Re: [R] Trellis.par.set/ family/ global change font?

[Prof Brian Ripley]

On Fri, 30 Jun 2006, Renaud Lancelot wrote:

> A radical solution is to edit the file .../etc/Rdevga and to change
> the definition of the first set of fonts, e.g.
>
> # TT Arial : plain
> # TT Arial : bold
> # TT Arial : italic
> # TT Arial : bold&italic
>
> TT Times New Roman : plain
> TT Times New Roman : bold
> TT Times New Roman : italic
> TT Times New Roman : bold&italic

He is on Linux, so that will not work.  We have not been told the graphics 
device, but both postscript() and pdf() allow the device to be set when 
the device is opened, and that works for me:

pdf(family="serif")
example(xyplot)
dev.off()


>
> Best,
>
> Renaud
>
> 2006/6/30, Deepayan Sarkar <[EMAIL PROTECTED]>:
>> On 6/29/06, McClatchie, Sam (PIRSA-SARDI)
>> <[EMAIL PROTECTED]> wrote:
>>> Background:
>>> OS: Linux Ubuntu Dapper 6.06
>>> release: R 2.3.1
>>> editor: GNU Emacs 21.4.1
>>> front-end: ESS 5.2.3
>>> -
>>>
>>> Colleagues
>>>
>>> I have a rather complicated trellis plot that a journal editor has 
>>> requested I edit and change all the fonts to times.
>>>
>>> I'd like to change all fonts globally for the plot, as in 
>>> par(family="serif") for non-trellis plots. Various experiments with 
>>> trellis.par.set after reading the help page have not solved the problem for 
>>> me. Even doing the local change
>>> trellis.par.set(par.xlab.text=list(cex=1.5, family="serif")) does not 
>>> change the font to times for xlab (I mean my syntax is wrong, not that 
>>> there is a bug).
>>>
>>> So I'm obviously misreading the help page or just missing the meaning. Any 
>>> suggestions?
>>
>> Lattice uses 'fontfamily' rather than 'family' (borrowed from grid, I
>> suppose). I don't think there's a way to set the family globally. You
>> might try
>>
>> trellis.par.set(grid.pars = list(fontfamily = "serif"))
>>
>> but I'm not sure if that will work.
>>
>> -Deepayan
>>
>> __
>> R-help@stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>>
>
>
>

-- 
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] Trellis.par.set/ family/ global change font?

[Renaud Lancelot]

A radical solution is to edit the file .../etc/Rdevga and to change
the definition of the first set of fonts, e.g.

# TT Arial : plain
# TT Arial : bold
# TT Arial : italic
# TT Arial : bold&italic

TT Times New Roman : plain
TT Times New Roman : bold
TT Times New Roman : italic
TT Times New Roman : bold&italic

Best,

Renaud

2006/6/30, Deepayan Sarkar <[EMAIL PROTECTED]>:
> On 6/29/06, McClatchie, Sam (PIRSA-SARDI)
> <[EMAIL PROTECTED]> wrote:
> > Background:
> > OS: Linux Ubuntu Dapper 6.06
> > release: R 2.3.1
> > editor: GNU Emacs 21.4.1
> > front-end: ESS 5.2.3
> > -
> >
> > Colleagues
> >
> > I have a rather complicated trellis plot that a journal editor has 
> > requested I edit and change all the fonts to times.
> >
> > I'd like to change all fonts globally for the plot, as in 
> > par(family="serif") for non-trellis plots. Various experiments with 
> > trellis.par.set after reading the help page have not solved the problem for 
> > me. Even doing the local change
> > trellis.par.set(par.xlab.text=list(cex=1.5, family="serif")) does not 
> > change the font to times for xlab (I mean my syntax is wrong, not that 
> > there is a bug).
> >
> > So I'm obviously misreading the help page or just missing the meaning. Any 
> > suggestions?
>
> Lattice uses 'fontfamily' rather than 'family' (borrowed from grid, I
> suppose). I don't think there's a way to set the family globally. You
> might try
>
> trellis.par.set(grid.pars = list(fontfamily = "serif"))
>
> but I'm not sure if that will work.
>
> -Deepayan
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>


-- 
Renaud LANCELOT
Département Elevage et Médecine Vétérinaire (EMVT) du CIRAD
Directeur adjoint chargé des affaires scientifiques

CIRAD, Animal Production and Veterinary Medicine Department
Deputy director for scientific affairs

Campus international de Baillarguet
TA 30 / B (Bât. B, Bur. 214)
34398 Montpellier Cedex 5 - France
Tél   +33 (0)4 67 59 37 17
Secr. +33 (0)4 67 59 39 04
Fax   +33 (0)4 67 59 37 95

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[R] Empirical CDF

[Augusto.Sanabria]

Good day everyone,

I want to assess the error when fitting a Gram-Charlier
CDF to some data 'ws', that is, I want to calculate:

 Err = |ecdf(ws) - GCh_ser(ws)|

The problem is, I cannot get the F(x) values from the
ecdf.

'Summary(ecdf())' returns some of the x-axis values,
but how do you get the F(x) values?

Thank you for any help you can provide.

Regards,

Augusto



Augusto Sanabria. MSc, PhD.
Mathematical Modeller
Risk Research Group
Geospatial & Earth Monitoring Division
Geoscience Australia (www.ga.gov.au)
Cnr. Jerrabomberra Av. & Hindmarsh Dr.
Symonston ACT 2609
Ph. (02) 6249-9155

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Re: [R] aggregate data.frame by one column

[Guo Wei-Wei]

Hi Andrew,

Thank you very much! It works so well than I can expect.

All the best,
Wei-Wei

2006/6/30, Andrew Robinson <[EMAIL PROTECTED]>:
> Hi Wei-Wei,
>
> try this:
>
> eva.agg <- aggregate(x = list(
>VC1=eva$VC1,
>EO1=eva$EO1,
>EO2=eva$EO2,
>EO3=eva$EO3,
>EO4=eva$EO4,
>EO5=eva$EO5
>),
>  by = list(PARTNO=eva$PARTNO),
>  FUN = mean, na.rm = TRUE)
>
> eva.agg$NUM <- aggregate(eva$PARTNO, list(eva$PARTNO), length)
>
> Cheers
>
> Andrew
>

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Re: [R] aggregate data.frame by one column

[Andrew Robinson]

Hi Wei-Wei,

try this:

eva.agg <- aggregate(x = list(
   VC1=eva$VC1,
   EO1=eva$EO1,
   EO2=eva$EO2,
   EO3=eva$EO3,
   EO4=eva$EO4,
   EO5=eva$EO5
   ),
 by = list(PARTNO=eva$PARTNO),
 FUN = mean, na.rm = TRUE)

eva.agg$NUM <- aggregate(eva$PARTNO, list(eva$PARTNO), length)


Cheers

Andrew


On Fri, Jun 30, 2006 at 10:54:47AM +0800, Guo Wei-Wei wrote:
> Hi, everyone,
> 
> I have a data.frame named "eva" like this:
> 
> IND PARTNO VC1 EO1 EO2 EO3 EO4 EO5
> 114 114001   2   5   4   4   5   4
> 114 114001   2   4   4   4   4   4
> 114 114001   2   4  NA  NA  NA  NA
> 112 112002   2   3   3   6   2   6
> 112 112002   2   1   1   3   4   4
> 112 112003   2   6   6   6   5   6
> 112 112003   2   5   7   6   6   6
> 112 112003   2   6   6   6   4   5
> 114 114004   2   2   3   3   2   4
> 114 114004   2   5   3   4   4   2
> 114 114004   2  NA  NA  NA  NA  NA
> 113 113005   2   5   5   6   6   5
> 113 113005   2   7   7   4   7   6
> 111 111006   2   5   7   7   7   7
> 112 112007   2   7   7   7   2   2
> 112 112007   2   6   6   6   1   2
> 112 112007   2   7   6   6   2   2
> 111 111008   2   4   1   3   1   4
> 111 111008   2   3   1   5   3   2
> 
> This is only a small part of the whole data. "PARTNO" is a digit variable
> and I want to use it as a group variable to aggreate other variables.
> What I want to get looks like this:
> 
> IND PARTNO NUM VC1 EO1 EO2 EO3 EO4 EO5
> 114 114001   3   2 4.3   4   4 4.5   4
> 112 112002   2   2   2   2 4.5   3   5
> 112 112003   3   2 5.7 6.3   6   5 5.7
> 114 114004   3   2 3.5   3 3.5   3   3
> 113 113005   2   2   6   6   5 6.5 5.5
> 111 111006   1   2   5   7   7   7   7
> 112 112007   3   2 6.7 6.3 6.3 1.7   2
> 111 111008   2   2 3.5   1   4   2   3
> 
> "NUM" is a newly added variable which indicates the case number
> of each group grouped by "PARTNO".
> 
> I have two questions on this manipulation.
> 
> The first is how to get the newly added variable "NUM". I have no idea
> on this question.
> 
> The second is how to average other variables by group. If there are
> "NA", I want
> the average operation is done on other cases. For example, the
> variable "EO1" has
> values of 2, 5, and "NA" on case 114004. What I have done is
> 
> > aggregate(eva[,-2], by=eva[,-2], mean)
> 
> But it seems because there are "NA"s, the "aggregate" cannot process.
> Because the "NA" values are not a small part, I cannot use imputation
> methods. I'm not sure whether my operation is right.
> 
> Does anyone have any suggestion on the two problems? Thanks in advance!
> 
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

-- 
Andrew Robinson  
Department of Mathematics and StatisticsTel: +61-3-8344-9763
University of Melbourne, VIC 3010 Australia Fax: +61-3-8344-4599
Email: [EMAIL PROTECTED] http://www.ms.unimelb.edu.au

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Re: [R] Trellis.par.set/ family/ global change font?

[Deepayan Sarkar]

On 6/29/06, McClatchie, Sam (PIRSA-SARDI)
<[EMAIL PROTECTED]> wrote:
> Background:
> OS: Linux Ubuntu Dapper 6.06
> release: R 2.3.1
> editor: GNU Emacs 21.4.1
> front-end: ESS 5.2.3
> -
>
> Colleagues
>
> I have a rather complicated trellis plot that a journal editor has requested 
> I edit and change all the fonts to times.
>
> I'd like to change all fonts globally for the plot, as in par(family="serif") 
> for non-trellis plots. Various experiments with trellis.par.set after reading 
> the help page have not solved the problem for me. Even doing the local change
> trellis.par.set(par.xlab.text=list(cex=1.5, family="serif")) does not change 
> the font to times for xlab (I mean my syntax is wrong, not that there is a 
> bug).
>
> So I'm obviously misreading the help page or just missing the meaning. Any 
> suggestions?

Lattice uses 'fontfamily' rather than 'family' (borrowed from grid, I
suppose). I don't think there's a way to set the family globally. You
might try

trellis.par.set(grid.pars = list(fontfamily = "serif"))

but I'm not sure if that will work.

-Deepayan

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[R] aggregate data.frame by one column

[Guo Wei-Wei]

Hi, everyone,

I have a data.frame named "eva" like this:

IND PARTNO VC1 EO1 EO2 EO3 EO4 EO5
114 114001   2   5   4   4   5   4
114 114001   2   4   4   4   4   4
114 114001   2   4  NA  NA  NA  NA
112 112002   2   3   3   6   2   6
112 112002   2   1   1   3   4   4
112 112003   2   6   6   6   5   6
112 112003   2   5   7   6   6   6
112 112003   2   6   6   6   4   5
114 114004   2   2   3   3   2   4
114 114004   2   5   3   4   4   2
114 114004   2  NA  NA  NA  NA  NA
113 113005   2   5   5   6   6   5
113 113005   2   7   7   4   7   6
111 111006   2   5   7   7   7   7
112 112007   2   7   7   7   2   2
112 112007   2   6   6   6   1   2
112 112007   2   7   6   6   2   2
111 111008   2   4   1   3   1   4
111 111008   2   3   1   5   3   2

This is only a small part of the whole data. "PARTNO" is a digit variable
and I want to use it as a group variable to aggreate other variables.
What I want to get looks like this:

IND PARTNO NUM VC1 EO1 EO2 EO3 EO4 EO5
114 114001   3   2 4.3   4   4 4.5   4
112 112002   2   2   2   2 4.5   3   5
112 112003   3   2 5.7 6.3   6   5 5.7
114 114004   3   2 3.5   3 3.5   3   3
113 113005   2   2   6   6   5 6.5 5.5
111 111006   1   2   5   7   7   7   7
112 112007   3   2 6.7 6.3 6.3 1.7   2
111 111008   2   2 3.5   1   4   2   3

"NUM" is a newly added variable which indicates the case number
of each group grouped by "PARTNO".

I have two questions on this manipulation.

The first is how to get the newly added variable "NUM". I have no idea
on this question.

The second is how to average other variables by group. If there are
"NA", I want
the average operation is done on other cases. For example, the
variable "EO1" has
values of 2, 5, and "NA" on case 114004. What I have done is

> aggregate(eva[,-2], by=eva[,-2], mean)

But it seems because there are "NA"s, the "aggregate" cannot process.
Because the "NA" values are not a small part, I cannot use imputation
methods. I'm not sure whether my operation is right.

Does anyone have any suggestion on the two problems? Thanks in advance!

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Re: [R] lme convergence

[Spencer Graves]

  Does anyone know how to obtain the 'returnObject' from an 'lme' run 
that fails to converge?  An argument of this name is described on the 
'lmeControl' help page as, "a logical value indicating whether the 
fitted object should be returned when the maximum number of iterations 
is reached without convergence of the algorithm. Default is 'FALSE'."

  Unfortunately, I've so far been unable to get it to work, as 
witnessed by the following modification of an example from the '?lme' 
help page:

 > library(nlme)
 > fm1 <- lme(distance ~ age, data = Orthodont,
+control=lmeControl(msMaxIter=1))
Error in lme.formula(distance ~ age, data = Orthodont, control = 
lmeControl(msMaxIter = 1)) :
iteration limit reached without convergence (9)
 > fm1
Error: object "fm1" not found
 > fm1 <- lme(distance ~ age, data = Orthodont,
+control=lmeControl(msMaxIter=1,
+  returnObject=TRUE))
Error in lme.formula(distance ~ age, data = Orthodont, control = 
lmeControl(msMaxIter = 1,  :
iteration limit reached without convergence (9)
 > fm1
Error: object "fm1" not found   

  I might be able to fix the problem myself, working through the 'lme' 
code line by line, e.g., using 'debug'.  However, I'm not ready to do 
that just now.

  Best Wishes,
  Spencer Graves

Ravi Varadhan wrote:
> Use "try" to capture error messages without breaking the loop.
> ?try
> 
> --
> Ravi Varadhan, Ph.D.
> Assistant Professor,  The Center on Aging and Health
> Division of Geriatric Medicine and Gerontology
> Johns Hopkins University
> Ph: (410) 502-2619
> Fax: (410) 614-9625
> Email:  [EMAIL PROTECTED]
> Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html 
> --
> 
>> -Original Message-
>> From: [EMAIL PROTECTED] [mailto:r-help-
>> [EMAIL PROTECTED] On Behalf Of Pryseley Assam
>> Sent: Wednesday, June 28, 2006 12:18 PM
>> To: R-Users
>> Subject: [R] lme convergence
>>
>> Dear R-Users,
>>
>>   Is it possible to get the covariance matrix from an lme model that did
>> not converge ?
>>
>>   I am doing a simulation which entails fitting linear mixed models, using
>> a "for loop".
>>   Within each loop, i generate a new data set and analyze it using a mixed
>> model.  The loop stops When the "lme function" does not converge for a
>> simulated dataset. I want to inquire if there is a method to suppress the
>> error message from the lme function, or better still, a way of going about
>> this issue of the loop ending once the lme function does not converge.
>>
>>   Thanks in advance,
>>   Pryseley
>>
>>
>> -
>>
>>
>>  [[alternative HTML version deleted]]
>>
>> __
>> R-help@stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide! http://www.R-project.org/posting-
>> guide.html
> 
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

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[R] Trellis.par.set/ family/ global change font?

[McClatchie, Sam \(PIRSA-SARDI\)]

Background:
OS: Linux Ubuntu Dapper 6.06
release: R 2.3.1
editor: GNU Emacs 21.4.1
front-end: ESS 5.2.3
-

Colleagues

I have a rather complicated trellis plot that a journal editor has requested I 
edit and change all the fonts to times. 

I'd like to change all fonts globally for the plot, as in par(family="serif") 
for non-trellis plots. Various experiments with trellis.par.set after reading 
the help page have not solved the problem for me. Even doing the local change 
trellis.par.set(par.xlab.text=list(cex=1.5, family="serif")) does not change 
the font to times for xlab (I mean my syntax is wrong, not that there is a bug).

So I'm obviously misreading the help page or just missing the meaning. Any 
suggestions?

Thanks

Sam

Sam McClatchie,
Oceanography subprogram 
South Australian Aquatic Sciences Centre
PO Box 120, Henley Beach 5022
Adelaide, South Australia
email <[EMAIL PROTECTED]>
Cellular: 0431 304 497 
Telephone: (61-8) 8207 5448
FAX: (61-8) 8207 5481
Research home page 
  
   /\
  ...>> 
 
   <°)Xx><<
  /  \\
><(((°> 
  >><(((°>   ...>>O<°)Xx><<


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Re: [R] How to use a for loop to generate two sequences

[Gabor Grothendieck]

On 6/29/06, Xiaohua Dai <[EMAIL PROTECTED]> wrote:
> I followed your method but there was an error on FUN get:
>
> > nm <- paste("test", 1:1000, sep = "")
> > lapply(nm, get)
> Error in get(x, envir, mode, inherits) : variable "test1" was not found
> > L <- sapply(paste("test", 1:1000, sep = ""), get, simplify = FALSE)
> Error in get(x, envir, mode, inherits) : variable "test1" was not found
>
> But lapply(nm, as.name) worked well. Are there any problem with my R env?

These are different things.  Using as.name gives you a list of names
but I am assuming you are looking for a list of the objects themselves
so you need to have those objects defined.  Here is a reproducible
example:

> test1 <- test2 <- 1
> sapply(paste("test", 1:2, sep = ""), get, simplify = FALSE)
$test1
[1] 1

$test2
[1] 1





>
> > traceback()
> 2: FUN(X[[1]], ...)
> 1: lapply(nm, get)
>
> > sessionInfo()
> Version 2.3.1 (2006-06-01)
> i386-pc-mingw32
>
> attached base packages:
> [1] "methods"   "stats" "graphics"  "grDevices" "utils" "datasets"
> [7] "base"
>
> > win.version()
> [1] "Windows XP Professional (build 2600) Service Pack 2.0"
>
>
> Thanks
> Xiaohua
>
>
> On 6/30/06, Gabor Grothendieck <[EMAIL PROTECTED]> wrote:
> > A vector of character strings:
> >
> >  nm <- paste("test", 1:1000, sep = "")
> >
> > A list whose components are the objects: test1, test2, ...
> >
> >  lapply(nm, get)
> >
> > or if you do it this way the list will have 'test1', 'test2', ... as the
> > component names:
> >
> >  L <- sapply(paste("test", 1:1000, sep = ""), get, simplify = FALSE)
> >
> > and then
> >
> >  names(L)
> >
> > gives the vector of names.
> >
> >
> > Also note that
> >
> >  apropos("^test[0-9]+")
> >
> > will give a vector of object names corresponding to objects
> >  in the current workspace whose names
> > are "test" followed by a number.
> >
> > On 6/29/06, Xiaohua Dai <[EMAIL PROTECTED]> wrote:
> > > Hi R users,
> > >
> > > Hope the question is not too simple:
> > >
> > > How to use a for loop to generate two lists as below:
> > >
> > > testlist <- list(test1, test2, ..., test1000)
> > > stringlist <- list("test1","test2",...,"test1000")
> > >
> > > Thanks
> > > Xiaohua
> > >
> > > __
> > > R-help@stat.math.ethz.ch mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide! 
> > > http://www.R-project.org/posting-guide.html
> > >
>

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Re: [R] Extracting R plots from MS Word

[Gabor Grothendieck]

I think these are zipped emf and wmf files.  Google for emz extension.

On 6/29/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
> Thanks to all those who responded to my request about extracting R plots
> from MS Word. I decided to try Gabor Grothendieck's second suggestion and
> saved the Word document as html. (I may yet try some of the other
> suggestions.)
>
> Saving the .doc as .htm indeed produced a folder with many of the images
> in .gif form. However some of my images seemed to be described by files
> with .wmz or .emz extensions. I am not quite sure how to change these into
> .gif or .eps or anything useful!
>
> Cheers,  Murray Jorgensen
>
> > Click the graphic, press ctrl-C to copy it to the clipboard and then
> > using ctrl-V paste it into mspaint or Xnview (free, find it via google) or
> > other
> > graphics program and then save it from there.   Which program will
> > work will depend on the format of the image.
> >
> > Another possibility is to save the Word file in HTML format.  In
> > Word, choose File | SaveAs and choose the Save As Type to be Web Page.
> > That will create an HTML file plus it will create a folder with
> > one file per image.
> >
> > On 6/29/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
> >> Hi,
> >>
> >> I am revising a paper that I am a co-author of. The figures are plots
> >> generated from R but at the moment I do not have the R code that
> >> generates
> >> them.
> >>
> >> As this is time critical I would like to slightly abuse the list by
> >> asking
> >> whether anyone knows how to extract from MS Word into a stand-alone
> >> graphics file a plot that was pasted into Word from R (probably as a
> >> Windows Metafile, but possibly as a bitmap).
> >>
> >> I would be very grateful for help with this.
> >>
> >> Regards,  Murray Jorgensen
> >>
> >> __
> >> R-help@stat.math.ethz.ch mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide!
> >> http://www.R-project.org/posting-guide.html
> >>
> >
>
>
>

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Re: [R] Extracting R plots from MS Word

[maj]

Thanks to all those who responded to my request about extracting R plots
from MS Word. I decided to try Gabor Grothendieck's second suggestion and
saved the Word document as html. (I may yet try some of the other
suggestions.)

Saving the .doc as .htm indeed produced a folder with many of the images
in .gif form. However some of my images seemed to be described by files
with .wmz or .emz extensions. I am not quite sure how to change these into
.gif or .eps or anything useful!

Cheers,  Murray Jorgensen

> Click the graphic, press ctrl-C to copy it to the clipboard and then
> using ctrl-V paste it into mspaint or Xnview (free, find it via google) or
> other
> graphics program and then save it from there.   Which program will
> work will depend on the format of the image.
>
> Another possibility is to save the Word file in HTML format.  In
> Word, choose File | SaveAs and choose the Save As Type to be Web Page.
> That will create an HTML file plus it will create a folder with
> one file per image.
>
> On 6/29/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
>> Hi,
>>
>> I am revising a paper that I am a co-author of. The figures are plots
>> generated from R but at the moment I do not have the R code that
>> generates
>> them.
>>
>> As this is time critical I would like to slightly abuse the list by
>> asking
>> whether anyone knows how to extract from MS Word into a stand-alone
>> graphics file a plot that was pasted into Word from R (probably as a
>> Windows Metafile, but possibly as a bitmap).
>>
>> I would be very grateful for help with this.
>>
>> Regards,  Murray Jorgensen
>>
>> __
>> R-help@stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide!
>> http://www.R-project.org/posting-guide.html
>>
>

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Re: [R] How to use a for loop to generate two sequences

[Xiaohua Dai]

I followed your method but there was an error on FUN get:

> nm <- paste("test", 1:1000, sep = "")
> lapply(nm, get)
Error in get(x, envir, mode, inherits) : variable "test1" was not found
> L <- sapply(paste("test", 1:1000, sep = ""), get, simplify = FALSE)
Error in get(x, envir, mode, inherits) : variable "test1" was not found

But lapply(nm, as.name) worked well. Are there any problem with my R env?

> traceback()
2: FUN(X[[1]], ...)
1: lapply(nm, get)

> sessionInfo()
Version 2.3.1 (2006-06-01)
i386-pc-mingw32

attached base packages:
[1] "methods"   "stats" "graphics"  "grDevices" "utils" "datasets"
[7] "base"

> win.version()
[1] "Windows XP Professional (build 2600) Service Pack 2.0"


Thanks
Xiaohua


On 6/30/06, Gabor Grothendieck <[EMAIL PROTECTED]> wrote:
> A vector of character strings:
>
>  nm <- paste("test", 1:1000, sep = "")
>
> A list whose components are the objects: test1, test2, ...
>
>  lapply(nm, get)
>
> or if you do it this way the list will have 'test1', 'test2', ... as the
> component names:
>
>  L <- sapply(paste("test", 1:1000, sep = ""), get, simplify = FALSE)
>
> and then
>
>  names(L)
>
> gives the vector of names.
>
>
> Also note that
>
>  apropos("^test[0-9]+")
>
> will give a vector of object names corresponding to objects
>  in the current workspace whose names
> are "test" followed by a number.
>
> On 6/29/06, Xiaohua Dai <[EMAIL PROTECTED]> wrote:
> > Hi R users,
> >
> > Hope the question is not too simple:
> >
> > How to use a for loop to generate two lists as below:
> >
> > testlist <- list(test1, test2, ..., test1000)
> > stringlist <- list("test1","test2",...,"test1000")
> >
> > Thanks
> > Xiaohua
> >
> > __
> > R-help@stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide! 
> > http://www.R-project.org/posting-guide.html
> >

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Re: [R] NLME Fitting

[Spencer Graves]

  I'm not certain what you want, but it sounds like the answer might be 
in '?nlme' help page.  Toward the end, it describes the 'Value' returned 
as follows:

an object of class 'nlme' representing the nonlinear mixed-effects
  model fit. Generic functions such as 'print', 'plot' and 'summary'
  have methods to show the results of the fit. See 'nlmeObject' for
  the components of the fit. The functions 'resid', 'coef',
  'fitted', 'fixed.effects', and 'random.effects'  can be used to
  extract some of its components.

  Also, 'str' might help you find what you want.

  Spencer Graves
p.s.  If you'd like further help from this listserve, PLEASE do read the 
posting guide! "www.R-project.org/posting-guide.html".  This might help 
you write a question so it is easier for others to understand, thereby 
increasing the chances for a quick and useful reply.

F Monadjemi wrote:
> Dear Reader,
> 
> Is it possible to extract the random part of nlme fitting analysis (non linear
> mixed effect model) i.e.sigma(b), in R?
> 
> Thank you for respond
> 
> 
> Farinaz
> 
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Re: [R] Reporting ppr fits and using them externally.

[Robert Chatfield]

A couple days of detective work have gone along way to reveal how one  
may
recover the actual knots and coefficients of the splines used in ppr.
It's not finished yet, but I may be due some mid-course correction.

First, ... I was asked, ... why?

On Jun 27, 2006, at 11:50 PM, Prof Brian Ripley wrote:

> It is normal to report smooth curves via plots of smooth curves.  
> There are examples for ppr in MASS4 p.241 (referenced on the help  
> page).  This is done by the plot() method.
>
> Please do consult the references in the documentation: those who  
> very carefully documented these tools put them there because they  
> do give additional information.

This  reading and plotting of course was all done before contacting r- 
help.

The plots of the smooth curves will be used to communicate with most  
readers of our
publication.  However, reviewers for J. Geophysical Research and  
Atmospheric Environment
will require specifics of the fit performed.  We hope that the  
results will be used
to greatly improve our understanding of smog ozone formation, and for  
field use,
the pure spline fit is required, unencumbered by the ~2000 fitted  
points of our estimation
data set.

So, we have found that (my colleague Bob E's words)
> Both smooth.spline and ppr, with spline or gcvspline option,
> eventually come to a call to qsbart.f. Therefore, find out
> which parameters ppr is using in the qsbart call, and
> determine which parameters to smooth.spline cause the
> same arguments to qsbart.
>
>
> From ppr, qsbart is called from at
> the end of the chain (some wrappers left out):
> ppr -> smart1 -> {subfit, fulfit} -> onetrm -> oneone -> supsmu ->  
> spline -> qsbart
> Nearly all the code in the fortran routines deals with the
> supersmoother case.
>
> smooth.spline (stats/R/smspline.R) calls subroutine spline directly.

I have found that qsbart is  in this file  /library/stats/src/ 
sbart.c

and that the inputs and outputs seem to be clearly documented at the  
beginning
of the code:

> /* A Cubic B-spline Smoothing routine.
>
>The algorithm minimises:
>
> (1/n) * sum ws(i)^2 * (ys(i)-sz(i))^2 + lambda* int  
> ( s"(x) )^2 dx
>
>lambda is a function of the spar which is assumed to be between  
> 0 and 1
>
> INPUT
> -
>penalt   A penalty > 1 to be used in the gcv criterion
>dofoff   either `df.offset' for GCV or `df' (to be matched).
>nnumber of data points
>ys(n)vector of length n containing the observations
>ws(n)vector containing the weights given to each data point
>xs(n)vector containing the ordinates of the observations
>ssw  `centered weighted sum of y^2'
>nk   number of b-spline coefficients to be estimated
> nk <= n+2
>knot(nk+4)   vector of knot points defining the cubic b-spline  
> basis.
> To obtain full cubic smoothing splines one might
> have (provided the xs-values are strictly increasing)
>spar penalised likelihood smoothing parameter
>isparindicating if spar is supplied (ispar=1) or to be  
> estimated
>lspar, uspar lower and upper values for spar search;  0.,1. are  
> good values
>tol, eps used in Golden Search routine
>isetup   setup indicator [initially 0
>icritindicator saying which cross validation score is to  
> be computed
> 0: none ;  1: GCV ;  2: CV ;  3: 'df matching'
>ld4  the leading dimension of abd (ie ld4=4)
>ldnk the leading dimension of p2ip (not referenced)
>
> OUTPUT
> --
>coef(nk) vector of spline coefficients
>sz(n)vector of smoothed z-values
>lev(n)   vector of leverages
>crit either ordinary or generalized CV score
>spar if ispar != 1
>lspar == lambda (a function of spar and the design)
>iter number of iterations needed for spar search (if  
> ispar != 1)
>ier  error indicator
> ier = 0 ___  everything fine
> ier = 1 ___  spar too small or too big
> problem in cholesky decomposition

These are returned to the calling FORTRAN code (we should note the  
need to
respect FORTRAN<->C array and call conventions).

So it remains for us to find either the results of the last call to  
qsbart.f
made from  subroutine spline (n, x, y, w, smo, edf) in  the ppr.f
code "spline"
>   subroutine spline (n, x, y, w, smo, edf)
> c
> c--
> c
> c input:
> cn : number of observations.
> cx(n) : ordered abscissa values.
> cy(n) : corresponding ordinate (response) values.
> cw(n) : weight for each (x,y) observation.
> c output:
> c   smo(n) : smoothed ordinate (response) values.
> c   edf : equivalent degrees of freedom
> c
> c--

Note that coe

Re: [R] How to use a for loop to generate two sequences

[Gabor Grothendieck]

A vector of character strings:

  nm <- paste("test", 1:1000, sep = "")

A list whose components are the objects: test1, test2, ...

  lapply(nm, get)

or if you do it this way the list will have 'test1', 'test2', ... as the
component names:

  L <- sapply(paste("test", 1:1000, sep = ""), get, simplify = FALSE)

and then

  names(L)

gives the vector of names.


Also note that

  apropos("^test[0-9]+")

will give a vector of object names corresponding to objects
 in the current workspace whose names
are "test" followed by a number.

On 6/29/06, Xiaohua Dai <[EMAIL PROTECTED]> wrote:
> Hi R users,
>
> Hope the question is not too simple:
>
> How to use a for loop to generate two lists as below:
>
> testlist <- list(test1, test2, ..., test1000)
> stringlist <- list("test1","test2",...,"test1000")
>
> Thanks
> Xiaohua
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>

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Re: [R] Passing argument in nested function calls

[Gabor Grothendieck]

getArgs should be:

getArgs <- function(...) extractArgs(...)

# test
extractArgs(x = 3)
getArgs(x = 3)


On 6/29/06, Aarti Dahiya <[EMAIL PROTECTED]> wrote:
> Please, do not ask why you would do this.  I have simplified my complicated
> code to just the basic problem occuring to be able to make it easier to
> understand the actual problem.
>
> I have two function getArgs() and extractArgs() - code and test results
> provided below.
> I test them using getArgs(id = 's1002') from the command line.
>
> getArgs() prints the name of the argument as id and the actual argument as
> s1002, which is correct.
>
> But, when I call extractArgs() from within getArgs() passing value of passed
> (stored in passed, passed is created from paste(names(args),"=",
> sQuote(args))); extractArgs() treats the value of passed as a string "id =
> 's1002'" and treats the whole thing as one argument.  So, it prints
> args[[1]] as the whole thing id = 's1002'", but prints blank for
> names(args[[1]]), obviously beacuse it cannot find a name for the argument.
>
> If I call extractArgs(id = 's1002') from the command line, it works just
> fine, prints the name of the argument as id and the actual argument as
> s1002, which is correct.
>
> How do I fix the problem so that when extractArgs() is called within
> getArgs(), it behaves the same way as getArgs() and extracts the argument
> and argument name?  Can we unstring passed or change it into another mode?
>
> I'll appreciate any help or pointers.  Thanks.  Aarti
>
> getArgs <- function(...)
> {
>cat("\nEntering getArgs()\n\n")
>
>args <- list(...)
>
>cat("In getArgs(), names(args[1]) is ")
>cat(names(args[1]))
>cat(" and args[[1]] is ")
>cat(args[[1]])
>cat("\n")
>
>passed <- paste(names(args),"=", sQuote(args))
>
>extractArgs(passed)
>
>cat("Exiting getArgs()\n\n")
> }
>
> extractArgs <- function(...)
> {
>cat("\nEntering extractArgs()\n\n")
>
>args <- list(...)
>
>cat("In extractArgs(), names(args[1]) is ")
>cat(names(args[1]))
>cat(" and args[[1]] is ")
>cat(args[[1]])
>cat("\n")
>
>cat("\nExiting extractArgs()\n\n")
> }
>
> Test:
>
> >getArgs(id = 's1002')
>
> Entering getArgs()
>
> In getArgs(), names(args[1]) is id and args[[1]] is s1002
>
> Entering extractArgs()
>
> In extractArgs(), names(args[1]) is  and args[[1]] is id = 's1002'
>
> Exiting extractArgs()
>
> Exiting getArgs()
>
> >extractArgs(id = 's1002')
>
> Entering extractArgs()
>
> In extractArgs(), names(args[1]) is id and args[[1]] is s1002
>
> Exiting extractArgs()
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>

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[R] help with coxme

[Lei Liu]

Hi there,

I have a question on fitting data by coxme. In particular I want to fit a 
random intercept and random slope cox model. Using the rats dataset as an 
example, I generated another covariate x2 and want to specify a random slope 
for x2. Here is my code:

x2=matrix(rep(runif(50), 3), 50, 3)
x2=as.vector(t(x2))

rats2=cbind(rats, x2)

But when I used the coxme function as follows, it gave an error message. 
What is the right way to do it? Thanks a lot!

  coxme(Surv(time, status) ~ rx+x2, data=rats2, random=~ (1+x2)|litter )


Lei Liu
Assistant Professor
Division of Biostatistics and Epidemiology
Dept. of Public Health Sciences
School of Medicine
University of Virginia

3181 Hospital West Complex
Charlottesville, VA 22908-0717

1-434-982-3364 (o)
1-434-806-8086 (c)

[EMAIL PROTECTED]
[EMAIL PROTECTED]

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Re: [R] Transform Normal Dist to ArcTan Dist

[Ben Bolker]

Luis Cota  avmltd.com> writes:

> 
> I have a set of data that is distributed normally.  How can I transform
> this data to fit an ArcTan distribution?
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-help  stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
> 
> 

  we need more information.  This is a stats question more than an R
question, and there isn't enough context here to know either (1) what
arctangent distribution you're talking about (it may be the Cauchy/
t-distribution with 1 df, or it may be something else) or (2) why
you want to transform the distribution, and whether it's a sensible
thing to do in the first place ... (see what the posting guide has
to say about statistical questions ...)

  Ben Bolker

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[R] Passing argument in nested function calls

[Aarti Dahiya]

Please, do not ask why you would do this.  I have simplified my complicated 
code to just the basic problem occuring to be able to make it easier to 
understand the actual problem.

I have two function getArgs() and extractArgs() - code and test results 
provided below.
I test them using getArgs(id = 's1002') from the command line.

getArgs() prints the name of the argument as id and the actual argument as 
s1002, which is correct.

But, when I call extractArgs() from within getArgs() passing value of passed 
(stored in passed, passed is created from paste(names(args),"=", 
sQuote(args))); extractArgs() treats the value of passed as a string "id = 
's1002'" and treats the whole thing as one argument.  So, it prints 
args[[1]] as the whole thing id = 's1002'", but prints blank for 
names(args[[1]]), obviously beacuse it cannot find a name for the argument.

If I call extractArgs(id = 's1002') from the command line, it works just 
fine, prints the name of the argument as id and the actual argument as 
s1002, which is correct.

How do I fix the problem so that when extractArgs() is called within 
getArgs(), it behaves the same way as getArgs() and extracts the argument 
and argument name?  Can we unstring passed or change it into another mode?

I'll appreciate any help or pointers.  Thanks.  Aarti

getArgs <- function(...)
{
cat("\nEntering getArgs()\n\n")

args <- list(...)

cat("In getArgs(), names(args[1]) is ")
cat(names(args[1]))
cat(" and args[[1]] is ")
cat(args[[1]])
cat("\n")

passed <- paste(names(args),"=", sQuote(args))

extractArgs(passed)

cat("Exiting getArgs()\n\n")
}

extractArgs <- function(...)
{
cat("\nEntering extractArgs()\n\n")

args <- list(...)

cat("In extractArgs(), names(args[1]) is ")
cat(names(args[1]))
cat(" and args[[1]] is ")
cat(args[[1]])
cat("\n")

cat("\nExiting extractArgs()\n\n")
}

Test:

>getArgs(id = 's1002')

Entering getArgs()

In getArgs(), names(args[1]) is id and args[[1]] is s1002

Entering extractArgs()

In extractArgs(), names(args[1]) is  and args[[1]] is id = 's1002'

Exiting extractArgs()

Exiting getArgs()

>extractArgs(id = 's1002')

Entering extractArgs()

In extractArgs(), names(args[1]) is id and args[[1]] is s1002

Exiting extractArgs()

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Re: [R] cat and positioning of the output

[Michael H. Prager]

It works on Windows (rgui.exe) with this change:

 for ( i in 1:10 ) { cat("Number",i,"\r"); flush.console(); Sys.sleep(1) 
}; cat("\n")

MHP


on 6/29/2006 4:33 PM Dan Gunter said the following:
> =?ANSI_X3.4-1968?Q?J=3Frn_Schulz?= wrote:
>   
>> Hello R users!
>>
>> I like to use cat in a loop. I know, loops are not the best way in R ... but
>> my question: It is possible to overwrite the expression "Reading row: i" in
>> each iteration of the loop (print out in the below loop on the screen) or
>> more particulary to overwrite the counter "i".
>>
>> for(i in 1:header$M){
>>cat("Reading row: ", i)
>>SparseIndex[[i]] <- readBin( con, integer(), n=MIndexNumber[i], size=4 )
>>SparseSignal[[i]] <- readBin( con, numeric(), n=MIndexNumber[i], size=4 )
>> }
>>
>> Many thanks
>> J?rn Schulz.
>>   
>> 
> On a UNIX terminal, adding '\r' will cause the cursor to go back to the 
> beginning of the same line. I can't speak for Windows.
>
> e.g.
>
> for ( i in 1:10 ) { cat("Number",i,"\r"); Sys.sleep(1) }; cat("\n")
>
> -Dan
>
>   

-- 
Michael Prager, Ph.D.
Southeast Fisheries Science Center
NOAA Center for Coastal Fisheries and Habitat Research
Beaufort, North Carolina  28516
** Opinions expressed are personal, not official.  No
** official endorsement of any product is made or implied.

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Re: [R] cat and positioning of the output

[Philippe Grosjean]

Dan Gunter wrote:
> =?ANSI_X3.4-1968?Q?J=3Frn_Schulz?= wrote:
> 
>>Hello R users!
>>
>>I like to use cat in a loop. I know, loops are not the best way in R ... but
>>my question: It is possible to overwrite the expression "Reading row: i" in
>>each iteration of the loop (print out in the below loop on the screen) or
>>more particulary to overwrite the counter "i".
>>
>>for(i in 1:header$M){
>>   cat("Reading row: ", i)
>>   SparseIndex[[i]] <- readBin( con, integer(), n=MIndexNumber[i], size=4 )
>>   SparseSignal[[i]] <- readBin( con, numeric(), n=MIndexNumber[i], size=4 )
>>}
>>
>>Many thanks
>>J?rn Schulz.
>>  
> 
> On a UNIX terminal, adding '\r' will cause the cursor to go back to the 
> beginning of the same line. I can't speak for Windows.
> 
> e.g.
> 
> for ( i in 1:10 ) { cat("Number",i,"\r"); Sys.sleep(1) }; cat("\n")
> 
> -Dan

It works, but I don't like much strange things that can happen with "\r" 
because the caret is located at the beginning of the line. Look at what 
happens if you forgot the latests 'cat("\n")'. Also, note that for RGui 
under windows, you must use flush.console(). So:

 > for (i in 1:10) {
 >cat("Number",i,"\r")
 >flush.console()
 >Sys.sleep(1)
 > }
 > cat("\n")

does the job. The alternative is to use "\b" repeatedly, which is done 
in progress() indeed.
Best,

Philippe Grosjean

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Re: [R] cat and positioning of the output

[Dan Gunter]

=?ANSI_X3.4-1968?Q?J=3Frn_Schulz?= wrote:
> Hello R users!
>
> I like to use cat in a loop. I know, loops are not the best way in R ... but
> my question: It is possible to overwrite the expression "Reading row: i" in
> each iteration of the loop (print out in the below loop on the screen) or
> more particulary to overwrite the counter "i".
>
> for(i in 1:header$M){
>cat("Reading row: ", i)
>SparseIndex[[i]] <- readBin( con, integer(), n=MIndexNumber[i], size=4 )
>SparseSignal[[i]] <- readBin( con, numeric(), n=MIndexNumber[i], size=4 )
> }
>
> Many thanks
> J?rn Schulz.
>   
On a UNIX terminal, adding '\r' will cause the cursor to go back to the 
beginning of the same line. I can't speak for Windows.

e.g.

for ( i in 1:10 ) { cat("Number",i,"\r"); Sys.sleep(1) }; cat("\n")

-Dan

-- 
Dan Gunter. voice:510-495-2504 fax:510-486-6363 dsd.lbl.gov/~dang

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Re: [R] cat and positioning of the output

[Philippe Grosjean]

=?ANSI_X3.4-1968?Q?J=3Frn_Schulz?= wrote:
> Hello R users!
> 
> I like to use cat in a loop. I know, loops are not the best way in R ... but
> my question: It is possible to overwrite the expression "Reading row: i" in
> each iteration of the loop (print out in the below loop on the screen) or
> more particulary to overwrite the counter "i".

In package svMisc (SciViews bundle):

 > ?progress
 > example(progress)
Best,

Philippe Grosjean


> for(i in 1:header$M){
>cat("Reading row: ", i)
>SparseIndex[[i]] <- readBin( con, integer(), n=MIndexNumber[i], size=4 )
>SparseSignal[[i]] <- readBin( con, numeric(), n=MIndexNumber[i], size=4 )
> }
> 
> Many thanks
> J?rn Schulz.

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Re: [R] cat and positioning of the output

[Gabor Grothendieck]

On Windows XP this works for me:

for(i in 1:3) { if (i > 1) cat("\b"); cat(i); flush.console();
Sys.sleep(1) }; cat("\n")

It displays 1, then it overwrites it with 2 and then overwrites that with 3.


On 6/29/06, J?rn Schulz <[EMAIL PROTECTED]> wrote:
>
> Hello R users!
>
> I like to use cat in a loop. I know, loops are not the best way in R ... but
> my question: It is possible to overwrite the expression "Reading row: i" in
> each iteration of the loop (print out in the below loop on the screen) or
> more particulary to overwrite the counter "i".
>
> for(i in 1:header$M){
>   cat("Reading row: ", i)
>   SparseIndex[[i]] <- readBin( con, integer(), n=MIndexNumber[i], size=4 )
>   SparseSignal[[i]] <- readBin( con, numeric(), n=MIndexNumber[i], size=4 )
> }
>
> Many thanks
> J?rn Schulz.
> --
> View this message in context: 
> http://www.nabble.com/cat-and-positioning-of-the-output-tf1869521.html#a5109359
> Sent from the R help forum at Nabble.com.
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>

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[R] cat and positioning of the output

[J?rn Schulz]

Hello R users!

I like to use cat in a loop. I know, loops are not the best way in R ... but
my question: It is possible to overwrite the expression "Reading row: i" in
each iteration of the loop (print out in the below loop on the screen) or
more particulary to overwrite the counter "i".

for(i in 1:header$M){
   cat("Reading row: ", i)
   SparseIndex[[i]] <- readBin( con, integer(), n=MIndexNumber[i], size=4 )
   SparseSignal[[i]] <- readBin( con, numeric(), n=MIndexNumber[i], size=4 )
}

Many thanks
J?rn Schulz.
-- 
View this message in context: 
http://www.nabble.com/cat-and-positioning-of-the-output-tf1869521.html#a5109359
Sent from the R help forum at Nabble.com.

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Re: [R] How to use a for loop to generate two sequences

[Thomas Lumley]

On Thu, 29 Jun 2006, Xiaohua Dai wrote:

> Hi R users,
>
> Hope the question is not too simple:
>
> How to use a for loop to generate two lists as below:
>
> testlist <- list(test1, test2, ..., test1000)
> stringlist <- list("test1","test2",...,"test1000")

I don't know why you would want to use a for loop:

  stringlist<-as.list(paste("test",1:1000,sep=""))
  testlist<-lapply(stringlist, as.name)


-thomas

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[R] How to use a for loop to generate two sequences

[Xiaohua Dai]

Hi R users,

Hope the question is not too simple:

How to use a for loop to generate two lists as below:

testlist <- list(test1, test2, ..., test1000)
stringlist <- list("test1","test2",...,"test1000")

Thanks
Xiaohua

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Re: [R] Biobass, SAGx, and Jonckheere-Terpstra test

[Prof Brian Ripley]

It is *Biobase*.  That is part of BioC (www.bioconductor.org), although I 
agree that it should make clear where to get non-CRAN packages. (Worse: 
SAGx used not to require it, and only the update to the most recent 
version does.)

On Thu, 29 Jun 2006, Horace Tso wrote:

> Hi list,
>
> I tried to load the package SAGx and failed because it complains it's
> looking for the Biobass which is not there. Then I looked up the package
> list and Biobass is not found.
>
> I'm trying to run the Jonckheere-Terpstra test and from what I see in
> the R archive, SAGx is the only place it's been implemented.
>
>> library(SAGx)
> Loading required package: multtest
> Loading required package: survival
> Loading required package: splines
> Loading required package: sma
> Error in loadNamespace(i, c(lib.loc, .libPaths())) :
>there is no package called 'Biobase'
> Error: package/namespace load failed for 'SAGx'
>
>
> Horace W. Tso
>
> __
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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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[R] Cointegration Test in R

[Dennis Heidemann]

Hello!

I'm using the blrtest() function in the urca package
to test cointegration relationships.
Unfortunately, the hypothesis (restrictions on beta) 
specifies the same restriction on all cointegration vectors.
Is there any possibility to specify different restrictions on
the cointegration vectors?
Are there any other packages in R using cointegration tests?

Thanks and best regards.
Dennis Heidemann
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Re: [R] RCOM Package

[Gabor Grothendieck]

Go into Excel, turn on macro recording, perform whatever operations
you want and look at whatever code is generated for you.

On 6/29/06, Thomas Sudler <[EMAIL PROTECTED]> wrote:
> Hi list,
>
> I just installed the rcom package and tried to read/give out some values
> from/to Excel. Altogether it works great... but nevertheless I don't know
> how the syntax works or in other words: "Which command needs which
> parameters?"
>
> Is there somwhere a manual about this package with good examples? I've read
> the Package description... but there are not really good
> descriptions/examples.
>
> I know the following parameters/commands:
>
> #Connect to the active Workbook
> excel <- comGetObject("Excel.Application")
>
> #Set the active sheet
> sheet <- comGetProperty(excel,"ActiveSheet")
>
> #Set a specific sheet
> sheet <- comGetProperty(excel,"Worksheets","WorksheetXY")
>
> #Create a new Worksheet
> comInvoke(comGetProperty(excel,"Worksheets"),"Add")
>
> #Define a range in a defined sheet
> range1 <- comGetProperty(sheet,"Range","A1","A20")
>
> #Read out this range from Excel
> val1 <- as.double(comGetProperty(range1,"Value"))
>
> #Give back the results to Excel
> comSetProperty(range1,"Value",val1)
>
> Some of my questions are:
>
> - How can I rename a worksheet?
> - How can I define the name of a new worksheet?
> - How can I delete a worksheet?
> - How can I connect to a specific Workbook, if more than one is opened?
> - ...
>
> Can someone help me?
>
> Thanks,
> Thomas
>
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>

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[R] RCOM Package

[Thomas Sudler]

Hi list,

I just installed the rcom package and tried to read/give out some values 
from/to Excel. Altogether it works great... but nevertheless I don't know 
how the syntax works or in other words: "Which command needs which 
parameters?"

Is there somwhere a manual about this package with good examples? I've read 
the Package description... but there are not really good 
descriptions/examples.

I know the following parameters/commands:

#Connect to the active Workbook
excel <- comGetObject("Excel.Application")

#Set the active sheet
sheet <- comGetProperty(excel,"ActiveSheet")

#Set a specific sheet
sheet <- comGetProperty(excel,"Worksheets","WorksheetXY")

#Create a new Worksheet
comInvoke(comGetProperty(excel,"Worksheets"),"Add")

#Define a range in a defined sheet
range1 <- comGetProperty(sheet,"Range","A1","A20")

#Read out this range from Excel
val1 <- as.double(comGetProperty(range1,"Value"))

#Give back the results to Excel
comSetProperty(range1,"Value",val1)

Some of my questions are:

- How can I rename a worksheet?
- How can I define the name of a new worksheet?
- How can I delete a worksheet?
- How can I connect to a specific Workbook, if more than one is opened?
- ...

Can someone help me?

Thanks,
Thomas

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[R] Biobass, SAGx, and Jonckheere-Terpstra test

[Horace Tso]

Hi list,

I tried to load the package SAGx and failed because it complains it's
looking for the Biobass which is not there. Then I looked up the package
list and Biobass is not found. 

I'm trying to run the Jonckheere-Terpstra test and from what I see in
the R archive, SAGx is the only place it's been implemented.

> library(SAGx)
Loading required package: multtest
Loading required package: survival
Loading required package: splines
Loading required package: sma
Error in loadNamespace(i, c(lib.loc, .libPaths())) : 
there is no package called 'Biobase'
Error: package/namespace load failed for 'SAGx'


Horace W. Tso

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Re: [R] Internet Problem in R

[Liaw, Andy]

It could well be a firewall issue.  Try adding --internet2 as argument to
Rgui.exe in the target field of the shortcut for Rgui.

Andy 

From: Elizabeth Purdom
> 
> Hi,
> 
> I have a student who's R seems to be unable to connect to the 
> internet. I have verified that her computer has internet 
> access that's working fine, but that R is not able to 
> establish connections. For example, she cannot download 
> packages for R from the URL site, cannot source webpages, or 
> read.table from a webpage (all of these give errors of not 
> being able to establish a connection). Right now I have shown 
> her how to manually download the zip file for the package and 
> install it from the local file, but she wants Bioconductor -- 
> the instructions for which seem to require the usual internet 
> access. Does anyone have any troubleshooting suggestions? 
> (I've never had problems with the internet interface with R, 
> so I don't even know where to start to try to fix it or even 
> diagnose the problem). Could a firewall have this effect? Wireless?
> 
> Her computer is running version R.2.3.1, on a Windows XP.
> 
> Thanks,
> Elizabeth Purdom
> 
> __
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> PLEASE do read the posting guide! 
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> 
>

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[R] Internet Problem in R

[Elizabeth Purdom]

Hi,

I have a student who's R seems to be unable to connect to the internet. I 
have verified that her computer has internet access that's working fine, 
but that R is not able to establish connections. For example, she cannot 
download packages for R from the URL site, cannot source webpages, or 
read.table from a webpage (all of these give errors of not being able to 
establish a connection). Right now I have shown her how to manually 
download the zip file for the package and install it from the local file, 
but she wants Bioconductor -- the instructions for which seem to require 
the usual internet access. Does anyone have any troubleshooting 
suggestions? (I've never had problems with the internet interface with R, 
so I don't even know where to start to try to fix it or even diagnose the 
problem). Could a firewall have this effect? Wireless?

Her computer is running version R.2.3.1, on a Windows XP.

Thanks,
Elizabeth Purdom

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Re: [R] specify y axis values

[jim holtman]

?axis

> curve(2*x  + 3, 0,10,xaxt='n',yaxt='n')
> axis(1, at=seq(0,10))
> axis(2, at=seq(5,10))
>



On 6/29/06, Marc Bernard <[EMAIL PROTECTED]> wrote:
>
> Dear All,
>
> I am looking how to specify the values on the y axis and x axis for a
> curve function.
> example:
>
> curve(2*x  + 3, 0,10) gives me  a range of x axis in (0,2,4,6,8,10) amd
> for yaxis (5,10,15,20). How to do in order to have the x axis in
> (0,1,2,3,4,5,6,7,8,9,10) and y axis in (5,6,7,8,.., 10).
>
>
> Thanks a lot,
>
> Bernard
>
>
>
> -
>
>[[alternative HTML version deleted]]
>
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>



-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390 (Cell)
+1 513 247 0281 (Home)

What is the problem you are trying to solve?

[[alternative HTML version deleted]]

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Re: [R] R server

[Gabor Csardi]

One approach would be to install R on a unix machine and let other machines
connect to it via a standard X server.
There might be other approaches though

Gabor

On Thu, Jun 29, 2006 at 12:05:40PM -0400, Li, Mike wrote:
> Hi, 
> 
> I just installed R in Windows, it seems to me that R is a standalone
> desktop application. Do you know if R has its server version which could
> handle multi-users, have several distinct R sessions and their own
> variables in Unix or Windows? 
> 
> I saw OpenStatServer, RStatServer available, can those handle
> multi-sessions?
> 
> Thanks
> 
> Mike
> 
> 
>   [[alternative HTML version deleted]]
> 
> __
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-- 
Csardi Gabor <[EMAIL PROTECTED]>MTA RMKI, ELTE TTK

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[R] R server

[Li, Mike]

Hi, 

I just installed R in Windows, it seems to me that R is a standalone
desktop application. Do you know if R has its server version which could
handle multi-users, have several distinct R sessions and their own
variables in Unix or Windows? 

I saw OpenStatServer, RStatServer available, can those handle
multi-sessions?

Thanks

Mike


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Re: [R] Problems Creating an R package

[Prof Brian Ripley]

On Thu, 29 Jun 2006, Thomas Petzoldt wrote:

> Hi Aarti
>
> src/  if you have source files in C or Fortran.
> R/for the R sources.
>
> If you have no C or Fortran files, you should delete the src/ directory.
>
> The syntax error in your R function is simply that the "," is on a new
> line so R "thinks" that the line above is complete.

R does know it is waiting for a ')'.  The error is exactly where it says, at
>> 6: , .env = <

and of course

>> , .env = , class = c("Class", "Object"), ...instanciationTime =
 ^
which is not valid R.

>
> Hope it helps
>
> Thomas P.
>
>
> Aarti Dahiya wrote:
>> Hi all,
>>
>> When I check my package using "Rcmd check ..\myPackage\R.mykg" on Windows in
>> Command Prompt, this is what get:-
>>
>> * using log directory 'C:/R/bin/R.getdata.Rcheck'
>> * using Version 2.3.1 (2006-06-01)
>> * checking for file 'R.getdata/DESCRIPTION' ... OK
>> * checking extension type ... Package
>> * this is package 'R.getdata' version '1.0'
>> * checking package dependencies ... OK
>> * checking if this is a source package ... OK
>> * checking whether package 'R.getdata' can be installed ... OK
>> * checking package directory ... OK
>> * checking for portable file names ... OK
>> * checking DESCRIPTION meta-information ... OK
>> * checking top-level files ... OK
>> * checking index information ... OK
>> * checking package subdirectories ... WARNING
>> Subdirectory 'src' contains no source files.
>> * checking R files for syntax errors ... ERROR
>> Syntax error in file 'R/ConnectionFactory.R'
>>
>> Q1. What should I put in 'src'.  I did put two of my source .R files, it
>> still does not work.
>>
>> Q2. This is what I get if I source R/ConnectionFactory.R.
>> Error in parse(file, n = -1, NULL, "?") : syntax error at
>> 5: }
>> 6: , .env = <
>>
>> These are the contents of R/ConnectionFactory.R.
>>
>> "ConnectionFactory" <-
>> structure(function()
>> {
>>  extend(Object(), "ConnectionFactory")
>> }
>> , .env = , class = c("Class", "Object"), ...instanciationTime =
>
>
>> structure(1151521420.604, class = c("POSIXt",
>> "POSIXct")), formals = c("public", "class"), modifiers = c("public",
>> "class")
>>
>> Please note that this file is one that was automatically generated in
>> R.mykg/R.  My source file ConnectionFactory.R has the actual R code which
>> sources just fine.
>>
>> I will greatly appreciate any help!  Thank you.
>>
>> Aarti
>>
>> __
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>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
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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] initializing table and filling it out

[Gabor Grothendieck]

If you use lapply you don't have to set up the storage area.

Here is an example.  I have used textConnection with character
strings to make this reproducible but you can replace conn with
a vector of filenames,

# test data
Lines1 <- "
1 2
3 4
"

Lines2 <- "
11 12
13 14
"

conn <- list(textConnection(Lines1), textConnection(Lines2))

# this is code
f <- function(f) with(read.table(f), c(a = mean(V1), b = sd(V2)))
do.call(rbind, lapply(conn, f))



On 6/29/06, Cuau <[EMAIL PROTECTED]> wrote:
>
>   Hi everyone,
>
> I'm writting a script that will open multiple files in a  single folder 
> and then will do some calculations to finally save  everything in a big table.
>   So here  is the pseudo code
>
>  #read all files in the given directory
>  myfiles <-list.files("c:\\myDir")
>
>  #initialize table
>  ???
>
>  #loop through files
>  for(f in myfiles[-1]) {
>netMat <- read.table( f, sep" " )
>netMat <-as.matrix(netMat)
>
>   # calculate the needed Stats
>   gden(netMat)->density
>   centralization(netMat, degree) -> Gdegree
>   centralization(netMat, betweenness) -> Gbetweenness
>   centralization(netMat, closeness) -> Gcloseness
>
>  #store into table
>  
>
>  }
>
>So my questions are two
>
>   First how can I initialize the table (it will be a 4 X 1001 table) without 
> filling it out first.
>  Second how can I store each value in the table (i.e. in each round I'll  be 
> adding one full column with density and the 3 different  centralizations)?
>
>  thks
>
>  -Cuau
>
>
>
>
> -
>
>
>[[alternative HTML version deleted]]
>
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Re: [R] superimposing histograms con't

[Martin Maechler]

> "Jeff" == Jeff Miller <[EMAIL PROTECTED]>
> on Wed, 28 Jun 2006 16:20:39 -0400 writes:

Jeff> I was just thinking about this last night.
Jeff> I would like to do the same but WITH overlapping.

Jeff> For example, I graph 2 sets of count data. Say the
Jeff> bars for the 1`s overlap...I would like to show that
Jeff> with a different shading for the group that has the
Jeff> higher frequency. For example, it could be black up to
Jeff> a frequency of 5 followed by diagonal-dashes from 5-7
Jeff> representing the higher frequency of a second group.

Just 5 minutes ago, I've posted a reply to Bill's message
containing R code which I think also solves the above problem.

Solving overlapping visually either by
  (old style) shading  or by
  (new style) transparent colors -- unfortunately only available
  on pdf(version >= 1.4), png(), and quartz(), AFAIK.

Martin Maechler

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Re: [R] Problems Creating an R package

[Thomas Petzoldt]

Hi Aarti

src/  if you have source files in C or Fortran.
R/for the R sources.

If you have no C or Fortran files, you should delete the src/ directory.

The syntax error in your R function is simply that the "," is on a new
line so R "thinks" that the line above is complete.

Hope it helps

Thomas P.


Aarti Dahiya wrote:
> Hi all,
> 
> When I check my package using "Rcmd check ..\myPackage\R.mykg" on Windows in 
> Command Prompt, this is what get:-
> 
> * using log directory 'C:/R/bin/R.getdata.Rcheck'
> * using Version 2.3.1 (2006-06-01)
> * checking for file 'R.getdata/DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'R.getdata' version '1.0'
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking whether package 'R.getdata' can be installed ... OK
> * checking package directory ... OK
> * checking for portable file names ... OK
> * checking DESCRIPTION meta-information ... OK
> * checking top-level files ... OK
> * checking index information ... OK
> * checking package subdirectories ... WARNING
> Subdirectory 'src' contains no source files.
> * checking R files for syntax errors ... ERROR
> Syntax error in file 'R/ConnectionFactory.R'
> 
> Q1. What should I put in 'src'.  I did put two of my source .R files, it 
> still does not work.
> 
> Q2. This is what I get if I source R/ConnectionFactory.R.
> Error in parse(file, n = -1, NULL, "?") : syntax error at
> 5: }
> 6: , .env = <
> 
> These are the contents of R/ConnectionFactory.R.
> 
> "ConnectionFactory" <-
> structure(function()
> {
>   extend(Object(), "ConnectionFactory")
> }
> , .env = , class = c("Class", "Object"), ...instanciationTime = 


> structure(1151521420.604, class = c("POSIXt",
> "POSIXct")), formals = c("public", "class"), modifiers = c("public",
> "class")
> 
> Please note that this file is one that was automatically generated in 
> R.mykg/R.  My source file ConnectionFactory.R has the actual R code which 
> sources just fine.
> 
> I will greatly appreciate any help!  Thank you.
> 
> Aarti
> 
> __
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Re: [R] superimposing histograms con't

[Martin Maechler]

> "Bill" == Bill Shipley <[EMAIL PROTECTED]>
> on Wed, 28 Jun 2006 15:53:35 -0400 writes:

Bill> Earlier, I posted the following question:

Bill> I want to superimpose histograms from three
Bill> populations onto the same graph, changing the shading
Bill> of the bars for each population. After consulting the
Bill> help files and the archives I cannot find out how to
Bill> do this (seemly) simple graph. To be clear, I want

Bill> - a single x axis (from -3 to 18)
Bill> - three groups of bars forming the histograms of each population
Bill>   (they will not overlap much, but this is a detail)
Bill> - the bars from each histogram having different
Bill>   shadings or other  visually distinguishing features.
 
Bill> Gabor Grothendieck [EMAIL PROTECTED] pointed
Bill> to some code to to this but I have found another way
Bill> that works even easier.
 

Bill> hist(x[sel1],xlim=c(a,b),ylim=c(A,B))  - this plots the histogram for 
the
Bill> first group (indexed by sel1) but with an x axis and a y axis that 
spans the
Bill> entire range.
 
Bill> par(new=T)  - to keep on the same graph
 
Bill> hist(x[sel2],main=Null,xlab=NULL,ylab=NULL,axes=F) -superimposes the 
second
Bill> histogram
 
Bill> par(new=T)  - to keep on the same graph
 
Bill> hist(x[sel3],main=Null,xlab=NULL,ylab=NULL,axes=F) -superimposes the 
third
Bill> histogram
 
Hmm, the above does not work (because of 'Null' instead of  'NULL')
but even if you fix that, I'm pretty sure you get pretty wrong
plots.

par(new = TRUE) is quite often a bad choice.
In the present case, plot 2 and 3 use different
coordinate systems than plot 1.

The "correct" solution -- apart from using  lattice::histogram()
with the correct 'superpose' panel is really to make use of the
fact that

  1) hist() returns a "histogram" (S3) object which is plotted by
 
  2) plot.histogram() which has a nice help page even though
 the funcion is namespace-hidden.

Here's a reproducible solution --- with quite a bit of extra
code in order to show two ``colorizations'' for overplotting,
in particular one with ``transparent colors'' :


##MM: construct reproducible example data
set.seed(1)
x <- c(rnorm(50), (rnorm(60) +3.5), (rnorm(40) +3.5 + 3))
str(grouping <- factor(c(rep(1,50), rep(2,60), rep(3,40
(n.gr <- length(table(grouping))) # 3

xr <- range(x)
## Compute all three histograms objects but without plotting:
histL <- tapply(x, grouping, hist, plot = FALSE)
maxC <- max(print( sapply(lapply(histL, "[[", "counts"), max)) ) # 14 15 15

pdf("3histo.pdf", version = "1.4") # >= 1.4 is needed
## or try the default x11()

if((TC <- transparent.cols <- .Device %in% c("pdf", "png"))) {
cols <- hcl(h = seq(30, by=360 / n.gr, length = n.gr), l = 65,
alpha = 0.5) ## << transparency
} else {
h.den <- c(10, 15, 20)
h.ang <- c(45, 15, -30)
}

## Plots the histogram for the
## first group (indexed by sel1) but with an x axis and a y axis that spans the
## entire range.
if(TC) {
plot(histL[[1]], xlim = xr, ylim= c(0, maxC), col = cols[1],
 xlab = "x", main = "3 Histograms of 3 Selections from 'x'")
} else
plot(histL[[1]], xlim = xr, ylim= c(0, maxC), density = h.den[1], angle = 
h.ang[1],
 xlab = "x", main = "Histogram of 3 selections from 'x'")
## Using density instead of color make these *add*

if(!transparent.cols) {
for(j in 2:n.gr)
plot(histL[[j]], add = TRUE, density = h.den[j], angle = h.ang[j])
} else { ## use semi-translucent colors (available only for PDF >= 1.4 and PNG 
devices):
for(j in 2:n.gr)
plot(histL[[j]], add = TRUE, col = cols[j])
}

if(.Device == "pdf") { ## you have set it above
  dev.off()
  system("gv 3histo.pdf &")## or use 'acroread' ;  'xpdf' does not show 
transparent colors...
}

1 ##--- Martin Maechler, ETH Zurich

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[R] initializing table and filling it out

[Cuau]

   Hi everyone,
  
 I'm writting a script that will open multiple files in a  single folder 
and then will do some calculations to finally save  everything in a big table.
   So here  is the pseudo code
  
  #read all files in the given directory
  myfiles <-list.files("c:\\myDir")
  
  #initialize table
  ???
  
  #loop through files
  for(f in myfiles[-1]) {
netMat <- read.table( f, sep" " )
netMat <-as.matrix(netMat)
  
   # calculate the needed Stats
   gden(netMat)->density
   centralization(netMat, degree) -> Gdegree
   centralization(netMat, betweenness) -> Gbetweenness
   centralization(netMat, closeness) -> Gcloseness
  
  #store into table
  
  
  }
  
So my questions are two
  
   First how can I initialize the table (it will be a 4 X 1001 table) without 
filling it out first. 
  Second how can I store each value in the table (i.e. in each round I'll  be 
adding one full column with density and the 3 different  centralizations)?
  
  thks
  
  -Cuau
  
  
  

-


[[alternative HTML version deleted]]

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Re: [R] Extracting R plots from MS Word

[Philipp Pagel]

On Thu, Jun 29, 2006 at 05:15:08PM +1200, [EMAIL PROTECTED] wrote:
> I am revising a paper that I am a co-author of. The figures are plots
> generated from R but at the moment I do not have the R code that generates
> them.
> 
> As this is time critical I would like to slightly abuse the list by asking
> whether anyone knows how to extract from MS Word into a stand-alone
> graphics file a plot that was pasted into Word from R (probably as a
> Windows Metafile, but possibly as a bitmap).

Open the doc file in OpenOffice, save in sxw format (openoffice's old 
native format), unpack the file with unzip and find the figure in the
resulting directory.

I'm not sure if and how this works with the new odt format used by
openoffice now, but sxw will work.

cu
Philipp

-- 
Dr. Philipp PagelTel.  +49-8161-71 2131
Dept. of Genome Oriented Bioinformatics  Fax.  +49-8161-71 2186
Technical University of Munich
Science Center Weihenstephan
85350 Freising, Germany

 and

Institute for Bioinformatics / MIPS  Tel.  +49-89-3187 3675
GSF - National Research Center   Fax.  +49-89-3187 3585
  for Environment and Health
Ingolstädter Landstrasse 1
85764 Neuherberg, Germany
http://mips.gsf.de/staff/pagel

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[R] Problems Creating an R package

[Aarti Dahiya]

Hi all,

When I check my package using "Rcmd check ..\myPackage\R.mykg" on Windows in 
Command Prompt, this is what get:-

* using log directory 'C:/R/bin/R.getdata.Rcheck'
* using Version 2.3.1 (2006-06-01)
* checking for file 'R.getdata/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R.getdata' version '1.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'R.getdata' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Subdirectory 'src' contains no source files.
* checking R files for syntax errors ... ERROR
Syntax error in file 'R/ConnectionFactory.R'

Q1. What should I put in 'src'.  I did put two of my source .R files, it 
still does not work.

Q2. This is what I get if I source R/ConnectionFactory.R.
Error in parse(file, n = -1, NULL, "?") : syntax error at
5: }
6: , .env = <

These are the contents of R/ConnectionFactory.R.

"ConnectionFactory" <-
structure(function()
{
extend(Object(), "ConnectionFactory")
}
, .env = , class = c("Class", "Object"), ...instanciationTime = 
structure(1151521420.604, class = c("POSIXt",
"POSIXct")), formals = c("public", "class"), modifiers = c("public",
"class")

Please note that this file is one that was automatically generated in 
R.mykg/R.  My source file ConnectionFactory.R has the actual R code which 
sources just fine.

I will greatly appreciate any help!  Thank you.

Aarti

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Re: [R] Problems using na.include

[Frank E Harrell Jr]

Greg Distiller wrote:
> Hi
> I am having problems using na.action=na.include in a nlme call. Basically I 
> am trying to run a particular model without including any covariates but my 
> dataset does include some covariates (factors) with missing values. My 
> understanding from the Pinheiro and Bates book is that one would use 
> na.action=na.include in order to treat the missing values as another factor 
> level and then one can also use naPattern to specify which rows must be 
> excluded from the calculation of the objective function.

The approach of adding new categories for missing values has been shown 
to be highly problematic, completely changing the interpretation of the 
predictor and causing biases.  See an article by Werner Vach on this in 
the Encyclopedia of Biostatistics.

> 
> I have tried this but keep getting error messages about being unable to find 
> the object or the function "na.include". I have also tried to replicate the 
> particular Phenobarbital example verbatim from the book but am getting the 
> same error message. Could it be that my version of the nlme package is 
> outdated? I also cannot find any help on na.include...
> 
> Thanks
> 
> Greg
> 
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> 


-- 
Frank E Harrell Jr   Professor and Chair   School of Medicine
  Department of Biostatistics   Vanderbilt University

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Re: [R] Help needed understanding eval,quote,expression

[toby_marks]

Great help, & thanks to both of you.  I actually think I get it. 

I think I was locked into eval(expression  ... ) as the solution.  I did 
search the archives for this question, but it must not have clicked with 
me.The  Thomas Lumley R-help (February 2005) was on the money.  I was 
missing the power & flexibility of the [[ operation.  It is certainly more 
direct.

I do believe this pattern will satisfy my original problem.

> x = list(y=list(y1="hello",y2="world"),z=list(z1="foo",z2="bar"))
> ids = list( zIds=c("z1","z2"),yIds=c("y1","y2"))
> str="y1"
> x$y[[str]]
[1] "hello"


btw:  I set my prompt to $, so the first post, the $ at the beginning of 
the line was the prompt.  apologies for the confusion.


cheers.





Prof Brian Ripley <[EMAIL PROTECTED]> 
06/29/2006 04:06 AM





To
Joerg van den Hoff <[EMAIL PROTECTED]>
cc
[EMAIL PROTECTED], r-help@stat.math.ethz.ch
Subject
Re: [R] Help needed understanding eval,quote,expression






On Thu, 29 Jun 2006, Joerg van den Hoff wrote:

> Prof Brian Ripley wrote:
>> You are missing eval(parse(text=)). E.g.
>> 
>>> x <- list(y=list(y1="hello",y2="world"),z=list(z1="foo",z2="bar"))
>> (what do you mean by the $ at the start of these lines?)
>>> eval(parse(text="x$y$y1"))
>> [1] "hello"
>> 
>> However, bear in mind
>> 
>>> fortune("parse")
>> 
>> If the answer is parse() you should usually rethink the question.
>> -- Thomas Lumley
>>R-help (February 2005)
>> 
>> In your indicated example you could probably use substitute() as 
>> effectively.
>> 
>> 
>> On Wed, 28 Jun 2006, [EMAIL PROTECTED] wrote:
>> 
>>> I am trying to build up a quoted or character expression representing 
a
>>> component in a list  in order to reference it indirectly.
>>> For instance, I have a list that has data I want to pull, and another 
list
>>> that has character vectors and/or lists of characters containing the 
names
>>> of the components in the first list.
>>> 
>>> It seems that the way to do this is as evaluating expressions, but I 
seem
>>> to be missing something.  The concept should be similar to the snippet
>>> below:
>>> 
>>> 
>>> For instance:
>>> 
>>> $x = list(y=list(y1="hello",y2="world"),z=list(z1="foo",z2="bar"))
>>> $y = quote(x$y$y1)
>>> $eval(y)
>>> [1] "hello"
>>> 
>>> 
>>> but, I'm trying to accomplish this by building up y as a character and
>>> then evaluating it, and having no success.
>>> 
>>> $y1=paste("x$y$","y1",sep="")
>>> $y1
>>> [1] "x$y$y1"
>>> 
>>> 
>>> How can I evaluate y1 as I did with y previously?  or can I?
>>> 
>>> 
>>> Much Thanks !
>>> 
>>> 
>
> if I understand you correctly you can achieve your goal much easier than 
with 
> eval, parse, substitute and the like:
>
> x <- list(y=list(y1="hello",y2="world"),z=list(z1="foo",z2="bar"))
>
> s1 <- 'y'
> s2 <- 'y1'
>
> x[[s1]][[s2]]
>
> i.e. using `[[' instead of `$' for list component extraction allows to 
use 
> characters for indexing (in other words: x$y == x[['y']])


But what he actually asked for was

>>> I am trying to build up a quoted or character expression representing 
a
>>> component in a list  in order to reference it indirectly.

You just typed in x[[s1]][[s2]], not 'built [it] up'.  Suppose the 
specification had been

r <- "x"
s <- c("y", "y1")

and s was of variable length?  Then you need to construct a call similar 
to x[["y"]][["y1"]] from r and s.

[There was another reason for sticking with $ rather than using [[: the 
latter makes unnecessary copies in released versions 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



CONFIDENTIALITY NOTICE: This electronic mail transmission (i...{{dropped}}

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[R] multivariate normality test

[Remigijus Lapinskas]

Hello,

Could someone help me to explain the VERY big difference in applying two
tests on multivariate normality:

library(mvnormtest)
data(EuStockMarkets)
mshapiro.test(t(EuStockMarkets[15:29,1:4]))


 Shapiro-Wilk normality test
data:  Z
W = 0.8161, p-value = 0.005955

and

library(energy)
mvnorm.etest( EuStockMarkets[15:29,1:4] )

 Energy test of multivariate normality: estimated parameters

data:  x, sample size 15, dimension 4, replicates 999
E-statistic = 1.0041, p-value = 0.2482



Many thanks,
Rem

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Re: [R] smoothing splines and degrees of freedom

[Spencer Graves]

  The help page for 'smooth.spline' says the argument 'df' is 'the 
desired equivalent number of degrees of freedom (trace of the smoother 
matrix).'  It also explains that the output of 'smooth.spline' includes 
a component 'fit', and two components of 'fit' are 'knot' and 'coef'. 
To learn more, you can run the examples, examine 'str(cars.spl)' and the 
other objects produced by those examples.  You can also read more in the 
references cited there.

  If you would like further help from this group, please submit another 
question, preferably after first reading the posting guide! 
"www.R-project.org/posting-guide.html".  There is substantial but 
anecdotal evidence to suggest that posts more consistent with that guide 
tend to get better answers quicker.  For example, if the above does NOT 
answer your question, I believe you would have gotten a better reply if 
you had provided a simple, self-contained example, rather than having me 
rely on one from the 'example' section of the 'smooth.spline' help page.

  Hope this helps.
  Spencer Graves


Steven Shechter wrote:
> Hi,
> If I set df=2 in my smooth.spline function, is that equivalent to running
> a linear regression through my data?  It appears that df=# of data points
> gives the interpolating spline and that df = 2 gives the linear
> regression, but I just want to confirm this.
> 
> Thank you,
> Steven
> 
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[R] function in boot

[YIHSU CHEN]

Dear R users:

I'm trying to use "boot" function under the package boot to run some 
bootstrapping.

Basically, I have a df as follows. (The data is simplified for illustrative 
purpose.) 

V1 V2 V3
1  2  3 
4  5  7
3  5  2

Say that I want bootrap among (V1,V2,V3) for 1000 times and calculate the 
average of them, ie., v_bar still has lenght of 3. I think my question is 
really how to write bf function below. 

bf <- function(d,f)
{
gp1 <- 1:3 #indicate random draw from three series
dmean <- apply(d[,gp1]*f[gp1],1,mean)  
}
a <- boot(df,bf, R=1000, stype="f")


Any help or suggestions? Many thanks.

Yihsu

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Re: [R] lmer - Is this reasonable output?

[Dimitris Rizopoulos]

Hello Rick,

some comments below:

o in lmer(), 'method = "ML"' and its counterpart "REML" refer to the 
case of linear mixed models; for GLMMs the methods currently available 
are PQL and Laplace. The control argument 'usePQL = FALSE' can be used 
when 'method = Laplace', and in fact specifies not to use PQL as a 
refinement to the initial values.

o SAS proc NLMIXED performs (adaptive) Gaussian Quadrature and is 
conceptually closer to 'method = Laplace' in lmer(); for PQL you have 
to use proc GLIMMIX.

o for GLMMs both lmer() and NLMIXED work with an approximation to the 
observed data likelihood, since this likelihood involves an integral 
with no closed-form solution (except from very specific cases).

o with only 4 clusters I think it'd be difficult to estimate variance 
components; If you want to correct for site, you could just put it as 
an ordinary covariate in your logistic regression.

I hope my comments help.

Best,
Dimitris


Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven

Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://med.kuleuven.be/biostat/
 http://www.student.kuleuven.be/~m0390867/dimitris.htm


- Original Message - 
From: "Rick Bilonick" <[EMAIL PROTECTED]>
To: "R Help" 
Sent: Thursday, June 29, 2006 3:52 PM
Subject: [R] lmer - Is this reasonable output?


> I'm estimating two models for data with n = 179 with four clusters 
> (21,
> 70, 36, and 52) named siteid. I'm estimating a logistic regression 
> model
> with random intercept and another version with random intercept and
> random slope for one of the independent variables.
>
>
> fit.1 <- lmer(glaucoma~(1|siteid)+x1
> +x2,family=binomial,data=set1,method="ML",
>  control=list(usePQL=FALSE,msVerbose=TRUE))
>
> Generalized linear mixed model fit using PQL
> Formula: glaucoma ~ (1 | siteid) + x1 + x2
>  Data: set1
> Family: binomial(logit link)
>  AIC  BIClogLik deviance
> 236.7448 249.4944 -114.3724 228.7448
> Random effects:
> Groups NameVariance Std.Dev.
> siteid (Intercept) 0.05959  0.24411
> number of obs: 179, groups: siteid, 4
>
> Estimated scale (compare to 1)  0.464267
>
> Fixed effects:
> Estimate Std. Error z value Pr(>|z|)
> (Intercept) -2.213779   0.688158 -3.2170 0.001296 **
> x1   0.609028   0.293250  2.0768 0.037818 *
> x2   0.025027   0.009683  2.5846 0.009749 **
> ---
> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
> Correlation of Fixed Effects:
>   (Intr) x1
> x1 -0.871
> x2 -0.372 -0.024
>
>> ranef(fit.1)
> An object of class “ranef.lmer”
> [[1]]
>  (Intercept)
> 1 -0.05053772
> 2 -0.21592157
> 3  0.36643051
> 4 -0.04141520
>
>
> fit.2 <- lmer(glaucoma~(x1|siteid)+x1
> +x2,family=binomial,data=set1,method="ML",
>  control=list(usePQL=FALSE,msVerbose=TRUE))
>
> Generalized linear mixed model fit using PQL
> Formula: glaucoma ~ (x1 | siteid) + x1 + x2
>  Data: set1
> Family: binomial(logit link)
>  AIC  BIClogLik deviance
> 239.3785 258.5029 -113.6893 227.3785
> Random effects:
> Groups NameVariance Std.Dev. Corr
> siteid (Intercept) 0.059590 0.24411
>x1  0.013079 0.11436  0.000
> number of obs: 179, groups: siteid, 4
>
> Estimated scale (compare to 1)  0.4599856
>
> Fixed effects:
>  Estimate Std. Error z value Pr(>|z|)
> (Intercept) -2.2137787  0.6911360 -3.2031 0.001360 **
> x1   0.6090279  0.2995553  2.0331 0.042042 *
> x2   0.0250268  0.0097569  2.5650 0.010316 *
> ---
> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
> Correlation of Fixed Effects:
>   (Intr) x1
> x1 -0.854
> x2 -0.372 -0.023
>
>> ranef(fit.2)
> An object of class “ranef.lmer”
> [[1]]
>  (Intercept)   x1
> 1 -0.05534800  0.009265667
> 2 -0.16991678 -0.052723584
> 3  0.27692026  0.137597965
> 4  0.01648737 -0.062232012
>
> Note that the fixed coefficient estimates are identical for both 
> models
> and they are exactly equal to what glm gives ignoring the sites (but 
> the
> standard errors given by lmer are definitely larger - which would 
> seem
> reasonable). The se's for the fixed factors differ slightly between 
> the
> two models. Note also that the estimated random effect sd for siteid
> intercept is identical for both models.
>
> I ran both models using PROC NLMIXED in SAS. It gives be similar
> estimates but not identical for the fixed effects and random 
> effects.
> The confidence intervals on the random effects for each site are 
> very
> large.
>
> Am I getting these results because I don't really need to fit a 
> random
> effect for siteid? The estimated random effects for slope seem to 
> say
> that siteid matters. When I plot the data for each site with 
> smoothing
> splines it indicates reasonably different patterns between sites.
>
> I don't think these models are that complicated and I have a 
>

[R] lmer - Is this reasonable output?

[Rick Bilonick]

I'm estimating two models for data with n = 179 with four clusters (21,
70, 36, and 52) named siteid. I'm estimating a logistic regression model
with random intercept and another version with random intercept and
random slope for one of the independent variables.


fit.1 <- lmer(glaucoma~(1|siteid)+x1
+x2,family=binomial,data=set1,method="ML",
  control=list(usePQL=FALSE,msVerbose=TRUE))

Generalized linear mixed model fit using PQL
Formula: glaucoma ~ (1 | siteid) + x1 + x2
  Data: set1
 Family: binomial(logit link)
  AIC  BIClogLik deviance
 236.7448 249.4944 -114.3724 228.7448
Random effects:
 Groups NameVariance Std.Dev.
 siteid (Intercept) 0.05959  0.24411
number of obs: 179, groups: siteid, 4

Estimated scale (compare to 1)  0.464267

Fixed effects:
 Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.213779   0.688158 -3.2170 0.001296 **
x1   0.609028   0.293250  2.0768 0.037818 *
x2   0.025027   0.009683  2.5846 0.009749 **
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Correlation of Fixed Effects:
   (Intr) x1
x1 -0.871
x2 -0.372 -0.024

> ranef(fit.1)
An object of class “ranef.lmer”
[[1]]
  (Intercept)
1 -0.05053772
2 -0.21592157
3  0.36643051
4 -0.04141520


fit.2 <- lmer(glaucoma~(x1|siteid)+x1
+x2,family=binomial,data=set1,method="ML",
  control=list(usePQL=FALSE,msVerbose=TRUE))

Generalized linear mixed model fit using PQL
Formula: glaucoma ~ (x1 | siteid) + x1 + x2
  Data: set1
 Family: binomial(logit link)
  AIC  BIClogLik deviance
 239.3785 258.5029 -113.6893 227.3785
Random effects:
 Groups NameVariance Std.Dev. Corr
 siteid (Intercept) 0.059590 0.24411
x1  0.013079 0.11436  0.000
number of obs: 179, groups: siteid, 4

Estimated scale (compare to 1)  0.4599856

Fixed effects:
  Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.2137787  0.6911360 -3.2031 0.001360 **
x1   0.6090279  0.2995553  2.0331 0.042042 *
x2   0.0250268  0.0097569  2.5650 0.010316 *
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Correlation of Fixed Effects:
   (Intr) x1
x1 -0.854
x2 -0.372 -0.023

> ranef(fit.2)
An object of class “ranef.lmer”
[[1]]
  (Intercept)   x1
1 -0.05534800  0.009265667
2 -0.16991678 -0.052723584
3  0.27692026  0.137597965
4  0.01648737 -0.062232012

Note that the fixed coefficient estimates are identical for both models
and they are exactly equal to what glm gives ignoring the sites (but the
standard errors given by lmer are definitely larger - which would seem
reasonable). The se's for the fixed factors differ slightly between the
two models. Note also that the estimated random effect sd for siteid
intercept is identical for both models.

I ran both models using PROC NLMIXED in SAS. It gives be similar
estimates but not identical for the fixed effects and random effects.
The confidence intervals on the random effects for each site are very
large.

Am I getting these results because I don't really need to fit a random
effect for siteid? The estimated random effects for slope seem to say
that siteid matters. When I plot the data for each site with smoothing
splines it indicates reasonably different patterns between sites.

I don't think these models are that complicated and I have a reasonable
amount of data. I fit the fixed and random curves to the separate sites
(along with separate glm estimates for each site). As would be expected,
the random curves lie between the fixed effect curve and the glm curve.
But there seems to be a lot of shrinkage toward the fixed effect curve.
(The fixed effect curve fits the smoothing spline curve for all sites
combined very closely.)

If I specify method="ML" and use PQL, I get similar fixed effect
estimates (but not identical to glm). The random intercept sd about
doubles. I think SAS NLMIXED uses an approximation to the likelihood so
that may explain some of the differences.

One other thing that seems odd to me is the random intercept sd for site
id. It equals 0.24411 in both models. If I change x1 to, say x3 (an
entirely different variable), I still get 0.24411. However, the random
slope sd does change.

I just want to make sure I'm fitting a reasonable model and getting
reasonable estimates.

Rick B.

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Re: [R] boxplot of subset of factors, in an order of my choice [B roadcast]

[Liaw, Andy]

1. Use something like 

  with(testResults, boxplot(score[test == "rTest"]))

2. testResults$test <- factor(as.character(testResults$test),
  levels=c("rTest", "gTest", "fTest"))

[Substitute any order you like in the last line.]

Andy

From: Sumitrajit Dhar
> 
> Hi Folks,
> 
> Say I am working with the following data set:
> testResults:
>   studtestscore
> 1 1   fTest   43
> 2 1   rTest   39
> 3 1   gTest   43
> 4 2   fTest   23
> 5 2   rTest   33
> 6 2   gTest   41
> .
> .
> .
> N n   gTest   47
> 
> I would like to generate a boxplot of rTest only. Here is 
> what I have done after reading the data in and attaching the object.
> 
> test <- factor(test)
> 
> Now when I try
> 
> boxplot(score ~ test, subset = test=="rTest")
> 
> 1. I still see the tick marks for the other factors on the 
> x-axis although no data are plotted. Can I eliminate these 
> extra markers (and the space for these faactors) and just 
> have the tick marker and the label for "rTest"?
> 
> 2. I would also like to be able to rearrange the tests as 
> they appear from left to right on the graph. I read the hints 
> and help about reorder.factor but it does not seem to be the 
> solution in this case.  
> I am wanting to re-order the boxes without any logic 
> (statistical anyways). Can this be done?
> 
> Thanks in advance,
> Sumit
> 
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>

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[R] boxplot of subset of factors, in an order of my choice

[Sumitrajit Dhar]

Hi Folks,

Say I am working with the following data set:
testResults:
studtestscore
1   1   fTest   43
2   1   rTest   39
3   1   gTest   43
4   2   fTest   23
5   2   rTest   33
6   2   gTest   41
.
.
.
N   n   gTest   47

I would like to generate a boxplot of rTest only. Here is what I have  
done after reading the data in and attaching the object.

test <- factor(test)

Now when I try

boxplot(score ~ test, subset = test=="rTest")

1. I still see the tick marks for the other factors on the x-axis  
although no data are plotted. Can I eliminate these extra markers  
(and the space for these faactors) and just have the tick marker and  
the label for "rTest"?

2. I would also like to be able to rearrange the tests as they appear  
from left to right on the graph. I read the hints and help about  
reorder.factor but it does not seem to be the solution in this case.  
I am wanting to re-order the boxes without any logic (statistical  
anyways). Can this be done?

Thanks in advance,
Sumit

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[R] Problems using na.include

[Greg Distiller]

Hi
I am having problems using na.action=na.include in a nlme call. Basically I 
am trying to run a particular model without including any covariates but my 
dataset does include some covariates (factors) with missing values. My 
understanding from the Pinheiro and Bates book is that one would use 
na.action=na.include in order to treat the missing values as another factor 
level and then one can also use naPattern to specify which rows must be 
excluded from the calculation of the objective function.

I have tried this but keep getting error messages about being unable to find 
the object or the function "na.include". I have also tried to replicate the 
particular Phenobarbital example verbatim from the book but am getting the 
same error message. Could it be that my version of the nlme package is 
outdated? I also cannot find any help on na.include...

Thanks

Greg

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[R] specify y axis values

[Marc Bernard]

Dear All,
   
  I am looking how to specify the values on the y axis and x axis for a curve 
function.
  example:
   
  curve(2*x  + 3, 0,10) gives me  a range of x axis in (0,2,4,6,8,10) amd for 
yaxis (5,10,15,20). How to do in order to have the x axis in 
(0,1,2,3,4,5,6,7,8,9,10) and y axis in (5,6,7,8,.., 10).
   
   
  Thanks a lot,
   
  Bernard
   


-

[[alternative HTML version deleted]]

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Re: [R] Running R

[Pramod Anugu]

Thank you Andy for your suggestion. I used the  method 2 and was able to go
upto Step 8. But When I type R

# R
Fatal error: unable to open the base package
 
1.  Tell configure exactly where to find the readline header files (by
something like --with-readline=/where/the/files/are, check configure
--help).
 
2.  Compile R without readline; i.e., configure --with-readline=no.
 
Andy



   1. gunzip  R-patched.tar.gz
   2. tar -xvf R-patched.tar
   3. changed the directory to the newly created directory R-patched
   4. Typed ./configure 
   5. Typed make 
   6. Make check 
   7. make check-all 
   8. Typed make install 
   *9. Typed R

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Re: [R] numerical integration problem

[Duncan Murdoch]

On 6/29/2006 7:38 AM, Sundar Dorai-Raj wrote:
> 
> przeszczepan wrote:
>> Hi,
>> 
>> I have got problems integrating the following function using "integrate": 
>> 
>> lambdat<-function(t){
>> tempT<-T[k,][!is.na(T[k,])]#available values from k-th row of matrix T
>> tempJ<-J[k,][!is.na(J[k,])]
>> 
>> hg<-length(tempT[tempT<=t & tempJ==0])#counts observations satisfing the 
>> conditions
>> ag<-length(tempT[tempT<=t & tempJ==1])
>> 
>> lambdaXY[hg+1,ag+1]#takes  values from a 10x10 matrix
>> }
>> 
>> I keep receiving this message:
>> 
>> 1: longer object length
>> is not a multiple of shorter object length in: tempT <= t 
>> 2: longer object length
>> is not a multiple of shorter object length in: tempT <= t & tempJ == 
>> 0 
>> 
>> What I suspect is that the "integrate" function submits the whole vector of 
>> points at which the integral is to be evaluated at once. For my function to 
>> be integrated it would rather have to be evaluated at each point after 
>> another in a loop of some kind.
>> 
> 
> You suspect correctly. Best to read ?integrate too.
> 
>> Can you think of a way to solve this problem without me having to write the 
>> integrating procedure from scratch (I have no idea about FORTRAN and this is 
>> what the "integrate" description refers to)?
>> 
> 
> Just put a "for"-loop in your function to iterate over t.

Or use Vectorize().

vlambdat <- Vectorize(lambdat)

should give a function that can be passed to integrate(), assuming that 
lambdat works when given a length 1 vector as input.

Duncan Murdoch


> 
>n <- length(t)
>hg <- ag <- vector("numeric", n)
>for(i in seq(n)) {
>  hg[i] <- length(tempT[tempT <= t[i] & tempJ == 0])
>  ag[i] <- length(tempT[tempT <= t[i] & tempJ == 1])
>}
> 
> I doubt this will work because integrate is expecting a vector of 
> n=length(t) from lambdat. The last line of the function returns a nxn 
> matrix. Please submit data to run the function plus your call to 
> integrate in any subsequent postings.
> 
> HTH,
> 
> --sundar
> 
>> Thank you.
>> 
>> Kind Regards,
>> Lukasz Szczepanski
>> Student
>> 
>> __
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> 
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Re: [R] numerical integration problem

[Sundar Dorai-Raj]

przeszczepan wrote:
> Hi,
> 
> I have got problems integrating the following function using "integrate": 
> 
> lambdat<-function(t){
> tempT<-T[k,][!is.na(T[k,])]#available values from k-th row of matrix T
> tempJ<-J[k,][!is.na(J[k,])]
> 
> hg<-length(tempT[tempT<=t & tempJ==0])#counts observations satisfing the 
> conditions
> ag<-length(tempT[tempT<=t & tempJ==1])
> 
> lambdaXY[hg+1,ag+1]#takes  values from a 10x10 matrix
> }
> 
> I keep receiving this message:
> 
> 1: longer object length
> is not a multiple of shorter object length in: tempT <= t 
> 2: longer object length
> is not a multiple of shorter object length in: tempT <= t & tempJ == 
> 0 
> 
> What I suspect is that the "integrate" function submits the whole vector of 
> points at which the integral is to be evaluated at once. For my function to 
> be integrated it would rather have to be evaluated at each point after 
> another in a loop of some kind.
> 

You suspect correctly. Best to read ?integrate too.

> Can you think of a way to solve this problem without me having to write the 
> integrating procedure from scratch (I have no idea about FORTRAN and this is 
> what the "integrate" description refers to)?
> 

Just put a "for"-loop in your function to iterate over t.

   n <- length(t)
   hg <- ag <- vector("numeric", n)
   for(i in seq(n)) {
 hg[i] <- length(tempT[tempT <= t[i] & tempJ == 0])
 ag[i] <- length(tempT[tempT <= t[i] & tempJ == 1])
   }

I doubt this will work because integrate is expecting a vector of 
n=length(t) from lambdat. The last line of the function returns a nxn 
matrix. Please submit data to run the function plus your call to 
integrate in any subsequent postings.

HTH,

--sundar

> Thank you.
> 
> Kind Regards,
> Lukasz Szczepanski
> Student
> 
> __
> R-help@stat.math.ethz.ch mailing list
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[R] numerical integration problem

[przeszczepan]

Hi,

I have got problems integrating the following function using "integrate": 

lambdat<-function(t){
tempT<-T[k,][!is.na(T[k,])]#available values from k-th row of matrix T
tempJ<-J[k,][!is.na(J[k,])]

hg<-length(tempT[tempT<=t & tempJ==0])#counts observations satisfing the 
conditions
ag<-length(tempT[tempT<=t & tempJ==1])

lambdaXY[hg+1,ag+1]#takes  values from a 10x10 matrix
}

I keep receiving this message:

1: longer object length
is not a multiple of shorter object length in: tempT <= t 
2: longer object length
is not a multiple of shorter object length in: tempT <= t & tempJ == 0 

What I suspect is that the "integrate" function submits the whole vector of 
points at which the integral is to be evaluated at once. For my function to be 
integrated it would rather have to be evaluated at each point after another in 
a loop of some kind.

Can you think of a way to solve this problem without me having to write the 
integrating procedure from scratch (I have no idea about FORTRAN and this is 
what the "integrate" description refers to)?

Thank you.

Kind Regards,
Lukasz Szczepanski
Student

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[R] Package Spatialkernel Annocement

[Pingping Zheng]

Hi,

A new R package spatialkernel has been accepted by CRAN. Spatialkernel
focuses on implementation of kernel regression methods proposed in
Diggle P.J. et al (2005), J. R. Stat. Soc. C, 54, 3, 645-658
and kernel density estimation of inhomogeneous Poisson point process
with edge-correction proposed by
M. Berman and P.J. Diggle (1989), J. R. Stat. Soc, B, 51, 81–92,
for an arbitrary polygonal area.

The package source and Windows binary are available at
http://www.maths.lancs.ac.uk/~zhengp1/spatialkernel/
Examples in spatialkernel-package shows a quick run of some basic
functionality.

Sorry for the wrong linked URL address at CRAN archives.

Best wishes


-- 
Dr Pingping Zheng
Department of Mathematics and Statistics
Fylde College
Lancaster University
Lancaster LA1 4YF
UK

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Re: [R] using "rbinom" in C code gives me erroneous results... random variable is not random (always zero)...

[Prof Brian Ripley]

Your text has lost almost all the carriage returns: please do as we ask 
and not send HTML code.

You appear not to be initializing the random seed in your code: the manual 
says:

   The C code behind @R{}'s @[EMAIL PROTECTED] functions can be accessed by
   including the header file @file{Rmath.h}; @xref{Distribution
   functions}.  Those calls generate a single variate and should also be
   enclosed in calls to @code{GetRNGstate} and @code{PutRNGstate}.

Why have you not done so?

On Thu, 29 Jun 2006, Vumani Dlamini wrote:

> Dear Listers,
> I am trying to use "rbinom" in my C code, but i always get zeros as output no 
> matter the probability. Am not sure what I am doing wrong because the 
> function has worked before. Attached in an example. Noticed that "rbinom" 
> expects 'n' to be REAL.
> Regards, Vumani
>
> R  2.3.1 (2006-06-01)
> Windows XP
> Gcc
> /* Called this file binom.c and then ran rcmd shlib on it */#include 
> #include #include #include SEXP 
> binomial(SEXP r, SEXP n, SEXP p){ int i; SEXP out; PROTECT(out = 
> allocVector(REALSXP,INTEGER(r)[0]));  for(i = 0; i < INTEGER(r)[0]; ++i){  
> REAL(out)[i] = rbinom(REAL(n)[0],REAL(p)[0]); } Rprintf("%d   %f   
> %f\n",INTEGER(r)[0],REAL(n)[0],REAL(p)[0]); UNPROTECT(1); return(out);}
>
> ### used theses line in R
> dyn.load("binom.dll").Call("binomial",as.integer(10),as.double(1),as.double(0.4))dyn.unload("binom.dll")
> _
> Try Live.com - your fast, personalized homepage with all the things you care 
> about in one place.
> http://www.live.com/getstarted
>   [[alternative HTML version deleted]]
>
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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 R plots from MS Word

[Jonathan Baron]

Another way to do this is with OpenOffice (OO).  Read the Word file
into OO Writer.  Cut the figure.  Open OO Draw.  Click Paste, and 
the figure appears in Draw.  Save it as EPS, or whatever you
like.  This works for both EMF and WMF.

> * [EMAIL PROTECTED] <[EMAIL PROTECTED]> [060629 08:30]:
> > As this is time critical I would like to slightly abuse the list by asking
> > whether anyone knows how to extract from MS Word into a stand-alone
> > graphics file a plot that was pasted into Word from R (probably as a
> > Windows Metafile, but possibly as a bitmap).

-- 
Jonathan Baron, Professor of Psychology, University of Pennsylvania
Home page: http://www.sas.upenn.edu/~baron
Editor: Judgment and Decision Making (http://journal.sjdm.org)

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Re: [R] re-direct to "more" or "less"

[Gabor Grothendieck]

The first few lines or last few lines of an object can often be viewed
like this:

head(iris)
tail(iris)



On 6/28/06, Mike Wolfgang <[EMAIL PROTECTED]> wrote:
> Dear list,
>
> sometimes my function generates too much data and shows them on screen, i
> cannot view first several lines until program ends and I have to scroll my
> mouse up to get them. Is there any re-direction function in R to pipeline
> outputs to "more" or "less" type functions?
> Thanks
>
> mike
>
>[[alternative HTML version deleted]]
>
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Re: [R] Very slow read.table on Linux, compared to Win2000 [Broad cast]

[Alberto Murta]

On Wednesday 28 June 2006 15:45, Patrick Connolly wrote:
> On Wed, 28-Jun-2006 at 04:43PM -0700, Alberto Murta wrote:
> |> I have a pentium 4 pc with 256 MB of RAM, so I made a text file, tab
> |>
> |> separated, with column names and 15000 x 483 integers:
> |> > system("ls -l teste.txt")
> |>
> |> -rw-r--r--  1 amurta  amurta  16998702 Jun 28 16:08 teste.txt
> |>
> |> the time it took to import it was around 15 secs:
> |> > system.time(teste <- read.delim("teste.txt"))
> |>
> |> [1] 15.349  0.244 16.597  0.000  0.000
> |>
> |> so I think lack of RAM must not be the main problem.
> |> Cheers
> |>
> |> Alberto
> |>
> |> > version
> |>
> |>_
> |> platform   i386-unknown-freebsd6.1
> |> arch   i386
> |> os freebsd6.1
> |> system i386, freebsd6.1
> |> status
> |> major  2
> |> minor  3.1
> |> year   2006
> |> month  06
> |> day01
> |> svn rev38247
> |> language   R
> |> version.string Version 2.3.1 (2006-06-01)
>
> Doesn't tell us about your window manager.  I'd suspect you're using a
> light one.

I'm using KDE 3.5.2 (a not so light one) and running R in emacs.

-- 
  Alberto G. Murta
IPIMAR - Institute of Fisheries and Marine Research 
Avenida de Brasilia; 1449-006 Lisboa; Portugal
Tel: +351 213027120; Fax: +351 213015948

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Re: [R] Extracting R plots from MS Word

[Gabor Grothendieck]

Click the graphic, press ctrl-C to copy it to the clipboard and then
using ctrl-V paste it into mspaint or Xnview (free, find it via google) or other
graphics program and then save it from there.   Which program will
work will depend on the format of the image.

Another possibility is to save the Word file in HTML format.  In
Word, choose File | SaveAs and choose the Save As Type to be Web Page.
That will create an HTML file plus it will create a folder with
one file per image.

On 6/29/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
> Hi,
>
> I am revising a paper that I am a co-author of. The figures are plots
> generated from R but at the moment I do not have the R code that generates
> them.
>
> As this is time critical I would like to slightly abuse the list by asking
> whether anyone knows how to extract from MS Word into a stand-alone
> graphics file a plot that was pasted into Word from R (probably as a
> Windows Metafile, but possibly as a bitmap).
>
> I would be very grateful for help with this.
>
> Regards,  Murray Jorgensen
>
> __
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>

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[R] using "rbinom" in C code gives me erroneous results... random variable is not random (always zero)...

[Vumani Dlamini]

Dear Listers,
I am trying to use "rbinom" in my C code, but i always get zeros as output no 
matter the probability. Am not sure what I am doing wrong because the function 
has worked before. Attached in an example. Noticed that "rbinom" expects 'n' to 
be REAL.
Regards, Vumani
 
R  2.3.1 (2006-06-01)
Windows XP
Gcc
/* Called this file binom.c and then ran rcmd shlib on it */#include 
#include #include #include SEXP binomial(SEXP 
r, SEXP n, SEXP p){ int i; SEXP out; PROTECT(out = 
allocVector(REALSXP,INTEGER(r)[0]));  for(i = 0; i < INTEGER(r)[0]; ++i){  
REAL(out)[i] = rbinom(REAL(n)[0],REAL(p)[0]); } Rprintf("%d   %f   
%f\n",INTEGER(r)[0],REAL(n)[0],REAL(p)[0]); UNPROTECT(1); return(out);}
 
### used theses line in R
dyn.load("binom.dll").Call("binomial",as.integer(10),as.double(1),as.double(0.4))dyn.unload("binom.dll")
_
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Re: [R] zero.print in print.table after adding margins

[Peter Dalgaard]

"BXC (Bendix Carstensen)" <[EMAIL PROTECTED]> writes:

> The function addmargins() adds margins to a table, but returns a matrix.
> But even after converted to a table the print.zero="." option of
> print.table() does not work:
> 
> > x <- sample( 1:7, 20, replace=T )
> > y <- sample( 1:7, 20, replace=T )
> > tt <- table( x, y )
> > tx <- as.table( addmargins( table( x, y ) ) )
> > print( tt, zero.print="." )
>y
> x   1 2 3 4 5 6 7
>   1 1 2 2 . . 1 .
>   2 1 . . 1 . . .
>   3 . . . . . . 2
>   4 1 . . . . 1 .
>   5 1 . 1 . . 1 .
>   6 . 1 . 1 . . .
>   7 . . 1 . 1 1 .
> > print( tx, zero.print="." )
>  y
> x  1  2  3  4  5  6  7 Sum
>   11  2  2  0  0  1  0   6
>   21  0  0  1  0  0  0   2
>   30  0  0  0  0  0  2   2
>   41  0  0  0  0  1  0   2
>   51  0  1  0  0  1  0   3
>   60  1  0  1  0  0  0   2
>   70  0  1  0  1  1  0   3
>   Sum  4  3  4  2  1  4  2  20
> 
> Is this a facility of print.table?
> The attributes() of tt and tx have identical stucture. 

It appears to be intentional.

print.table has

if (is.integer(x) && zero.print != "0" && any(i0 <- !ina &
x == 0))
xx[i0] <- sub("0", zero.print, xx[i0])

and of course,

> storage.mode(tx)
[1] "double"
> storage.mode(tt)
[1] "integer"

The reason could be that it is not entirely clear what to expect for
values that are zero up to round-off.

storage.mode(tx) <- "integer" fixes things up.

-- 
   O__   Peter Dalgaard Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark  Ph:  (+45) 35327918
~~ - ([EMAIL PROTECTED])  FAX: (+45) 35327907

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Re: [R] Running R [Broadcast]

[Peter Dalgaard]

"Liaw, Andy" <[EMAIL PROTECTED]> writes:

> You have two choices (AFAIK): 
>  
> 1.  Tell configure exactly where to find the readline header files (by
> something like --with-readline=/where/the/files/are, check configure
> --help).
>  
> 2.  Compile R without readline; i.e., configure --with-readline=no.
>  
> Andy


But first check sequencing - I'm pretty sure that configure can find
header files on RedHat if they are there. 

He's not too good at interpreting his output:

> --One suggestion was to install readline-devel. But according to the below I
> 
> already have readline-devel. 
> 
> # find . -iname readline-devel\* 
>  find -iname readline-devel\* 
> ./os/4.1/x86_64/RedHat/RPMS/readline-devel-4.3-13.x86_64.rpm 
> 
> #rpm -ivh readline*.rpm 
> Preparing...### 
> [100%] 
> package readline-4.3-13 is already installed 

and as far as I can see, this means that readline-devel got installed
and readline (NOT -devel) was there already. So readline-devel is
there now, but wasn't there before. Now did he rerun configure? If so,
did it fail with a different message?



-- 
   O__   Peter Dalgaard Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark  Ph:  (+45) 35327918
~~ - ([EMAIL PROTECTED])  FAX: (+45) 35327907

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Re: [R] Mixing grid and base graphics--need help understanding this quirk

[Paul Murrell]

Hi


Kevin Wright wrote:
> My setup: Windows 2000, R 2.3.1
> 
> When I start a brand new session of R and paste the code below into R,
> the graphic device shows "Some text" in the lower left corner.  If I
> paste the code into the command window again, then "Some text" does
> not appear in the lower left corner.  Why is this?
> 
> require(grid)
> par(mfrow=c(1,2))
> plot(1:10)
> plot(-10:1)
> par(mfrow=c(1,1))
> pushViewport(viewport(.04, .04, width=stringWidth("Some text"),
> height=unit(2,"lines"),
>   name="pagenum", gp=gpar(fontsize=10)))
> grid.text("Some text", gp=gpar(col="gray30"),
>   just=c("left","bottom"))
> popViewport()


Good question! :)

Short answer:
Traditional and grid graphics are fighting each other for control of the
clipping region.

Simple fix/workaround:
Explicitly set the clipping region for the grid output, like this ...

require(grid)
par(mfrow=c(1,2))
plot(1:10)
plot(-10:1)
par(mfrow=c(1,1))
# Requires R >= 2.3.0
grid.clip()
pushViewport(viewport(.04, .04, width=stringWidth("Some text"),
height=unit(2,"lines"),
  name="pagenum", gp=gpar(fontsize=10)))
grid.text("Some text", gp=gpar(col="gray30"),
  just=c("left","bottom"))
popViewport()

Long answer:
The first time you run the code, the pushViewport() call is the first
grid operation on the graphics device, so some initial grid set up
occurs, *including setting the clipping region to the whole device*.
The second time you run the code, the pushViewport() call just inherits
the current clipping region (which is the one set by the last
traditional plot) so the text gets clipped.  You can see this effect,
with the following code (the text does not even appear the first time
because the grid initialisation occurs before the traditional plots) ...

require(grid)
grid.newpage()
par(mfrow=c(1,2))
plot(1:10)
plot(-10:1)
par(mfrow=c(1,1))
pushViewport(viewport(.04, .04, width=stringWidth("Some text"),
height=unit(2,"lines"),
  name="pagenum", gp=gpar(fontsize=10)))
grid.text("Some text", gp=gpar(col="gray30"),
  just=c("left","bottom"))
popViewport()

... so really the problem is that the text should never appear.

Interestingly, if you run your original code (text is drawn), then run
it again (text is not drawn), then ONLY run the grid part (push, text,
pop) the text DOES get drawn!  This happens because the popViewport()
restores the clipping region of the previous grid viewport (which is the
whole device).

I need to think a bit more about whether this behaviour can be "fixed",
whether it should be fixed, or whether the current "user beware" warning
about mixing traditional and grid graphics is sufficient.

Paul
-- 
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
[EMAIL PROTECTED]
http://www.stat.auckland.ac.nz/~paul/

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[R] zero.print in print.table after adding margins

[BXC (Bendix Carstensen)]

The function addmargins() adds margins to a table, but returns a matrix.
But even after converted to a table the print.zero="." option of
print.table() does not work:

> x <- sample( 1:7, 20, replace=T )
> y <- sample( 1:7, 20, replace=T )
> tt <- table( x, y )
> tx <- as.table( addmargins( table( x, y ) ) )
> print( tt, zero.print="." )
   y
x   1 2 3 4 5 6 7
  1 1 2 2 . . 1 .
  2 1 . . 1 . . .
  3 . . . . . . 2
  4 1 . . . . 1 .
  5 1 . 1 . . 1 .
  6 . 1 . 1 . . .
  7 . . 1 . 1 1 .
> print( tx, zero.print="." )
 y
x  1  2  3  4  5  6  7 Sum
  11  2  2  0  0  1  0   6
  21  0  0  1  0  0  0   2
  30  0  0  0  0  0  2   2
  41  0  0  0  0  1  0   2
  51  0  1  0  0  1  0   3
  60  1  0  1  0  0  0   2
  70  0  1  0  1  1  0   3
  Sum  4  3  4  2  1  4  2  20

Is this a facility of print.table?
The attributes() of tt and tx have identical stucture. 

Best,
Bendix
--
Bendix Carstensen
Senior Statistician
Steno Diabetes Center
Niels Steensens Vej 2
DK-2820 Gentofte
Denmark
tel: +45 44 43 87 38
mob: +45 30 75 87 38
fax: +45 44 43 07 06
[EMAIL PROTECTED]
www.biostat.ku.dk/~bxc

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Re: [R] Very slow read.table on Linux, compared to Win2000 [Broad cast]

[Patrick Connolly]

On Wed, 28-Jun-2006 at 04:43PM -0700, Alberto Murta wrote:

|> I have a pentium 4 pc with 256 MB of RAM, so I made a text file, tab 
|> separated, with column names and 15000 x 483 integers:
|> 
|> > system("ls -l teste.txt")
|> -rw-r--r--  1 amurta  amurta  16998702 Jun 28 16:08 teste.txt
|> 
|> the time it took to import it was around 15 secs:
|> 
|> > system.time(teste <- read.delim("teste.txt"))
|> [1] 15.349  0.244 16.597  0.000  0.000
|> 
|> so I think lack of RAM must not be the main problem.
|> Cheers
|> 
|> Alberto
|> 
|> 
|> > version
|>_
|> platform   i386-unknown-freebsd6.1
|> arch   i386
|> os freebsd6.1
|> system i386, freebsd6.1
|> status
|> major  2
|> minor  3.1
|> year   2006
|> month  06
|> day01
|> svn rev38247
|> language   R
|> version.string Version 2.3.1 (2006-06-01)

Doesn't tell us about your window manager.  I'd suspect you're using a
light one.



-- 
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.   
   ___Patrick Connolly   
 {~._.~} Great minds discuss ideas
 _( Y )_Middle minds discuss events 
(:_~*~_:)Small minds discuss people  
 (_)-(_)   . Anon
  
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Re: [R] kmeans clustering

[Andrej Kastrin]

richard mendes wrote:
> Hello R list members,
>
> I'm a bio informatics student from the Leiden university
> (netherlands). We were asked to make a program with different
> clustering methods. The problem we are experiencing is the following.
>
> we have a matrix with data like the following
>
>  research1research2research3enz
> sample1  0.5 0.2  0.4
>
> sample2  0.4 0.4  0.3
>
> sample3  0.7 0.2  0.8
>
> enz
>
>
> now if we use kmeans(matrix,3,20) the clustering method will cluster
> only on rows by using the columns values as multiple variables. The
> output from this syntax is for example
>
> sample1 = 1
> sample2 = 2
> sample3 = 3
> enz
>
> Is there a method that will use the rows and columns as seperate
> values so that every variable in the matrix will be assigned to a
> cluster instead of a row.
>
> the output then could be interperted as a heatmap.
>
> thank you in advance for your time,
>
> Richard Mendes
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
>   
You mean something like:?
kmeans(dataMatrix,5) ## clustering by rows
kmeans(t(dataMatrix),5) ## clustering by attribute

HTH, Andrej

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[R] kmeans clustering

[richard mendes]

Hello R list members,

I'm a bio informatics student from the Leiden university
(netherlands). We were asked to make a program with different
clustering methods. The problem we are experiencing is the following.

we have a matrix with data like the following

 research1research2research3enz
sample1  0.5 0.2  0.4

sample2  0.4 0.4  0.3

sample3  0.7 0.2  0.8

enz


now if we use kmeans(matrix,3,20) the clustering method will cluster
only on rows by using the columns values as multiple variables. The
output from this syntax is for example

sample1 = 1
sample2 = 2
sample3 = 3
enz

Is there a method that will use the rows and columns as seperate
values so that every variable in the matrix will be assigned to a
cluster instead of a row.

the output then could be interperted as a heatmap.

thank you in advance for your time,

Richard Mendes

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Re: [R] Running R [Broadcast]

[Liaw, Andy]

You have two choices (AFAIK): 
 
1.  Tell configure exactly where to find the readline header files (by
something like --with-readline=/where/the/files/are, check configure
--help).
 
2.  Compile R without readline; i.e., configure --with-readline=no.
 
Andy

  _  

From: [EMAIL PROTECTED] on behalf of Pramod Anugu
Sent: Wed 6/28/2006 4:18 PM
To: r-help@stat.math.ethz.ch
Subject: Re: [R] Running R [Broadcast]



[EMAIL PROTECTED] R-2.3.0]# ./configure 
checking build system type... x86_64-unknown-linux-gnu 
checking host system type... x86_64-unknown-linux-gnu 
loading site script './config.site' 
loading build specific script './config.site' 
checking for pwd... /bin/pwd 
checking whether builddir is srcdir... yes 
checking for working aclocal... found 
checking for working autoconf... found 
checking for working automake... found 
checking for working autoheader... found 
checking for working makeinfo... found 
checking for gawk... gawk 
checking for egrep... grep -E 
checking whether ln -s works... yes 
checking for ranlib... ranlib 
checking for bison... no 
checking for byacc... no 
checking for ar... ar 
checking for a BSD-compatible install... /usr/bin/install -c 
checking for sed... /bin/sed 
checking for less... /usr/bin/less 
checking for perl... /usr/bin/perl 
checking whether perl version is at least 5.004... yes 
checking for dvips... /usr/bin/dvips 
checking for tex... /usr/bin/tex 
checking for latex... /usr/bin/latex 
checking for makeindex... /usr/bin/makeindex 
checking for pdftex... /usr/bin/pdftex 
checking for pdflatex... /usr/bin/pdflatex 
checking for makeinfo... /usr/bin/makeinfo 
checking for unzip... /usr/bin/unzip 
checking for zip... /usr/bin/zip 
checking for gzip... /bin/gzip 
checking for firefox... /usr/bin/firefox 
using default browser ... /usr/bin/firefox 
checking for acroread... no 
checking for acroread4... no 
checking for xpdf... no 
checking for gv... no 
checking for gnome-gv... no 
checking for ggv... /usr/bin/ggv 
checking for gcc... gcc 
checking for C compiler default output file name... a.out 
checking whether the C compiler works... yes 
checking whether we are cross compiling... no 
checking for suffix of executables... 
checking for suffix of object files... o 
checking whether we are using the GNU C compiler... yes 
checking whether gcc accepts -g... yes 
checking for gcc option to accept ANSI C... none needed 
checking how to run the C preprocessor... gcc -E 
checking whether gcc needs -traditional... no 
checking how to run the C preprocessor... gcc -E 
checking for g77... g77 
checking whether we are using the GNU Fortran 77 compiler... yes 
checking whether g77 accepts -g... yes 
checking for g++... g++ 
checking whether we are using the GNU C++ compiler... yes 
checking whether g++ accepts -g... yes 
checking how to run the C++ preprocessor... g++ -E 
checking whether __attribute__((visibility())) is supported... yes 
checking whether gcc accepts -fvisibility... yes 
checking whether g77 accepts -fvisibility... yes 
checking for a sed that does not truncate output... /bin/sed 
checking for ld used by gcc... /usr/bin/ld 
checking if the linker (/usr/bin/ld) is GNU ld... yes 
checking for /usr/bin/ld option to reload object files... -r 
checking for BSD-compatible nm... /usr/bin/nm -B 
checking how to recognise dependent libraries... pass_all 
checking for ANSI C header files... yes 
checking for sys/types.h... yes 
checking for sys/stat.h... yes 
checking for stdlib.h... yes 
checking for string.h... yes 
checking for memory.h... yes 
checking for strings.h... yes 
checking for inttypes.h... yes 
checking for stdint.h... yes 
checking for unistd.h... yes 
checking dlfcn.h usability... yes 
checking dlfcn.h presence... yes 
checking for dlfcn.h... yes 
checking the maximum length of command line arguments... 32768 
checking command to parse /usr/bin/nm -B output from gcc object... ok 
checking for objdir... .libs 
checking for ranlib... (cached) ranlib 
checking for strip... strip 
checking if gcc static flag  works... yes 
checking if gcc supports -fno-rtti -fno-exceptions... no 
checking for gcc option to produce PIC... -fPIC 
checking if gcc PIC flag -fPIC works... yes 
checking if gcc supports -c -o file.o... yes 
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared 
libraries... yes 
checking whether -lc should be explicitly linked in... no 
checking dynamic linker characteristics... GNU/Linux ld.so 
checking how to hardcode library paths into programs... immediate 
checking whether stripping libraries is possible... yes 
checking if libtool supports shared libraries... yes 
checking whether to build shared libraries... yes 
checking whether to build static libraries... no 
configure: creating libtool 
appending configuration tag "CXX" to libtool 
checking for ld used by g++... /usr/bin/ld -m elf_x86_64 
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes 
checking whether the g++ linker (/usr/bin/ld -m el

Re: [R] re-direct to "more" or "less"

[Prof Brian Ripley]

Please read the help before replying ...


page(iris, method="print")


does exactly what I understand was asked for.

On Thu, 29 Jun 2006, Søren Højsgaard wrote:


No - not like page(). Page (on windows) gives

structure(list(Sepal.Length = c(5.1, 4.9, 4.7, 4.6, 5, 5.4, 4.6,
5, 4.4, 4.9, 5.4, 4.8, 4.8, 4.3, 5.8, 5.7, 5.4, 5.1, 5.7, 5.1,
5.4, 5.1, 4.6, 5.1, 4.8, 5, 5, 5.2, 5.2, 4.7, 4.8, 5.4, 5.2, .

while the less() function below gives

Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1 5.1 3.5 1.4 0.2 setosa
2 4.9 3 1.4 0.2 setosa
3 4.7 3.2 1.3 0.2 setosa
4 4.6 3.1 1.5 0.2 setosa


Regards
Søren





-Oprindelig meddelelse-
Fra: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] På vegne
af Peter Dalgaard
Sendt: 29. juni 2006 10:31
Til: Søren Højsgaard
Cc: Mike Wolfgang; R-help list
Emne: Re: [R] re-direct to "more" or "less"

Søren Højsgaard <[EMAIL PROTECTED]> writes:


Something like

less <- function(a){
  fn <- paste(tempdir(),"\\dataframe.txt",sep='',collapse='')
  write.table(a, quote=F, file=fn)
  system(paste("less ",fn))
}

could perhaps help you (assuming that you have less on your

computer). I agree that it would be very nice to have a
built-in version...


Like page(), you mean... ?

:-)

(This goes via file.show, so Windows GUI users get a separate
window, I suppose.)


Regards
Søren




-Oprindelig meddelelse-
Fra: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] På vegne af

Mike Wolfgang

Sendt: 29. juni 2006 04:29
Til: R-help list
Emne: [R] re-direct to "more" or "less"

Dear list,

sometimes my function generates too much data and shows them on
screen, i cannot view first several lines until program

ends and I

have to scroll my mouse up to get them. Is there any re-direction
function in R to pipeline outputs to "more"
or "less" type functions?
Thanks

mike

[[alternative HTML version deleted]]

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--
   O__   Peter Dalgaard Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark  Ph:
(+45) 35327918
~~ - ([EMAIL PROTECTED])  FAX:
(+45) 35327907



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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] Help needed understanding eval,quote,expression

[Prof Brian Ripley]

On Thu, 29 Jun 2006, Joerg van den Hoff wrote:

> Prof Brian Ripley wrote:
>> You are missing eval(parse(text=)). E.g.
>> 
>>> x <- list(y=list(y1="hello",y2="world"),z=list(z1="foo",z2="bar"))
>> (what do you mean by the $ at the start of these lines?)
>>> eval(parse(text="x$y$y1"))
>> [1] "hello"
>> 
>> However, bear in mind
>> 
>>> fortune("parse")
>> 
>> If the answer is parse() you should usually rethink the question.
>> -- Thomas Lumley
>>R-help (February 2005)
>> 
>> In your indicated example you could probably use substitute() as 
>> effectively.
>> 
>> 
>> On Wed, 28 Jun 2006, [EMAIL PROTECTED] wrote:
>> 
>>> I am trying to build up a quoted or character expression representing a
>>> component in a list  in order to reference it indirectly.
>>> For instance, I have a list that has data I want to pull, and another list
>>> that has character vectors and/or lists of characters containing the names
>>> of the components in the first list.
>>> 
>>> It seems that the way to do this is as evaluating expressions, but I seem
>>> to be missing something.  The concept should be similar to the snippet
>>> below:
>>> 
>>> 
>>> For instance:
>>> 
>>> $x = list(y=list(y1="hello",y2="world"),z=list(z1="foo",z2="bar"))
>>> $y = quote(x$y$y1)
>>> $eval(y)
>>> [1] "hello"
>>> 
>>> 
>>> but, I'm trying to accomplish this by building up y as a character and
>>> then evaluating it, and having no success.
>>> 
>>> $y1=paste("x$y$","y1",sep="")
>>> $y1
>>> [1] "x$y$y1"
>>> 
>>> 
>>> How can I evaluate y1 as I did with y previously?  or can I?
>>> 
>>> 
>>> Much Thanks !
>>> 
>>> 
>
> if I understand you correctly you can achieve your goal much easier than with 
> eval, parse, substitute and the like:
>
> x <- list(y=list(y1="hello",y2="world"),z=list(z1="foo",z2="bar"))
>
> s1 <- 'y'
> s2 <- 'y1'
>
> x[[s1]][[s2]]
>
> i.e. using `[[' instead of `$' for list component extraction allows to use 
> characters for indexing (in other words: x$y == x[['y']])


But what he actually asked for was

>>> I am trying to build up a quoted or character expression representing a
>>> component in a list  in order to reference it indirectly.

You just typed in x[[s1]][[s2]], not 'built [it] up'.  Suppose the 
specification had been

r <- "x"
s <- c("y", "y1")

and s was of variable length?  Then you need to construct a call similar 
to x[["y"]][["y1"]] from r and s.

[There was another reason for sticking with $ rather than using [[: the 
latter makes unnecessary copies in released versions 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] re-direct to "more" or "less"

[Peter Dalgaard]

Søren Højsgaard <[EMAIL PROTECTED]> writes:

> No - not like page(). Page (on windows) gives
> 
> structure(list(Sepal.Length = c(5.1, 4.9, 4.7, 4.6, 5, 5.4, 4.6, 
> 5, 4.4, 4.9, 5.4, 4.8, 4.8, 4.3, 5.8, 5.7, 5.4, 5.1, 5.7, 5.1, 
> 5.4, 5.1, 4.6, 5.1, 4.8, 5, 5, 5.2, 5.2, 4.7, 4.8, 5.4, 5.2, .
> 
> while the less() function below gives
> 
> Sepal.Length Sepal.Width Petal.Length Petal.Width Species
> 1 5.1 3.5 1.4 0.2 setosa
> 2 4.9 3 1.4 0.2 setosa
> 3 4.7 3.2 1.3 0.2 setosa
> 4 4.6 3.1 1.5 0.2 setosa
> 


If all else fails, read the manual...: page() has a method= argument.
(It might not be a bad idea to switch the default, though).

> > -Oprindelig meddelelse-
> > Fra: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] På vegne 
> > af Peter Dalgaard
> > Sendt: 29. juni 2006 10:31
> > Til: Søren Højsgaard
> > Cc: Mike Wolfgang; R-help list
> > Emne: Re: [R] re-direct to "more" or "less"
> > 
> > Søren Højsgaard <[EMAIL PROTECTED]> writes:
> > 
> > > Something like
> > > 
> > > less <- function(a){
> > >   fn <- paste(tempdir(),"\\dataframe.txt",sep='',collapse='')
> > >   write.table(a, quote=F, file=fn)
> > >   system(paste("less ",fn))
> > > }
> > > 
> > > could perhaps help you (assuming that you have less on your 
> > computer). I agree that it would be very nice to have a 
> > built-in version...
> > 
> > 
> > Like page(), you mean... ?
> > 
> > :-)
> > 
> > (This goes via file.show, so Windows GUI users get a separate 
> > window, I suppose.) 
> > 
> > > Regards
> > > Søren
> > > 
> > >  
> > > 
> > > > -Oprindelig meddelelse-
> > > > Fra: [EMAIL PROTECTED] 
> > > > [mailto:[EMAIL PROTECTED] På vegne af 
> > Mike Wolfgang
> > > > Sendt: 29. juni 2006 04:29
> > > > Til: R-help list
> > > > Emne: [R] re-direct to "more" or "less"
> > > > 
> > > > Dear list,
> > > > 
> > > > sometimes my function generates too much data and shows them on 
> > > > screen, i cannot view first several lines until program 
> > ends and I 
> > > > have to scroll my mouse up to get them. Is there any re-direction 
> > > > function in R to pipeline outputs to "more"
> > > > or "less" type functions?
> > > > Thanks
> > > > 
> > > > mike
> > > > 
> > > > [[alternative HTML version deleted]]
> > > > 
> > > > __
> > > > R-help@stat.math.ethz.ch mailing list 
> > > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > > PLEASE do read the posting guide! 
> > > > http://www.R-project.org/posting-guide.html
> > > >
> > > 
> > > __
> > > R-help@stat.math.ethz.ch mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide! 
> > > http://www.R-project.org/posting-guide.html
> > > 
> > 
> > -- 
> >O__   Peter Dalgaard Øster Farimagsgade 5, Entr.B
> >   c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
> >  (*) \(*) -- University of Copenhagen   Denmark  Ph:  
> > (+45) 35327918
> > ~~ - ([EMAIL PROTECTED])  FAX: 
> > (+45) 35327907
> > 
> 

-- 
   O__   Peter Dalgaard Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark  Ph:  (+45) 35327918
~~ - ([EMAIL PROTECTED])  FAX: (+45) 35327907

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Re: [R] Help needed understanding eval,quote,expression

[Joerg van den Hoff]

Prof Brian Ripley wrote:
> You are missing eval(parse(text=)). E.g.
> 
>> x <- list(y=list(y1="hello",y2="world"),z=list(z1="foo",z2="bar"))
> (what do you mean by the $ at the start of these lines?)
>> eval(parse(text="x$y$y1"))
> [1] "hello"
> 
> However, bear in mind
> 
>> fortune("parse")
> 
> If the answer is parse() you should usually rethink the question.
> -- Thomas Lumley
>R-help (February 2005)
> 
> In your indicated example you could probably use substitute() as 
> effectively.
> 
> 
> On Wed, 28 Jun 2006, [EMAIL PROTECTED] wrote:
> 
>> I am trying to build up a quoted or character expression representing a
>> component in a list  in order to reference it indirectly.
>> For instance, I have a list that has data I want to pull, and another list
>> that has character vectors and/or lists of characters containing the names
>> of the components in the first list.
>>
>>
>> It seems that the way to do this is as evaluating expressions, but I seem
>> to be missing something.  The concept should be similar to the snippet
>> below:
>>
>>
>> For instance:
>>
>> $x = list(y=list(y1="hello",y2="world"),z=list(z1="foo",z2="bar"))
>> $y = quote(x$y$y1)
>> $eval(y)
>> [1] "hello"
>>
>>
>> but, I'm trying to accomplish this by building up y as a character and
>> then evaluating it, and having no success.
>>
>> $y1=paste("x$y$","y1",sep="")
>> $y1
>> [1] "x$y$y1"
>>
>>
>> How can I evaluate y1 as I did with y previously?  or can I?
>>
>>
>> Much Thanks !
>>
>>

if I understand you correctly you can achieve your goal much easier than 
with eval, parse, substitute and the like:

x <- list(y=list(y1="hello",y2="world"),z=list(z1="foo",z2="bar"))

s1 <- 'y'
s2 <- 'y1'

x[[s1]][[s2]]

i.e. using `[[' instead of `$' for list component extraction allows to 
use characters for indexing (in other words: x$y == x[['y']])

joerg

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Re: [R] re-direct to "more" or "less"

[Søren Højsgaard]

No - not like page(). Page (on windows) gives

structure(list(Sepal.Length = c(5.1, 4.9, 4.7, 4.6, 5, 5.4, 4.6, 
5, 4.4, 4.9, 5.4, 4.8, 4.8, 4.3, 5.8, 5.7, 5.4, 5.1, 5.7, 5.1, 
5.4, 5.1, 4.6, 5.1, 4.8, 5, 5, 5.2, 5.2, 4.7, 4.8, 5.4, 5.2, .

while the less() function below gives

Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1 5.1 3.5 1.4 0.2 setosa
2 4.9 3 1.4 0.2 setosa
3 4.7 3.2 1.3 0.2 setosa
4 4.6 3.1 1.5 0.2 setosa


Regards
Søren


 

> -Oprindelig meddelelse-
> Fra: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] På vegne 
> af Peter Dalgaard
> Sendt: 29. juni 2006 10:31
> Til: Søren Højsgaard
> Cc: Mike Wolfgang; R-help list
> Emne: Re: [R] re-direct to "more" or "less"
> 
> Søren Højsgaard <[EMAIL PROTECTED]> writes:
> 
> > Something like
> > 
> > less <- function(a){
> >   fn <- paste(tempdir(),"\\dataframe.txt",sep='',collapse='')
> >   write.table(a, quote=F, file=fn)
> >   system(paste("less ",fn))
> > }
> > 
> > could perhaps help you (assuming that you have less on your 
> computer). I agree that it would be very nice to have a 
> built-in version...
> 
> 
> Like page(), you mean... ?
> 
> :-)
> 
> (This goes via file.show, so Windows GUI users get a separate 
> window, I suppose.) 
> 
> > Regards
> > Søren
> > 
> >  
> > 
> > > -Oprindelig meddelelse-
> > > Fra: [EMAIL PROTECTED] 
> > > [mailto:[EMAIL PROTECTED] På vegne af 
> Mike Wolfgang
> > > Sendt: 29. juni 2006 04:29
> > > Til: R-help list
> > > Emne: [R] re-direct to "more" or "less"
> > > 
> > > Dear list,
> > > 
> > > sometimes my function generates too much data and shows them on 
> > > screen, i cannot view first several lines until program 
> ends and I 
> > > have to scroll my mouse up to get them. Is there any re-direction 
> > > function in R to pipeline outputs to "more"
> > > or "less" type functions?
> > > Thanks
> > > 
> > > mike
> > > 
> > >   [[alternative HTML version deleted]]
> > > 
> > > __
> > > R-help@stat.math.ethz.ch mailing list 
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide! 
> > > http://www.R-project.org/posting-guide.html
> > >
> > 
> > __
> > R-help@stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide! 
> > http://www.R-project.org/posting-guide.html
> > 
> 
> -- 
>O__   Peter Dalgaard Øster Farimagsgade 5, Entr.B
>   c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
>  (*) \(*) -- University of Copenhagen   Denmark  Ph:  
> (+45) 35327918
> ~~ - ([EMAIL PROTECTED])  FAX: 
> (+45) 35327907
>

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Re: [R] re-direct to "more" or "less"

[Peter Dalgaard]

Søren Højsgaard <[EMAIL PROTECTED]> writes:

> Something like
> 
> less <- function(a){
>   fn <- paste(tempdir(),"\\dataframe.txt",sep='',collapse='')
>   write.table(a, quote=F, file=fn)
>   system(paste("less ",fn))
> }
> 
> could perhaps help you (assuming that you have less on your computer). I 
> agree that it would be very nice to have a built-in version...


Like page(), you mean... ?

:-)

(This goes via file.show, so Windows GUI users get a separate window,
I suppose.) 

> Regards
> Søren
> 
>  
> 
> > -Oprindelig meddelelse-
> > Fra: [EMAIL PROTECTED] 
> > [mailto:[EMAIL PROTECTED] På vegne af Mike Wolfgang
> > Sendt: 29. juni 2006 04:29
> > Til: R-help list
> > Emne: [R] re-direct to "more" or "less"
> > 
> > Dear list,
> > 
> > sometimes my function generates too much data and shows them 
> > on screen, i cannot view first several lines until program 
> > ends and I have to scroll my mouse up to get them. Is there 
> > any re-direction function in R to pipeline outputs to "more" 
> > or "less" type functions?
> > Thanks
> > 
> > mike
> > 
> > [[alternative HTML version deleted]]
> > 
> > __
> > R-help@stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide! 
> > http://www.R-project.org/posting-guide.html
> >
> 
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
> 

-- 
   O__   Peter Dalgaard Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark  Ph:  (+45) 35327918
~~ - ([EMAIL PROTECTED])  FAX: (+45) 35327907

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Re: [R] Extracting R plots from MS Word

[Johannes Ranke]

Hi,

I would also like to know how to do this with MS products alone.

However, a nice tool to do this is wmf2eps (http://www.wmf2eps.de.vu/).
You can paste windows vector graphics into wmf2eps, and it first saves
it as EMF (enhanced metafile), before it creates EPS, which is what I
use it for.

Maybe your publisher will be even more happy if you supply EPS.

Best regards,

Johannes Ranke


* [EMAIL PROTECTED] <[EMAIL PROTECTED]> [060629 08:30]:
> Hi,
> 
> I am revising a paper that I am a co-author of. The figures are plots
> generated from R but at the moment I do not have the R code that generates
> them.
> 
> As this is time critical I would like to slightly abuse the list by asking
> whether anyone knows how to extract from MS Word into a stand-alone
> graphics file a plot that was pasted into Word from R (probably as a
> Windows Metafile, but possibly as a bitmap).
> 
> I would be very grateful for help with this.
> 
> Regards,  Murray Jorgensen
> 
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

-- 
Dr. Johannes Ranke [EMAIL PROTECTED]
UFT Bremen, Leobenerstr. 1 +49 421 218 8971 
D-28359 Bremen http://www.uft.uni-bremen.de/chemie/ranke

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Re: [R] Problem running one of the rgl demo scripts...

[Brian Lunergan]

Duncan Murdoch wrote:
> Brian Lunergan wrote:
>> Afternoon folks:
>>
>> I'm getting a program crash when I try to run demo(rgl). The following 
>> error details result:
>>
>> RGUI caused a stack fault in module NVOPENGL.DLL at 017f:695280f0.
>> Registers:
>> EAX=0002 CS=017f EIP=695280f0 EFLGS=00010246
>> EBX=0001 SS=0187 ESP=00572000 EBP=004d1208
>> ECX=042f1f01 DS=0187 ESI=004d1208 FS=5d1f
>> EDX=00442d84 ES=0187 EDI=042f1f3c GS=5d0e
>> Bytes at CS:EIP:
>> 53 56 8b 5c 24 0c 57 83 bb 9c 39 00 00 02 0f 84
>> Stack dump:
>> 69541be5 004d1208 004d1208 0001 69541bef 0001 004d1208 
>> 0001 69541bef 0001 004d1208 0001 69541bef 0001 
>> 004d1208 0001
>>
>> Setup details are:
>>
>> R version: 2.2.1
>> OS: win98se
>> RGL file name: rgl_0.66.zip
>>
>> It appears to be gagging on an Nvidia opengl driver file, NVIDIA 
>> Compatible OpenGL ICD, version 4.12.01.0631. The video card is 
>> recorded as:
>>
>> 3DForce2 MX Series,NVIDIA GeForce2 MX (Ver 4.12.01.0631 ,9/20/2000)
>>
>> I also tried this with version 2.3.1 of R with the same results.
>>
>> Anyone have any thoughts or ideas on the subject? Has it occurred any 
>> place else? Is there a workaround or solution, or should I perhaps 
>> turf the package and forgo its abilities since it appears my system as 
>> it stands may not be able to support it?
> You could try a newer build, available on my web page 
> (http://www.stats.uwo.ca/faculty/murdoch/software).  If it dies the same 
> way, you could perhaps try to diagnose what is going wrong and send a 
> patch if it's an rgl bug.  Given the age of your video driver 
> (9/20/2000), you might be able to update it and fix a bug there.

Just downloaded and installed a new video driver (file the demo originally 
reporting choking on now showing v4.14.10.8198, December 10, 2005 03:06:00) 
and things seemed to have settled down. The demo now runs through fully 
without complaint.

-- 
Brian Lunergan
Nepean, Ontario
Canada


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Re: [R] Help needed understanding eval,quote,expression

[Prof Brian Ripley]

You are missing eval(parse(text=)). E.g.

> x <- list(y=list(y1="hello",y2="world"),z=list(z1="foo",z2="bar"))
(what do you mean by the $ at the start of these lines?)
> eval(parse(text="x$y$y1"))
[1] "hello"

However, bear in mind

> fortune("parse")

If the answer is parse() you should usually rethink the question.
-- Thomas Lumley
   R-help (February 2005)

In your indicated example you could probably use substitute() as 
effectively.


On Wed, 28 Jun 2006, [EMAIL PROTECTED] wrote:

> I am trying to build up a quoted or character expression representing a
> component in a list  in order to reference it indirectly.
> For instance, I have a list that has data I want to pull, and another list
> that has character vectors and/or lists of characters containing the names
> of the components in the first list.
>
>
> It seems that the way to do this is as evaluating expressions, but I seem
> to be missing something.  The concept should be similar to the snippet
> below:
>
>
> For instance:
>
> $x = list(y=list(y1="hello",y2="world"),z=list(z1="foo",z2="bar"))
> $y = quote(x$y$y1)
> $eval(y)
> [1] "hello"
>
>
> but, I'm trying to accomplish this by building up y as a character and
> then evaluating it, and having no success.
>
> $y1=paste("x$y$","y1",sep="")
> $y1
> [1] "x$y$y1"
>
>
> How can I evaluate y1 as I did with y previously?  or can I?
>
>
> Much Thanks !
>
>
>
>
>
>
>
>
> 
> CONFIDENTIALITY NOTICE: This electronic mail transmission (i...{{dropped}}
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>

-- 
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] Error: evaluation nested too deeply: infinite recursion / options(expressions=)?

[Uwe Ligges]

Aarti Dahiya wrote:
> I am getting this error:- Error: evaluation nested too deeply: infinite 
> recursion / options(expressions=)? The reason is probbaly because I am 
> calling methods within methods.

Maybe at some point you get an infinite recursion because you forgot to 
"unclass" something?


> I read related posts.  It said the solution is to set  options(expressions = 
> 1000). I wanted to know where in my code or system to set 
> options(expressions = 1000)?


Bewore you start the problematic code, but probably you really have 
infinite recursion 

Uwe Ligges


> Thanks.
> 
> Aarti
> 
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Re: [R] re-direct to "more" or "less"

[Søren Højsgaard]

Something like

less <- function(a){
  fn <- paste(tempdir(),"\\dataframe.txt",sep='',collapse='')
  write.table(a, quote=F, file=fn)
  system(paste("less ",fn))
}

could perhaps help you (assuming that you have less on your computer). I agree 
that it would be very nice to have a built-in version...
Regards
Søren

 

> -Oprindelig meddelelse-
> Fra: [EMAIL PROTECTED] 
> [mailto:[EMAIL PROTECTED] På vegne af Mike Wolfgang
> Sendt: 29. juni 2006 04:29
> Til: R-help list
> Emne: [R] re-direct to "more" or "less"
> 
> Dear list,
> 
> sometimes my function generates too much data and shows them 
> on screen, i cannot view first several lines until program 
> ends and I have to scroll my mouse up to get them. Is there 
> any re-direction function in R to pipeline outputs to "more" 
> or "less" type functions?
> Thanks
> 
> mike
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html
>

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Re: [R] Question on memory allocation & loop

[Prof Brian Ripley]

On Thu, 29 Jun 2006, Manoj wrote:

> Hello All,
>  I am trying to work on writing the following piece of (pseudo)
> code in an optimal fashion:
>
> 
> # Two data frames with some data
>
> a = data.frame(somedata)
> b = data.frame(somedata)
>
> for(i in 1:nrow(dt) {
>  # Merge dates for a given date into a new data frame
>   c = merge(a[a$dt==dt[i],),b[b$dt == dt[i],], by=c(some column));
> }

Note that only the last iteration of that loop is actually needed.

What are you really trying to do, and why are you worrying about memory? 
E.g. merge() in R-devel is a lot more efficient for some operations, 
including perhaps your example.

> 
>
>
> Now, my understanding is that the data frame c in the above code is
> malloc'ed in every count of the loop.  Is that assumption correct?

No.  Here 'c' is just a symbol, and assignment (please use <- in public 
code, it is easier to read) binds the symbol to the data frame returned by 
merge().  So the allocation (not 'malloc' necessarily) is going on inside 
merge(). Also, 'c' is a system object, so you are confusing people by 
using its name for your own object.

When you assign to 'c' you change the binding to a different already 
allocated object.  Eventually garbage collection will recover (to R) the 
memory allocated to objects which are no longer bound to symbols.

I am not aware of any account which describes in detail how R works at 
this level, and end users do not need to know it.  (It is also the case 
that R maintains a number of illusions and internally may not do what it 
appears to do.)

>
> Is the following attempt a better way of doing things?
>
> 
> a = data.frame(somedata)
> b = data.frame(somedata)
>
> # Pre-allocate data frame c
>
> c = data.frame(for some size);
>
> for(i in 1:nrow(dt) {
>  # Merge dates for a given date into a new data frame
>   # and copy the result into c
>
>  copy(c, merge(a[a$dt==dt[i],),b[b$dt == dt[i],], by=c(some column));
>
> }
> 
>
> Now the question is, How can I copy the merged data into my
> pre-allocated data frame c ? I tried rbind/cbind but they are pretty
> fuzzy about having the right names and dimension hence it fails.
>
> Any help would be greatly appreciated!
>
> Thanks.
>
> Manoj
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>

-- 
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] Help needed understanding eval,quote,expression

[toby_marks]

I am trying to build up a quoted or character expression representing a 
component in a list  in order to reference it indirectly. 
For instance, I have a list that has data I want to pull, and another list 
that has character vectors and/or lists of characters containing the names 
of the components in the first list.


It seems that the way to do this is as evaluating expressions, but I seem 
to be missing something.  The concept should be similar to the snippet 
below:


For instance:

$x = list(y=list(y1="hello",y2="world"),z=list(z1="foo",z2="bar"))
$y = quote(x$y$y1)
$eval(y)
[1] "hello"


but, I'm trying to accomplish this by building up y as a character and 
then evaluating it, and having no success. 

$y1=paste("x$y$","y1",sep="")
$y1
[1] "x$y$y1"


How can I evaluate y1 as I did with y previously?  or can I? 


Much Thanks !









CONFIDENTIALITY NOTICE: This electronic mail transmission (i...{{dropped}}

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Re: [R] re-direct to "more" or "less"

[Dimitris Rizopoulos]

maybe ?sink() or ?capture.output() could be useful, in this case.


Best,
Dimitris


Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven

Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://med.kuleuven.be/biostat/
 http://www.student.kuleuven.be/~m0390867/dimitris.htm


- Original Message - 
From: "Mike Wolfgang" <[EMAIL PROTECTED]>
To: "R-help list" 
Sent: Thursday, June 29, 2006 4:28 AM
Subject: [R] re-direct to "more" or "less"


> Dear list,
>
> sometimes my function generates too much data and shows them on 
> screen, i
> cannot view first several lines until program ends and I have to 
> scroll my
> mouse up to get them. Is there any re-direction function in R to 
> pipeline
> outputs to "more" or "less" type functions?
> Thanks
>
> mike
>
> [[alternative HTML version deleted]]
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html
> 


Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

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[R] Building R: use the current version! {was " Running R"}

[Martin Maechler]

I'm not really answering your question, but if you install from
the sources -- always a useful experience in finding out if your
computer is well equipped with software -- 
*PLEASE* use the latest aka "current" version of R.
Currently, that's 2.3.1 and not 2.3.0.

A very reasonable alternative is also to work with R-patched
(i.e. 'R 2.3.1 patched' at the moment), since we (aim to) ensure
that R-patched only contains simple well tested bug fixes in
addition to the respective released version.

(Contrary to "R-devel" which always contains the current R
 development version with all potential new features and which
 is hence also designated 'unstable'.)

Martin Maechler, 
ETH Zurich (and R-core)


> "Pramod" == Pramod Anugu <[EMAIL PROTECTED]>
> on Wed, 28 Jun 2006 15:18:10 -0500 writes:

Pramod> [EMAIL PROTECTED] R-2.3.0]# ./configure

  .
  .

Pramod> 1. tar -zxvf R-2.3.0.tar.gz
Pramod> 2. changed the directory to the newly created directory R-2.3.0

   .
   .

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