Re: [R] Assist on R-2.0.0 /64 bit AMD/SuSE 9.1

[Prof Brian Ripley]

What is Assist-0.1.0?  It's not part of R and it is not a CRAN nor 
Bioconductor package.  

There is a CRAN package `assist', and if you mean that please follow the
advice in the posting guide and contact the maintainer.  Now, that package
says

Title: A Suite of S-Plus Functions Implementing Smoothing Splines

and S-PLUS functions don't run on 64-bit versions of R.  I suggest you and
the maintainer look for the use of `long *' in .C calls: S-PLUS uses `long 
*' where R uses `int *'.

On Thu, 21 Oct 2004, Simon Frost wrote:

 I compiled and installed Assist-0.1.0; I'm using R-2.0.0 running on SuSe 
 Linux, on a dual AMD64 machine. However, I (apparently randomly) get 
 segmentation faults when I use cubic2. Any ideas?

-- 
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] How to draw x-axis time label.

[Ivy_Li]

Thank you for helping me.
I have modified this part of code.

Time - c(2004-08-05 09:08:48, 2004-08-13 20:53:38,
2004-08-14 13:57:23, 2004-08-12 16:17:41, 
2004-08-12 16:15:27, 2004-08-11 21:38:24,
2004-08-12 14:28:41, 2004-08-18 18:04:47,
2004-08-13 15:23:14, 2004-08-14 02:36:33)
Time - as.POSIXct(Time)
x - data.frame(main.name=AAA, fruit.name=rep(c(Apply,Watermelon),each=5), 
x.name=Time, y.name=(1:10))
par(las=3,mai=c(1,.7,.5,.3))
plot(x$x.name,as.character(x$y.name),pch=26, xlab=Process Time, xaxt = 'n')
axis.POSIXct(1, at=seq(min(x$x.name), max(x$x.name), days),format=%d /%m)
fruit.class - table(x$fruit.name)
color.code - c(611,552,656,121,451,481,28,652,32,550,90,401,150,12,520,8)
for(j in 1:length(fruit.class))
{
fruit - names(fruit.class)[j]
lines(smooth.spline(x[x$fruit.name==fruit, x.name],
x[x$fruit.name==fruit, y.name],df=5),
col=colors()[color.code[j]],lwd=5)
}

Run above code , you will find the Process Time is close to the x-label, I want to 
move it down . And How can I reduce font?
Thank you very much!


Best Regards!
Ivy Li
YMS in Production  Testing
Semiconductor Manufactory International(ShangHai) Corporation
#18 ZhangJiang Road, PuDong New Area, Shanghai, China
Tel: 021-5080-2000 *11754
Email: [EMAIL PROTECTED]



--
: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED]
: 20041019 18:17
: Ivy_Li
: Re: : : : [R] How to draw x-axis time label.


In this case,  don't draw x-axis:

plot(x$x.name,as.character(x$y.name),pch=26, xaxt = 'n')

Then check out functin mtext() (to draw the xaxis yourself. It's not
diffucult but you have to try).
Luck
Huang Huan



Internet
[EMAIL PROTECTED] - 10/19/2004 10:23 AM


To:Huan HUANG

cc:r-help


Subject:: : : [R] How to draw x-axis time label.



Thank you !
I run your code. It have a graph with time(date) on x-axis. Thank you very
much!
Well,  Would you like to do me a favor again?
Most of times, the x-axis time data is lasted about 3 months. They are too
much. I must select some of them marking in x-axis,and they are must
reasonable and  human-readable. Now I have tried the pretty  function,
But as soon as I run it,  the format of data changed to numeric ,I don't
know what should I do. Is there exist other functions can get the same
result?



Best Regards!
Ivy Li
YMS in Production  Testing
Semiconductor Manufactory International(ShangHai) Corporation
#18 ZhangJiang Road, PuDong New Area, Shanghai, China
Tel: 021-5080-2000 *11754
Email: [EMAIL PROTECTED]



--
: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED]
: 20041019 16:43
: Ivy_Li
: Re: : : [R] How to draw x-axis time label.


Hi Li chen,

I mean you should run the code I sent you in my first email. It's here
again:

plot(x$x.name,as.character(x$y.name),pch=26)

By running this you should have a graph with time(date) on x-axis.

Give it a go? Let me know if it is not working.
Huang Huan



Internet
[EMAIL PROTECTED] - 10/19/2004 02:18 AM


To:Huan HUANG

cc:


Subject:: : [R] How to draw x-axis time label.


Put *time* on x-axis? Like this:

plot(time(x$x.name),as.character(x$y.name),pch=26)

but the x-axis is not real time , just some number.

I forgot your question in your previous mail. :-)
My chinese name is Li Chen
hello!

Best Regards!
Ivy Li
YMS in Production  Testing
Semiconductor Manufactory International(ShangHai) Corporation
#18 ZhangJiang Road, PuDong New Area, Shanghai, China
Tel: 021-5080-2000 *11754
Email: [EMAIL PROTECTED]



--
: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED]
: 20041018 18:35
: Ivy_Li
: Re: : [R] How to draw x-axis time label.


Come on, Ivy. Did you try the line in my previous email? That will put
*time* on x-axis. Give it a go?



Internet
[EMAIL PROTECTED] - 10/18/2004 10:24 AM


To:Huan HUANG

cc:


Subject:: [R] How to draw x-axis time label.



Thank you !
I know the oddness number are time calulated since 1970, but i need them to
be  x-axis .
What  should  I do ?

Best Regards!
Ivy Li
YMS in Production  Testing
Semiconductor Manufactory International(ShangHai) Corporation
#18 ZhangJiang Road, PuDong New Area, Shanghai, China
Tel: 021-5080-2000 *11754
Email: [EMAIL PROTECTED]



--
: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED]
: 20041018 16:50
: Ivy_Li
: Re: [R] How to draw x-axis time label.


Hi Ivy (any chinese name?)

I ran your codes. I found if I try:

plot(x$x.name,as.character(x$y.name),pch=26,)

It would put time as the x axis. The *odd* numbers showed in yoru graph as
the moment are numbers of seconds of those dates since the beginning of
1970.
Hope it helps.
Huang Huan



Internet
[EMAIL PROTECTED]@stat.math.ethz.ch - 10/18/2004 07:26 AM


Sent by:[EMAIL PROTECTED]

To:r-help

cc:


Subject:[R] How to draw x-axis time label.


Hi everybody,
 Could I consult one problem?
 It is about plot
 Now I do some analysis in plot . I need to draw a plot which x-axis is
 time . But when I run the funtion of 

Re: : [R] How to draw x-axis time label.

[Prof Brian Ripley]

On Fri, 22 Oct 2004, Ivy_Li wrote:

 Thank you for helping me.
 I have modified this part of code.
 
 Time - c(2004-08-05 09:08:48, 2004-08-13 20:53:38,
   2004-08-14 13:57:23, 2004-08-12 16:17:41, 
   2004-08-12 16:15:27, 2004-08-11 21:38:24,
   2004-08-12 14:28:41, 2004-08-18 18:04:47,
   2004-08-13 15:23:14, 2004-08-14 02:36:33)
 Time - as.POSIXct(Time)
 x - data.frame(main.name=AAA, fruit.name=rep(c(Apply,Watermelon),each=5), 
   x.name=Time, y.name=(1:10))
 par(las=3,mai=c(1,.7,.5,.3))
 plot(x$x.name,as.character(x$y.name),pch=26, xlab=Process Time, xaxt = 'n')
 axis.POSIXct(1, at=seq(min(x$x.name), max(x$x.name), days),format=%d /%m)
 fruit.class - table(x$fruit.name)
 color.code - c(611,552,656,121,451,481,28,652,32,550,90,401,150,12,520,8)
 for(j in 1:length(fruit.class))
 {
   fruit - names(fruit.class)[j]
   lines(smooth.spline(x[x$fruit.name==fruit, x.name],
   x[x$fruit.name==fruit, y.name],df=5),
   col=colors()[color.code[j]],lwd=5)
 }
 
 Run above code , you will find the Process Time is close to the
 x-label, I want to move it down . And How can I reduce font? Thank you

Process Time *is* the x-label!  You will find all this discussed in An
Introduction to R: you need to change the margins and to use title(xlab=,
line=) to place the x-label in another position.  And the font *size* is
set by cex*: see ?par and the An Introduction to R manual.

[Many, many unneeded lines removed.]


-- 
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] p-values for the dip test

[Martin Maechler]

Hmm, this is rather about reading the (Hartigan)^2 paper ...

 Kylie == Kylie Lange [EMAIL PROTECTED]
 on Fri, 22 Oct 2004 11:17:34 +0930 writes:

Kylie Hi all,

Kylie I am using Hartigan  Hartigan's [1] dip test of
Kylie unimodality via the diptest package in R. The
Kylie function dip() returns the value of the test
Kylie statistic but I am having problems calculating the
Kylie p-value associated with that value. I'm hoping
Kylie someone here is familiar with this process and can
Kylie explain it.

Kylie In the original article there is an example using
Kylie n=63 and a dip value of 0.059 - which I am able to
Kylie replicate using dip(). However the article then
Kylie states:

Kylie The dip illustrated in Figure 1 is 0.059 which has a
Kylie tail probability about 10% from Table 1. (
Kylie sqrt(63)*D*F(63) is distributed approximately as
Kylie sqrt(100)*D*F(100) which has 90% point 0.474. Thus
Kylie D*F(63) has 90% point 0.060. )

note:  sqrt(100) * D(F_100) =  10 * D(F_100)

   i.e. D(F_100) would have 90* point 0.0474

but the second 4 is a simple typo, (not the only one in the
paper, IIRC!);  s/4/1/ -- you get the correct 0.0471

Kylie It is the value of 0.474 that I am unable to
Kylie get. Table 1 is a table of percentage points for
Kylie various sample sizes. The same table is provided in
Kylie the diptest package as 'qDiptab' (but at greater
Kylie accuracy). n=63 is not tabled but n=50 and 100
Kylie are. In the table for n=100 the value given for 90%
Kylie is 0.0471 so where does the 0.474 come from?

(see above).

Kylie Any help appreciated!  

you're welcome.
Martin Maechler, ETH Zurich ('diptest' maintainer)


Kylie [1] Hartigan JA  Hartigan PM. The Dip Test of
Kylie Unimodality, The Annals of Statistics, v13(1):70-84, 1985.

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[R] Vector and String

[pbrouilly]

Hi everybody,

I'm using a vector to strore some strings.

I create a vector named seq2 :
 seq2-vector(length=0)

I have a string named b
 b
[1] CATGGTAGGAATAC

I put b in the vector
 seq2-c(seq2,b)

Finally I edit seq2
 seq2
[1] 14760

My question is why I obtained a number (14760) when I add a string (CATGGTAGGAATAC)

I have an idea : when I edit b, I see ( [1] CATGGTAGGAATAC ) 
and not ([1] CATGGTAGGAATAC) 

How can I convert b to a true string with  

Thank you very much

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Re: [R] Vector and String

[Prof Brian Ripley]

On Fri, 22 Oct 2004 [EMAIL PROTECTED] wrote:

 Hi everybody,
 
 I'm using a vector to strore some strings.
 
 I create a vector named seq2 :
  seq2-vector(length=0)

 typeof(seq2)
[1] logical

so you created a *logical vector*.  See ?vector.

 I have a string named b
  b
 [1] CATGGTAGGAATAC

I think you have a factor, not a `string'.  What does str(b) say?

 I put b in the vector
  seq2-c(seq2,b)
 
 Finally I edit seq2
  seq2
 [1] 14760
 
 My question is why I obtained a number (14760) when I add a string (CATGGTAGGAATAC)
 
 I have an idea : when I edit b, I see ( [1] CATGGTAGGAATAC ) 
 and not ([1] CATGGTAGGAATAC) 
 
 How can I convert b to a true string with  

seq2 - character()
seq2 - c(seq2, as.character(b))



-- 
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] Vector and String

[Marc Mamin]

Hello,
I'm looking for a procedure to detect trend changes or significant signals 
in time series as in the attached example.

Could you point me to a library or reference I can start with?
Thanks,
Marc Mamin__
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Re: libraries and references (was `[R] Vector and String')

[Prof Brian Ripley]

Have you read the R-posting guide which specifically asks you *not* to 
tack completely separate questions on to other threads, and to use a 
relevant subject line?

What has this to do with `[R] Vector and String'?

On Fri, 22 Oct 2004, Marc Mamin wrote:

 I'm looking for a procedure to detect trend changes or significant signals 
 in time series as in the attached example.
 
 Could you point me to a library or reference I can start with?

Two good references are the R posting guide at
http://www.r-project.org/posting-guide.html and the R FAQ at
http://cran.r-project.org/doc/FAQ/R-FAQ.html which lists some very
relevant R packages (and which the posting guide asks you to consult).
Please do start with those.

There are lots of good libraries in the world, but you need to visit one 
which will admit you.  They will probably insist that you read their usage 
conditions first.  So does this list.

-- 
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: libraries and references (was `[R] Vector and String')

[Pfaff, Bernhard]

  I'm looking for a procedure to detect trend changes or 
 significant signals 
  in time series as in the attached example.

Dear Marc,

it seems that your example have been removed, as stated in the posting
guide. Hence, I can only guess what your problem is and offer:

help.search(Goldfeld)
help.search(Chow)
help.search(structural change)

May be you can provide your example directly in a mail?

HTH,
Bernhard

  
  Could you point me to a library or reference I can start with?
 
 Two good references are the R posting guide at
 http://www.r-project.org/posting-guide.html and the R FAQ at
 http://cran.r-project.org/doc/FAQ/R-FAQ.html which lists some very
 relevant R packages (and which the posting guide asks you 
 to consult).
 Please do start with those.
 
 There are lots of good libraries in the world, but you need 
 to visit one 
 which will admit you.  They will probably insist that you 
 read their usage 
 conditions first.  So does this list.
 
 -- 
 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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The information contained herein is confidential and is inte...{{dropped}}

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[R] building an R package : where and how should my fortran library be loaded ?

[Gilles GUILLOT]

Hi ,

I'm currently trying to make available 
a few fortran subroutines and R functions 
(which make interface to these subroutines),
as an R package.
I'm doing it under linux with R 1.9.0 
(but hope to do it for windows too).
I have trouble for loading my fortran code.
Here are the steps involved :

1) In R: 
  # Create tree for package
# and include my R functions in it
R package.skeleton(name=Geneland,
 list=c(mcmcFmodel,
   simFmodel,
   rdiscr,
   tessel.post),
 path=/home/guillot/projets/flux/package/,
 force=T)

# copy my fortran code in the tree
Rsystem(cp /home/guillot/projets/flux/package/fortran/*.f   
/home/guillot/projets/flux/package/Geneland/src/)

R q()

2) In a Unix shell
$ R CMD build Geneland
$ R CMD check Geneland
$ R CMD build Geneland
$ R CMD INSTALL Geneland

3) Back to R
R library(Geneland)

So far, it's OK, pure R functions work fine.
But  R functions calling  some Fortran via .Fortran
do not work, I get an error message like :
Error in .Fortran(mcmc, ...
Fortran function name not in load table

If I make 
R dyn.load(/usr/lib/R/library/Geneland/libs/Geneland.so)

then it works .
I was thinking that my Geneland.so was loaded automatically
by the command library(Geneland)
Obviously, it's not.
Where and how should the library loaded ?


Gilles

_
Gilles GUILLOT
INRA -Département Mathématiques et Informatique Appliquées

Unité de Mixte de Recherche INRA - INAPG - ENGREF
Institut National Agronomique de Paris-Grignon
16 rue Claude Bernard
75231 Paris cedex 5

Aile Claude Bernard
Niveau cours +3 étages
tel : +33 (0)1 44 08 72 71
fax : +33 (0)1 44 08 16 66
http://www.inapg.fr/ens_rech/mathinfo/personnel/guillot/welcome.html
__
-- 
_
Gilles GUILLOT
INRA -Département Mathématiques et Informatique Appliquées

Unité de Mixte de Recherche INRA - INAPG - ENGREF
Institut National Agronomique de Paris-Grignon
16 rue Claude Bernard
75231 Paris cedex 5

Aile Claude Bernard
Niveau cours +3 étages
tel : +33 (0)1 44 08 72 71
fax : +33 (0)1 44 08 16 66
http://www.inapg.fr/ens_rech/mathinfo/personnel/guillot/welcome.html

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Re: [R] building an R package : where and how should my fortran library be loaded ?

[Prof Brian Ripley]

On Fri, 22 Oct 2004, Gilles GUILLOT wrote:

 I'm currently trying to make available 
 a few fortran subroutines and R functions 
 (which make interface to these subroutines),
 as an R package.
 I'm doing it under linux with R 1.9.0 

Please update, as few of us have such an old system in use.

 (but hope to do it for windows too).
 I have trouble for loading my fortran code.

[...]

 I was thinking that my Geneland.so was loaded automatically
 by the command library(Geneland)

`Thinking'?  `Hoping', perhaps, but where did you read that?

 Obviously, it's not.
 Where and how should the library loaded ?

By your R code, via library.dynam.  A common `spell' is for package foo to 
include in foo/src/zzz.R

.First.lib - function(libpath, pkgname)  
library.dynam(foo, pkgname, libpath)

and it described in `Writing R Extensions'.  That also explains the 
different rules for packages with namespaces.

-- 
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] cor, cov, method pairwise.complete.obs

[Eric Lecoutre]

Hi UseRs,
I don't want to die beeing idiot...
I dont understand the different results between:
cor() and cov2cov(cov()).
See this little example:
 x=matrix(c(0.5,0.2,0.3,0.1,0.4,NA,0.7,0.2,0.6,0.1,0.4,0.9),ncol=3)
 cov2cor(cov(x,use=pairwise.complete.obs))
   [,1]   [,2]   [,3]
[1,]  1.000  0.4653400 -0.1159542
[2,]  0.4653400  1.000 -0.7278728
[3,] -0.1159542 -0.7278728  1.000
 cor(x,use=pairwise.complete.obs)
   [,1]   [,2]   [,3]
[1,]  1.000  0.3973597 -0.1159542
[2,]  0.3973597  1.000 -0.9736842
[3,] -0.1159542 -0.9736842  1.000
My question arises in a context where cor(mydata, 
use=pairwise.complete.obs)  returns correlations on diagonal that are 
near 0.95 (where as my data do have 100 observations and only 12 missing 
values...).

Do cor() and cov() handle the same way the argument pairwise.complete.obs?
Eric
 R.version
 _
platform i386-pc-mingw32
arch i386
os   mingw32
system   i386, mingw32
status
major2
minor0.0
year 2004
month10
day  04
language R
Eric Lecoutre
UCL /  Institut de Statistique
Voie du Roman Pays, 20
1348 Louvain-la-Neuve
Belgium
tel: (+32)(0)10473050
[EMAIL PROTECTED]
http://www.stat.ucl.ac.be/ISpersonnel/lecoutre
If the statistics are boring, then you've got the wrong numbers. -Edward 
Tufte

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[R] Convert a list in a dataframe

[Vito Ricci]

Hi,

I've a list containing parameters (intercepts 
coefficients) of 12 regressions fitted

 coeff
[[1]]
 (Intercept) anno 
-427017.1740 217.0588 

[[2]]
 (Intercept) anno 
-39625.82146 21.78025 

.

[[12]]
(Intercept)anno 
257605.0343   -129.7646 

I want create a data frame with two columns (intercept
and anno)using data in these list.

Any help will be appreciated.
Best
Vito



=
Diventare costruttori di soluzioni

The business of the statistician is to catalyze 
the scientific learning process.  
George E. P. Box


Visitate il portale http://www.modugno.it/
e in particolare la sezione su Palese http://www.modugno.it/archivio/cat_palese.shtml

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[R] grouping for lme with nested repeated measurements

[Nicolaas Busscher]

I am using lme to handle repeated measurements.
So far i can follow the examples from the book from pinheiro and bates.
Now i get the problem , that i have nested repeated measuremnts, and i cant find out 
how to do the grouping part of the lme formula.

1.The simple problem ist that i have different Samples , from which i make repeated 
measurements (each sample is measured 6 times) and i repeat this experiment over 
several Days, so i get the lme grouping term random=~1|Days/Sample.

2. Now i am measuring with 2 different measuring Apparatus the same Sample each 6 
times, to see how big the difference from the appratus is. 
Because Apparatus is on the level of repeated measurements i cant write 
Days/Sample/Apparatus. the lme function offers a list() feature to design the 
grouping, but i didnt understand this, if it is the solution to the problem.

Maybe somebody had the same Problem?
best greetings
N.Busscher
-- 
#---
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##   Neue Telephon Nummer
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RE: [R] Convert a list in a dataframe

[Liaw, Andy]

Try something like:

as.data.frame(do.call(rbind, coeff))

HTH,
Andy

 From: Vito Ricci
 
 Hi,
 
 I've a list containing parameters (intercepts 
 coefficients) of 12 regressions fitted
 
  coeff
 [[1]]
  (Intercept) anno 
 -427017.1740 217.0588 
 
 [[2]]
  (Intercept) anno 
 -39625.82146 21.78025 
 
 .
 
 [[12]]
 (Intercept)anno 
 257605.0343   -129.7646 
 
 I want create a data frame with two columns (intercept
 and anno)using data in these list.
 
 Any help will be appreciated.
 Best
 Vito
 
 
 
 =
 Diventare costruttori di soluzioni
 
 The business of the statistician is to catalyze 
 the scientific learning process.  
 George E. P. Box
 
 
 Visitate il portale http://www.modugno.it/
 e in particolare la sezione su Palese 
 http://www.modugno.it/archivio/cat_palese.shtm l
 
 
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Re: [R] Convert a list in a dataframe

[Peter Dalgaard]

Vito Ricci [EMAIL PROTECTED] writes:

 Hi,
 
 I've a list containing parameters (intercepts 
 coefficients) of 12 regressions fitted
 
  coeff
 [[1]]
  (Intercept) anno 
 -427017.1740 217.0588 
 
 [[2]]
  (Intercept) anno 
 -39625.82146 21.78025 
 
 .
 
 [[12]]
 (Intercept)anno 
 257605.0343   -129.7646 
 
 I want create a data frame with two columns (intercept
 and anno)using data in these list.

data.frame(do.call(rbind,coeff))

Did this result from an lapply() construct? If so, consider using
sapply(); then you can just do

data.frame(t(coeff))

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

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Re: [R] Convert a list in a dataframe

[Uwe Ligges]

Vito Ricci wrote:
Hi,
I've a list containing parameters (intercepts 
coefficients) of 12 regressions fitted

coeff
[[1]]
 (Intercept) anno 
-427017.1740 217.0588 

[[2]]
 (Intercept) anno 
-39625.82146 21.78025 

.
[[12]]
(Intercept)anno 
257605.0343   -129.7646 

I want create a data frame with two columns (intercept
and anno)using data in these list.

coeffD - as.data.frame(t(matrix(unlist(coeff), , 2)))
names(coeffD) - names(coeff[[1]])
Uwe Ligges

Any help will be appreciated.
Best
Vito

=
Diventare costruttori di soluzioni
The business of the statistician is to catalyze 
the scientific learning process.  
George E. P. Box

Visitate il portale http://www.modugno.it/
e in particolare la sezione su Palese http://www.modugno.it/archivio/cat_palese.shtml
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[R] confidence interval

[lu kan]

I used a dataset to fit a linear model. For each new sample, a precition can be 
obtained using the fitted model. Now I wonder is there any way to calculate the 
confidence interval of the precition for new samples? Any suggestion or pointing to a 
reference would be very appreciated.
 
Lu
  
 
 



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[R] bquote inside a legend

[Jean Eid]

I am trying to automate an outide of the plot region table that has the
correlation coef. of the various variables in the plot. I am currently
using bquote to get the greek/latex representation of $\rho$. what I want
so what I have is the following

  rhoa - cor(x, data1$No.Msa.Hosp)
  rhon - cor(x, data1$N.Not.Profit.msa)
  rhop - cor(x, data1$N.Profit.msa)

 temp - bquote(list(rho[Not-profit]==.(rhon),rho[Profit]==.(rhop),
rho[All]==.(rhoa)))

everything works fine but the problem is that the following legend call
  legend(par(usr)[2]-a1,3*par(usr)[3]-b1,ex12, ncol=2)

does not respect the ncol argument. I am guessing it is respecting it but
bquote is of dimension 1 i.e just a big string. Does anyone know of a way
to break this into two columns


Thank you

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Re: [R] confidence interval

[Uwe Ligges]

lu kan wrote:
I used a dataset to fit a linear model. For each new sample, a precition can be obtained using the fitted model. Now I wonder is there any way to calculate the confidence interval of the precition for new samples? Any suggestion or pointing to a reference would be very appreciated.
 
Lu
You already found predict(), so read ?predict.lm carefully and find that 
there is a argument interval.

Uwe Ligges
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[R] Incompatibility between R-2.0.0 and Rggobi_1.0-0.

[Aruna Buddana]

Hello,
I was trying to install Rggobi in the latest version of R and it gave me 
a compilation error for
R CMD INSTALL Rggobi_1.0-0.tar.gz

RSGGobi.C: In function RS_GGOBI_init
(R_IsNaNorNA) undeclared (line 77)
I searched for this function in R src files and it was abandoned in 
~/R-2.0.0/src/include/R_ext/Arith.h file.
Only functions

int R_IsNA(double);/* True for R's NA only */
int R_IsNaN(double);/* True for special NaN, *not* for NA */
are declared leaving out R_IsNaNorNA.
This funcion was declared in R-1.9.1.
So I changed (R_IsNaNorNA) to (R_IsNA) in  ~/Rggobi/src. Then I built 
Rggobi and installed it using R CMD

Can anyone tell me if there is any other way to do it? Was I right?
Thanks,
Sincerely,
Aruna Buddana,
Intern, Statistics and Data Sciences
Oak Ridge National Laboratories.
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[R] ave gives unexpected NA's

[Wolfram Fischer]

[R 2.0.0 on Linux]

I tried:
 df - data.frame(
 grp1=factor( c('A' ,'A' ,'A' ,'D', 'D' ) ) ,
 grp2=factor( c('a1','a2','a2','d1','d1') )
 )
 df
  grp1 grp2 val
1A   a1   1
2A   a2   2
3A   a2   4
4D   d1   8
5D   d1  16

I got:
 with( df, ave( val, grp1, grp2, FUN=sum ) )
[1]  1 24 24 NA NA

I have expected to get:
[1]  1 6 24

Do I misunderstand something with `ave' or is there a bug?

Thanks - Wolfram

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[R] Interval Arithmetic Queueing Models

[Dominic Kay]

I want to do two things in R and have searched the mail archive and 
packages to see if they have been done before. I could not see anything. 
If anyone has tackled these problem domains before I would be grateful 
for help.

1.   Has anyone implemented interval arithmetic (see generally 
http://www.cs.utep.edu/interval-comp/ ) either directly in R code or by 
linking in an external C++/Fortran library?

2.  Has anyone implemented queueing modelling ( see e.g the software at 
http://www.perfdynamics.com/ ).

I would be grateful for pointers. Please include me as an addressee on 
any response as I am not on this mailing list.
regards
Dominic

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Re: [R] Incompatibility between R-2.0.0 and Rggobi_1.0-0.

[Prof Brian Ripley]

This is discussed in 200update.txt file on developer.r-project.org, which 
tells you the right way to do it.

BTW, the incompatility is of Rggobi_1.0-0 with R-2.0.0 and not the other 
way round.

On Fri, 22 Oct 2004, Aruna Buddana wrote:

 Hello,
 I was trying to install Rggobi in the latest version of R and it gave me 
 a compilation error for
  R CMD INSTALL Rggobi_1.0-0.tar.gz
 
 RSGGobi.C: In function RS_GGOBI_init
 (R_IsNaNorNA) undeclared (line 77)
 
 
 I searched for this function in R src files and it was abandoned in 
 ~/R-2.0.0/src/include/R_ext/Arith.h file.
 Only functions
 
 int R_IsNA(double);/* True for R's NA only */
 int R_IsNaN(double);/* True for special NaN, *not* for NA */
 
 
 are declared leaving out R_IsNaNorNA.
 This funcion was declared in R-1.9.1.
 
 So I changed (R_IsNaNorNA) to (R_IsNA) in  ~/Rggobi/src. Then I built 
 Rggobi and installed it using R CMD
 
 Can anyone tell me if there is any other way to do it? Was I right?

No.


-- 
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] bquote inside a legend

[Uwe Ligges]

Jean Eid wrote:
I am trying to automate an outide of the plot region table that has the
correlation coef. of the various variables in the plot. I am currently
using bquote to get the greek/latex representation of $\rho$. what I want
so what I have is the following
  rhoa - cor(x, data1$No.Msa.Hosp)
  rhon - cor(x, data1$N.Not.Profit.msa)
  rhop - cor(x, data1$N.Profit.msa)
 temp - bquote(list(rho[Not-profit]==.(rhon),rho[Profit]==.(rhop),
rho[All]==.(rhoa)))
everything works fine but the problem is that the following legend call
  legend(par(usr)[2]-a1,3*par(usr)[3]-b1,ex12, ncol=2)
does not respect the ncol argument. I am guessing it is respecting it but
bquote is of dimension 1 i.e just a big string. Does anyone know of a way
to break this into two columns

There is an example how to work with mathematical annotation in legend() 
in the Help Desk in R News 2/3.
Please specify easily reproducible examples (not examples with data we 
do not have) - according to the posting guide!

What you are probably going to do is something like:
plot(1:10)
rhoa - 1
rhon - 2
rhop - 3
exprhoa - substitute(rho[All]==.(rhoa), list(rhoa = rhoa))
exprhon - substitute(rho[Not-profit]==.(rhon), list(rhon = rhon))
exprhop - substitute(rho[Profit]==.(rhop), list(rhop = rhop))
legend(2, 8, do.call(expression, list(exprhon, exprhop, exprhoa)), 
ncol = 2)

Uwe Ligges

Thank you
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Re: [R] console under Mandrake

[Prof Brian Ripley]

On Fri, 22 Oct 2004, Adrian Dusa wrote:

 I recently compiled R 2.0.0 under Mandrake 9, but it won't run unless in a
 terminal; is there a way to run it in a console, like in Windows?

Yes.  Did you read the manual the INSTALL file pointed you to?
See appendix B.6 in the version I am looking at.

Or see `An Introduction to R' appendix B.1 and look for --gui.

[To run the GNOME console I think you need R-patched, not 2.0.0 as 
distributed.]

Another approach is to run John Fox's Rcmdr package that provides a 
console.

-- 
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] ave gives unexpected NA's

[Peter Dalgaard]

Wolfram Fischer [EMAIL PROTECTED] writes:

 [R 2.0.0 on Linux]
 
 I tried:
  df - data.frame(
  grp1=factor( c('A' ,'A' ,'A' ,'D', 'D' ) ) ,
  grp2=factor( c('a1','a2','a2','d1','d1') )
  )
  df
   grp1 grp2 val
 1A   a1   1
 2A   a2   2
 3A   a2   4
 4D   d1   8
 5D   d1  16
 
 I got:
  with( df, ave( val, grp1, grp2, FUN=sum ) )
 [1]  1 24 24 NA NA
 
 I have expected to get:
 [1]  1 6 24
 
 Do I misunderstand something with `ave' or is there a bug?

Both. You should have expected 1 6 6 24 24.

Apparently the culprit is this line inside ave()

  unlist(lapply(split(x, g), FUN))[g]

which acts up if there are empty levels of g. It works with

  unlist(lapply(split(x, g), FUN))[as.character(g)]

but that doesn't strike me as the right solution.

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

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Re: [R] confidence interval

[lu kan]

Is there the similar thing for non-linear 'nls'? 

Lu
Uwe Ligges [EMAIL PROTECTED] wrote:
lu kan wrote:

 I used a dataset to fit a linear model. For each new sample, a precition can be 
 obtained using the fitted model. Now I wonder is there any way to calculate the 
 confidence interval of the precition for new samples? Any suggestion or pointing to 
 a reference would be very appreciated.
 
 Lu

You already found predict(), so read ?predict.lm carefully and find that 
there is a argument interval.

Uwe Ligges


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Re: [R] console under Mandrake

[Peter Dalgaard]

Prof Brian Ripley [EMAIL PROTECTED] writes:

 On Fri, 22 Oct 2004, Adrian Dusa wrote:
 
  I recently compiled R 2.0.0 under Mandrake 9, but it won't run unless in a
  terminal; is there a way to run it in a console, like in Windows?
 
 Yes.  Did you read the manual the INSTALL file pointed you to?
 See appendix B.6 in the version I am looking at.
 
 Or see `An Introduction to R' appendix B.1 and look for --gui.
 
 [To run the GNOME console I think you need R-patched, not 2.0.0 as 
 distributed.]
 
 Another approach is to run John Fox's Rcmdr package that provides a 
 console.

Actually, that one is more of a script submission device. (It has
nowhere to just type and press Enter, you need to edit, select, and
press Submit. Which is a good thing for some modes of operation.)

You'll find that the Linux consoles are not nearly as developed as the
Windows one and hardly anyone is using --gui. There are two good reasons:

1) It's really not that horrible to use the command line in a terminal
   window on Linux. 

2) Many people like to use ESS (see the FAQ) and run everything from
   Emacs.

and of course the bad reason: That there isn't much there. However,
had there been a real need, someone would likely have put in the
relevant improvements. 

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

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[R] invalid for factors not really working

[stefan . albrecht]

Dear all,

I have the impression that the function invalid from gtools is not
really working as I would expect it to do for factors:

Browse[1] invalid(as.factor(NA))
[1] FALSE
Browse[1] invalid(as.numeric(NA))
[1] TRUE

I would exptect that
 invalid(as.factor(NA))
is also TRUE.

Maybe this should be changed in a consistent way which also works in
similar cases for other classes.
One could possibly use
 else return(all(is.na(as.vector(x

Any better suggestions?

Best regards,

Stefan

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RE: [R] confidence interval

[Liaw, Andy]

No, but this question has been asked fairly recently and work-around posted.
Please search the archive.

Andy

 From: lu kan
 
 Is there the similar thing for non-linear 'nls'? 
 
 Lu
 Uwe Ligges [EMAIL PROTECTED] wrote:
 lu kan wrote:
 
  I used a dataset to fit a linear model. For each new 
 sample, a precition can be obtained using the fitted model. 
 Now I wonder is there any way to calculate the confidence 
 interval of the precition for new samples? Any suggestion or 
 pointing to a reference would be very appreciated.
  
  Lu
 
 You already found predict(), so read ?predict.lm carefully 
 and find that 
 there is a argument interval.
 
 Uwe Ligges
 
   
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Re: [R] Assist on R-2.0.0 /64 bit AMD/SuSE 9.1

[Simon Frost]

Dear Brian,

Apologies;I do mean 'assist' rather than 'Assist'; there are versions for R 
and for SPlus. I doubt whether it's to do with calling conventions; the 
functions sometimes work, sometimes they don't, and cause a segmentation 
fault.

Thanks
Simon
-- 
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Adjunct Assistant Professor
Department of Pathology
University of California, San Diego
UCSD Antiviral Research Center
150 W. Washington St.
San Diego, CA 92103
USA
Tel: +1 619 543 8080 Ext 275
Fax: +1 619 298 0177
Email: [EMAIL PROTECTED]

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[R] R

[songj]

Hi, Everyone:

We are installing R package in our Sun Solaris 9, and falling in trouble. We 
downloaded all package from bioconductor, the R can not be installed in Sun 
Solaris 9. We greatly appreciated if you could give us any suggestions. 
Thanks.

Yours

Song

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[R] How to save a complete image of the current state of R ?

[Andreas Buness]

Hello,
I like to save the complete state of R, i.e. including
all environments, objects/workspaces, loaded packages etc..
This wish has arisen since I am not able to reproduce
an error which occurs when running R CMD check.
Many thanks for your advice in advance.
Best Regards
Andreas
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Re: [R] How to save a complete image of the current state of R ?

[Kevin Bartz]

Andreas Buness wrote:
Hello,
I like to save the complete state of R, i.e. including
all environments, objects/workspaces, loaded packages etc..
This wish has arisen since I am not able to reproduce
an error which occurs when running R CMD check.
Many thanks for your advice in advance.
Best Regards
Andreas
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Does save.image meet your needs?
Kevin
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Re: [R] confidence interval

[Prof Brian Ripley]

On Fri, 22 Oct 2004, lu kan wrote:

 Is there the similar thing for non-linear 'nls'? 

Do read the documentation for predict.nls, which also has an argument
interval, which is what you asked.

And this time, read even more carefully.  Then look in the recent
archives, as the posting guide asks, for this question was discussed
recently.

 Uwe Ligges [EMAIL PROTECTED] wrote:
 lu kan wrote:
 
  I used a dataset to fit a linear model. For each new sample, a precition can be 
  obtained using the fitted model. Now I wonder is there any way to calculate the 
  confidence interval of the precition for new samples? Any suggestion or pointing 
  to a reference would be very appreciated.
 
 You already found predict(), so read ?predict.lm carefully and find that 
 there is a argument interval.

 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] How to save a complete image of the current state of R ?

[Uwe Ligges]

Andreas Buness wrote:
Hello,
I like to save the complete state of R, i.e. including
all environments, objects/workspaces, loaded packages etc..
I think what you are going to do is not available.
You can save the workspace, attach the data and load formerly loaded 
packages again, of course.

Uwe Ligges
This wish has arisen since I am not able to reproduce
an error which occurs when running R CMD check.
Many thanks for your advice in advance.
Best Regards
Andreas
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Re: [R] not-mentioned problems on installing R under Solaris; was: R

[Uwe Ligges]

[EMAIL PROTECTED] wrote:
Hi, Everyone:
We are installing R package in our Sun Solaris 9, and falling in trouble. We 
downloaded all package from bioconductor, the R can not be installed in Sun 
Solaris 9. We greatly appreciated if you could give us any suggestions. 
Thanks.

Yours
Song
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Please read the line above which is appended at each R-help message for 
very well reasons. So PLEASE do read the posting guide! 
http://www.R-project.org/posting-guide.html;!

Please use a sensible subject!
Please tell us about your problems. Many users have installed both R and 
Bioconductor packages under Solaris.

So please specify the error messages that appear when you try to install 
R. And provide all information about versions and compiler you are using.

Also, please send Bioconductor related messages to the Bioconductor 
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Uwe Ligges
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Re: [R] R

[Adaikalavan Ramasamy]

You will need to get R working first before installing BioConductor
packages.

Please provide a more useful output (like the error message) if you want
useful help.

Have you tried reading the R manual or searching the mail archives [2].

[1] http://cran.r-project.org/doc/manuals/R-admin.pdf
[2] http://cran.r-project.org/search.html


On Fri, 2004-10-22 at 17:58, [EMAIL PROTECTED] wrote:
 Hi, Everyone:
 
 We are installing R package in our Sun Solaris 9, and falling in trouble. We 
 downloaded all package from bioconductor, the R can not be installed in Sun 
 Solaris 9. We greatly appreciated if you could give us any suggestions. 
 Thanks.
 
 Yours
 
 Song
 
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Re: [R] How to save a complete image of the current state of R ?

[Adaikalavan Ramasamy]

Perhaps save.image(file=lala.rda, compress=T) followed by
load(lala.rda) to re-load it.


On Fri, 2004-10-22 at 18:05, Andreas Buness wrote:
 Hello,
 
 I like to save the complete state of R, i.e. including
 all environments, objects/workspaces, loaded packages etc..
 
 This wish has arisen since I am not able to reproduce
 an error which occurs when running R CMD check.
 
 Many thanks for your advice in advance.
 Best Regards
 Andreas
 
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[R] [R-pkgs] New Package for Multivariate and Propensity Score Matching

[Jasjeet Singh Sekhon]

Matching version 0.48 is now available on CRAN.

Matching provides functions for estimating causal effects by
multivariate and propensity score matching. The package includes a
variety of univariate and multivariate tests to determine if balance
has been obtained by the matching procedure. These tests can also be
used to determine if an experiment or quasi-experiment is balanced on
baseline covariates.  The functions provide valid standard errors and
allow one to estimate various estimands.

For documentation and further details see:

http://jsekhon.fas.harvard.edu/matching

Cheers,
Jas.

==
Jasjeet S. Sekhon
Associate Professor
Harvard University
Center for Basic Research in the 
  Social Sciences
[EMAIL PROTECTED]
http://jsekhon.fas.harvard.edu/
Office: 617.496.2426 Fax: 617.507.5524

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Re: [R] R

[rongguiwong]

i think install.packages may help.
for example,if i want package car from www.cran.r-project.org
i can use 
install.packages(car)
you can use ?install.packages to see more details.


ÔÚ 2004Äê10ÔÂ23ÈÕ ÐÇÆÚÁù 00:[EMAIL PROTECTED] дµÀ£º
 Hi, Everyone:

 We are installing R package in our Sun Solaris 9, and falling in trouble.
 We downloaded all package from bioconductor, the R can not be installed in
 Sun Solaris 9. We greatly appreciated if you could give us any suggestions.
 Thanks.

 Yours

 Song

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RE: [R] console under Mandrake

[Adrian Dusa]

Thank you for your both answers,

As you might have guessed, I am initiating myself in the Linux wizardry. I
have absolutely nothing against command line, I was just heavily used to the
Windows console mode; a terminal window is just fine. Actually, I only used
the console to install packages from CRAN, anyway; I'm sure I'll find the
commands for this.
I read the manuals; it probably didn't work for me because I do not use GNOME
but KDE.

So command line it is... and most probably ESS.
Best regards,
Adrian

-Original Message-
From: Peter Dalgaard [mailto:[EMAIL PROTECTED]
Sent: 22 octombrie 2004 19:11
To: Adrian Dusa; [EMAIL PROTECTED]
Subject: Re: [R] console under Mandrake

Prof Brian Ripley [EMAIL PROTECTED] writes:

 On Fri, 22 Oct 2004, Adrian Dusa wrote:

  I recently compiled R 2.0.0 under Mandrake 9, but it won't run unless in a
  terminal; is there a way to run it in a console, like in Windows?

 Yes.  Did you read the manual the INSTALL file pointed you to?
 See appendix B.6 in the version I am looking at.

 Or see `An Introduction to R' appendix B.1 and look for --gui.

 [To run the GNOME console I think you need R-patched, not 2.0.0 as
 distributed.]

 Another approach is to run John Fox's Rcmdr package that provides a
 console.

Actually, that one is more of a script submission device. (It has
nowhere to just type and press Enter, you need to edit, select, and
press Submit. Which is a good thing for some modes of operation.)

You'll find that the Linux consoles are not nearly as developed as the
Windows one and hardly anyone is using --gui. There are two good reasons:

1) It's really not that horrible to use the command line in a terminal
   window on Linux.

2) Many people like to use ESS (see the FAQ) and run everything from
   Emacs.

and of course the bad reason: That there isn't much there. However,
had there been a real need, someone would likely have put in the
relevant improvements.

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

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[R] $B%a%C%;!<%8$rG[?.$G$-$^$;$s(B

[Yahoo!$B%0%k!<%W(B]

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[R] R2HTML installation on R 1.9.1

[Threefoot, Mark]

Hello,

I am trying to install R2HTML version 1.4-3, but am getting errors when I try to use 
it.  I am running R 1.9.1 on Redhat Linux Ent 3 AS x86_64.  I installed R2HTML using 
the following command R CMD INSTALL R2HTML_1.4-3.tar.gz.  I did not get any errors 
when installing it.  When I launch R and type library('R2HTML'), I get the following 
error:

 library('R2HTML')
Error in loadNamespace(i, c(lib.loc, .libPaths()), keep.source) :
There is no package called 'grDevices'
Error in library(R2HTML) : package/namespace load failed

Is there a dependency that I need to install prior to using R2HTML?  I could not find 
any dependencies in any of the R2HTML documentation.  I also could not find a package 
called grDevices on CRAN.  

Thanks for your help,
Mark

[[alternative HTML version deleted]]

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Re: [R] R2HTML installation on R 1.9.1

[Sundar Dorai-Raj]

Threefoot, Mark wrote:
Hello,
I am trying to install R2HTML version 1.4-3, but am getting errors when I try to use it.  I am 
running R 1.9.1 on Redhat Linux Ent 3 AS x86_64.  I installed R2HTML using the following command 
R CMD INSTALL R2HTML_1.4-3.tar.gz.  I did not get any errors when installing it.  
When I launch R and type library('R2HTML'), I get the following error:

library('R2HTML')
Error in loadNamespace(i, c(lib.loc, .libPaths()), keep.source) :
There is no package called 'grDevices'
Error in library(R2HTML) : package/namespace load failed
Is there a dependency that I need to install prior to using R2HTML?  I could not find any dependencies in any of the R2HTML documentation.  I also could not find a package called grDevices on CRAN.  

Thanks for your help,
Mark
grDevices is new for R-2.0.0. Either upgrade R or find an older version 
of R2HTML.

http://cran.r-project.org/src/contrib/Archive/
--sundar
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[R] Evaluate a function for various value of parameters

[Stephane DRAY]

Hello list,
I have a problem ... and do not know how to solve it.
I would like create a function that estimate the quality of the fit of 
different functions with different values of parameters.
This problem is related to the following one:
I would like to create a function evaluatemyfunction which evaluate a 
function f for different values of parameters. For instance, if
f=function(a,b) a*b
evaluatemyfunction(f,1:10,5) would return:
5
10
15...

I would like that f could have a variable number of arguments. I have begin 
to write a function:

evaluatemyfunction=function(f,...){
b=match.call(expand.dot=F)$...
myg=expand.grid(lapply(b,eval)) #contains all combinations of parameters
for (i in 1:nrow(myg)){
argsasname=paste(paste(names(myg),myg[1,],sep==),collapse=,)
# ??
}
}
I have try to construct arguments of the function as character, then parse 
and pass it to f but parse doesn't work:

 parse(text=paste(paste(names(myg),myg[i,],sep==),collapse=,))
Error in parse(file, n, text, prompt) : parse error
Any ideas ??
Thanks in advance,
sincerely
Stéphane DRAY
-- 

Département des Sciences Biologiques
Université de Montréal, C.P. 6128, succursale centre-ville
Montréal, Québec H3C 3J7, Canada
Tel : (514) 343-6111 poste 1233 Fax : (514) 343-2293
E-mail : [EMAIL PROTECTED]
-- 

Web  http://www.steph280.freesurf.fr/
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[R] dotplot lattice problems: y axis values and bg color output in jpg

[Paul Johnson]

I have a linux system with Fedora Core 2 and R-2.0.
I was comparing plots made with plot() and dotplot() and discovered a 
problem. Although the dots are positioned correctly, the numerical 
labels in the dotplot y axis are not correct.

I put copies here:
http://lark.cc.ku.edu/~pauljohn/R/plotTrouble1.jpg
That is the correct one from plot, with the higest value on y showing 
at 18.

http://lark.cc.ku.edu/~pauljohn/R/plotTrouble2.jpg
That is the dotplot one. The picture is basically the same, except the 
numbers on the y axis only go up to 8.  But the dots are in the correct 
spots and the x axis is labeled correctly.

On the screen, the plots have white backgrounds, but the picture from 
the dotplot turns out gray. Why is that?  Sometimes, if I run another 
lattice plot in the same session, the colors change to the dark 
background, and I suppose the same trouble is happening.  Isn't 
trellis.par.set() going to remain in place for all following trellis plots?

Here's the code I used to make these 2 graphs.
x11(height=6.5,width=6.5)
data2003- subset(elaine1,POLCYEAR==2003)
plot(data2003$OLDCRASH,data2003$RENUCYC)
modall - lm(RENUCYC~OLDCRASH,data=data2003)
abline(modall)
dev.copy(device=jpeg,file=plotTrouble1.jpg)
dev.off()
dev.off()
trellis.par.set(theme=col.whitebg(),height=9,width=6.5)
dotplot (RENUCYC~OLDCRASH, data=elaine1, xlab=ECR, 
as.table=T,subset=POLCYEAR==2003,
panel=function(x,y)
{
  panel.dotplot(x,y,cex=0.2);
  panel.lmline(x,y);
}
   )

jpeg(file=plotTrouble2.jpg,bg=white,height=480,width=480)
trellis.last.object()
dev.off()
dev.off()
I tried to force the ylim on the dotplot up to 18, but it just produced 
this even uglier result.

http://lark.cc.ku.edu/~pauljohn/R/plotTrouble3.jpg
--
Paul E. Johnson   email: [EMAIL PROTECTED]
Dept. of Political Sciencehttp://lark.cc.ku.edu/~pauljohn
1541 Lilac Lane, Rm 504
University of Kansas  Office: (785) 864-9086
Lawrence, Kansas 66044-3177   FAX: (785) 864-5700
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Re: [R] Evaluate a function for various value of parameters

[Olaf Mersmann]

Hi Stephane,

* Stephane DRAY [EMAIL PROTECTED] [041023 00:20]:
 Hello list,
 
 I have a problem ... and do not know how to solve it.
 I would like create a function that estimate the quality of the fit of 
 different functions with different values of parameters.
 This problem is related to the following one:
 I would like to create a function evaluatemyfunction which evaluate a 
 function f for different values of parameters. For instance, if
 f=function(a,b) a*b
 evaluatemyfunction(f,1:10,5) would return:
 5
 10
 15...
 
 I would like that f could have a variable number of arguments. I have begin 
 to write a function:

That function has already been written for you. Lookup 'mapply' in the
online help.

HTH
Olaf

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Re: [R] dotplot lattice problems: y axis values and bg color output in jpg

[Sundar Dorai-Raj]

Paul Johnson wrote:
I have a linux system with Fedora Core 2 and R-2.0.
I was comparing plots made with plot() and dotplot() and discovered a 
problem. Although the dots are positioned correctly, the numerical 
labels in the dotplot y axis are not correct.

I put copies here:
http://lark.cc.ku.edu/~pauljohn/R/plotTrouble1.jpg
That is the correct one from plot, with the higest value on y showing 
at 18.

http://lark.cc.ku.edu/~pauljohn/R/plotTrouble2.jpg
That is the dotplot one. The picture is basically the same, except the 
numbers on the y axis only go up to 8.  But the dots are in the correct 
spots and the x axis is labeled correctly.

On the screen, the plots have white backgrounds, but the picture from 
the dotplot turns out gray. Why is that?  Sometimes, if I run another 
lattice plot in the same session, the colors change to the dark 
background, and I suppose the same trouble is happening.  Isn't 
trellis.par.set() going to remain in place for all following trellis plots?

Here's the code I used to make these 2 graphs.
x11(height=6.5,width=6.5)
data2003- subset(elaine1,POLCYEAR==2003)
plot(data2003$OLDCRASH,data2003$RENUCYC)
modall - lm(RENUCYC~OLDCRASH,data=data2003)
abline(modall)
dev.copy(device=jpeg,file=plotTrouble1.jpg)
dev.off()
dev.off()
trellis.par.set(theme=col.whitebg(),height=9,width=6.5)
dotplot (RENUCYC~OLDCRASH, data=elaine1, xlab=ECR, 
as.table=T,subset=POLCYEAR==2003,
panel=function(x,y)
{
  panel.dotplot(x,y,cex=0.2);
  panel.lmline(x,y);
}
   )

jpeg(file=plotTrouble2.jpg,bg=white,height=480,width=480)
trellis.last.object()
dev.off()
dev.off()
I tried to force the ylim on the dotplot up to 18, but it just produced 
this even uglier result.

http://lark.cc.ku.edu/~pauljohn/R/plotTrouble3.jpg
Paul,
dotplot is not doing what you think it's doing. RENUCYC is being forced 
to a factor with 9 levels. I think what you intending to use is xyplot. 
Just

trellis.par.set(theme=col.whitebg(),height=9,width=6.5)
xyplot(RENUCYC~OLDCRASH, data=elaine1, xlab=ECR,
   as.table=T,subset=POLCYEAR==2003,
   panel=function(x,y) {
 panel.dotplot(x,y,cex=0.2) #; no need for semi-colons
 panel.lmline(x,y)
   })
As for your second question, when you call jpeg a new device is called. 
You need to reset the theme after opening the device, or just use 
trellis.device:

trellis.device(jpeg, file=plotTrouble2.jpg,
   theme = col.whitebg(),height=480,width=480)
trellis.last.object()
dev.off()
--sundar
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Re: [R] dotplot lattice problems: y axis values and bg color output in jpg

[Olaf Mersmann]

Hi Paul.
* Paul Johnson [EMAIL PROTECTED] [041023 00:24]:
*snip*

 That is the dotplot one. The picture is basically the same, except the 
 numbers on the y axis only go up to 8.  But the dots are in the correct 
 spots and the x axis is labeled correctly.

Unless RENUCYC is a factor, a dotplot makes little sense. Afaik you're
looking for an xyplot. 

 On the screen, the plots have white backgrounds, but the picture from 
 the dotplot turns out gray. Why is that?  

It's the default lattice color sheme which makes for easier viewing on
computer screens.

 Sometimes, if I run another
 lattice plot in the same session, the colors change to the dark 
 background, and I suppose the same trouble is happening.  Isn't 
 trellis.par.set() going to remain in place for all following trellis plots?

To quote the manual:
Once a device is open, it's settings can be modified. When another
instance of the same device is opened later using trellis.device, the
settings for that device are reset to its defaults, unless otherwise
specified in the call to trellis.device.

HTH
Olaf

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Re: [R] dotplot lattice problems: y axis values and bg color output in jpg

[Deepayan Sarkar]

On Friday 22 October 2004 17:16, Paul Johnson wrote:
 I have a linux system with Fedora Core 2 and R-2.0.

 I was comparing plots made with plot() and dotplot() and discovered a
 problem. Although the dots are positioned correctly, the numerical
 labels in the dotplot y axis are not correct.

That's comparing apples and oranges, sort of. You should use xyplot 
instead of dotplot if you want the equivalent of plot (more precisely, 
plot.default).

Although it's not obvious from your code, I'll bet your Y variable is 
numeric with 9 unique values. dotplot treats one of its variables as a 
factor. If neither variable are factors, it by default chooses the Y 
variable is a factor. If it is numeric, as in your case, it converts it 
into a 'shingle' (see ?shingle). This has almost the same effect as 
coercion to a factor, except the Y values are labeled 1,2,... instead 
of the levels.

 I put copies here:

 http://lark.cc.ku.edu/~pauljohn/R/plotTrouble1.jpg

 That is the correct one from plot, with the higest value on y
 showing at 18.

 http://lark.cc.ku.edu/~pauljohn/R/plotTrouble2.jpg

 That is the dotplot one. The picture is basically the same, except
 the numbers on the y axis only go up to 8.  But the dots are in the
 correct spots and the x axis is labeled correctly.

They are not the same. The Y-spacing between the unique values are all 
equal in dotplot, unlike in the plot output.

 On the screen, the plots have white backgrounds, but the picture from
 the dotplot turns out gray. Why is that?  Sometimes, if I run another
 lattice plot in the same session, the colors change to the dark
 background, and I suppose the same trouble is happening.  Isn't
 trellis.par.set() going to remain in place for all following trellis
 plots?

Trellis settings are very much device-specific, and trellis.par.set only 
affects the currently open device (much like par). You call it to 
change the x11 settings, but you haven't changed the jpeg settings 
anywhere, so the defaults are used.

What happens for new instances of the same device is a bit more subtle. 
Once you change settings for a particular device type (say x11), 
lattice remembers these settings. However, if you open a new instance 
of this device with, say

trellis.device(x11)

the x11 settings revert back to the x11 defaults (this behaviour can 
be suppressed by an argument to trellis.device). Now, even if you don't 
do this explicitly, any attempt to create a Trellis plot while there's 
no currently active device results in a call to trellis.device, and 
hence results in a new instance with the settings reset to defaults. 
However, the settings are NOT reset if the device is already open.

An example to make things a bit less confusing (hopefully):

p - xyplot(1~1)
x11() 
p  ## default (grey) background
trellis.par.set(col.whitebg())
p  ## 'white' (actually transparent) background
dev.off()

x11()
p ## still white background, settings retained
dev.off()

p ## new instance of x11 started, settings reset, 
  ## hence grey background


If you find this surprising, it's basically because lattice has no way 
of knowing that a new device has been opened unless it's done through 
trellis.device. Otherwise, the idea is to be similar to par and reset 
the defaults everytime.

Deepayan

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Re: [R] How to calculate a double integral ...?

[cjosephlu]

Gabor Grothendieck [EMAIL PROTECTED] writes:
 cjlu cjlu at mail.ncku.edu.tw writes:
 : How can I calculate a double integral like
 : 
 :   \int_a^b \int_c^y g(x, y) dx dy
 : 
 : where a, b, c are constants, g(x, y), e.g.,
 : g(x, y) = tan(x + y).
 :  
 Integrate
 
g2 - function(x, y) g(x, y) * (x  y)
 
 over (a,b) x (a,c).
 
Thanks Gabor for your prompt and helpful response!

Later on, I realized that such an integration can be done by
the following way, provided function g(x, y) takes vector input, e.g.,
g(x, y) = tan(x + y)

 integrate(function(y) {
+   sapply(y, function(y) {
+ integrate(function(x) tan(x + y), -.5, y)$value
+   })
+ }, 0, .5)
0.07238855 with absolute error  1.1e-15

if g(x, y) can only take scalar input, we can do

 integrate(function(y) {
+   sapply(y, function(y) {
+ integrate(function(x) {
+   sapply(x, function(x) tan(x + y))
+ }, -.5, y)$value
+   })
+ }, 0, .5)
0.07238855 with absolute error  1.1e-15

Best regards,

C. Joseph Lu
Department of Statistics
National Cheng-Kung University
Tainan
Taiwan, ROC

-
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Re: [R] Evaluate a function for various value of parameters

[Gabor Grothendieck]

Stephane DRAY dray at biomserv.univ-lyon1.fr writes:
: I would like to create a function evaluatemyfunction which evaluate a 
: function f for different values of parameters. For instance, if
: f=function(a,b) a*b
: evaluatemyfunction(f,1:10,5) would return:
: 5
: 10
: 15...
: 

This is not a general solution (Olaf has already provided that) but 
in some cases you may simply be able to write your function f so that 
it takes vector arguments.  For example, with the f you have above 
one could write f(1:10,5) .

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[R] JDBC DB access in R

[zubin]

Hello, i see packages referencing using ODBC access to databases via R, are
there any packages that use JDBC to submit SQL to a database and return into
a data frame?  

-zubin

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