.

I there a solution?

Thanks.

Silvia

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--
O__ Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907

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Re: [R] Sweave and abbreviating output from R

2005-04-11 Thread Gavin Simpson

Gabor Grothendieck wrote:
On Apr 11, 2005 7:22 AM, Gavin Simpson [EMAIL PROTECTED] wrote:
Dear List,
I'm using Sweave to produce a series of class handouts for a course I am
running. The students in previous years have commented about wanting
output within the handouts so they can see what to expect the output to
look like. So Sweave is a godsend for producing this type of handout -
with one exception: Is there a way to suppress some rows of printed
output so as to save space in the printed documentation? E.g
snip
Any thoughts on this?

Maybe you could use head(rnorm(100)) instead.  Check ?head
for other arguments.

Thanks for this Gabor. Head/tail works just fine for my rnorm example, 
but for printed output from summary methods for example it doesn't quite 
work as I would like.

But that got me thinking a bit more and I remembered capture.output() 
and I saw that noquote() is used in head.function(). So, I can now get 
this far:

noquote(capture.output(summary(pondsca)))[1:10]
 [1] 

 [2] Call: 

 [3] 

 [4] Partitioning of mean squared contingency coefficient: 

 [5] 

 [6] Total 4.996 

 [7] Unconstrained 4.996 

 [8] 

 [9] Eigenvalues, and their contribution to the mean squared 
contingency coefficient
[10] 

Now all I need is to find out how to print without the indices 
[1],[2]...[n] being printed?

Also, I noticed that with some objects, more than one line of output 
is printed per line - just like a vector would. In the example below we 
see 3 lines of output printed per row.

x - rnorm(100)
y - rnorm(100)
noquote(capture.output(summary(lm(x ~ y[1:5]
[1] Call:   lm(formula = x ~ y)
[4] Residuals:
Is there a way to print only a single element of a vector per line?
Thanks in advance.
Gav
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Gavin Simpson [T] +44 (0)20 7679 5522
ENSIS Research Fellow [F] +44 (0)20 7679 7565
ENSIS Ltd.  ECRC [E] gavin.simpsonATNOSPAMucl.ac.uk
UCL Department of Geography   [W] http://www.ucl.ac.uk/~ucfagls/cv/
26 Bedford Way[W] http://www.ucl.ac.uk/~ucfagls/
London.  WC1H 0AP.
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
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Re: [R] ??

2005-04-11 Thread TEMPL Matthias

Hello Adrián,

Look e.g. at
http://tolstoy.newcastle.edu.au/R/help/04/06/0869.html
and use e.g. http://finzi.psych.upenn.edu/search.html for searching help files, 
manuals and mailing list archives.

Best,
Matthias

 
 R people,
 I'd like to know how can I make inequations with are

What is are?

 , specially work 
 with lineal programming.

Linear programming, not lineal.

 Thanks for your unvaluable help
 Adrián


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[R] How to suppress the printing of warnings (Windows)?

2005-04-11 Thread Jacho-Chavez,DT (pgr)

Dear all,

I'm a newbie in R. I am running simulations using a fixed bandwidth in 
nonparametric regressions, sending all the output to a file myoutput.txt using 
sink(myoutput.txt),  R is printing all warnings by the end of the simulation 
on the file. I know the source of the problem  can take care of it. However, 
finding a 50 MB file (where all the output is printed, e.g. myoutput.txt) by 
the end of the simulation exercise is not quite pleasant. How could I turn them 
off completely?, so they are not printed in myoutput.txt file.

Thanks in advanced for your help.


David

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Re: [R] Building R packages under Windows.

On Apr 11, 2005 2:58 AM, Duncan Golicher [EMAIL PROTECTED] wrote:
 Hello,
 
 My question is the following. Has anyone put together an idiots
 checklist of the steps needed to build a (small personal) package under
 Windows, or documented their own experiences of building packages under
 Windows?
 
 I ask this as last week there were some very interesting comments
 regarding the advantages of putting personally written functions
 together as a package rather than sourcing them in at the start of a
 session using .Rprofile. They inspired me to try to build my own package
 for a few functions I use in teaching on my laptop running Windows XP .
 I read and reread Writing R extensions I  installed Pearl and tried
 build on a modified package.skeleton. I fairly quickly worked out I
 needed to do things like setting Tmpdir as an environment variable, but
 then I got stuck and frustrated and gave up. I'm sure that with more
 time I would get things working, but I don't have more time. Could the
 process be made smoother through better documentation? This may sound
 like laziness, but I do guess that there are others are in the same
 position who find that the initiial hassles of building a package (under
 Windows) leads to a negative cost benefit balance over less elegant
 solutions.
 
 Thanks,

Other resources are:
- http://www.murdoch-sutherland.com/Rtools/
- README.packages in \Program Files\R\rw2001 or whatever version of R
- posts by me, John Fox, Andy Liao in r-help or r-devel

I use Windows XP and it also took me quite a bit of time until I 
figured it out too.  I was really wondering as I got frustrated how
it was possible that 500+ packages got developed for R when it
was so hard to figure out how to create a package, particularly
if you want to put in a vignette.  One of the problems is that its
dependent on so many other pieces of software and also there can
be path problems that you have to figure out.  I suspect that the process
is somewhat smoother under UNIX and maybe most people use
that.  

Fortunately, it does all work once you get it figured out
and its worth it if you are going to do a lot of development since
it really helps organize you.   If you are just going to use it briefly
or casually its probably not worth the hassle.  Once you do figure
it out it does work although there are a few annoyances.
R CMD CHECK is really great although I wish there were some 
way of telling it to ignore the files referenced in .Rbuildignore so 
one does not have to do a build first.  Also the error messages
from the process are often less than helpful but I suspect it would
be difficult to improve since it can go wrong at a point which is
different than the source of the problem.

I think the fixable problems are:
- a guide is needed, as you mention
- the prerequisites need to be reduced:
  -- significant portions are written in perl which is probably a 
 holdover from the days when R was less powerful and now
 could all be ported to R
  -- it would be nice it the tools were not needed either.  
  -- reduced functionality with no Microsoft style help should be
 possible to optionally allow one to create packages without
 downloading the Microsoft help compiler
- the TEXINPUTS problems with MiKTeX needs to be solved
  by MiKTeX (they know about it and intend to solve it but I am
  not sure how quickly that will happen.  In the meantime there
  are workarounds at:
 http://www.murdoch-sutherland.com/Rtools/miktex.html
  The fourth alternative is the easiest.  I think this only affects
  you if you are building vignettes.)

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Re: [R] How to change letters after space into capital letters

On Mon, 11 Apr 2005, Barry Rowlingson wrote:
Wolfram Fischer wrote:
What is the easiest way to change within vector of strings
each letter after a space into a capital letter?
[Example omitted, that did somthing different!
  c( this is an element of the vector of strings, second element )
becomes:
  c( This Is An Element Of The Vector Of Strings, Second Element )
]
Similarly, Gabor G is referring to a thread which answers a _different_ 
question.

This perl code seems to work:
#!/usr/bin/perl
$s1=this is a lower-cased string;
$s1=~s/ ([a-z])/ \u\1/g;
print $s1.\n;
producing:
this Is A Lower-cased String
But that is not what his example does, which capitalized the first word 
too.  I think he intended s/\b([a-z])/\u\1/g;

gannet% echo this is a lower-cased string | perl -p -e 's/\b([a-z])/\u\1/g'
This Is A Lower-Cased String
but sticking it in a gsub in R doesn't work, even with perl=TRUE:
s1
[1] this is a lowercased string
gsub( ([a-z]), \\u\\1,s1,perl=TRUE)
[1] this uis ua ulowercased ustrin
But ?gsub does warn you that perl REs may vary depending on the phase of the 
moon and the PCRE lib on your system.
This is not actually to do with REs, but substitutions.  \u is not 
interpreted in substitutions (and only \1 to \9 are, as documented).

I've just noticed the missing 'g' on the end. Anyone know where that went?
Yes. Use R-2.1.0 beta which has many bugs in gsub fixed.
--
Brian D. Ripley,  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595
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Re: [R] Sweave and abbreviating output from R

2005-04-11 Thread Sean Davis

On Apr 11, 2005, at 8:12 AM, Gavin Simpson wrote:
Gabor Grothendieck wrote:
On Apr 11, 2005 7:22 AM, Gavin Simpson [EMAIL PROTECTED] 
wrote:
Dear List,
I'm using Sweave to produce a series of class handouts for a course 
I am
running. The students in previous years have commented about wanting
output within the handouts so they can see what to expect the output 
to
look like. So Sweave is a godsend for producing this type of handout 
-
with one exception: Is there a way to suppress some rows of printed
output so as to save space in the printed documentation? E.g
snip
Any thoughts on this?
Maybe you could use head(rnorm(100)) instead.  Check ?head
for other arguments.

Any thought you would want to locally modify the print methods for 
object of interest?  I haven't tried it, but it might allow you to 
treat large objects like matrices, long vectors, and data.frames 
differently than objects like model.fits, etc.

Sean
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Re: [R] How to suppress the printing of warnings (Windows)?

try,
options(warn=-1)
I hope it helps.
Best,
Dimitris

Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/16/336899
Fax: +32/16/337015
Web: http://www.med.kuleuven.ac.be/biostat/
http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm
- Original Message - 
From: Jacho-Chavez,DT (pgr) [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Sent: Monday, April 11, 2005 2:14 PM
Subject: [R] How to suppress the printing of warnings (Windows)?


Dear all,
I'm a newbie in R. I am running simulations using a fixed bandwidth 
in nonparametric regressions, sending all the output to a file 
myoutput.txt using sink(myoutput.txt),  R is printing all 
warnings by the end of the simulation on the file. I know the source 
of the problem  can take care of it. However, finding a 50 MB file 
(where all the output is printed, e.g. myoutput.txt) by the end of 
the simulation exercise is not quite pleasant. How could I turn them 
off completely?, so they are not printed in myoutput.txt file.

Thanks in advanced for your help.
David
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[R] Trying to undo an assignment

2005-04-11 Thread Uzuner, Tolga

Hi,

I defined corr to be a function, not realising that this was also the name for
correlation in package=boot.

How do I explicitly call the corr function within package boot (so, scope up
over the current frame, I guess is another way of saying it) without removing
my new corr function ? 

Thanks,
Tolga

Please follow the attached hyperlink to an important disclaimer
http://www.csfb.com/legal_terms/disclaimer_europe.shtml



==
This message is for the sole use of the intended recipient. ...{{dropped}}

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RE: [R] How to suppress the printing of warnings (Windows)?

2005-04-11 Thread abunn


 I'm a newbie in R. I am running simulations using a fixed 
 bandwidth in nonparametric regressions, sending all the output to 
 a file myoutput.txt using sink(myoutput.txt),  R is printing 
 all warnings by the end of the simulation on the file. I know the 
 source of the problem  can take care of it. However, finding a 
 50 MB file (where all the output is printed, e.g. myoutput.txt) 
 by the end of the simulation exercise is not quite pleasant. How 
 could I turn them off completely?, so they are not printed in 
 myoutput.txt file.


Look at ?options and scroll to 'warn.' Also, ?warnings gives an example.


HTH, Andy

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Re: [R] dealing with multicollinearity

2005-04-11 Thread John Sorkin

Manuel,
The problem you describe does not sound like it is due to
multicolinearity. I state this because you variance inflation factor is
modest (1.1) and, more importantly, the correlation between your
independent variables (x1 and x2) is modest, -0.25. I suspect the
problem is due to one, or more, observations having a disproportionally
large influence on your coefficients. I suggest you plot your residuals
vs. predicted values. I would also do a formal analysis of the influence
each observation has on the reported coefficients. You might consider
computing Cook's distance for each observation.
 
I hope this has helped.
 
John
 
John Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
Baltimore VA Medical Center GRECC and
University of Maryland School of Medicine Claude Pepper OAIC
 
University of Maryland School of Medicine
Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
 
410-605-7119 
- NOTE NEW EMAIL ADDRESS:
[EMAIL PROTECTED]

 Manuel Gutierrez [EMAIL PROTECTED] 4/11/2005
6:22:55 AM 



I have a linear model y~x1+x2 of some data where the
coefficient for
x1 is higher than I would have expected from theory
(0.7 vs 0.88)
I wondered whether this would be an artifact due to x1
and x2 being correlated despite that the variance
inflation factor is not too high (1.065):
I used perturbation analysis to evaluate collinearity
library(perturb)
P-perturb(A,pvars=c(x1,x2),prange=c(1,1))
 summary(P)
Perturb variables:
x1 normal(0,1) 
x2 normal(0,1) 

Impact of perturbations on coefficients:
mean s.d. min  max 
(Intercept)  -26.0670.270  -27.235  -25.481
x1 0.7260.0250.6720.882
x2 0.0600.0110.0370.082

I get a mean for x1 of 0.726 which is closer to what
is expected.
I am not an statistical expert so I'd like to know if
my evaluation of the effects of collinearity is
correct and in that case any solutions to obtain a
reliable linear model.
Thanks,
Manuel

Some more detailed information:

 A-lm(y~x1+x2)
 summary(A)

Call:
lm(formula = y ~ x1 + x2)

Residuals:
  Min1QMedian3Q   Max 
-4.221946 -0.484055 -0.004762  0.397508  2.542769 

Coefficients:
 Estimate Std. Error t value Pr(|t|)
(Intercept) -27.234720.27996 -97.282   2e-16 ***
x10.882020.02475  35.639   2e-16 ***
x20.081800.01239   6.604 2.53e-10 ***
---
Signif. codes:  0 `***' 0.001 `**' 0.01 `*' 0.05 `.'
0.1 ` ' 1 

Residual standard error: 0.823 on 241 degrees of
freedom
Multiple R-Squared: 0.8411,Adjusted R-squared: 0.8398

F-statistic: 637.8 on 2 and 241 DF,  p-value: 
2.2e-16 

 cor.test(x1,x2)

Pearson's product-moment correlation

data:  x1 and x2 
t = -3.9924, df = 242, p-value = 8.678e-05
alternative hypothesis: true correlation is not equal
to 0 
95 percent confidence interval:
-0.3628424 -0.1269618 
sample estimates:
  cor 
-0.248584

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[[alternative HTML version deleted]]

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Re: [R] How to suppress the printing of warnings (Windows)?

On Mon, 11 Apr 2005, Jacho-Chavez,DT  (pgr) wrote:
Dear all,
I'm a newbie in R. I am running simulations using a fixed bandwidth in 
nonparametric regressions, sending all the output to a file myoutput.txt 
using sink(myoutput.txt),  R is printing all warnings by the end of 
the simulation on the file. I know the source of the problem  can take 
care of it. However, finding a 50 MB file (where all the output is 
printed, e.g. myoutput.txt) by the end of the simulation exercise is not 
quite pleasant. How could I turn them off completely?, so they are not 
printed in myoutput.txt file.
options(warn=-1)
However, warnings and errors are sent to stderr not stdout except on 
obselete versions (95/98/ME) of Windows, and so not redirected by that 
sink() call. For me (Windows XP)

sink(foo.out)
warning(test)
Warning message:
test
as expected.  So is this an obsolete version of Windows or a very old 
version of R?

--
Brian D. Ripley,  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595
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Re: [R] Trying to undo an assignment

2005-04-11 Thread Sundar Dorai-Raj


Uzuner, Tolga wrote on 4/11/2005 7:33 AM:
Hi,
I defined corr to be a function, not realising that this was also the name for
correlation in package=boot.
How do I explicitly call the corr function within package boot (so, scope up
over the current frame, I guess is another way of saying it) without removing
my new corr function ? 

Thanks,
Tolga
Tolga,
You can use the :: operator, as in `boot::corr'.
--sundar
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RE: [R] How to suppress the printing of warnings (Windows)?

2005-04-11 Thread Jacho-Chavez,DT (pgr)

I'm running R v2.0.0 on Windows 2000. The command options(warn=-1) did the 
trick. However, is there a way I may also stop these warnings from printing on 
my screen while using R interactively. I am working with the LOCFIT library.

I'm also planning to run my simulations in my department's Unix machine (R 
v1.9.0) in batch mode, would `option(warn=-1)' do the trick there as well?

David

-Original Message-
From: Prof Brian Ripley [mailto:[EMAIL PROTECTED]
Sent: 11 April 2005 13:48
To: Jacho-Chavez,DT (pgr)
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] How to suppress the printing of warnings (Windows)?


On Mon, 11 Apr 2005, Jacho-Chavez,DT  (pgr) wrote:

 Dear all,

 I'm a newbie in R. I am running simulations using a fixed bandwidth in 
 nonparametric regressions, sending all the output to a file myoutput.txt 
 using sink(myoutput.txt),  R is printing all warnings by the end of 
 the simulation on the file. I know the source of the problem  can take 
 care of it. However, finding a 50 MB file (where all the output is 
 printed, e.g. myoutput.txt) by the end of the simulation exercise is not 
 quite pleasant. How could I turn them off completely?, so they are not 
 printed in myoutput.txt file.

options(warn=-1)

However, warnings and errors are sent to stderr not stdout except on 
obselete versions (95/98/ME) of Windows, and so not redirected by that 
sink() call. For me (Windows XP)

 sink(foo.out)
 warning(test)
Warning message:
test

as expected.  So is this an obsolete version of Windows or a very old 
version of R?


-- 
Brian D. Ripley,  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595

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[R] TSeries GARCH Estimates accuracy

2005-04-11 Thread Sanjay Kumar Singh

Hi,

I am trying to fit a GARCH(1,1) model to a financial timeseries using the 
'garch' function in the tseries package. However the parameter estimates 
obtained sometimes match with those obtained using SAS or S-Plus (Finmetrics) 
and sometimes show a completely different result. I understand that this could 
be due to the way optimization of MLEs are done, however, I would appreciate 
any help to obtain consistent results using R. 

Also is there any garch simulation function available other than garchSim from 
fseries package?

Thanks in advance,
Sanjay

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RE: [R] How to suppress the printing of warnings (Windows)?

On Mon, 11 Apr 2005, Jacho-Chavez,DT  (pgr) wrote:
I'm running R v2.0.0 on Windows 2000. The command options(warn=-1) did 
the trick. However, is there a way I may also stop these warnings from 
printing on my screen while using R interactively. I am working with the 
LOCFIT library.
Then sink() is not sinking warnings on that OS, so something else is 
wrong.

Yes, option(warn=-1) works in interactive sessions too.
I'm also planning to run my simulations in my department's Unix machine 
(R v1.9.0) in batch mode, would `option(warn=-1)' do the trick there as 
well?
Yes.
David
-Original Message-
From: Prof Brian Ripley [mailto:[EMAIL PROTECTED]
Sent: 11 April 2005 13:48
To: Jacho-Chavez,DT (pgr)
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] How to suppress the printing of warnings (Windows)?
On Mon, 11 Apr 2005, Jacho-Chavez,DT  (pgr) wrote:
Dear all,
I'm a newbie in R. I am running simulations using a fixed bandwidth in
nonparametric regressions, sending all the output to a file myoutput.txt
using sink(myoutput.txt),  R is printing all warnings by the end of
the simulation on the file. I know the source of the problem  can take
care of it. However, finding a 50 MB file (where all the output is
printed, e.g. myoutput.txt) by the end of the simulation exercise is not
quite pleasant. How could I turn them off completely?, so they are not
printed in myoutput.txt file.
options(warn=-1)
However, warnings and errors are sent to stderr not stdout except on
obselete versions (95/98/ME) of Windows, and so not redirected by that
sink() call. For me (Windows XP)
sink(foo.out)
warning(test)
Warning message:
test
as expected.  So is this an obsolete version of Windows or a very old
version of R?
--
Brian D. Ripley,  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595

--
Brian D. Ripley,  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595
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[R] Error on X11 or on R?

2005-04-11 Thread Elio Mineo

Dear list,
I am using R version 2.0.0 under Linux Mandrake 10.0. I have installed R 
by using the rpm file on CRAN.
By executing the following code, I have this output (the text file 
formaggio.txt is attached):

 dati - read.table(formaggio.txt, header=TRUE)
 plot(dati)
Error in text.default(x, y, txt, cex = cex, font = font) :
   X11 font at size 16 could not be loaded
Is it a X11 problem or a R problem? What can I do to solve this problem?
Thanks in advance,
Elio
Taste  Acetic  H2S  Lactic
12.3   4.543  3.135  0.86
20.9   5.159  5.043  1.53
39 5.366  5.438  1.57
47.9   5.759  7.496  1.81
5.64.663  3.807  0.99
25.9   5.697  7.601  1.09
37.3   5.892  8.726  1.29
21.9   6.078  7.966  1.78
18.1   4.898  3.85   1.29
21 5.242  4.174  1.58
34.9   5.74  6.142   1.68
57.2   6.446  7.908  1.9
0.74.477  2.996  1.06
25.9   5.236  4.942  1.3
54.9   6.151  6.752  1.52
40.9   6.365  9.588  1.74
15.9   4.787  3.912  1.16
6.45.412  4.71.49
18 5.247  6.174  1.63
38.9   5.438  9.064  1.99
14 4.564  4.949  1.15
15.2   5.298  5.22   1.33
32 5.455  9.242  1.44
56.7   5.855  10.199 2.01
16.8   5.366  3.664  1.31
11.6   6.043  3.219  1.46
26.5   6.458  6.962  1.72
0.75.328  3.912  1.25
13.4   5.802  6.685  1.08
5.56.176  4.787  1.25__
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Re: [R] dealing with multicollinearity

2005-04-11 Thread ronggui

why not use vif command (from car library) to caculate the VIF to help you 
assess is a collinearity is infulential?

I have never  seen any book dealling with this topics by perturbation analysis.

the VIF,tolerance,principal component analysis are the tools dealing with 
collinearity.you can get the information from john fox's book.

generally,caculating the correlation directly is not essential.

one more thing,if your purpose of modeling is  prediction but not 
interpretation,collinearity does not matter much.


On Mon, 11 Apr 2005 12:22:55 +0200 (CEST)
Manuel Gutierrez [EMAIL PROTECTED] wrote:

 
 I have a linear model y~x1+x2 of some data where the
 coefficient for
 x1 is higher than I would have expected from theory
 (0.7 vs 0.88)
 I wondered whether this would be an artifact due to x1
 and x2 being correlated despite that the variance
 inflation factor is not too high (1.065):
 I used perturbation analysis to evaluate collinearity
 library(perturb)
 P-perturb(A,pvars=c(x1,x2),prange=c(1,1))
  summary(P)
 Perturb variables:
 x1 normal(0,1) 
 x2 normal(0,1) 
 
 Impact of perturbations on coefficients:
 mean s.d. min  max 
 (Intercept)  -26.0670.270  -27.235  -25.481
 x1 0.7260.0250.6720.882
 x2 0.0600.0110.0370.082
 
 I get a mean for x1 of 0.726 which is closer to what
 is expected.
 I am not an statistical expert so I'd like to know if
 my evaluation of the effects of collinearity is
 correct and in that case any solutions to obtain a
 reliable linear model.
 Thanks,
 Manuel
 
 Some more detailed information:
 
  A-lm(y~x1+x2)
  summary(A)
 
 Call:
 lm(formula = y ~ x1 + x2)
 
 Residuals:
   Min1QMedian3Q   Max 
 -4.221946 -0.484055 -0.004762  0.397508  2.542769 
 
 Coefficients:
  Estimate Std. Error t value Pr(|t|)
 (Intercept) -27.234720.27996 -97.282   2e-16 ***
 x10.882020.02475  35.639   2e-16 ***
 x20.081800.01239   6.604 2.53e-10 ***
 ---
 Signif. codes:  0 `***' 0.001 `**' 0.01 `*' 0.05 `.'
 0.1 ` ' 1 
 
 Residual standard error: 0.823 on 241 degrees of
 freedom
 Multiple R-Squared: 0.8411,   Adjusted R-squared: 0.8398
 
 F-statistic: 637.8 on 2 and 241 DF,  p-value: 
 2.2e-16 
 
  cor.test(x1,x2)
 
   Pearson's product-moment correlation
 
 data:  x1 and x2 
 t = -3.9924, df = 242, p-value = 8.678e-05
 alternative hypothesis: true correlation is not equal
 to 0 
 95 percent confidence interval:
  -0.3628424 -0.1269618 
 sample estimates:
   cor 
 -0.248584
 
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Re: [R] Sweave and abbreviating output from R

2005-04-11 Thread Gavin Simpson

Roger Bivand wrote:
On Mon, 11 Apr 2005, Gavin Simpson wrote:

Dear List,
I'm using Sweave to produce a series of class handouts for a course I am 
running. The students in previous years have commented about wanting 
output within the handouts so they can see what to expect the output to 
look like. So Sweave is a godsend for producing this type of handout - 
with one exception: Is there a way to suppress some rows of printed 
output so as to save space in the printed documentation? E.g
snip

Semi-automatic is:

res - capture.output(rnorm(100))
cat(res[1:2], ..., res[length(res)], sep=\n)

but I've found that 1) it needs masking from the users, and 2) it is 
difficult to automate when the numbers of output lines generated by print 
methods vary with input data (like in print.htest()). But capture.output 
is very useful.

Roger
Thanks Roger - that got it! using combinations of:
echo=true,eval=FALSE=
summary(pondspca, scaling = 2)
@
echo=false,eval=true=
out - capture.output(summary(pondspca))
cat(out[1:27], , out[43:48], , sep = \n)
@
displays the relevant commands to the user but hides the semi-automatic 
printing of the selected sections.

All the best,
Gav
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Gavin Simpson [T] +44 (0)20 7679 5522
ENSIS Research Fellow [F] +44 (0)20 7679 7565
ENSIS Ltd.  ECRC [E] gavin.simpsonATNOSPAMucl.ac.uk
UCL Department of Geography   [W] http://www.ucl.ac.uk/~ucfagls/cv/
26 Bedford Way[W] http://www.ucl.ac.uk/~ucfagls/
London.  WC1H 0AP.
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
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[R] Two y-axis in lattice

2005-04-11 Thread Sharon Kuhlmann

Hi,

I am trying to plot two time series in each panel of an xyplot in lattice, 
but I need a different y-axis for each time series. Is this possible? How?

Thanks for any suggestions.

Sincerely,

Sharon Kühlmann


Sharon Kühlmann Berenzon
Biostatistics/Epidemiology
Swedish Institute for Infectious Disease Control (SMI) 

[EMAIL PROTECTED]
tel. +46-8-457 2376;  fax. +46-8-32 83 30

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[R] static analysis tools for R code?

2005-04-11 Thread Vivek Rao

An R script will terminate when one tries to use an
undefined variable, with a message such as 

Error in print(x) : Object x not found

This run-time error might occur after the script has
already been running for some time. In some cases it
would be nice to get such warnings before the script
is run, just as a syntax error caused by a missing
parenthesis is caught.

Are there any static analysis tools for R? Such a
tool would not have to be perfect to be useful.
Besides using undefined variables, defining variables
that are never used is something I'd like to be warned
about.

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[R] how to use the hmm packgae?

2005-04-11 Thread Eric()

Hi all,
Can someone  help me how to use the hmm package?
I see the description,but i didnot know how to use it.
I  got the y.sim value for the sim.hmm function, 
then I want  the example try - hmm(y.sim,K=2,verb=T  to work ,
How can I do it successly?
Thank's for your help.

   Eric
[[alternative HTML version deleted]]

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Re: [R] static analysis tools for R code?

If I understand well what you need then (I think) the answer is No; 
this is a feature of the language called Lazy Evaluation. For more 
info look at e.g., the R Language Definition document, section 
4.3.3.

Best,
Dimitris

Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/16/336899
Fax: +32/16/337015
Web: http://www.med.kuleuven.ac.be/biostat/
http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm
- Original Message - 
From: Vivek Rao [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Sent: Monday, April 11, 2005 4:18 PM
Subject: [R] static analysis tools for R code?


An R script will terminate when one tries to use an
undefined variable, with a message such as
Error in print(x) : Object x not found
This run-time error might occur after the script has
already been running for some time. In some cases it
would be nice to get such warnings before the script
is run, just as a syntax error caused by a missing
parenthesis is caught.
Are there any static analysis tools for R? Such a
tool would not have to be perfect to be useful.
Besides using undefined variables, defining variables
that are never used is something I'd like to be warned
about.
__
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Re: [R] Trying to undo an assignment

On Mon, 11 Apr 2005, Uzuner, Tolga wrote:
Hi,
I defined corr to be a function, not realising that this was also the name for
correlation in package=boot.
How do I explicitly call the corr function within package boot (so, scope up
over the current frame, I guess is another way of saying it) without removing
my new corr function ?
boot::corr
--
Brian D. Ripley,  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595
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Re: [R] static analysis tools for R code?

2005-04-11 Thread Luke Tierney

There are some preliminary tools available in the codetools package
at
http://www.stat.uiowa.edu/~luke/R/codetools/
Hopefully these will be cleaned up and released via CRAN or
incorporated into R this summer.
luke
On Mon, 11 Apr 2005, Dimitris Rizopoulos wrote:
If I understand well what you need then (I think) the answer is No; this is a 
feature of the language called Lazy Evaluation. For more info look at e.g., 
the R Language Definition document, section 4.3.3.

Best,
Dimitris

Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/16/336899
Fax: +32/16/337015
Web: http://www.med.kuleuven.ac.be/biostat/
   http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm
- Original Message - From: Vivek Rao [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Sent: Monday, April 11, 2005 4:18 PM
Subject: [R] static analysis tools for R code?

An R script will terminate when one tries to use an
undefined variable, with a message such as
Error in print(x) : Object x not found
This run-time error might occur after the script has
already been running for some time. In some cases it
would be nice to get such warnings before the script
is run, just as a syntax error caused by a missing
parenthesis is caught.
Are there any static analysis tools for R? Such a
tool would not have to be perfect to be useful.
Besides using undefined variables, defining variables
that are never used is something I'd like to be warned
about.
__
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--
Luke Tierney
Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa  Phone: 319-335-3386
Department of Statistics andFax:   319-335-3017
   Actuarial Science
241 Schaeffer Hall  email:  [EMAIL PROTECTED]
Iowa City, IA 52242 WWW:  http://www.stat.uiowa.edu
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Re: [R] static analysis tools for R code?

Look at Luke Tierney's codetools package.
https://stat.ethz.ch/pipermail/r-devel/2003-July/027103.html
It is useful, and has been run over R itself several times.
On Mon, 11 Apr 2005, Vivek Rao wrote:
An R script will terminate when one tries to use an
undefined variable, with a message such as
Error in print(x) : Object x not found
This run-time error might occur after the script has
already been running for some time. In some cases it
would be nice to get such warnings before the script
is run, just as a syntax error caused by a missing
parenthesis is caught.
Are there any static analysis tools for R? Such a
tool would not have to be perfect to be useful.
Besides using undefined variables, defining variables
that are never used is something I'd like to be warned
about.
--
Brian D. Ripley,  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595
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Re: [R] Two y-axis in lattice

2005-04-11 Thread Deepayan Sarkar

On Monday 11 April 2005 08:58, Sharon Kuhlmann wrote:
 Hi,

 I am trying to plot two time series in each panel of an xyplot in
 lattice, but I need a different y-axis for each time series. Is this
 possible? 

Depends. How do you want the axes to be displayed? A small reproducible 
example that we can work with would be helpful.

Deepayan

 How? 

 Thanks for any suggestions.

 Sincerely,

 Sharon Kühlmann

 
 Sharon Kühlmann Berenzon
 Biostatistics/Epidemiology
 Swedish Institute for Infectious Disease Control (SMI)

 [EMAIL PROTECTED]
 tel. +46-8-457 2376;  fax. +46-8-32 83 30

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Re: [R] Building R packages under Windows.

2005-04-11 Thread Duncan Murdoch

Gabor Grothendieck wrote:
Other resources are:
- http://www.murdoch-sutherland.com/Rtools/
My plan is that this is only going to include updates of the information 
in the R Admin manual, e.g. when a new version of one of the tools is 
available, this page will give advice on whether to use it or not.

- README.packages in \Program Files\R\rw2001 or whatever version of R
As mentioned, all of this has moved into the admin manual.
- posts by me, John Fox, Andy Liao in r-help or r-devel
I use Windows XP and it also took me quite a bit of time until I 
figured it out too.  I was really wondering as I got frustrated how
it was possible that 500+ packages got developed for R when it
was so hard to figure out how to create a package, particularly
if you want to put in a vignette.  One of the problems is that its
dependent on so many other pieces of software and also there can
be path problems that you have to figure out.  I suspect that the process
is somewhat smoother under UNIX and maybe most people use
that.  

Fortunately, it does all work once you get it figured out
and its worth it if you are going to do a lot of development since
it really helps organize you.   If you are just going to use it briefly
or casually its probably not worth the hassle.  Once you do figure
it out it does work although there are a few annoyances.
R CMD CHECK is really great although I wish there were some 
way of telling it to ignore the files referenced in .Rbuildignore so 
one does not have to do a build first.  Also the error messages
from the process are often less than helpful but I suspect it would
be difficult to improve since it can go wrong at a point which is
different than the source of the problem.

I think the fixable problems are:
- a guide is needed, as you mention
Comments on the new organization are welcome.  They'll be unlikely to 
make it into 2.1.0, but 2.1.1 or 2.2.0 will benefit from them.

- the prerequisites need to be reduced:
  -- significant portions are written in perl which is probably a 
 holdover from the days when R was less powerful and now
 could all be ported to R
This would be nice, but, as you say, there's a significant amount of 
work there.  It seems to me that giving instructions on how to install 
Perl is a lot easier, and the work a user does in installing Perl is 
small compared to all the other things someone writing a package would 
be doing, and only needs to be done once.  So I have no intention of 
redoing this, and wouldn't even be all that enthusiastic about testing a 
submission of rewrites from someone else.

  -- it would be nice it the tools were not needed either. 
I don't think this is likely any time soon.  The tools are there to 
provide make and a Unix-like environment in which to run it.  I don't 
think it's likely anyone would rewrite make in R.  Some of the other 
tools could be replaced with R code, but since you're installing one, 
why not install several?

  -- reduced functionality with no Microsoft style help should be
 possible to optionally allow one to create packages without
 downloading the Microsoft help compiler
This is possible, by editing the MkRules file and/or using the --docs=normal
option to BUILD or INSTALL.  I've just fixed up the R-admin description 
a bit to make this clearer.

- the TEXINPUTS problems with MiKTeX needs to be solved
  by MiKTeX (they know about it and intend to solve it but I am
  not sure how quickly that will happen.  In the meantime there
  are workarounds at:
 http://www.murdoch-sutherland.com/Rtools/miktex.html
  The fourth alternative is the easiest.  I think this only affects
  you if you are building vignettes.)
I'm no longer sure they intend to fix it.  Since I wrote those 
instructions, they came out with a new release that breaks one of the 
workarounds.

Duncan Murdoch
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Re: [R] how to use the hmm packgae?

2005-04-11 Thread Rolf Turner

``Eric'' ([EMAIL PROTECTED]) wrote:

 Hi all,
 Can someone  help me how to use the hmm package?
 I see the description,but i didnot know how to use it.
 I  got the y.sim value for the sim.hmm function, 
 then I want  the example try - hmm(y.sim,K=2,verb=T  to work ,
 How can I do it successly?
 Thank's for your help.

Your posting is very un-helpful.  Please read the Posting
Guide.

What goes wrong?  The example ``works'' precisely as
specified --- provided you remember to close your
parentheses!

cheers,

Rolf Turner
[EMAIL PROTECTED]

P. S. Questions about contributed packages should be directed
to the maintainers of those packages (in this case me) and
NOT to the list.

R. T.

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Re: [R] Error on X11 or on R?

Elio Mineo [EMAIL PROTECTED] writes:

 Dear list,
 I am using R version 2.0.0 under Linux Mandrake 10.0. I have installed
 R by using the rpm file on CRAN.
 By executing the following code, I have this output (the text file
 formaggio.txt is attached):
 
   dati - read.table(formaggio.txt, header=TRUE)
   plot(dati)
 Error in text.default(x, y, txt, cex = cex, font = font) :
 X11 font at size 16 could not be loaded
 
 Is it a X11 problem or a R problem? What can I do to solve this problem?

It's a buglet in R, but it is easily fixed by ensuring that you
install both 75dpi and 100dpi X11 fonts, or stop telling your font
server not to scale fonts.

-- 
   O__   Peter Dalgaard Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics 2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark  Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907

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RE: [R] embedding fonts in eps files

2005-04-11 Thread Rudi Alberts

Hi,

I'm again struggling with embedding of fonts in eps files using R. Is
this really possible? I don't agree with prof. Ripley saying that all
necessary information is in the help file. The aim is to include the
complete definitions of the fonts (eventually only the used characters),
not only the DSC comments (Document Structuring Conventions), so that
we don't use the font definitions of the PS interpreter who renders the
eps file.

I tried this command

postscript(fig2.eps, width = 6.50, height = 3.43, pointsize =
10,horizontal = FALSE, onefile = TRUE, paper = special,
family=Times, fonts=Times)

I also tried the same command, except for that I gave the following
value to the family and to the fonts arguments:
c(tir_.afm,tib_.afm,tii_.afm,tibi.afm,
sy__.afm)

After reading the help file (again) I hoped setting the fonts argument
should do what I want. It doesn't. Probably it only includes the DSC
comments in the eps .?

Prof. Ripley refers to this sentence:
 The software including the PostScript plot file should either embed
 the font outlines (usually from '.pfb' or '.pfa' files) or use DSC
 comments to instruct the print spooler to do so.
The question then is: how to make the software including the PostScript
plot file embed the font oulines..?

Do you have any clue?

I work on SUSE Linux 8.1 and I use R 2.0.0.


kind regards,

Rudi Alberts.





On Tue, 2005-01-18 at 03:48, [EMAIL PROTECTED] wrote:
 On 18-Jan-05 Rudi Alberts wrote:
  Hi,
  
  I have to make eps files with fonts embedded. 
  I use the following postscript command:
  
  
  postscript(fig3a.eps, width = 5.2756, height = 7.27, pointsize =
  7,horizontal = FALSE, onefile = FALSE, paper = special,family =
  Times)
  
  plot(...)
  
  dev.off()
  
  
  Are fonts automatically embedded in this way?
  How can I see that?
  If not, how to do it?
 
 Well, it seems to have set Times as the working font family
 when I used your postscript(...) command above; but see further
 down. I viewed the resulting .eps file (using 'less' in Linux
 but Windows users should also have some way of looking into a
 text file).
 
 The first few lines of the file are:
 
 %!PS-Adobe-3.0 EPSF-3.0
 %%DocumentNeededResources: font Times-Roman
 %%+ font Times-Bold
 %%+ font Times-Italic
 %%+ font Times-BoldItalic
 %%+ font Symbol
 %%Title: R Graphics Output
 ...
 
 These are so-called DSC (Document Structuring Conventions)
 comments and are not directly executed by whatever renders
 the PostScript code. They do, however, provided useful
 information for programs which have to handle the PS file.
 
 From the above, it can be seen that R's postscript() function
 has taken note of the 'family=Times' option.
 
 Further down the .eps file are the lines
 
 %%IncludeResource: font Times-Roman
 /Times-Roman findfont
 dup length dict begin
   {1 index /FID ne {def} {pop pop} ifelse} forall
   /Encoding ISOLatin1Encoding def
   currentdict
   end
 /Font1 exch definefont pop
 %%IncludeResource: font Times-Bold
 /Times-Bold findfont
 dup length dict begin
   {1 index /FID ne {def} {pop pop} ifelse} forall
   /Encoding ISOLatin1Encoding def
   currentdict
   end
 /Font2 exch definefont pop
 %%IncludeResource: font Times-Italic
 /Times-Italic findfont
 dup length dict begin
   {1 index /FID ne {def} {pop pop} ifelse} forall
   /Encoding ISOLatin1Encoding def
   currentdict
   end
 /Font3 exch definefont pop
 %%IncludeResource: font Times-BoldItalic
 /Times-BoldItalic findfont
 dup length dict begin
   {1 index /FID ne {def} {pop pop} ifelse} forall
   /Encoding ISOLatin1Encoding def
   currentdict
   end
 /Font4 exch definefont pop
 %%IncludeResource: font Symbol
 /Symbol findfont
 dup length dict begin
   {1 index /FID ne {def} {pop pop} ifelse} forall
   currentdict
   end
 /Font5 exch definefont pop
 
 Apart from the %% DSC comments, this is executable PS
 code which calls on the interpreter to set up the Times
 fonts Times-Roman as Font1, Times-Bold as Font2,
 Times-Italic as Font3, Times-BoldItalic as Font4,
 and Symbol (not a Times font) as Font5.
 
 If, instead of 'family=Times', you had used the option
 'family=Helvetica', you would have got (try it and see)
 exactly the same with Helvetica substituted for Times
 throughout.
 
 So far so good. Now comes the crunch.
 
 The above (and this is the only part of the .eps file
 which has anything to do with setting up fonts) assumes
 that the PS interpreter (i.e. the program, including
 printer firmware, which renders the PS visible) already
 has access to the PostScript definitions of these fonts.
 
 There is a default assumption (not just in R but in
 practically any software which outputs PostScript) that
 the rendering device will have built-in access to the
 Standard Adobe Font Set -- a set of 13 fonts comprising
 the Times, Helvetica and Courier families, and the Symbol
 font, together with the encoding vectors StandardEncoding
 and ISOLatin1Encoding; most software also assumes the
 presence

Re: [R] Error on X11 or on R?

2005-04-11 Thread Elio Mineo

Ok. Thanks Peter.
Peter Dalgaard wrote:
Elio Mineo [EMAIL PROTECTED] writes:
 

Dear list,
I am using R version 2.0.0 under Linux Mandrake 10.0. I have installed
R by using the rpm file on CRAN.
By executing the following code, I have this output (the text file
formaggio.txt is attached):
 dati - read.table(formaggio.txt, header=TRUE)
 plot(dati)
Error in text.default(x, y, txt, cex = cex, font = font) :
   X11 font at size 16 could not be loaded
Is it a X11 problem or a R problem? What can I do to solve this problem?
   

It's a buglet in R, but it is easily fixed by ensuring that you
install both 75dpi and 100dpi X11 fonts, or stop telling your font
server not to scale fonts.
 

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[R] Re: [R-SIG-Mac] BUG in RODBC with OS X?

2005-04-11 Thread Simon Urbanek

Drew,
On Apr 8, 2005, at 11:53 AM, Drew Balazs wrote:
This is my second posting on this topic, the first recieved no
replies.  Has anyone successfully used RODBC on the OS X platform?
Yes - it works pretty much out of the box. I tested it with the  
Actual drivers and they work pretty well (although I don't have any  
MS box to test the MS SQL part of it).

If I try to connect through the GUI using  chan -
odbcConnect(drewdb, uid=user, pwd =pwd) it simply crashes R with
the following crash report:
Well, you didn't send the crash report, but only a small  
(unfortunately useless) part of it. Given the error below, chances  
are that the error is caused by the driver. As of the GUI, you should  
include the version (and possibly revision) of the GUI along with the  
full report so we can try to track it down. However, this won't help  
with the ODBC problem you have.

However, if I try it through an xterm (command line), I get the  
following:

Warning messages:
1: [RODBC] ERROR: state IM004, code 0, message [iODBC][Driver  
Manager]Driver's SQLAllocEnv() failed
If you think this is not a driver problem, you should consider  
contacting the package maintainer, although I don't give it much hope  
as most ODBC problems are driver-related (and most drivers have very  
little OS X support). Alternatively you could ask on the  iODBC pages.

Cheers,
Simon
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[R] (no subject)

2005-04-11 Thread Cerviño Beresi Ulises

Hello R-people,

I have searched the mailing list messages and the R site (through the
web search and google) I didnt find anything related to Particle Swarm
Optimization (PSO) for R. Is there a package that implements such
algorithm?

Thanks in advance,

Ulises

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Re: [R] How to change letters after space into capital letters

2005-04-11 Thread Martin Maechler

 Gabor == Gabor Grothendieck [EMAIL PROTECTED]
 on Mon, 11 Apr 2005 07:31:00 -0400 writes:

Gabor On Apr 11, 2005 6:22 AM, Wolfram Fischer [EMAIL PROTECTED] wrote:
 What is the easiest way to change within vector of strings
 each letter after a space into a capital letter?
 
 E.g.:
 c( this is an element of the vector of strings, second element )
 becomes:
 c( This Is An Element Of The Vector Of Strings, Second Element )
 
 My reason to try to do this is to get more readable abbreviations.
 (A suggestion would be to add an option to abbreviate() which changes
 letters after space to uppercase letters before executing the 
abbreviation
 algorithm.)
 

Gabor Look for the thread titled

Gabor String manipulation---mixed case

Gabor in the r-help archives.

Indeed!  Thank you, Gabor.

If you use R 2.1.0 beta  (which you should consider seriously as
a good netizen ;-),  this is as simple as

   RSiteSearch(String manipulation---mixed case)
  A search query has been submitted to http://search.r-project.org
  The results page should open in your browser shortly

Martin.

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Re: [R] Building R packages under Windows.

On Apr 11, 2005 10:58 AM, Duncan Murdoch [EMAIL PROTECTED] wrote:
 Gabor Grothendieck wrote:
 
  Other resources are:
  - http://www.murdoch-sutherland.com/Rtools/
 
 My plan is that this is only going to include updates of the information
 in the R Admin manual, e.g. when a new version of one of the tools is
 available, this page will give advice on whether to use it or not.
 
  - README.packages in \Program Files\R\rw2001 or whatever version of R
 
 As mentioned, all of this has moved into the admin manual.
 
  - posts by me, John Fox, Andy Liao in r-help or r-devel
 
  I use Windows XP and it also took me quite a bit of time until I
  figured it out too.  I was really wondering as I got frustrated how
  it was possible that 500+ packages got developed for R when it
  was so hard to figure out how to create a package, particularly
  if you want to put in a vignette.  One of the problems is that its
  dependent on so many other pieces of software and also there can
  be path problems that you have to figure out.  I suspect that the process
  is somewhat smoother under UNIX and maybe most people use
  that.
 
  Fortunately, it does all work once you get it figured out
  and its worth it if you are going to do a lot of development since
  it really helps organize you.   If you are just going to use it briefly
  or casually its probably not worth the hassle.  Once you do figure
  it out it does work although there are a few annoyances.
  R CMD CHECK is really great although I wish there were some
  way of telling it to ignore the files referenced in .Rbuildignore so
  one does not have to do a build first.  Also the error messages
  from the process are often less than helpful but I suspect it would
  be difficult to improve since it can go wrong at a point which is
  different than the source of the problem.
 
  I think the fixable problems are:
  - a guide is needed, as you mention
 
 Comments on the new organization are welcome.  They'll be unlikely to
 make it into 2.1.0, but 2.1.1 or 2.2.0 will benefit from them.

I am probably missing something here but is there some new
material that perhaps I am unaware of?

 
  - the prerequisites need to be reduced:
-- significant portions are written in perl which is probably a
   holdover from the days when R was less powerful and now
   could all be ported to R
 
 This would be nice, but, as you say, there's a significant amount of
 work there.  It seems to me that giving instructions on how to install
 Perl is a lot easier, and the work a user does in installing Perl is
 small compared to all the other things someone writing a package would
 be doing, and only needs to be done once.  So I have no intention of
 redoing this, and wouldn't even be all that enthusiastic about testing a
 submission of rewrites from someone else.
 

I assume you are primarily interested in working on the part that is
specific to Windows but this is not really a Windows job though
that would be a key application of it.  Its really a job for R in general 
since it affects all ports of R, not just Windows.   The biggest problem 
with porting this is that someone has to know R, perl and the scripts
themselves or else they have to learn some of these which would
be much more work.  Not only does it make it harder to create
packages but the package development tools are held back since
presumably few people know R, perl and the scripts.  The key growth 
of R will not be driven so much by changes to the core but by addon 
packages so making it easy to create such packages are key to the 
success of R, at least IMHO.

-- it would be nice it the tools were not needed either.
 
 I don't think this is likely any time soon.  The tools are there to
 provide make and a Unix-like environment in which to run it.  I don't
 think it's likely anyone would rewrite make in R.  Some of the other

There is a perl power tools project to rewrite all the UNIX tools in perl.  
   http://ppt.perl.org/
It does include make so I guess its doable.  It would be neat
if there were an R power tools project although even better would
just be to eliminate the need for the tools in the first place, if
feasible.

The path problems are annoying.  Maybe there is some way of
creating a package of tools that one simply installs in the same
way one installs other R packages even if the tools themselves
are not changed?  By the way, there is another free help compiler
on the net.  I have never really looked at it but its at vizacc.com .
Not sure if there are any implications to that.

 tools could be replaced with R code, but since you're installing one,
 why not install several?
 
-- reduced functionality with no Microsoft style help should be
   possible to optionally allow one to create packages without
   downloading the Microsoft help compiler
 
 This is possible, by editing the MkRules file and/or using the --docs=normal
 option to BUILD or INSTALL.  I've just fixed up the R-admin description

Re: [R] How to change letters after space into capital letters

On Apr 11, 2005 11:28 AM, Martin Maechler [EMAIL PROTECTED] wrote:
 
 If you use R 2.1.0 beta  (which you should consider seriously as
 a good netizen ;-),  this is as simple as
 
   RSiteSearch(String manipulation---mixed case)
  A search query has been submitted to http://search.r-project.org
  The results page should open in your browser shortly

It would be nice if RSiteSearch were an entry in the Help menu 
in the Windows GUI.

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[R] How to calculate the AUC in R

2005-04-11 Thread Dubas, João Paulo

Hello R-listers,
I'm working in an experiment that try to determine the degree of 
infection of different clones of a fungus and, one of the measures we 
use to determine these degree is the counting of antibodies in the 
plasma at different dilutions, in this experiment the maximum number of 
dilutions was eleven. I already checked for differences on the maximum 
concentration of the antibodies in function of each clone of the fungus. 
However one measure of interest is the area under the curve (AUC) for 
the counting of antibodies in function of dilution. Unfortunately I 
don't know how to calculate the AUC. Someone can point me an example of 
this procedure or a package that implements this calculation?

Thanks for the help,
João Paulo Dubas.
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Re: [R] How to calculate the AUC in R

2005-04-11 Thread Frank E Harrell Jr

Dubas, João Paulo wrote:
Hello R-listers,
I'm working in an experiment that try to determine the degree of 
infection of different clones of a fungus and, one of the measures we 
use to determine these degree is the counting of antibodies in the 
plasma at different dilutions, in this experiment the maximum number of 
dilutions was eleven. I already checked for differences on the maximum 
concentration of the antibodies in function of each clone of the fungus. 
However one measure of interest is the area under the curve (AUC) for 
the counting of antibodies in function of dilution. Unfortunately I 
don't know how to calculate the AUC. Someone can point me an example of 
this procedure or a package that implements this calculation?

Thanks for the help,
João Paulo Dubas.
One of many ways:
trap.rule - function(x,y) sum(diff(x)*(y[-1]+y[-length(y)]))/2
--
Frank E Harrell Jr   Professor and Chair   School of Medicine
 Department of Biostatistics   Vanderbilt University
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Re: [R] How to calculate the AUC in R

Also see the function AUC in the ROC package.


On Mon, 2005-04-11 at 13:34 -0400, Frank E Harrell Jr wrote:
 Dubas, Joo Paulo wrote:
  Hello R-listers,
  
  I'm working in an experiment that try to determine the degree of 
  infection of different clones of a fungus and, one of the measures we 
  use to determine these degree is the counting of antibodies in the 
  plasma at different dilutions, in this experiment the maximum number of 
  dilutions was eleven. I already checked for differences on the maximum 
  concentration of the antibodies in function of each clone of the fungus. 
  However one measure of interest is the area under the curve (AUC) for 
  the counting of antibodies in function of dilution. Unfortunately I 
  don't know how to calculate the AUC. Someone can point me an example of 
  this procedure or a package that implements this calculation?
  
  Thanks for the help,
  Joo Paulo Dubas.
  
 
 One of many ways:
 
 trap.rule - function(x,y) sum(diff(x)*(y[-1]+y[-length(y)]))/2
 


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[R] ANNOUNCE: S-PLUS 7.0

2005-04-11 Thread David Smith

Insightful is proud to announce a major update to S-PLUS available
today: S-PLUS 7. S-PLUS 7 was designed to enable statisticians to
create targeted statistical applications with large data sets that can
be deployed to business users, researchers, analysts and other end
users who do not have special expertise in statistical methods.

S-PLUS 7 is the result of scores of interviews with S-PLUS users which
drove the design and development of the new features.  S-PLUS 7 has
also benefited from an extensive beta test program involving many
participants on s-news and r-help, to whom I offer sincere thanks for
their feedback during the development process.

The S-PLUS 7 release includes a new member of the S-PLUS product
family, S-PLUS Enterprise Developer, that provides additional new
features to S-PLUS, including:

* PIPELINE ARCHITECTURE and BIG DATA LIBRARY: S-PLUS 7 Enterprise
  Developer introduces a new pipeline architecture by making it
  possible to process gigabyte-sized data sets, even on machines with
  modest amounts of RAM. With the new big data library, S-PLUS
  programmers can import or create extremely large data objects by
  using out-of-memory processing techniques. Instead of holding a
  large data set entirely in memory, the pipeline architecture caches
  the data file on disk and uses specialized streaming algorithms to
  process the data, reading only a small portion of the data into
  memory at a time.

* S-PLUS WORKBENCH INTEGRATED DEVELOPMENT ENVIRONMENT: an integrated
  environment for S code development, based on the Eclipse
  framework. This release offers the core functionality of code
  editing, syntax error detection, project and task management,
  interfaces with source code control systems, and interaction with
  the S language engine.

You can read about the new features of S-PLUS, including a link to a
detailed white paper about the new big data library at:

   www.insightful.com/products/splus/s7_features.asp

You can also learn more about the new capabilities of S-PLUS 7 at a
webinar I will be giving on April 19. More info at:

   www.insightful.com/news_events/webcasts/2005/04splus

Finally, my thanks to all the members of the S community -- including
R folk -- who have provided such great discussion and debate over the
years, which has helped make S-PLUS what it is today.

# David Smith

-- 
David M Smith [EMAIL PROTECTED]
Senior Product Manager, Insightful Corp, Seattle WA
Tel: +1 (206) 802 2360
Fax: +1 (206) 283 6310

New S-PLUS 7! Create advanced statistical applications with large data sets.
www.insightful.com/splus

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[R] nested random effects

2005-04-11 Thread Dede Greenstein

Hello
For an unbalanced longitudinal data set with subjects nested within 
family  as the random effect (random= ~1 | FAMILY/ID)-- I am unclear as to 
why the subject within family random coefficient is not zero when there is 
only one person in a family with only one data point.

Thanks
Dede Greenstein
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Re: [R] How to calculate the AUC in R

2005-04-11 Thread Dubas, João Paulo

Quoting Frank E Harrell Jr:
Dubas, João Paulo wrote:
Quoting Frank E Harrell Jr:
Do you know any book where I can get more information about the subject?
Thanks for the help
João Paulo Dubas.

No, other than an algebra or calculus book where numerical integration 
is discussion.
Thanks to all listers that helped me in this question.
The function AUC on the ROC package can be used for the analysis of of
the relationship sensitivity x sensibility of a test, I couldn't adjust
that function to my purpose.
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RE: [R] ANNOUNCE: S-PLUS 7.0

2005-04-11 Thread Vadim Ogranovich

David, From the white paper, the BIG DATA THING looks quite impressive.
IMHO, it addresses the biggest limitation the S family has had so far. I
could, of course, think of few features that I wish to see there, but
the existing functionality looks fairly complete. Congratulations! An R
folk Vadim

 -Original Message-
 From: [EMAIL PROTECTED] 
 [mailto:[EMAIL PROTECTED] On Behalf Of David Smith
 Sent: Monday, April 11, 2005 11:26 AM
 To: r-help@stat.math.ethz.ch
 Subject: [R] ANNOUNCE: S-PLUS 7.0
 
 Insightful is proud to announce a major update to S-PLUS available
 today: S-PLUS 7. S-PLUS 7 was designed to enable 
 statisticians to create targeted statistical applications 
 with large data sets that can be deployed to business users, 
 researchers, analysts and other end users who do not have 
 special expertise in statistical methods.
 
 S-PLUS 7 is the result of scores of interviews with S-PLUS 
 users which drove the design and development of the new 
 features.  S-PLUS 7 has also benefited from an extensive beta 
 test program involving many participants on s-news and 
 r-help, to whom I offer sincere thanks for their feedback 
 during the development process.
 
 The S-PLUS 7 release includes a new member of the S-PLUS 
 product family, S-PLUS Enterprise Developer, that provides 
 additional new features to S-PLUS, including:
 
 * PIPELINE ARCHITECTURE and BIG DATA LIBRARY: S-PLUS 7 Enterprise
   Developer introduces a new pipeline architecture by making it
   possible to process gigabyte-sized data sets, even on machines with
   modest amounts of RAM. With the new big data library, S-PLUS
   programmers can import or create extremely large data objects by
   using out-of-memory processing techniques. Instead of holding a
   large data set entirely in memory, the pipeline architecture caches
   the data file on disk and uses specialized streaming algorithms to
   process the data, reading only a small portion of the data into
   memory at a time.
 
 * S-PLUS WORKBENCH INTEGRATED DEVELOPMENT ENVIRONMENT: an integrated
   environment for S code development, based on the Eclipse
   framework. This release offers the core functionality of code
   editing, syntax error detection, project and task management,
   interfaces with source code control systems, and interaction with
   the S language engine.
 
 You can read about the new features of S-PLUS, including a 
 link to a detailed white paper about the new big data library at:
 
www.insightful.com/products/splus/s7_features.asp
 
 You can also learn more about the new capabilities of S-PLUS 
 7 at a webinar I will be giving on April 19. More info at:
 
www.insightful.com/news_events/webcasts/2005/04splus
 
 Finally, my thanks to all the members of the S community -- 
 including R folk -- who have provided such great discussion 
 and debate over the years, which has helped make S-PLUS what 
 it is today.
 
 # David Smith
 
 --
 David M Smith [EMAIL PROTECTED]
 Senior Product Manager, Insightful Corp, Seattle WA
 Tel: +1 (206) 802 2360
 Fax: +1 (206) 283 6310
 
 New S-PLUS 7! Create advanced statistical applications with 
 large data sets.
 www.insightful.com/splus
 
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[R] correlation range estimates with nlme::gls

2005-04-11 Thread Ben Bolker

  I'm trying to do a simple (?) analysis of a 1D spatial data set, 
allowing for spatial autocorrelation.  (Actually, I'm comparing expected 
vs. observed for a spatial model of a 1D spatial data set.)  I'm using 
models like

gls(obs~exp,correlation=corExp(form=~pos),data=data)
or
gls(obs~exp,correlation=corLin(form=~pos),data=data)
 This form is supposed to fit a linear model of obs=a*exp+b using an 
autocorrelation model based on the position variable pos.

  The problem: I get reasonable answers for the slope  intercept, but the 
estimated ranges for the autocorrelation functions are huge and seemingly 
unconnected to the pictures I get when I plot acf(resid(M0)) [where M0 is 
the OLS fit to the data].  I tried simulating a bunch of data with 
different data sizes: the disturbing thing is that the range results get 
(much) worse, not better, as the number of data points goes up [from n=30, 
around the real size, to n=50, to n=100].  When I am able to get 
confidence intervals on the range, they often don't make sense either. 
On the other hand, the estimates of slope and intercept are reasonable in 
reality and in the simulations.

  I've skipped the gory details at this point.  A more complete write-up 
is at http://www.zoo.ufl.edu/bolker/tiwari-new-reg.pdf if anyone wants 
more information ...

  Should I be concerned about this?  Are there any obvious diagnostics of 
non-convergence etc.?  (Reported AIC values suggest that the models with 
autocorrelation *are* preferable, by quite a bit -- I could pursue this 
further.)  Or should I just not worry about it and move on?

  Ben Bolker
--
simulation code:
library(MASS)
simdata - function(sd=200,range=2,n=NULL,mmin=0) {
  if (is.null(n)) mile - seq(mmin,17.5,by=0.5) else {
mile - seq(mmin,17.5,length=n)
  }
  mean - 3000-50*(mile-10)^2
  v - sd^2
  dist - abs(outer(mile,mile,-))
  Sigma - v*exp(-dist/range)
  X - mvrnorm(1,mu=mean,Sigma=Sigma)
  data.frame(mile=mile,X=X,mean=mean)
}
--
620B Bartram Hall[EMAIL PROTECTED]
Zoology Department, University of Floridahttp://www.zoo.ufl.edu/bolker
Box 118525   (ph)  352-392-5697
Gainesville, FL 32611-8525   (fax) 352-392-3704
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[R] dependent competing risks

2005-04-11 Thread Hein Goemans

I am a beginner in R. I want to estimate a dependent competing risks model 
as proposed by Han and Hausman (1990). Especially because I want to 
estimate a model with TVC, I write to inquire whether any one else has 
written up such a model in R and whether I could take a peek at snippets of 
code.

Thanks for any help!
Hein.
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[R] Regression and time series

2005-04-11 Thread Fernando Saldanha

Can someone shed some light on this obscure portion of the help for lm?

Considerable care is needed when using 'lm' with time series.

 Unless 'na.action = NULL', the time series attributes are stripped
 from the variables before the regression is done.  (This is
 necessary as omitting 'NA's would invalidate the time series
 attributes, and if 'NA's are omitted in the middle of the series
 the result would no longer be a regular time series.)

 Even if the time series attributes are retained, they are not used
 to line up series, so that the time shift of a lagged or
 differenced regressor would be ignored.  It is good practice to
 prepare a 'data' argument by 'ts.intersect(..., dframe = TRUE)',
 then apply a suitable 'na.action' to that data frame and call 'lm'
 with 'na.action = NULL' so that residuals and fitted values are
 time series.

I found that ts.intersect does not shorten a set of time series just
because the series has NAs. It only shortens a set of time series to
the length of the shortest time series (with NAs counting for the
length calculation). That being the case, the utility of ts.inersect
seems limited to me, unless I am missing something (which I probably
am).

In particular, I am currently having to pad the beginning of a time
series when I call diff. For example,

 a - ts(c(1, 2, 4))
 b - ts(c(NA, diff(a)))
 ab - ts.intersect(a, b)
 Time Series:
   Start = 1 
   End = 3 
   Frequency = 1 
  a  b
1 1 NA
2 2  1
3 4  2

I was hoping that something like ts.intersect would spare me the
trouble of explicitly padding b in the example above. However, if I
don't pad b the time series get misaligned:

 a - ts(c(1, 2, 4))
 b - ts(diff(a))
 ab - ts.intersect(a, b)
Time Series:
Start = 1 
End = 2 
Frequency = 1 
  a b
1 1 1
2 2 2

Any comments, suggestions?

FS

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[R] RE:Building R packages under Windows.

2005-04-11 Thread Duncan Golicher

Many, many thanks to Renaud Lancelot who sent me exactly the sort of 
guide I was looking for. It is in French, but exceptionally clear and 
easy to follow and I got a rough and ready test package built in no 
time. It really is not that hard if you don't bother with TeX/LaTeX. 
Most of my previous hassles seemed to have arisen from path problems.

Even so it would be nice to see the process streamlined a bit more in 
the future.

Thanks again to everyone,
Duncan Golicher
--
Dr Duncan Golicher
Ecologia y Sistematica Terrestre
Conservación de la Biodiversidad
El Colegio de la Frontera Sur
San Cristobal de Las Casas, Chiapas, Mexico
Tel. 967 1883 ext 1310
Celular 044 9671041021
[EMAIL PROTECTED]
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Re: [R] RE:Building R packages under Windows.

On Apr 11, 2005 8:55 PM, Duncan Golicher [EMAIL PROTECTED] wrote:
 Many, many thanks to Renaud Lancelot who sent me exactly the sort of
 guide I was looking for. It is in French, but exceptionally clear and
 easy to follow and I got a rough and ready test package built in no
 time. It really is not that hard if you don't bother with TeX/LaTeX.
 Most of my previous hassles seemed to have arisen from path problems.
 
 Even so it would be nice to see the process streamlined a bit more in
 the future.
 
 Thanks again to everyone,
 
 Duncan Golicher
 

Maybe this could be contributed?

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[R] calling svydesign function that uses model.frame

2005-04-11 Thread Richard Valliant

I need help on calling the svydesign function in the survey package
(although this error appears not to be specific to svydesign). I am
passing parameters incorrectly but am not sure how to correct the
problem.

## Call the main function PS.sim (one of mine).  The dots are
parameters I omitted to simplify the question.
## y.col, str.col, clus.id, and PS.col are names of columns in the
object pop.

PS.sim(pop=small, y.col=NOTCOV, 
...,str.col=new.str, clus.id=new.psu, 
PS.col=PS.var, ...)

## A data.frame called sam.dat is generated by PS.sim.  Its first 3
lines are:

 ID new.str PS.var new.psu NOTCOV   wts
213   1  32 2  37.7
236   1  32 2  37.7
286   1  22 2  37.7

## Next, try to generate a survey design object.
## This fails (note the use of the calling parms clus.id and str.col):
svydesign(id = ~clus.id, strata = ~str.col, weights = wts, 
 data = sam.dat, nest = TRUE)

## with this error: 
Error in model.frame(formula, rownames, variables, varnames, extras,
extranames,  : 
invalid variable type

## It looks like clus.id is substituted as new.psu, likewise for
str.col

## The call below works when I use the actual column names not the
calling parms:
svydesign(id = ~new.psu, strata = ~new.str, weights = wts,data =
sam.dat, nest = TRUE)


I need to call svydesign with the parms I use to invoke the main
function PS.sim, i.e., ~clus.id and ~str.col. 
How do I do that?

Thanks,
Richard

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[R] adding R site search to Rgui

2005-04-11 Thread Liaw, Andy

From: Gabor Grothendieck

 On Apr 11, 2005 11:28 AM, Martin Maechler maechler at stat.math.ethz.ch
wrote:
  
  If you use R 2.1.0 beta  (which you should consider seriously as
  a good netizen ;-),  this is as simple as
  
RSiteSearch(String manipulation---mixed case)
   A search query has been submitted to http://search.r-project.org
   The results page should open in your browser shortly
 
 It would be nice if RSiteSearch were an entry in the Help menu 
 in the Windows GUI.

One can easily add another menu (and menu item) for this in Rgui:

winSearch - function() {
string - winDialogString(Search string, )
RSiteSearch(string)
}

winMenuAdd(Search)
winMenuAddItem(Search, Search R Site, winSearch())

Andy

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[R] where is internal function of sample()?

2005-04-11 Thread Weijie Cai

Hi there,
I am trying to write a c++ shared library for R. I need a function which has 
the same functionality as sample() in R, i.e., does permutation, sample 
with/without replacement. Does R have internal sample routine so that I can 
call it directly?

I did not find it in R.h, Rinternal.h.
Thanks
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Re: [R] where is internal function of sample()?

2005-04-11 Thread Marc Schwartz

On Mon, 2005-04-11 at 23:04 -0400, Weijie Cai wrote:
 Hi there,
 
 I am trying to write a c++ shared library for R. I need a function which has 
 the same functionality as sample() in R, i.e., does permutation, sample 
 with/without replacement. Does R have internal sample routine so that I can 
 call it directly?
 
 I did not find it in R.h, Rinternal.h.
 
 Thanks

A quick grep of the source code tree tells you that the function is
in .../src/main/random.c

A general pattern for C .Internal functions is to use a prefix of do_
in conjunction with the R function name. So in this case, the C function
is called do_sample and begins at line 391 (for 2.0.1 patched) in the
aforementioned C source file.

HTH,

Marc Schwartz

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Re: [R] adding R site search to Rgui