[R] hashmap in R

[Qiang Li (Jonathan)]

Hi friends on R list,

Have people tried to implement a hashmap in R? What is the generic way to 
implement a lookup table in R?

Best,
Jonathan

 
===
Jonathan Qiang Li

===


  


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Re: [R] use of sequence on ridge regression

[Prof Brian Ripley]

On Wed, 7 May 2008, Rodrigo Briceño wrote:


Sorry to bother with this topic, but I'm still not clear about the
meaning of the value set that is used on lambda values. Is there a
correct way of doing that? My doubt is how to choose those 3 values
that appear in the example.


I think you have not yet read the help for seq(): try printing out
seq(0,0.1,0.001).  There are not '3 values' here, but 3 arguments to a 
function.


'lambda' values start at 0 (no shrinkage), and how large you want them to 
be is problem-specific.  How many you ask for (101 here) is also 
problem-specific, but around 100 values is often used.




Thanks.

On Wed, May 7, 2008 at 9:29 AM, Prof Brian Ripley <[EMAIL PROTECTED]> wrote:

On Wed, 7 May 2008, Rodrigo Briceño wrote:



Nice to meet you Brian. The question is about the numbers that appears
after lambda (0,0, 0.1, 0.0001). I know that seq is a set of values used
for testing which value fits best. But I'm not sure if I need to put
whatever I think or what. I tried also with a set of 5 values and I get
an error. Is there a maximum allowed?



 So you mean the set of values of lambda?  It is just a set to be use for a
plot and for searching in the select() methods.

 There is an R function called sequence(), and it is not the same as seq().






plot(lm.ridge(hipcenter ~ .,seatpos, lambda = seq(0,0.1,0.001)))
select(lm.ridge(hipcenter ~ ., seatpos,lambda = seq(0,0.1,0.001)))

__

Rodrigo Briceño
Project Manager
Sanigest Internacional

+506  22-91-12-00 ext. 113   Oficina Costa Rica
+506  22-32-08-30  Fax
+506  88-86-11-77  Celular
[EMAIL PROTECTED]
www.sanigest.com

MSN: [EMAIL PROTECTED]
SKYPE: rbriceno1087

_

This communication contains legal information which is privileged and
confidential. It is for the exclusive use of the address and
distribution, dissemination, copying or use by others is strictly
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para el uso exclusivo del destinatario. La distribución, diseminación,
copia u otro uso por terceras personas es estrictamente prohibida. Si
usted ha recibido esta comunicación por error, le rogamos borrar el
mensaje original y comunicárnoslo a esta misma dirección.



Prof Brian Ripley wrote:
 What do you mean by 'the sequence option'?

 The authot of lm.ridge

 On Wed, 7 May 2008, Rodrigo Briceño wrote:

   Dear R users. I have a doubt about the use of the
   sequence option on
   Ridge regression. I'm trying to understand the
   use of this option when
   variables are highly linear correlated. I'm
   running a model where the
   variables HtShoes and Ht have high VIF values. My
   program is written
   below, but I'm not sure about the correct way of
   using the sequence
   option:

   library (faraway)
   data (seatpos)
   attach (seatpos)
   spos.mod <- lm(hipcenter ~ .,seatpos) summary
   (spos.mod)
   library(MASS)
   lm.ridge(hipcenter ~ .,seatpos)
   plot(lm.ridge(hipcenter ~ .,seatpos, lambda =
   seq(0,0.1,0.001)))
   select(lm.ridge(hipcenter ~ ., seatpos,lambda =
   seq(0,0.1,0.001)))

   Any advice will be appreaciated. Rodrigo B.

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   PLEASE do read the posting guide
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   reproducible code.








 --
 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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--
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] Replicating Rows

[Jorge Ivan Velez]

Hi Marion,

Try this:

set.seed(123)
mydf=data.frame(trips=rpois(10,5), matrix(rnorm(10*5),ncol=5))
mydf
sapply(mydf[,-1],rep,mydf[,1])


HTH,

Jorge


On Wed, May 7, 2008 at 11:41 PM, <[EMAIL PROTECTED]> wrote:

>
>
> Hi,
>
>  I have a data matrix in which there are 1000 rows by 30 columns. The
> first
> column of each row is a numeric indicating the number of trips taken to a
> particular location with location attributes in the following column
> entries for
> that row.
>
> I want to repeat each row based on the number of trips taken (as indicated
> by
> the number in the first column)...i.e., if 1,1 indicates 4 trips, I want
> to
> replicate row 1 four times, and do this for each entry of column 1.
>
> I have played with rep command with little luck. Can anyone help? This is
> probably very simple.
>
> Thank you,
>
> mw
>
>
> Marion Wittmann, Ph.D. candidate
> Environmental Science and Management
> University of California
> Santa Barbara, CA 93106-5131
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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Re: [R] algorithmic or automatic differentiation

[Erin Hodgess]

Thanks to all!

Sincerely,
Erin

On Wed, May 7, 2008 at 10:35 PM, Simon Blomberg <[EMAIL PROTECTED]> wrote:
> No, computer algebra systems such as yacas do symbolic differentiation.
> Automatic differentiation is a numerical technique that can be used to
> find derivatives of functions that can be implemented as computer
> programs, through successive uses of the chain rule on the computer code
> itself. It would be cool if R could either do AD or interface to an AD
> package. R can be used with ADmodelbuilder (see
> http://otter-rsch.ca/admbre/examples/glmmadmb/glmmADMB.html) , a
> proprietry program, but an open source solution would be nice.
>
> Cheers,
>
> Simon.
>
>
> On Thu, 2008-05-08 at 03:09 +, David Winsemius wrote:
> > "Erin Hodgess" <[EMAIL PROTECTED]> wrote in
> > news:[EMAIL PROTECTED]:
> >
> > > Is there a package for automatic differentiation, please?
> > >
> >
> > Have you looked at Goedman, Grothendieck, Hojsgaard, and Pinkus' Ryacas?
> >
> > >From the Ryacas documentation:
> > Analytical derivatives of functions can be evaluated with the D() and
> > deriv() functions:
> >
> > > yacas("D(x) Sin(x)")
> >
> > expression(cos(x))
> >
> --
> Simon Blomberg, BSc (Hons), PhD, MAppStat.
> Lecturer and Consultant Statistician
> Faculty of Biological and Chemical Sciences
> The University of Queensland
> St. Lucia Queensland 4072
> Australia
> Room 320 Goddard Building (8)
> T: +61 7 3365 2506
> http://www.uq.edu.au/~uqsblomb
> email: S.Blomberg1_at_uq.edu.au
>
> Policies:
> 1.  I will NOT analyse your data for you.
> 2.  Your deadline is your problem.
>
> The combination of some data and an aching desire for
> an answer does not ensure that a reasonable answer can
> be extracted from a given body of data. - John Tukey.
>
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>



-- 
Erin Hodgess
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: [EMAIL PROTECTED]

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[R] Replicating Rows

[mwittmann]

Hi, 

 I have a data matrix in which there are 1000 rows by 30 columns. The first
column of each row is a numeric indicating the number of trips taken to a
particular location with location attributes in the following column entries for
that row. 

I want to repeat each row based on the number of trips taken (as indicated by
the number in the first column)...i.e., if 1,1 indicates 4 trips, I want to
replicate row 1 four times, and do this for each entry of column 1. 

I have played with rep command with little luck. Can anyone help? This is
probably very simple. 

Thank you,

mw


Marion Wittmann, Ph.D. candidate
Environmental Science and Management
University of California
Santa Barbara, CA 93106-5131

__
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Re: [R] algorithmic or automatic differentiation

[Simon Blomberg]

No, computer algebra systems such as yacas do symbolic differentiation.
Automatic differentiation is a numerical technique that can be used to
find derivatives of functions that can be implemented as computer
programs, through successive uses of the chain rule on the computer code
itself. It would be cool if R could either do AD or interface to an AD
package. R can be used with ADmodelbuilder (see
http://otter-rsch.ca/admbre/examples/glmmadmb/glmmADMB.html) , a
proprietry program, but an open source solution would be nice.

Cheers,

Simon.


On Thu, 2008-05-08 at 03:09 +, David Winsemius wrote:
> "Erin Hodgess" <[EMAIL PROTECTED]> wrote in 
> news:[EMAIL PROTECTED]:
> 
> > Is there a package for automatic differentiation, please?
> > 
> 
> Have you looked at Goedman, Grothendieck, Hojsgaard, and Pinkus' Ryacas?
> 
> >From the Ryacas documentation:
> Analytical derivatives of functions can be evaluated with the D() and 
> deriv() functions:
> 
> > yacas("D(x) Sin(x)")
> 
> expression(cos(x))
> 
-- 
Simon Blomberg, BSc (Hons), PhD, MAppStat. 
Lecturer and Consultant Statistician 
Faculty of Biological and Chemical Sciences 
The University of Queensland 
St. Lucia Queensland 4072 
Australia
Room 320 Goddard Building (8)
T: +61 7 3365 2506
http://www.uq.edu.au/~uqsblomb
email: S.Blomberg1_at_uq.edu.au

Policies:
1.  I will NOT analyse your data for you.
2.  Your deadline is your problem.

The combination of some data and an aching desire for 
an answer does not ensure that a reasonable answer can 
be extracted from a given body of data. - John Tukey.

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] algorithmic or automatic differentiation

[David Winsemius]

"Erin Hodgess" <[EMAIL PROTECTED]> wrote in 
news:[EMAIL PROTECTED]:

> Is there a package for automatic differentiation, please?
> 

Have you looked at Goedman, Grothendieck, Hojsgaard, and Pinkus' Ryacas?

>From the Ryacas documentation:
Analytical derivatives of functions can be evaluated with the D() and 
deriv() functions:

> yacas("D(x) Sin(x)")

expression(cos(x))

-- 
David Winsemius

__
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Re: [R] categorical data analysis

[David Winsemius]

David Winsemius <[EMAIL PROTECTED]> wrote in 
news:[EMAIL PROTECTED]:

> raymond chiruka <[EMAIL PROTECTED]> wrote in
> news:[EMAIL PROTECTED]: 
> 
>> i am trying to carry out a categorical data analysis but my problem
>> is that when in i use the chi squared  test some of my  expected
>> values are less than 5. is there a  test that can handle this
>> situation. the data is not a 2*2 table. its more from the social
>> sciences where you have from strongly agree to strongly disagree. i
>> know i can collapse vthe tables but there is a loss of information .
>> is the a test vthat i can for this kind of data. thanks in advancde.
>  
> In addition to Snow's suggestion of fisher.test, you may want to look 
> more closely at:
> ?chisq.test
snip

Another possibility for the analysis of ordered catergorical response 
might be proportional odds regression. The MASS package has polr:

library(MASS)
?polr

polr(formula, data, weights, start, ..., subset, na.action,
 contrasts = NULL, Hess = FALSE, model = TRUE,
 method = c("logistic", "probit", "cloglog", "cauchit"))

Arguments
formula: a formula expression as for regression models, of the form 
response ~ predictors. The response should be a factor (preferably an 
ordered factor), which will be interpreted as an ordinal response, with 
levels ordered as in the factor.  
-
My copy of Venables&Ripley's MASS is an older version and neither the 
index nor the TOC tells me where to find worked examples. Harrell's 
Regression Modeling Strategies has a case study illustrating the use of  
his lrm function. So you might also look at:

library(Design)
?lrm
-- 
David Winsemius

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Re: [R] cross-correlation lag.plot?

[David Stoffer]

http://www.stat.pitt.edu/stoffer/tsa2/Examples.htm


tom soyer wrote:
> 
> Hi,
> 
> Does anyone know if R has a function that is similar to lag.plot but
> instead
> of auto-correlation, it plots cross-correlation with lags?
> 
> Thanks,
> 
> -- 
> Tom
> 
>   [[alternative HTML version deleted]]
> 
> __
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 
> 


-
The power of accurate observation is commonly called cynicism 
by those who have not got it.  George Bernard Shaw
-- 
View this message in context: 
http://www.nabble.com/cross-correlation-lag.plot--tp17114046p17117624.html
Sent from the R help mailing list archive at Nabble.com.

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Re: [R] use of sequence on ridge regression

[Rodrigo Briceño]

Sorry to bother with this topic, but I'm still not clear about the
meaning of the value set that is used on lambda values. Is there a
correct way of doing that? My doubt is how to choose those 3 values
that appear in the example.
Thanks.

On Wed, May 7, 2008 at 9:29 AM, Prof Brian Ripley <[EMAIL PROTECTED]> wrote:
> On Wed, 7 May 2008, Rodrigo Briceño wrote:
>
>
> > Nice to meet you Brian. The question is about the numbers that appears
> > after lambda (0,0, 0.1, 0.0001). I know that seq is a set of values used
> > for testing which value fits best. But I'm not sure if I need to put
> > whatever I think or what. I tried also with a set of 5 values and I get
> > an error. Is there a maximum allowed?
> >
>
>  So you mean the set of values of lambda?  It is just a set to be use for a
> plot and for searching in the select() methods.
>
>  There is an R function called sequence(), and it is not the same as seq().
>
>
>
>
> >
> > plot(lm.ridge(hipcenter ~ .,seatpos, lambda = seq(0,0.1,0.001)))
> > select(lm.ridge(hipcenter ~ ., seatpos,lambda = seq(0,0.1,0.001)))
> >
> > __
> >
> > Rodrigo Briceño
> > Project Manager
> > Sanigest Internacional
> >
> > +506  22-91-12-00 ext. 113   Oficina Costa Rica
> > +506  22-32-08-30  Fax
> > +506  88-86-11-77  Celular
> > [EMAIL PROTECTED]
> > www.sanigest.com
> >
> > MSN: [EMAIL PROTECTED]
> > SKYPE: rbriceno1087
> >
> > _
> >
> > This communication contains legal information which is privileged and
> > confidential. It is for the exclusive use of the address and
> > distribution, dissemination, copying or use by others is strictly
> > prohibited. If you have received this communication by error, please
> > delete the original message and e-mail us.
> >
> >
> > Esta comunicación contiene información legal privilegiada y confidencial
> > para el uso exclusivo del destinatario. La distribución, diseminación,
> > copia u otro uso por terceras personas es estrictamente prohibida. Si
> > usted ha recibido esta comunicación por error, le rogamos borrar el
> > mensaje original y comunicárnoslo a esta misma dirección.
> >
> >
> >
> > Prof Brian Ripley wrote:
> >  What do you mean by 'the sequence option'?
> >
> >  The authot of lm.ridge
> >
> >  On Wed, 7 May 2008, Rodrigo Briceño wrote:
> >
> >Dear R users. I have a doubt about the use of the
> >sequence option on
> >Ridge regression. I'm trying to understand the
> >use of this option when
> >variables are highly linear correlated. I'm
> >running a model where the
> >variables HtShoes and Ht have high VIF values. My
> >program is written
> >below, but I'm not sure about the correct way of
> >using the sequence
> >option:
> >
> >library (faraway)
> >data (seatpos)
> >attach (seatpos)
> >spos.mod <- lm(hipcenter ~ .,seatpos) summary
> >(spos.mod)
> >library(MASS)
> >lm.ridge(hipcenter ~ .,seatpos)
> >plot(lm.ridge(hipcenter ~ .,seatpos, lambda =
> >seq(0,0.1,0.001)))
> >select(lm.ridge(hipcenter ~ ., seatpos,lambda =
> >seq(0,0.1,0.001)))
> >
> >Any advice will be appreaciated. Rodrigo B.
> >
> >__
> >R-help@r-project.org mailing list
> >https://stat.ethz.ch/mailman/listinfo/r-help
> >PLEASE do read the posting guide
> >http://www.R-project.org/posting-guide.html
> >and provide commented, minimal, self-contained,
> >reproducible code.
> >
> >
> >
> >
> >
>
>
>  --
>  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] anova p value extraction

[H. Paul Benton]

yep That worked Jorge. Thanks!

summary(pb)$"Pr(>F)1"
NULL
> summ<-summary(pb)
> class(unlist(summ))

[1] "numeric"
> unlist(summ)["Pr(>F)1"]

   Pr(>F)1
0.02533637
> names(summ)
NULL 



Jorge Ivan Velez wrote:
>
> Hi Paul,
>
> Perhaps
>
> # Data set
> set.seed(123)
> x=rnorm(100)
> y=x+2*rnorm(100)
>
> # ANOVA
> AOV=anova(lm (y ~ x))
> p1=AOV$"Pr(>F)"[1]
> p1
>  
> or
>
> # ANOVA 2
> AOV1=aov(y ~ x)
> p2=unlist(summary(AOV1))["Pr(>F)1"]
> p2
>
>
> HTH,
>
> Jorge
>
>
>
> On Wed, May 7, 2008 at 8:47 PM, Paul Benton <[EMAIL PROTECTED] 
> > wrote:
>
> hello all,
>
> Quick question, how do I get the p value out of the anova?
>
> Thanks,
>
> Paul
>
> > pb<-aov(as.numeric(diff[5,16:33]) ~ grF)
> > summary(pb)
>Df Sum SqMean Sq F value  Pr(>F)
> grF  3 2.7860e+10 9.2867e+09  4.2236 0.02534 *
> Residuals   14 3.0783e+10 2.1988e+09
> ---
> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> > str(summary(pb))
> List of 1
>  $ :Classes 'anova' and 'data.frame':   2 obs. of  5 variables:
>  ..$ Df : num [1:2] 3 14
>  ..$ Sum Sq : num [1:2] 2.79e+10 3.08e+10
>  ..$ Mean Sq: num [1:2] 9.29e+09 2.20e+09
>  ..$ F value: num [1:2] 4.22   NA
>  ..$ Pr(>F) : num [1:2] 0.0253 NA
>  - attr(*, "class")= chr [1:2] "summary.aov" "listof"
> > attr(summary(pb), "Pr(>F)")
> NULL
>
> __
> R-help@r-project.org  mailing list
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

[[alternative HTML version deleted]]

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Re: [R] anova p value extraction

[Abhijit Dasgupta]

What works, amazingly, is
summary(pb)$"Pr(>F)" [note the quotes]

Abhijit

On Wed, 07 May 2008 18:17:09 -0700
"H. Paul Benton" <[EMAIL PROTECTED]> wrote:

> Yea the anova object seems to be odd. It's not S4 so that's why I tried 
> originally the attr() funtion but
> 
> summary(pb)$Pr(>F)
> 
> Error: unexpected '>' in "summary(pb)$Pr(>"
> > summary(pb)$Pr
> 
> NULL
> > summary(pb)@Pr(>F)
> 
> Error: unexpected '>' in "summary(pb)@Pr(>"
> > summary(pb)@Pr(F)
> 
> Error: no slot of name "Pr" for this object of class "summary.aov"
> In addition: Warning message:
> trying to get slot "Pr" from an object (class "summary.aov") that is
> not an S4 object
> >
> 
> Research Programmer & Technician
> The Scripps Research Institute
> Mass Spectrometry Core Facility
>   o The
>  /
> o Scripps
>  \
>   o Research
>  /
> o Institute
> 
> 
> 
> [EMAIL PROTECTED] wrote:
> >  Hi: it's probably the Pr(> F) element so just access it by
> >
> > sum<-summary(whatever).
> >
> > then sum$Pr(>F) will probably work. But make sure that's it because 
> > usually the name is pval or pvalue etc so I'm
> > surprised about the weird name.
> >
> >
> >
> >
> > On Wed, May 7, 2008 at  8:47 PM, Paul Benton wrote:
> >
> >> hello all,
> >>
> >> Quick question, how do I get the p value out of the anova?
> >>
> >> Thanks,
> >>
> >> Paul
> >>
> >>> pb<-aov(as.numeric(diff[5,16:33]) ~ grF)
> >>> summary(pb)
> >> Df Sum SqMean Sq F value  Pr(>F)
> >> grF  3 2.7860e+10 9.2867e+09  4.2236 0.02534 *
> >> Residuals   14 3.0783e+10 2.1988e+09
> >> ---
> >> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> >>> str(summary(pb))
> >> List of 1
> >>  $ :Classes 'anova' and 'data.frame':   2 obs. of  5 variables:
> >>   ..$ Df : num [1:2] 3 14
> >>   ..$ Sum Sq : num [1:2] 2.79e+10 3.08e+10
> >>   ..$ Mean Sq: num [1:2] 9.29e+09 2.20e+09
> >>   ..$ F value: num [1:2] 4.22   NA
> >>   ..$ Pr(>F) : num [1:2] 0.0253 NA
> >>  - attr(*, "class")= chr [1:2] "summary.aov" "listof"
> >>> attr(summary(pb), "Pr(>F)")
> >> NULL
> >>
> >> __
> >> R-help@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide 
> >> http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >
> >
> 
>   [[alternative HTML version deleted]]
> 
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


-- 
Abhijit Dasgupta

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Re: [R] anova p value extraction

[Jorge Ivan Velez]

Hi Paul,

Perhaps

# Data set
set.seed(123)
x=rnorm(100)
y=x+2*rnorm(100)

# ANOVA
AOV=anova(lm (y ~ x))
p1=AOV$"Pr(>F)"[1]
p1

or

# ANOVA 2
AOV1=aov(y ~ x)
p2=unlist(summary(AOV1))["Pr(>F)1"]
p2


HTH,

Jorge



On Wed, May 7, 2008 at 8:47 PM, Paul Benton <[EMAIL PROTECTED]> wrote:

> hello all,
>
> Quick question, how do I get the p value out of the anova?
>
> Thanks,
>
> Paul
>
> > pb<-aov(as.numeric(diff[5,16:33]) ~ grF)
> > summary(pb)
>Df Sum SqMean Sq F value  Pr(>F)
> grF  3 2.7860e+10 9.2867e+09  4.2236 0.02534 *
> Residuals   14 3.0783e+10 2.1988e+09
> ---
> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> > str(summary(pb))
> List of 1
>  $ :Classes 'anova' and 'data.frame':   2 obs. of  5 variables:
>  ..$ Df : num [1:2] 3 14
>  ..$ Sum Sq : num [1:2] 2.79e+10 3.08e+10
>  ..$ Mean Sq: num [1:2] 9.29e+09 2.20e+09
>  ..$ F value: num [1:2] 4.22   NA
>  ..$ Pr(>F) : num [1:2] 0.0253 NA
>  - attr(*, "class")= chr [1:2] "summary.aov" "listof"
> > attr(summary(pb), "Pr(>F)")
> NULL
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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Re: [R] anova p value extraction

[H. Paul Benton]

Yea the anova object seems to be odd. It's not S4 so that's why I tried 
originally the attr() funtion but

summary(pb)$Pr(>F)

Error: unexpected '>' in "summary(pb)$Pr(>"
> summary(pb)$Pr

NULL
> summary(pb)@Pr(>F)

Error: unexpected '>' in "summary(pb)@Pr(>"
> summary(pb)@Pr(F)

Error: no slot of name "Pr" for this object of class "summary.aov"
In addition: Warning message:
trying to get slot "Pr" from an object (class "summary.aov") that is
not an S4 object
>

Research Programmer & Technician
The Scripps Research Institute
Mass Spectrometry Core Facility
  o The
 /
o Scripps
 \
  o Research
 /
o Institute



[EMAIL PROTECTED] wrote:
>  Hi: it's probably the Pr(> F) element so just access it by
>
> sum<-summary(whatever).
>
> then sum$Pr(>F) will probably work. But make sure that's it because 
> usually the name is pval or pvalue etc so I'm
> surprised about the weird name.
>
>
>
>
> On Wed, May 7, 2008 at  8:47 PM, Paul Benton wrote:
>
>> hello all,
>>
>> Quick question, how do I get the p value out of the anova?
>>
>> Thanks,
>>
>> Paul
>>
>>> pb<-aov(as.numeric(diff[5,16:33]) ~ grF)
>>> summary(pb)
>> Df Sum SqMean Sq F value  Pr(>F)
>> grF  3 2.7860e+10 9.2867e+09  4.2236 0.02534 *
>> Residuals   14 3.0783e+10 2.1988e+09
>> ---
>> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
>>> str(summary(pb))
>> List of 1
>>  $ :Classes 'anova' and 'data.frame':   2 obs. of  5 variables:
>>   ..$ Df : num [1:2] 3 14
>>   ..$ Sum Sq : num [1:2] 2.79e+10 3.08e+10
>>   ..$ Mean Sq: num [1:2] 9.29e+09 2.20e+09
>>   ..$ F value: num [1:2] 4.22   NA
>>   ..$ Pr(>F) : num [1:2] 0.0253 NA
>>  - attr(*, "class")= chr [1:2] "summary.aov" "listof"
>>> attr(summary(pb), "Pr(>F)")
>> NULL
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide 
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>

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[R] SVD for a 500, 000* 500, 000 matrix (singular value decomposition)

[kayj]

Hi,


I tried to run SVD on a  500,000* 500,000 matrix and i get a message that it
can  not allocate a vector of length 270 mb 

doe snayone know how to solve this problem? any ideas on other softwares
where I can do this? 
I appreciate your help
thanks 
-- 
View this message in context: 
http://www.nabble.com/SVD-for-a-500%2C000*-500%2C000-matrix-%28singular-value-decomposition%29-tp17115286p17115286.html
Sent from the R help mailing list archive at Nabble.com.

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[R] anova p value extraction

[Paul Benton]

hello all,

Quick question, how do I get the p value out of the anova?

Thanks,

Paul

> pb<-aov(as.numeric(diff[5,16:33]) ~ grF)
> summary(pb)
Df Sum SqMean Sq F value  Pr(>F)
grF  3 2.7860e+10 9.2867e+09  4.2236 0.02534 *
Residuals   14 3.0783e+10 2.1988e+09
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> str(summary(pb))
List of 1
 $ :Classes 'anova' and 'data.frame':   2 obs. of  5 variables:
  ..$ Df : num [1:2] 3 14
  ..$ Sum Sq : num [1:2] 2.79e+10 3.08e+10
  ..$ Mean Sq: num [1:2] 9.29e+09 2.20e+09
  ..$ F value: num [1:2] 4.22   NA
  ..$ Pr(>F) : num [1:2] 0.0253 NA
 - attr(*, "class")= chr [1:2] "summary.aov" "listof"
> attr(summary(pb), "Pr(>F)")
NULL

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Re: [R] Estimating QAIC using glm with the quasibinomial family

[Kunio takezawa]

R-users
E-mail: r-help@r-project.org

>but I was specificly interested in calculating QAIC and QAICc from
>a glm fitted with the "family=quasibinomial" option.

If you use "family=quasibinomial(link = "logit")" in glm(),
the program will be:

function ()
{
   xx <- c(1,2,3,4,5,6,7,8,9,10)
   yy <- c(1,0,1,0,0,1,0,1,1,1)
   data1 <- data.frame(x=xx, y=yy)
   out1 <- glm(y~x, data=data1, family=quasibinomial(link = "logit"))
   print(out1)
   aic0 <- out1$aic
   print("aic0")
   print(aic0)

   dev1 <- out1$deviance
   aic1 <-  dev1+ 2*2
   print("aic1")
   print(aic1)

   c1 <- 2.5
   qaic1 <-  dev1/c1+ 2*2
   print("qaic1")
   print(qaic1)
}

The result is:
Call:  glm(formula = y ~ x, family = quasibinomial(link = "logit"),
data = data1)

Coefficients:
(Intercept)x
-0.7300   0.2131

Degrees of Freedom: 9 Total (i.e. Null);  8 Residual
Null Deviance:  13.46
Residual Deviance: 12.63AIC: NA
[1] "aic0"
[1] NA
[1] "aic1"
[1] 16.63054
[1] "qaic1"
[1] 9.052216

   As you pointed out, glm() does not output the value of either AIC or
QAIC.
You are supposed to calculate those values. I guess that it is because AIC
is not
appropriate for this case, and the concept of QAIC has not been authorized
yet.

K. Takezawa

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Re: [R] Sweave, xtable and font size

[Duncan Murdoch]

On 07/05/2008 7:34 PM, Peter Jepsen wrote:

Hi,

I'm using Sweave with xtable to generate Latex tables. My problem is that some of the tables are too wide, and I would like to use the tiny font for these tables, but not for the others nor for the text. I can't work out how to accomplish that. 


The Latex code below does what I want it to, but I have to insert the "\tiny{" and the 
closing  "}" by hand. It originated from these commands in my .Rnw-file:

<>=
yearmale <- with(chol, table(year,male))
yearmale <- rowpct(yearmale) <>= 
print(xtable(yearmale,caption="My caption"))

$


See ?print.xtable.  You can use

print(xtable(yearmale,caption="My caption"), size="\\tiny")

Duncan Murdoch



LATEX CODE:

\begin{table}[ht]
\begin{center}
\tiny{
\begin{tabular}{rlll}
  \hline
 & Kvinder & Mænd & Total \\
  \hline
1998 & 1335 (75\%) & 437 (25\%) & 1772 (100\%) \\
  1999 & 1232 (74\%) & 425 (26\%) & 1657 (100\%) \\
  2000 & 1427 (74\%) & 502 (26\%) & 1929 (100\%) \\
  2001 & 1407 (74\%) & 493 (26\%) & 1900 (100\%) \\
  2002 & 1493 (71\%) & 611 (29\%) & 2104 (100\%) \\
  2003 & 1684 (75\%) & 566 (25\%) & 2250 (100\%) \\
  2004 & 1565 (73\%) & 567 (27\%) & 2132 (100\%) \\
  2005 & 1629 (74\%) & 586 (26\%) & 2215 (100\%) \\
  2006 & 1448 (72\%) & 553 (28\%) & 2001 (100\%) \\
  2007 & 1582 (73\%) & 590 (27\%) & 2172 (100\%) \\
  Total & 14802 (74\%) & 5330 (26\%) & 20132 (100\%) \\
   \hline
\end{tabular}
}
\caption{My caption}
\end{center}
\end{table}


Can anybody help me? Thank you in advance.

Best regards,
Peter.

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[R] Sweave, xtable and font size

[Peter Jepsen]

Hi,

I'm using Sweave with xtable to generate Latex tables. My problem is that some 
of the tables are too wide, and I would like to use the tiny font for these 
tables, but not for the others nor for the text. I can't work out how to 
accomplish that. 

The Latex code below does what I want it to, but I have to insert the "\tiny{" 
and the closing  "}" by hand. It originated from these commands in my .Rnw-file:

<>=
yearmale <- with(chol, table(year,male))
yearmale <- rowpct(yearmale) <>= 
print(xtable(yearmale,caption="My caption"))
$

LATEX CODE:

\begin{table}[ht]
\begin{center}
\tiny{
\begin{tabular}{rlll}
  \hline
 & Kvinder & Mænd & Total \\
  \hline
1998 & 1335 (75\%) & 437 (25\%) & 1772 (100\%) \\
  1999 & 1232 (74\%) & 425 (26\%) & 1657 (100\%) \\
  2000 & 1427 (74\%) & 502 (26\%) & 1929 (100\%) \\
  2001 & 1407 (74\%) & 493 (26\%) & 1900 (100\%) \\
  2002 & 1493 (71\%) & 611 (29\%) & 2104 (100\%) \\
  2003 & 1684 (75\%) & 566 (25\%) & 2250 (100\%) \\
  2004 & 1565 (73\%) & 567 (27\%) & 2132 (100\%) \\
  2005 & 1629 (74\%) & 586 (26\%) & 2215 (100\%) \\
  2006 & 1448 (72\%) & 553 (28\%) & 2001 (100\%) \\
  2007 & 1582 (73\%) & 590 (27\%) & 2172 (100\%) \\
  Total & 14802 (74\%) & 5330 (26\%) & 20132 (100\%) \\
   \hline
\end{tabular}
}
\caption{My caption}
\end{center}
\end{table}


Can anybody help me? Thank you in advance.

Best regards,
Peter.

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Re: [R] Gravity (spatial interaction) models in R

[Farley, Robert]

There may already be tools for gravity model APPLICATION, which is
simply an exercise in normalization.  Perhaps if I describe the gory
details, someone will recognize the problem by another name.
  

A singly constrained gravity model is simply an exercise in normalizing
the rows of a matrix (your "F-Factors") to match a vector (your
Productions).


A doubly constrained model ("Fratar" or "Furness") is simply an
iterative exercise of normalizing Rows (Productions) and Columns
(Attractions), stopping when the maximum error is within some predefined
limit.


I'm only a newbie, but from what I've seen on the list, this should be
simple to do


As to calibrating F-Factor functions: one often "chooses" a functional
F-Factor form, then "adjusts" the coefficients, until the weighted trip
length distribution of the resulting trip table matches the observed
data.




 
Robert Farley
Metro
www.Metro.net 
 
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Roger Bivand
Sent: Tuesday, May 06, 2008 06:37
To: [EMAIL PROTECTED]
Subject: Re: [R] Gravity (spatial interaction) models in R

Melanie Murphy  turbonet.com> writes:

> 
> I was wondering if anyone has developed (or is developing) an
> implementation for gravity models (spatial interaction) in R.  I
> conducted several searches on the CRAN website with no luck.
Currently
> I am estimating parameters via linearization.

There isn't anything (yet) in the Spatial task view on CRAN, and I'm not
aware
of the topic coming up on the R-sig-geo list either. The nearest sign of
transport planning is perhaps the emme2 package for interfacing EMME/2
software.
As you are aware, there are many almost equivalent ways of fitting
gravity
models, so many R functions are feasible. But no dedicated functions so
far, I'm
afraid - if I'm wrong, please let me know, and I'll update the task
view.

Roger

> 
> Thank you in advance
> 
> Melanie Murphy
>

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Re: [R] dlm with constant terms

[Giovanni Petris]

> Date: Wed, 07 May 2008 13:03:14 -0400
> From: "Stoyanov, Tsvetan (MSCIBARRA)" <[EMAIL PROTECTED]>
> Importance: normal
> Priority: normal
> Thread-topic: dlm with constant terms
> Thread-index: AciwZDz3Kl800OdmR4CQkEC8PUECZg==
> 
> Hi,
> I am trying to figure how to use dlm with constant terms
> (possibly time-dependent) added to both equations
>   y_t = c_t + F_t\theta_t + v_t
>   \theta_t = d_t + G_t\theta_{t-1} + w_t,
> in the way that S-PLUS Finmetrics does?
> 
> Is there any straightforward way to transform the above to
> the default setup?

I think you can do it by extending the state vector and defining a new
dlm with

\theta^*_t = (1  1  \theta_t')'

F^*_t = [c_t  0  F_t],

G^*_t = [100 ]
[010 ]
[0   d_t  G_t]

W^*_t = [0   0   0 ]
[0   0   0 ]
[0   0  W_t]

m^*_0 = (1  1  m_0)

C^*_0 = [e   0   0 ]
[0   e   0 ]
[0   0  C_0]

The 'e' on the diagonal of C^*_0 should be zero, but since the matrix
must be nonsingular youcan put a very small number, such as e = 1e-8. 

Best,
Giovanni Petris


> Thanks,
> Tsvetan
> 
> 
> NOTICE: If received in error, please destroy and notify sender. Sender does 
> not intend to waive confidentiality or privilege. Use of this email is 
> prohibited when received in error.
> 
> 

-- 

Giovanni Petris  <[EMAIL PROTECTED]>
Associate Professor
Department of Mathematical Sciences
University of Arkansas - Fayetteville, AR 72701
Ph: (479) 575-6324, 575-8630 (fax)
http://definetti.uark.edu/~gpetris/

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Re: [R] function in nls argument

[Katharine Mullen]

The error message means that the gradient (first derivative of residual
vector with respect to the parameter vector) is not possible to work with;
calling the function qr on the gradient multiplied by the square root of
the weight vector .swts (in your case all 1's) fails.

If you want concrete advice it would be helpful to provide the commented,
minimal, self-contained, reproducible code that the posting guide
requests.  what are the values of ST04, SM08b, ch2no, and tower?

General comments:  If your goal is to minimize sum( (observed -
predicted)^2), the function you give nls to minimize (optim.fun in your
case) should return the vector (observed - predicted), not the scalar sum(
(observed - predicted)^2).  You may want to see the nls.lm function in
package minpack.lm for another way to deal with the problem.

On Wed, 7 May 2008, Fernando Moyano wrote:

> Greetings R users, maybe there is someone who can help
> me with this problem:
>
> I define a function "optim.fun" and want as output the
> sum of squared errors between predicted and measured
> values, as follows:
>
> optim.fun <- function (ST04, SM08b, ch2no, a, b, d, E)
> {
> predR <-
> (a*SM08b^I(2)+b*SM08b+d)*exp(E*((1/(283.15-227.13))-(1/(ST04+273.15-227.13
> abserr <- abs(ch2no-predR)
> qnum <- quantile(abserr, probs=0.95, na.rm=T)
>
> is.na(abserr) <- (abserr > qnum)
> errsq <- sum(abserr^2, na.rm=T)
> errsq
> }
>
> Then I want to optimize parameters a,b,d and E as to
> minimize the function output with the following:
>
> optim.model<-nls(nulldat ~ optim.fun(ST04, SM08b,
> ch2no, a, b, d, E), data=tower,
> start=list(a=-0.003,b=0.13,d=0.50, E=400), na.action =
> na.exclude )
>
> were nulldat=0
> At this point I get the following error message:
>
> Error in qr.default(.swts * attr(rhs, "gradient")) :
>   NA/NaN/Inf in foreign function call (arg 1)
> Warning messages:
> 1: In if (na.rm) x <- x[!is.na(x)] else if
> (any(is.na(x))) stop("missing values and NaN's not
> allowed if 'na.rm' is FALSE") ... :
>   the condition has length > 1 and only the first
> element will be used
> (this warning is repeated 12 times)
>
> Question: what does the error mean? What am I doing
> wrong?
> Thanks a bunch.
> Nano
> Jen, Germany
> Max Planck for Biogeochemistry
>
>
>
>
>   
> 
>
> [[elided Yahoo spam]]
>
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> and provide commented, minimal, self-contained, reproducible code.
>

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[R] help with regsubsets

[Edwards, David J]

Hi,
 
I'm new to R and this mailing list, so I will attempt to state my question as 
appropriately as possible. 
 
I am running R version 2.7 with Windows XP and have recently been exploring the 
use of the function regsubsets in the leaps package in order to perform 
all-subsets regression. 
 
So, I'm calling the function as:
 
sub=regsubsets(X,Y,nbest=5,nvmax=maxnv,method="exhaustive",really.big=F)
 
I'm dealing with 14 observations and 23 variables and I'm aware of the linear 
dependencies that arise in these situations.  I also know that regsubsets 
performs a branch-and-bound algorithm and that at times it is necessary to 
reorder the variables. 
 
However, anytime I get the message: "Reordering variables and trying again" the 
R^2 for a model chosen by regsubsets does not match the R^2 I get from fitting 
the same model using the usual linear model function (lm).  If I don't get the 
"Reordering variables and trying again" message, I don't have any problems with 
R^2 (i.e. regubsets and lm match). 
 
Just for example, suppose the best 1-variable model chosen by regsubsets gives 
me an R^2 of 0.665. Fitting that same model using lm gives me an R^2 of 0.6317. 
 
 
Does anyone have any insight on why this may be happening? 
 

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Re: [R] predict lmer

[Kingsford Jones]

One question that arises is: at what level is the prediction desired?
Within a given ID:TRKPT2 level?  Within a given ID level?  At the
marginal level (which Bert's code appears to produce).  Also, there is
the question:  how confident can you be in your predictions.  This
thread discusses possible ways to get prediction intervals:

https://stat.ethz.ch/pipermail/r-sig-mixed-models/2008q2/thread.html#841

Finally, why assume a Poisson error distribution for a binary response?

Kingsford Jones

On Wed, May 7, 2008 at 10:13 AM, Bert Gunter <[EMAIL PROTECTED]> wrote:
> Sorry, my reply below may be too terse. You'll need to also construct the
>  appropriate design matrix to which to apply the fixef() results to.
>
>  If newDat is a data.frame containing **exactly the same named regressor and
>  response columns** as your original vdata dataframe, and if me.fit.of is
>  your fitted lmer object as you have defined it below, then
>
>   model.matrix(terms(me.fit.of),newDat) %*% fixef(me.fit.of)
>
>  gives your predictions. Note that while the response column in newDat is
>  obviously unnecessary for prediction (you can fill it with 0's,say), it is
>  nevertheless needed for model.matrix to work. This seems clumsy to me, so
>  there may well be better ways to do this, and **I would appreciate
>  suggestions for improvement.***
>
>
>  Cheers,
>  Bert
>
>
>
>
>  -Original Message-
>  From: bgunter
>  Sent: Wednesday, May 07, 2008 9:53 AM
>  To: May, Roel; r-help@r-project.org
>  Subject: RE: [R] predict lmer
>
>  ?fixef
>
>  gets you the coefficient vector, from which you can make your predictions.
>
>  -- Bert Gunter
>  Genentech
>
>  -Original Message-
>  From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
>  Behalf Of May, Roel
>  Sent: Wednesday, May 07, 2008 7:23 AM
>  To: r-help@r-project.org
>  Subject: [R] predict lmer
>
>
>
> Hi,
>
>  I am using lmer to analyze habitat selection in wolverines using the
>  following model:
>
>  (me.fit.of <-
>  lmer(USED~1+STEP+ALT+ALT2+relM+relM:ALT+(1|ID)+(1|ID:TRKPT2),data=vdata,
>  control=list(usePQL=TRUE),family=poisson,method="Laplace"))
>
>  Here, the habitat selection is calaculated using a so-called discrete
>  choice model where each used location has a certain number of
>  alternatives which the animal could have chosen. These sets of locations
>  are captured using the TRKPT2 random grouping. However, these sets are
>  also clustered over the different individuals (ID). USED is my binary
>  dependent variable which is 1 for used locations and zero for unused
>  locations. The other are my predictors.
>
>  I would like to predict the model fit at different values of the
>  predictors, but does anyone know whether it is possible to do this? I
>  have looked around at the R-sites and in help but it seems that there
>  doesn't exist a predict function for lmer???
>
>  I hope someone can help me with this; point me to the right functions or
>  tell me to just forget it
>
>  Thanks in advance!
>
>  Cheers Roel
>
>  Roel May
>  Norwegian Institute for Nature Research
>  Tungasletta 2, NO-7089 Trondheim, Norway
>
>
> [[alternative HTML version deleted]]
>
>  __
>  R-help@r-project.org mailing list
>  https://stat.ethz.ch/mailman/listinfo/r-help
>  PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>  and provide commented, minimal, self-contained, reproducible code.
>
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>  R-help@r-project.org mailing list
>  https://stat.ethz.ch/mailman/listinfo/r-help
>  PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>  and provide commented, minimal, self-contained, reproducible code.
>

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Re: [R] Problem installing tseries under FC7 x86_64

[Gavin Simpson]

On Wed, 2008-05-07 at 21:09 +0100, Michael Steinbeck-Reeves wrote:
> I have just installed the 64 bit version of R, using yum. The version
> is: 2.6.2-1.fc7.1.x86_64.

Could it be that you don't have the development "headers" for R? Try:

yum install R-devel

as root in a console and then try installing tseries within R.

HTH

G

> 
> I installed zoo without any major problem and the same with quadprog (a
> few warnings). However, when I came to install tseries I get the
> following:
> 
>  install.packages()
> Warning in install.packages() :
>   argument 'lib' is missing: using
> '/home/xx/R/x86_64-redhat-linux-gnu-library/2.6'
> trying URL
> 'http://cran.uk.r-project.org/src/contrib/tseries_0.10-14.tar.gz'
> Content type 'application/x-gzip' length 171219 bytes (167 Kb)
> opened URL
> ==
> downloaded 167 Kb
> 
> * Installing *source* package 'tseries' ...
> ** libs
> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/include/R
> -I/usr/local/include-fpic  -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m64 -mtune=generic -c arma.c -o arma.o
> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/include/R
> -I/usr/local/include-fpic  -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m64 -mtune=generic -c bdstest.c -o bdstest.o
> bdstest.c:25:15: error: R.h: No such file or directory
> bdstest.c: In function ‘freeall’:
> bdstest.c:86: warning: implicit declaration of function ‘Free’
> bdstest.c: In function ‘evalc’:
> bdstest.c:172: warning: implicit declaration of function ‘Rprintf’
> bdstest.c: In function ‘fkc’:
> bdstest.c:289: warning: implicit declaration of function ‘Calloc’
> bdstest.c:289: error: expected expression before ‘int’
> bdstest.c:289: warning: assignment makes pointer from integer without a
> cast
> bdstest.c:290: error: expected expression before ‘int’
> bdstest.c:290: warning: assignment makes pointer from integer without a
> cast
> bdstest.c:295: error: expected expression before ‘struct’
> bdstest.c:295: warning: assignment makes pointer from integer without a
> cast
> bdstest.c:300: error: expected expression before ‘short’
> bdstest.c:300: warning: assignment makes pointer from integer without a
> cast
> bdstest.c:307: error: expected expression before ‘short’
> bdstest.c:307: warning: assignment makes pointer from integer without a
> cast
> bdstest.c:309: warning: implicit declaration of function ‘error’
> bdstest.c:352: warning: implicit declaration of function ‘qsort’
> make: *** [bdstest.o] Error 1
> ERROR: compilation failed for package 'tseries'
> ** Removing '/home/x/R/x86_64-redhat-linux-gnu-library/2.6/tseries'
> 
> The downloaded packages are in
> /tmp/RtmpocpCZU/downloaded_packages
> Warning message:
> In install.packages() :
>   installation of package 'tseries' had non-zero exit status
> 
> I realise that R.h is missing and is not on my machine anywhere. What
> have I missed?
> 
> Thanks,
> 
> Michael
> 
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
-- 
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 Dr. Gavin Simpson [t] +44 (0)20 7679 0522
 ECRC, UCL Geography,  [f] +44 (0)20 7679 0565
 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
 Gower Street, London  [w] http://www.ucl.ac.uk/~ucfagls/
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Re: [R] cross-correlation lag.plot?

[Erin Hodgess]

Hi!

Try ?ccf

HTH,
Erin


On 5/7/08, tom soyer <[EMAIL PROTECTED]> wrote:
> Hi,
>
> Does anyone know if R has a function that is similar to lag.plot but instead
> of auto-correlation, it plots cross-correlation with lags?
>
> Thanks,
>
> --
> Tom
>
>[[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
Erin Hodgess
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: [EMAIL PROTECTED]

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Re: [R] rggobi is crashing R-2.7.0

[Michael Lawrence]

On Wed, May 7, 2008 at 11:40 AM, Mark Kimpel <[EMAIL PROTECTED]> wrote:

> Uninstalling and reinstalling ggobi via Synaptic solved the problem, at
> least for the demo data mtcars. Rotation works fine. No crashes on exit.
>
> Thanks for the good advice.
>

I am pretty sure what Paul is referring to is the graphics device stuff.
GGobi does not link against R anyway, so R would not be the problem here.

The reason rebuilding GGobi fixed it, is that your GGobi binary was linked
against an old version of graphviz. The new version broke binary
compatibility, thus you needed to install a GGobi binary built against the
new version.


> Mark
>
> On Wed, May 7, 2008 at 2:12 PM, Paul Johnson <[EMAIL PROTECTED]> wrote:
>
> > On Tue, May 6, 2008 at 12:32 PM, Mark Kimpel <[EMAIL PROTECTED]> wrote:
> > > I am running 64-bit Ubuntu 8.04 and when I invoke rggobi the
> interactive
> > >  graph displays but R crashes. See my sessionInfo() and a short
> example
> > >  below. Ggobi and rggobi installed without complaints. Mark
> > >
> > >  > sessionInfo()
> > >  R version 2.7.0 Patched (2008-05-04 r45620)
> > >  x86_64-unknown-linux-gnu
> > >
> >
> > In the R 2.7 release notes, there is a comment about a change in the
> > GUI libraries and it says that one must recompile everything that
> > relies on R.  If your R 2.7 was an upgrade, not a fresh install, it
> > could explain why this is happening.  If there's some old library or R
> > package sitting around, it could account for this.
> >
> > The part that concerned me about the R release note is that they don't
> > give a very clear guide on how far back in the toolchain we are
> > supposed to go.  Certainly, ggobi has to be rebuilt from scratch.  But
> > are any of the things on which ggobi depends needing recompliation as
> > well.
> >
> > pj
> >
> >
> > --
> > Paul E. Johnson
> > Professor, Political Science
> > 1541 Lilac Lane, Room 504
> > University of Kansas
> >
>
>
>
> --
> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
> Indiana University School of Medicine
>
> 15032 Hunter Court, Westfield, IN 46074
>
> (317) 490-5129 Work, & Mobile & VoiceMail
> (317) 663-0513 Home (no voice mail please)
>
> **
>
>[[alternative HTML version deleted]]
>
> __
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

[[alternative HTML version deleted]]

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[R] solution to differences in sequential and marginal ANOVA using a mixed model

[Bill Shipley]

Yesterday I posted the following question to the help list.  Thanks to John
Fox (copied below) who pointed out the solution.

 

Original question:

 

I have come across a result that I cannot explain, and am hopingthat someone
else can provide an answer.  A student fitted a mixed model  usingthe lme
function: out<- lme(fixed=Y~A+B+A:B, random=~1|Site).  Y is a continuous
variable while A and B are factors.  The data set is balanced with the same
number of observations in each combination of A and B.  There are two
hierarchical levels: Site and plots nested in site. 

He tried two different ways of getting theANOVA table: anova(out) and
anova(out, type="marginal"). Since the data were balanced, these two ways
should (I think) give the same output since they correspond to Type I and
III sums of squares in the SAS terminology.  At least, this is the case with
normal (i.e. not mixed) linear models.  However, he finds very different
results of these two types of ANOVA tables.  Why?

 

Response of John Fox:

 

Dear Bill,

 

I expect that the problem is in the contrasts that your student used for A
and B, though I haven't thought specifically about the context of a mixed
model. If he or she used the default contr.treatment(), then the contrasts
for different factors (and the interaction) are not orthogonal in the row
basis of the model matrix and hence are not orthogonal, even for balanced
data. Using, e.g., contr.sum() should provide A, B, and A:B contrasts that
are orthogonal to each other.

 

Indeed, changing to an appropriate type of contrast did solve the problem!
My problem was in forgetting that R uses treatment contrasts by default
while SPLUS uses Helmert contrasts by default (which would have worked as
well as sum contrasts).


[[alternative HTML version deleted]]

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[R] cross-correlation lag.plot?

[tom soyer]

Hi,

Does anyone know if R has a function that is similar to lag.plot but instead
of auto-correlation, it plots cross-correlation with lags?

Thanks,

-- 
Tom

[[alternative HTML version deleted]]

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[R] Problem installing tseries under FC7 x86_64

[Michael Steinbeck-Reeves]

I have just installed the 64 bit version of R, using yum. The version
is: 2.6.2-1.fc7.1.x86_64.

I installed zoo without any major problem and the same with quadprog (a
few warnings). However, when I came to install tseries I get the
following:

 install.packages()
Warning in install.packages() :
  argument 'lib' is missing: using
'/home/xx/R/x86_64-redhat-linux-gnu-library/2.6'
trying URL
'http://cran.uk.r-project.org/src/contrib/tseries_0.10-14.tar.gz'
Content type 'application/x-gzip' length 171219 bytes (167 Kb)
opened URL
==
downloaded 167 Kb

* Installing *source* package 'tseries' ...
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/include/R
-I/usr/local/include-fpic  -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c arma.c -o arma.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/include/R
-I/usr/local/include-fpic  -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c bdstest.c -o bdstest.o
bdstest.c:25:15: error: R.h: No such file or directory
bdstest.c: In function ‘freeall’:
bdstest.c:86: warning: implicit declaration of function ‘Free’
bdstest.c: In function ‘evalc’:
bdstest.c:172: warning: implicit declaration of function ‘Rprintf’
bdstest.c: In function ‘fkc’:
bdstest.c:289: warning: implicit declaration of function ‘Calloc’
bdstest.c:289: error: expected expression before ‘int’
bdstest.c:289: warning: assignment makes pointer from integer without a
cast
bdstest.c:290: error: expected expression before ‘int’
bdstest.c:290: warning: assignment makes pointer from integer without a
cast
bdstest.c:295: error: expected expression before ‘struct’
bdstest.c:295: warning: assignment makes pointer from integer without a
cast
bdstest.c:300: error: expected expression before ‘short’
bdstest.c:300: warning: assignment makes pointer from integer without a
cast
bdstest.c:307: error: expected expression before ‘short’
bdstest.c:307: warning: assignment makes pointer from integer without a
cast
bdstest.c:309: warning: implicit declaration of function ‘error’
bdstest.c:352: warning: implicit declaration of function ‘qsort’
make: *** [bdstest.o] Error 1
ERROR: compilation failed for package 'tseries'
** Removing '/home/x/R/x86_64-redhat-linux-gnu-library/2.6/tseries'

The downloaded packages are in
/tmp/RtmpocpCZU/downloaded_packages
Warning message:
In install.packages() :
  installation of package 'tseries' had non-zero exit status

I realise that R.h is missing and is not on my machine anywhere. What
have I missed?

Thanks,

Michael

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[R] Advanced R/S-Plus Course by XLSolutions Corp / May 2008 in San Francisco & Boston

[Sue Turner]

Please check out these upcoming courses offered by  XLSolutions
Corporation.

**Payments due after the class

R/Splus Advanced Programming course: May 29-30, 2008 in  San Francisco -
4 seats left.


R/Splus Advanced Programming course: May 29-30, 2008 in  Boston - 2
seats left.


R/Splus Fundamentals and Programming Techniques: June 19-20  in Boston


Payment due AFTER the class
Email us for group discounts.
Email Sue Turner: [EMAIL PROTECTED]
Phone: 206-686-1578
Visit us: www.xlsolutions-corp.com/courselist.htm
Please let us know if you and your colleagues are interested in this
class to take advantage of group discount. 

Register now to secure your seat!

Cheers,
Elvis Miller, PhD
Manager Training.
XLSolutions Corporation
206 686 1578
www.xlsolutions-corp.com

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[R] 2D correlation/convolution ?

[H. Paul Benton]

What is the command for 2D fft? Or 2D convolution and or auto-correlation?

Thanks,

Paul

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[R] coxph - weights- robust SE

[willy . wynant . chum]

Hi,

I am using coxph with weights to represent sampling fraction of subjects. 
Our simulation results show that the robust SE of beta systematically 
under-estimate the empirical SD of beta. 
Does anyone know how the robust SE are estimated in coxph using weights? 
Is there any analytical formula for the “weighted” robust SE?

Any help is appreciated!

Thanks so much in advance

Willy

[[alternative HTML version deleted]]

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Re: [R] pivoting - summing up factors

[Yasir Kaheil]

assuming what you have is a dataframe called x
try:
table(Plant=x$plant,Location=x$location)
 Location
Plant x y z
a 1 1 2
b 2 2 0

or simply:
table(x$plant,x$location)
   
x y z
  a 1 1 2
  b 2 2 0

thanks


juanita choo wrote:
> 
> Hi
> I would like to know how to pivot a table that will sum the number of
> plants
> (a or b) for each location (x,y,z)
> I have read on the listserve similar questions but which involve summing
> up
> numbers rather than factors.  I have also read about the R package reshape
> on the listserve but wanted to know if there's a way to do it easily
> without
> the package
> Thanks for the help!
> 
> location  plant
>  x a
>  x b
>  x b
>  y b
>  y b
>  y a
>  z a
>  z a
> 
> into a table like this
> 
> 
>xy   z
> a 11   2
> b 22   0
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 
> 


-
Yasir H. Kaheil, Ph.D.
Catchment Research Facility
The University of Western Ontario 

-- 
View this message in context: 
http://www.nabble.com/pivoting---summing-up-factors-tp17112158p17112407.html
Sent from the R help mailing list archive at Nabble.com.

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Re: [R] pivoting - summing up factors

[jim holtman]

Is this what you want:

> x
  location plant
1x a
2x b
3x b
4y b
5y b
6y a
7z a
8z a

> table(x$plant,x$location)

x y z
  a 1 1 2
  b 2 2 0
>


On Wed, May 7, 2008 at 2:56 PM, juanita choo <[EMAIL PROTECTED]> wrote:
> Hi
> I would like to know how to pivot a table that will sum the number of plants
> (a or b) for each location (x,y,z)
> I have read on the listserve similar questions but which involve summing up
> numbers rather than factors.  I have also read about the R package reshape
> on the listserve but wanted to know if there's a way to do it easily without
> the package
> Thanks for the help!
>
> location  plant
>  x a
>  x b
>  x b
>  y b
>  y b
>  y a
>  z a
>  z a
>
> into a table like this
>
>
>   xy   z
> a 11   2
> b 22   0
>
>[[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>



-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem you are trying to solve?

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[R] pivoting - summing up factors

[juanita choo]

Hi
I would like to know how to pivot a table that will sum the number of plants
(a or b) for each location (x,y,z)
I have read on the listserve similar questions but which involve summing up
numbers rather than factors.  I have also read about the R package reshape
on the listserve but wanted to know if there's a way to do it easily without
the package
Thanks for the help!

location  plant
 x a
 x b
 x b
 y b
 y b
 y a
 z a
 z a

into a table like this


   xy   z
a 11   2
b 22   0

[[alternative HTML version deleted]]

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Re: [R] help with updating to R2.7

[Gabor Grothendieck]

There are a few different methods discussed in the README to the batchfiles
distribution.  Home page at:

http://batchfiles.googlecode.com


On Wed, May 7, 2008 at 12:51 PM, ravi <[EMAIL PROTECTED]> wrote:
> Hi,
> >From R 2.6, I would like to update to R2.7. I would like to have some tips 
> >on the recommended method of installing the latest versions of an entire 
> >list of packages in R2.7 - i.e. all the packages that I have presently 
> >installed in R2.6.
> I am hoping that there is an easier method than fetching the packages 
> individually as I did, to begin with, for R2.6.
> Additionally, I would like to install R2.7 on another pc which is not 
> connected to the internet. I have previously installed R2.6 on it by fetching 
> the zip files from another pc and installed them from the local zip files. I 
> would like to know if there is a method of transferring an entire 
> installation (base+selected packages) from one pc to another. Will there be a 
> special problem if the first is a win vista pc and the 2nd has win 2000?
> One problem that I have in continuing to use R2.6 is in getting compatible 
> versions of a new package that happens to attract my interest. For example, I 
> was interested in getting the arm package for R2.6.1. I could not find the 
> package in the "R Binaries" list on CRAN webpage. In the packages list, I did 
> find old versions in the "arm archive". However, the files were in 
> ".tar.gz" format. How does one install from this format? It does not 
> appear to be as straightforward as in installing from the zip format 
> files.Recently, I had the same problem in installing a compatible version of 
> the "norm" package also. I am interested to know how I can tackle these 
> problems.
> I will appreciate all the help that I can get.
> Thanks,
> Ravi
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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Re: [R] rggobi is crashing R-2.7.0

[Mark Kimpel]

Uninstalling and reinstalling ggobi via Synaptic solved the problem, at
least for the demo data mtcars. Rotation works fine. No crashes on exit.

Thanks for the good advice.

Mark

On Wed, May 7, 2008 at 2:12 PM, Paul Johnson <[EMAIL PROTECTED]> wrote:

> On Tue, May 6, 2008 at 12:32 PM, Mark Kimpel <[EMAIL PROTECTED]> wrote:
> > I am running 64-bit Ubuntu 8.04 and when I invoke rggobi the interactive
> >  graph displays but R crashes. See my sessionInfo() and a short example
> >  below. Ggobi and rggobi installed without complaints. Mark
> >
> >  > sessionInfo()
> >  R version 2.7.0 Patched (2008-05-04 r45620)
> >  x86_64-unknown-linux-gnu
> >
>
> In the R 2.7 release notes, there is a comment about a change in the
> GUI libraries and it says that one must recompile everything that
> relies on R.  If your R 2.7 was an upgrade, not a fresh install, it
> could explain why this is happening.  If there's some old library or R
> package sitting around, it could account for this.
>
> The part that concerned me about the R release note is that they don't
> give a very clear guide on how far back in the toolchain we are
> supposed to go.  Certainly, ggobi has to be rebuilt from scratch.  But
> are any of the things on which ggobi depends needing recompliation as
> well.
>
> pj
>
>
> --
> Paul E. Johnson
> Professor, Political Science
> 1541 Lilac Lane, Room 504
> University of Kansas
>



-- 
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN 46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 663-0513 Home (no voice mail please)

**

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Re: [R] rggobi is crashing R-2.7.0

[Paul Johnson]

On Tue, May 6, 2008 at 12:32 PM, Mark Kimpel <[EMAIL PROTECTED]> wrote:
> I am running 64-bit Ubuntu 8.04 and when I invoke rggobi the interactive
>  graph displays but R crashes. See my sessionInfo() and a short example
>  below. Ggobi and rggobi installed without complaints. Mark
>
>  > sessionInfo()
>  R version 2.7.0 Patched (2008-05-04 r45620)
>  x86_64-unknown-linux-gnu
>

In the R 2.7 release notes, there is a comment about a change in the
GUI libraries and it says that one must recompile everything that
relies on R.  If your R 2.7 was an upgrade, not a fresh install, it
could explain why this is happening.  If there's some old library or R
package sitting around, it could account for this.

The part that concerned me about the R release note is that they don't
give a very clear guide on how far back in the toolchain we are
supposed to go.  Certainly, ggobi has to be rebuilt from scratch.  But
are any of the things on which ggobi depends needing recompliation as
well.

pj


-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas

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[R] algorithmic or automatic differentiation

[Erin Hodgess]

Hi R People:

Is there a package for automatic differentiation, please?

thanks in advance,
Erin


-- 
Erin Hodgess
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: [EMAIL PROTECTED]

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Re: [R] Estimating QAIC using glm with the quasibinomial family

[Darren Gillis]

Thank you for the rapid response.  I have no trouble in following your
example, but I was specificly interested in calculating QAIC and QAICc from
a glm fitted with the "family=quasibinomial" option.  This provides an
estimate of dispersion, but does not contain an explicit value for AIC or
log-likelihood.  Do you have any insights into how to deal with the output
from this specific option?  Or are you suggesting not to use
family=quasibinomial when faced with potential overdispersion?  Regardless,
thank you again for your response.

Cheers, Darren


-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Kunio takezawa
Sent: Tuesday, May 06, 2008 8:41 PM
To: r-help@r-project.org
Subject: Re: [R] Estimating QAIC using glm with the quasibinomial family

R-users
E-mail: r-help@r-project.org

>My question is: Will this calculation be valid with the residual 
>deviance returned by the glm() function using the quasibinomial family 
>as reported in R?

   Let me show you a simple example, assuming c=2.5:

function ()
{
   xx <- c(1,2,3,4,5,6,7,8,9,10)
   yy <- c(1,0,1,0,0,1,0,1,1,1)
   data1 <- data.frame(x=xx, y=yy)
   out1 <- glm(y~x, data=data1, family=binomial)
   print(out1)
   aic0 <- out1$aic
   print("aic0")
   print(aic0)

   dev1 <- out1$deviance
   aic1 <-  dev1+ 2*2
   print("aic1")
   print(aic1)

   c1 <- 2.5
   qaic1 <-  dev1/c1+ 2*2
   print("qaic1")
   print(qaic1)
}

The result is:

Call:  glm(formula = y ~ x, family = binomial, data = data1)

Coefficients:
(Intercept)x
-0.7300   0.2131

Degrees of Freedom: 9 Total (i.e. Null);  8 Residual
Null Deviance:  13.46
Residual Deviance: 12.63AIC: 16.63
[1] "aic0"
[1] 16.63054
[1] "aic1"
[1] 16.63054
[1] "qaic1"
[1] 9.052216

   I hope that this R program will be of some help to you.

K. Takezawa

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Re: [R] PC configuration you are using

[Jorge Ivan Velez]

Hi Endre,

I'm not sure if my configuration is typical. I'm running XP SP2, 4GB RAM and
Intel Core 2-Duo Processor of 2.4 GHz with 200GB HDD. My R version is R
2.7.0 Patched.

HTH,

Jorge


On Wed, May 7, 2008 at 12:49 PM, Endre Domiczi <[EMAIL PROTECTED]> wrote:

> Hello,
>
> As I mentioned in the previous message we are developing solution for
> wholesale companies to analyze their sales transactions by associative
> rules. I would very much appreciated if the community could give us
> some hint of what is a typical PC configuration of a professional
> statist (processor, RAM, HDD...)?
>
> Thanks a lot in advance and I highly appreciate your feedback!
>
> Kind regards,
> endre
>
> --
> Endre Domiczi, CEO
> Sevana Oy, http://www.sevana.fi
> Email : [EMAIL PROTECTED]
> GSM   : +372 53485178
> Skype : emddom
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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[R] dlm with constant terms

[Stoyanov, Tsvetan (MSCIBARRA)]

Hi,
I am trying to figure how to use dlm with constant terms
(possibly time-dependent) added to both equations
y_t = c_t + F_t\theta_t + v_t
\theta_t = d_t + G_t\theta_{t-1} + w_t,
in the way that S-PLUS Finmetrics does?

Is there any straightforward way to transform the above to
the default setup?
Thanks,
Tsvetan


NOTICE: If received in error, please destroy and notify sender. Sender does not 
intend to waive confidentiality or privilege. Use of this email is prohibited 
when received in error.

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[R] help with updating to R2.7

[ravi]

Hi,
>From R 2.6, I would like to update to R2.7. I would like to have some tips on 
>the recommended method of installing the latest versions of an entire list of 
>packages in R2.7 - i.e. all the packages that I have presently installed in 
>R2.6.
I am hoping that there is an easier method than fetching the packages 
individually as I did, to begin with, for R2.6.
Additionally, I would like to install R2.7 on another pc which is not connected 
to the internet. I have previously installed R2.6 on it by fetching the zip 
files from another pc and installed them from the local zip files. I would like 
to know if there is a method of transferring an entire installation 
(base+selected packages) from one pc to another. Will there be a special 
problem if the first is a win vista pc and the 2nd has win 2000?
One problem that I have in continuing to use R2.6 is in getting compatible 
versions of a new package that happens to attract my interest. For example, I 
was interested in getting the arm package for R2.6.1. I could not find the 
package in the "R Binaries" list on CRAN webpage. In the packages list, I did 
find old versions in the "arm archive". However, the files were in 
".tar.gz" format. How does one install from this format? It does not appear 
to be as straightforward as in installing from the zip format files.Recently, I 
had the same problem in installing a compatible version of the "norm" package 
also. I am interested to know how I can tackle these problems.
I will appreciate all the help that I can get.
Thanks,
Ravi

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Re: [R] use list elements to subtract values from the dataframe

[Julian Burgos]

Try
get(paste("wf$",fl[[1]],sep=""))

See ?get

Julian


Dirkheld wrote:

Hi,

I have a dataframe wf existing of a header with different labels and beneath
the values of those labels :
wf:
label1  label2  ...
0,450,21
0,100,45 
  


I have a list
fl <- c("label2","label3",..)

Isn't possible to use the list elements in the list in order to subtract
values from the dataframe? like :
wf$fl[[1]] 
When I do in R I get :NULL

fl[[1]] gives  "label2"  so no problem here...

While wf$label1 works fine.





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Re: [R] categorical data analysis - fisher.exact for 2x2 and greater

[Brian S Cade]

Jeff and others:

Paul Mielke and Ken Berry at Colorado State University developed very fast 
Fortran routines for doing Fisher exact tests (as well as some others like 
Chi-square and Zelterman's statistics).   Their book (Permutation Methods: 
A Distance Function Approach, 2nd ed.  2007. Springer) indicates that 
these algorithms were only efficient for <= 5 conditional loops so 2x2, 
3x2, 4x2, 5x2, 6x2, 3x3, and 2x2x2 were feasible back in the 1990's.   I'm 
not sure whether more recent computing capability permits larger tables 
now. 

Brian

Brian S. Cade

U. S. Geological Survey
Fort Collins Science Center
2150 Centre Ave., Bldg. C
Fort Collins, CO  80526-8818

email:  [EMAIL PROTECTED]
tel:  970 226-9326



"Dr. Jeff Miller" <[EMAIL PROTECTED]> 
Sent by: [EMAIL PROTECTED]
05/07/2008 09:56 AM

To
"'Greg Snow'" <[EMAIL PROTECTED]>, "'David Winsemius'" 
<[EMAIL PROTECTED]>, <[EMAIL PROTECTED]>
cc

Subject
Re: [R] categorical data analysis - fisher.exact for 2x2 and greater






Hi Simon and all,

I'm pretty sure that you are correct about this. I think it is a
misconception to say that the fisher exact test is only for a 2 by 2 
table.
It is presented that way in textbooks because, for a 2x2 table, it is easy
to perform.  For larger tables, it becomes complex quickly due to the rate
at which the permutations increase.

 When I use it for larger tables, it is hit or miss as to whether R will 
be
able to do it.  It's not uncommon to get an error implying that R is out 
of
memory. 

Check out Agresti's Categorical Data Analysis on the use of the fisher 
exact
for larger than 2x2 tables, and check out the R archives (and Google 
search)
for all the posts about the error message people run into sometimes.

On April 29th, Marc Schwartz replied to my question about this as follows:

Take a look at the 'workspace' argument in ?fisher.test and review the
second paragraph in Details:

"For 2 by 2 cases, p-values are obtained directly using the (central or
non-central) hypergeometric distribution. Otherwise, computations are 
based
on a C version of the FORTRAN subroutine FEXACT which implements the 
network
developed by Mehta and Patel (1986) and improved by Clarkson, Fan and Joe
(1993). The FORTRAN code can be obtained from
http://www.netlib.org/toms/643. Note this fails (with an error message) 
when
the entries of the table are too large. (It transposes the table if
necessary so it has no more rows than columns. One constraint is that the
product of the row marginals be less than 2^31 - 1.)"



Thank you,
Jeff



-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] 
On
Behalf Of Greg Snow
Sent: Wednesday, May 07, 2008 9:55 AM
To: David Winsemius; [EMAIL PROTECTED]
Subject: Re: [R] categorical data analysis

The last example in ?fisher.test is not a 2x2 table, in fact it uses 
levels
with a natural ordering similar to the original question.  Why would this
not be applicable to the situation?


From: [EMAIL PROTECTED] [EMAIL PROTECTED] On 
Behalf
Of David Winsemius [EMAIL PROTECTED]
Sent: Wednesday, May 07, 2008 7:34 AM
To: [EMAIL PROTECTED]
Subject: Re: [R] categorical data analysis

Simon Blomberg <[EMAIL PROTECTED]> wrote in
news:[EMAIL PROTECTED]:

> But see these posts:
>
> http://finzi.psych.upenn.edu/R/Rhelp02a/archive/119079.html
>
> http://finzi.psych.upenn.edu/R/Rhelp02a/archive/119080.html
>
> Simon.

Interesting reading, but the OP specifically said he was not dealing with
2x2 tables, so neither fisher.test nor the suggested alternatives would
be applicable to his data situation.

--
David Winsemius

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Internal Virus Database is out-of-date.


11:27 AM
 

Internal Virus Database is out-of-date.


11:27 AM

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Re: [R] help with the unique function

[Phil Spector]

Another way to produce the data frame is

subset(as.data.frame(table(x)),Freq>0)

   - Phil Spector
 Statistical Computing Facility
 Department of Statistics
 UC Berkeley
 [EMAIL PROTECTED]


On Wed, 7 May 2008, ravi wrote:


Hi,
The unique function is easy to understand and use. Beyond that, I want to get 
also the frequency of repetition of each individual row in a data frame
Let me explain with an example :
x<-data.frame(a=c(1,2,3,1,2),b=c(2,3,4,2,3),c=c(10,20,30,10,20))
xu<-unique(x)
We have,

x

  a b  c
1 1 2 10
2 2 3 20
3 3 4 30
4 1 2 10
5 2 3 20

xu

  a b  c
1 1 2 10
2 2 3 20
3 3 4 30

I want to get the following data frame :
  a b  c    Freq
1 1 2 10    2
2 2 3 20    2
3 3 4 30    1
That is, in addition to the unique rows, I want to get the frequency of 
repetion of each individual row.
I will appreciate all the help that I can get.
Thank You,
Ravi

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Re: [R] predict lmer

[Bert Gunter]

Sorry, my reply below may be too terse. You'll need to also construct the
appropriate design matrix to which to apply the fixef() results to.

If newDat is a data.frame containing **exactly the same named regressor and
response columns** as your original vdata dataframe, and if me.fit.of is
your fitted lmer object as you have defined it below, then

 model.matrix(terms(me.fit.of),newDat) %*% fixef(me.fit.of)

gives your predictions. Note that while the response column in newDat is
obviously unnecessary for prediction (you can fill it with 0's,say), it is
nevertheless needed for model.matrix to work. This seems clumsy to me, so
there may well be better ways to do this, and **I would appreciate
suggestions for improvement.*** 


Cheers,
Bert



-Original Message-
From: bgunter 
Sent: Wednesday, May 07, 2008 9:53 AM
To: May, Roel; r-help@r-project.org
Subject: RE: [R] predict lmer

?fixef

gets you the coefficient vector, from which you can make your predictions.

-- Bert Gunter
Genentech

-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of May, Roel
Sent: Wednesday, May 07, 2008 7:23 AM
To: r-help@r-project.org
Subject: [R] predict lmer

Hi,
 
I am using lmer to analyze habitat selection in wolverines using the
following model:
 
(me.fit.of <-
lmer(USED~1+STEP+ALT+ALT2+relM+relM:ALT+(1|ID)+(1|ID:TRKPT2),data=vdata,
control=list(usePQL=TRUE),family=poisson,method="Laplace"))
 
Here, the habitat selection is calaculated using a so-called discrete
choice model where each used location has a certain number of
alternatives which the animal could have chosen. These sets of locations
are captured using the TRKPT2 random grouping. However, these sets are
also clustered over the different individuals (ID). USED is my binary
dependent variable which is 1 for used locations and zero for unused
locations. The other are my predictors.
 
I would like to predict the model fit at different values of the
predictors, but does anyone know whether it is possible to do this? I
have looked around at the R-sites and in help but it seems that there
doesn't exist a predict function for lmer???
 
I hope someone can help me with this; point me to the right functions or
tell me to just forget it
 
Thanks in advance!
 
Cheers Roel
 
Roel May
Norwegian Institute for Nature Research
Tungasletta 2, NO-7089 Trondheim, Norway


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Re: [R] predict lmer

[Bert Gunter]

?fixef

gets you the coefficient vector, from which you can make your predictions.

-- Bert Gunter
Genentech

-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of May, Roel
Sent: Wednesday, May 07, 2008 7:23 AM
To: r-help@r-project.org
Subject: [R] predict lmer

Hi,
 
I am using lmer to analyze habitat selection in wolverines using the
following model:
 
(me.fit.of <-
lmer(USED~1+STEP+ALT+ALT2+relM+relM:ALT+(1|ID)+(1|ID:TRKPT2),data=vdata,
control=list(usePQL=TRUE),family=poisson,method="Laplace"))
 
Here, the habitat selection is calaculated using a so-called discrete
choice model where each used location has a certain number of
alternatives which the animal could have chosen. These sets of locations
are captured using the TRKPT2 random grouping. However, these sets are
also clustered over the different individuals (ID). USED is my binary
dependent variable which is 1 for used locations and zero for unused
locations. The other are my predictors.
 
I would like to predict the model fit at different values of the
predictors, but does anyone know whether it is possible to do this? I
have looked around at the R-sites and in help but it seems that there
doesn't exist a predict function for lmer???
 
I hope someone can help me with this; point me to the right functions or
tell me to just forget it
 
Thanks in advance!
 
Cheers Roel
 
Roel May
Norwegian Institute for Nature Research
Tungasletta 2, NO-7089 Trondheim, Norway


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Re: [R] help with the unique function

[Ted Harding]

On 07-May-08 16:31:23, Erik Iverson wrote:
> ravi -
> This may get you started
> 
> count.reps <- function(df) {
>hash  <- do.call("paste", c(df, sep = "\r"))
>cbind(unique(df), Freq = unclass(table(hash)))
> }
> 
> test <- data.frame(a = rep(1:10, 2), b = rep(1:10, 2))
> count.reps(test)

That doesn't work: It muddles the Association of the "unique"
values with the counts:

  A<-sample(c(0,1),100,replace=TRUE)
  B<-sample(c(0,1),100,replace=TRUE)
  C<-sample(c(0,1),100,replace=TRUE)
  sum((A==0)&(B==0)&(C==0))  ## [1] 26
  sum((A==0)&(B==0)&(C==1))  ## [1]  9
  sum((A==0)&(B==1)&(C==0))  ## [1] 10
  sum((A==0)&(B==1)&(C==1))  ## [1]  7
  sum((A==1)&(B==0)&(C==0))  ## [1] 15
  sum((A==1)&(B==0)&(C==1))  ## [1] 11
  sum((A==1)&(B==1)&(C==0))  ## [1]  5
  sum((A==1)&(B==1)&(C==1))  ## [1] 17

  test<-data.frame(A=A,B=B,C=C)
  count.reps(test)
#A B C Freq
# 1  0 0 1   26
# 2  0 1 09
# 3  1 0 1   10
# 4  1 0 07
# 5  1 1 1   15
# 6  0 0 0   11
#14  1 1 05
#25  0 1 1   17

So the freqencies come out in the order I found them ("binary
counting": ABC=000,001,010,011,100,101,110,111) but with the
(A,B,C) values in a quite different order.

I can't, myself, make out why this is happening, but no doubt
someone else can, and may sugest a correction!

Ted.








> Best,
> Erik Iverson
> 
> ravi wrote:
>> Hi,
>> The unique function is easy to understand and use. Beyond that, I want
>> to get also the frequency of repetition of each individual row in a
>> data frame
>> Let me explain with an example :
>> x<-data.frame(a=c(1,2,3,1,2),b=c(2,3,4,2,3),c=c(10,20,30,10,20))
>> xu<-unique(x)
>> We have,
>>> x
>>   a b  c
>> 1 1 2 10
>> 2 2 3 20
>> 3 3 4 30
>> 4 1 2 10
>> 5 2 3 20
>>> xu
>>   a b  c
>> 1 1 2 10
>> 2 2 3 20
>> 3 3 4 30
>> 
>> I want to get the following data frame :
>>   a b  cFreq
>> 1 1 2 102
>> 2 2 3 202
>> 3 3 4 301
>> That is, in addition to the unique rows, I want to get the frequency
>> of repetion of each individual row.
>> I will appreciate all the help that I can get.
>> Thank You,
>> Ravi
>> 
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
> 
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


E-Mail: (Ted Harding) <[EMAIL PROTECTED]>
Fax-to-email: +44 (0)870 094 0861
Date: 07-May-08   Time: 18:02:09
-- XFMail --

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[R] how to define .Renviron to work with different R-versions

[Poornima Reddy]

Hi,

I have a simple R script for printing arguments
cat > printargs.R << EOF
args = commandArgs()
print(args)
q()
EOF

   To run this script, first I set PATH to ~/src/R-2.6.2 and execute >
R --no-save < printargs.R

   I want to run this script with different R versions by defining an
.Renviron file in the same directory as printargs.R

   cat > .Renviron << EOF
   R_VERISON=R-2.7.0
   R_HOME=~/src/${R_VERSION}
   PATH=${R_HOME}/bin:${PATH}
   R_LIBS=${R_HOME}/library
   EOF

   Now when I run > R --no-save < printargs.R, I get
   Error in gzfile(file, "rb") : cannot open the connection
   In addition: Warning message:
   In gzfile(file, "rb") :  cannot open compressed file
'/home/ppreddy/src//library/base/R/base.rdx', probable reason 'No such
file or directory'
   Execution halted

   I do not know for sure, if I can define R_VERSION, R_HOME, and PATH
in .Renviron. All I have seen is defining R_LIBS/JAV_HOME in r-help
archives.
   So, please explain how to use the .Renviron to work with
R-different R-versions and also Should I place .Renviron in the home
dir instead of cwd?

Thanks,
Poornima.

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Re: [R] Solution of function

[Megh Dal]

I think I should be clear exactly what I want :

take following example :

a = b = seq(1, 5, by=500)
 v = matrix(0, nrow=length(a), ncol=length(a))
 for (i in 1:length(a))
   {
for (j in 1:length(a))
   {
d = c(17989*a[i], -18109*b[j])
v[i,j] = t(d) %*% matrix(c(0.0001741, 0.0001280, 0.0001280,
0.0002570), nrow=2) %*% d
   }
   }
 library("rgl")
 open3d()
 persp3d(a,b,v,col="green",alpha=0.7,aspect=c(1,1,0.5))
shade <- outer(a, b, function(x,y) (0 < (x-y)) & ((x-y) < 2))
  persp3d(a,b,v,col=ifelse(shade, "red", "green"), alpha=0.7,aspect=c(1,1,0.5))


Here you see that the surface is the plot of a x'Cx for different values of 
components of x. And the red region is the portion of that plot that satisfy 0 
 wrote: Megh Dal wrote:
> Hi,
>
>   I want to find solution of function :  f(x,y) = x'Cx - a under constraints :
>
>   0 < x,y < p
>   0 < x-y< q
>
>   where a, p,q are given constants and x = (x, y) and C is a 2X2 matrix 
> (given)
>
>   Can anyone suggest me any R function to do that?
>
>   
Not likely. What you have (if C is  positive definite) is the
intersection between the boundary of an ellipse and the interior of a
parallelepiped, where the center of the ellipse and one corner of the
parallelepiped is at (0,0).

This is the union of between zero and three curve segments (hmm, maybe
only two) and I don't think any of the standard solvers and minimizers
can come up with that kind of result.

-- 
   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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[R] PC configuration you are using

[Endre Domiczi]

Hello,

As I mentioned in the previous message we are developing solution for
wholesale companies to analyze their sales transactions by associative
rules. I would very much appreciated if the community could give us
some hint of what is a typical PC configuration of a professional
statist (processor, RAM, HDD...)?

Thanks a lot in advance and I highly appreciate your feedback!

Kind regards,
endre

-- 
Endre Domiczi, CEO
Sevana Oy, http://www.sevana.fi
Email : [EMAIL PROTECTED]
GSM   : +372 53485178
Skype : emddom

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Re: [R] help with the unique function

[Marc Schwartz]

ravi wrote:

Hi,
The unique function is easy to understand and use. Beyond that, I want to get 
also the frequency of repetition of each individual row in a data frame
Let me explain with an example :
x<-data.frame(a=c(1,2,3,1,2),b=c(2,3,4,2,3),c=c(10,20,30,10,20))
xu<-unique(x)
We have,

x

  a b  c
1 1 2 10
2 2 3 20
3 3 4 30
4 1 2 10
5 2 3 20

xu

  a b  c
1 1 2 10
2 2 3 20
3 3 4 30

I want to get the following data frame :
  a b  cFreq
1 1 2 102
2 2 3 202
3 3 4 301
That is, in addition to the unique rows, I want to get the frequency of 
repetion of each individual row.
I will appreciate all the help that I can get.
Thank You,
Ravi


As usual in R, there are several options:

> table(apply(x, 1, paste, collapse = ","))

1,2,10 2,3,20 3,4,30
 2  2  1

or:

> table(interaction(x, sep = ",", drop = TRUE))

1,2,10 2,3,20 3,4,30
 2  2  1


So:

> cbind(unique(x),
Freq = as.vector(table(apply(x, 1, paste, collapse = ","
  a b  c Freq
1 1 2 102
2 2 3 202
3 3 4 301

or:

> cbind(unique(x),
Freq = as.vector(table(interaction(x, sep = ",", drop = TRUE
  a b  c Freq
1 1 2 102
2 2 3 202
3 3 4 301


HTH,

Marc Schwartz

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Re: [R] help with the unique function

[Erik Iverson]

ravi -

This may get you started

count.reps <- function(df) {
  hash  <- do.call("paste", c(df, sep = "\r"))
  cbind(unique(df), Freq = unclass(table(hash)))
}

test <- data.frame(a = rep(1:10, 2), b = rep(1:10, 2))
count.reps(test)

Best,
Erik Iverson

ravi wrote:

Hi,
The unique function is easy to understand and use. Beyond that, I want to get 
also the frequency of repetition of each individual row in a data frame
Let me explain with an example :
x<-data.frame(a=c(1,2,3,1,2),b=c(2,3,4,2,3),c=c(10,20,30,10,20))
xu<-unique(x)
We have,

x

  a b  c
1 1 2 10
2 2 3 20
3 3 4 30
4 1 2 10
5 2 3 20

xu

  a b  c
1 1 2 10
2 2 3 20
3 3 4 30

I want to get the following data frame :
  a b  cFreq
1 1 2 102
2 2 3 202
3 3 4 301
That is, in addition to the unique rows, I want to get the frequency of 
repetion of each individual row.
I will appreciate all the help that I can get.
Thank You,
Ravi

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Re: [R] help with the unique function

[Jorge Ivan Velez]

Hi Ravi,

Try this:

x<-data.frame(a=c(1,2,3,1,2),b=c(2,3,4,2,3),c=c(10,20,30,10,20))
cbind(unique(x),lapply(x,table)$c)[,-4]
a b  c Freq
1 1 2 102
2 2 3 202
3 3 4 301


HTH,

Jorge


On Wed, May 7, 2008 at 12:11 PM, ravi <[EMAIL PROTECTED]> wrote:

> Hi,
> The unique function is easy to understand and use. Beyond that, I want to
> get also the frequency of repetition of each individual row in a data frame
> Let me explain with an example :
> x<-data.frame(a=c(1,2,3,1,2),b=c(2,3,4,2,3),c=c(10,20,30,10,20))
> xu<-unique(x)
> We have,
> > x
>   a b  c
> 1 1 2 10
> 2 2 3 20
> 3 3 4 30
> 4 1 2 10
> 5 2 3 20
> > xu
>   a b  c
> 1 1 2 10
> 2 2 3 20
> 3 3 4 30
>
> I want to get the following data frame :
>   a b  cFreq
> 1 1 2 102
> 2 2 3 202
> 3 3 4 301
> That is, in addition to the unique rows, I want to get the frequency of
> repetion of each individual row.
> I will appreciate all the help that I can get.
> Thank You,
> Ravi
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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[R] help with the unique function

[ravi]

Hi,
The unique function is easy to understand and use. Beyond that, I want to get 
also the frequency of repetition of each individual row in a data frame
Let me explain with an example :
x<-data.frame(a=c(1,2,3,1,2),b=c(2,3,4,2,3),c=c(10,20,30,10,20))
xu<-unique(x)
We have,
> x
  a b  c
1 1 2 10
2 2 3 20
3 3 4 30
4 1 2 10
5 2 3 20
> xu
  a b  c
1 1 2 10
2 2 3 20
3 3 4 30

I want to get the following data frame :
  a b  c    Freq
1 1 2 10    2
2 2 3 20    2
3 3 4 30    1
That is, in addition to the unique rows, I want to get the frequency of 
repetion of each individual row.
I will appreciate all the help that I can get.
Thank You,
Ravi

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Re: [R] use of sequence on ridge regression

[Rodrigo Briceño]

Nice to meet you Brian. The question is about the numbers that appears 
after lambda (0,0, 0.1, 0.0001). I know that seq is a set of values used 
for testing which value fits best. But I'm not sure if I need to put 
whatever I think or what. I tried also with a set of 5 values and I get 
an error. Is there a maximum allowed?

plot(lm.ridge(hipcenter ~ .,seatpos, lambda = seq(0,0.1,0.001)))
select(lm.ridge(hipcenter ~ ., seatpos,lambda = seq(0,0.1,0.001)))

__

*Rodrigo Briceño*
Project Manager
Sanigest Internacional

+506  22-91-12-00 ext. 113  * Oficina* *Costa Rica*
+506  22-32-08-30  *Fax
*+506  88-86-11-77*  Celular**
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delete the original message and e-mail us.


Esta comunicación contiene información legal privilegiada y confidencial 
para el uso exclusivo del destinatario. La distribución, diseminación, 
copia u otro uso por terceras personas es estrictamente prohibida. Si 
usted ha recibido esta comunicación por error, le rogamos borrar el 
mensaje original y comunicárnoslo a esta misma dirección.



Prof Brian Ripley wrote:
> What do you mean by 'the sequence option'?
>
> The authot of lm.ridge
>
> On Wed, 7 May 2008, Rodrigo Briceño wrote:
>
>> Dear R users. I have a doubt about the use of the sequence option on
>> Ridge regression. I'm trying to understand the use of this option when
>> variables are highly linear correlated. I'm running a model where the
>> variables HtShoes and Ht have high VIF values. My program is written
>> below, but I'm not sure about the correct way of using the sequence
>> option:
>>
>> library (faraway)
>> data (seatpos)
>> attach (seatpos)
>> spos.mod <- lm(hipcenter ~ .,seatpos) summary (spos.mod)
>> library(MASS)
>> lm.ridge(hipcenter ~ .,seatpos)
>> plot(lm.ridge(hipcenter ~ .,seatpos, lambda = seq(0,0.1,0.001)))
>> select(lm.ridge(hipcenter ~ ., seatpos,lambda = seq(0,0.1,0.001)))
>>
>> Any advice will be appreaciated. Rodrigo B.
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide 
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>

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[R] predict lmer

[May, Roel]

Hi,
 
I am using lmer to analyze habitat selection in wolverines using the
following model:
 
(me.fit.of <-
lmer(USED~1+STEP+ALT+ALT2+relM+relM:ALT+(1|ID)+(1|ID:TRKPT2),data=vdata,
control=list(usePQL=TRUE),family=poisson,method="Laplace"))
 
Here, the habitat selection is calaculated using a so-called discrete
choice model where each used location has a certain number of
alternatives which the animal could have chosen. These sets of locations
are captured using the TRKPT2 random grouping. However, these sets are
also clustered over the different individuals (ID). USED is my binary
dependent variable which is 1 for used locations and zero for unused
locations. The other are my predictors.
 
I would like to predict the model fit at different values of the
predictors, but does anyone know whether it is possible to do this? I
have looked around at the R-sites and in help but it seems that there
doesn't exist a predict function for lmer???
 
I hope someone can help me with this; point me to the right functions or
tell me to just forget it
 
Thanks in advance!
 
Cheers Roel
 
Roel May
Norwegian Institute for Nature Research
Tungasletta 2, NO-7089 Trondheim, Norway


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Re: [R] categorical data analysis - fisher.exact for 2x2 and greater

[Dr. Jeff Miller]

Hi Simon and all,

I'm pretty sure that you are correct about this. I think it is a
misconception to say that the fisher exact test is only for a 2 by 2 table.
It is presented that way in textbooks because, for a 2x2 table, it is easy
to perform.  For larger tables, it becomes complex quickly due to the rate
at which the permutations increase.

 When I use it for larger tables, it is hit or miss as to whether R will be
able to do it.  It's not uncommon to get an error implying that R is out of
memory. 

Check out Agresti's Categorical Data Analysis on the use of the fisher exact
for larger than 2x2 tables, and check out the R archives (and Google search)
for all the posts about the error message people run into sometimes.

On April 29th, Marc Schwartz replied to my question about this as follows:

Take a look at the 'workspace' argument in ?fisher.test and review the
second paragraph in Details:

"For 2 by 2 cases, p-values are obtained directly using the (central or
non-central) hypergeometric distribution. Otherwise, computations are based
on a C version of the FORTRAN subroutine FEXACT which implements the network
developed by Mehta and Patel (1986) and improved by Clarkson, Fan and Joe
(1993). The FORTRAN code can be obtained from
http://www.netlib.org/toms/643. Note this fails (with an error message) when
the entries of the table are too large. (It transposes the table if
necessary so it has no more rows than columns. One constraint is that the
product of the row marginals be less than 2^31 - 1.)"



Thank you,
Jeff



-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Greg Snow
Sent: Wednesday, May 07, 2008 9:55 AM
To: David Winsemius; [EMAIL PROTECTED]
Subject: Re: [R] categorical data analysis

The last example in ?fisher.test is not a 2x2 table, in fact it uses levels
with a natural ordering similar to the original question.  Why would this
not be applicable to the situation?


From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf
Of David Winsemius [EMAIL PROTECTED]
Sent: Wednesday, May 07, 2008 7:34 AM
To: [EMAIL PROTECTED]
Subject: Re: [R] categorical data analysis

Simon Blomberg <[EMAIL PROTECTED]> wrote in
news:[EMAIL PROTECTED]:

> But see these posts:
>
> http://finzi.psych.upenn.edu/R/Rhelp02a/archive/119079.html
>
> http://finzi.psych.upenn.edu/R/Rhelp02a/archive/119080.html
>
> Simon.

Interesting reading, but the OP specifically said he was not dealing with
2x2 tables, so neither fisher.test nor the suggested alternatives would
be applicable to his data situation.

--
David Winsemius

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Internal Virus Database is out-of-date.


11:27 AM
 

Internal Virus Database is out-of-date.


11:27 AM

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[R] function in nls argument

[Fernando Moyano]

Greetings R users, maybe there is someone who can help
me with this problem:

I define a function "optim.fun" and want as output the
sum of squared errors between predicted and measured
values, as follows:

optim.fun <- function (ST04, SM08b, ch2no, a, b, d, E)
{
predR <-
(a*SM08b^I(2)+b*SM08b+d)*exp(E*((1/(283.15-227.13))-(1/(ST04+273.15-227.13
abserr <- abs(ch2no-predR)
qnum <- quantile(abserr, probs=0.95, na.rm=T) 
  
is.na(abserr) <- (abserr > qnum)
errsq <- sum(abserr^2, na.rm=T)
errsq
}

Then I want to optimize parameters a,b,d and E as to
minimize the function output with the following:

optim.model<-nls(nulldat ~ optim.fun(ST04, SM08b,
ch2no, a, b, d, E), data=tower,
start=list(a=-0.003,b=0.13,d=0.50, E=400), na.action =
na.exclude )

were nulldat=0
At this point I get the following error message:

Error in qr.default(.swts * attr(rhs, "gradient")) : 
  NA/NaN/Inf in foreign function call (arg 1)
Warning messages:
1: In if (na.rm) x <- x[!is.na(x)] else if
(any(is.na(x))) stop("missing values and NaN's not
allowed if 'na.rm' is FALSE") ... :
  the condition has length > 1 and only the first
element will be used
(this warning is repeated 12 times)

Question: what does the error mean? What am I doing
wrong?
Thanks a bunch.
Nano
Jen, Germany
Max Planck for Biogeochemistry




  


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Re: [R] use of sequence on ridge regression

[Prof Brian Ripley]

On Wed, 7 May 2008, Rodrigo Briceño wrote:


Nice to meet you Brian. The question is about the numbers that appears
after lambda (0,0, 0.1, 0.0001). I know that seq is a set of values used
for testing which value fits best. But I'm not sure if I need to put
whatever I think or what. I tried also with a set of 5 values and I get
an error. Is there a maximum allowed?


So you mean the set of values of lambda?  It is just a set to be use for a 
plot and for searching in the select() methods.


There is an R function called sequence(), and it is not the same as seq().



plot(lm.ridge(hipcenter ~ .,seatpos, lambda = seq(0,0.1,0.001)))
select(lm.ridge(hipcenter ~ ., seatpos,lambda = seq(0,0.1,0.001)))

__

Rodrigo Briceño
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Prof Brian Ripley wrote:
  What do you mean by 'the sequence option'?

  The authot of lm.ridge

  On Wed, 7 May 2008, Rodrigo Briceño wrote:

Dear R users. I have a doubt about the use of the
sequence option on
Ridge regression. I'm trying to understand the
use of this option when
variables are highly linear correlated. I'm
running a model where the
variables HtShoes and Ht have high VIF values. My
program is written
below, but I'm not sure about the correct way of
using the sequence
option:

library (faraway)
data (seatpos)
attach (seatpos)
spos.mod <- lm(hipcenter ~ .,seatpos) summary
(spos.mod)
library(MASS)
lm.ridge(hipcenter ~ .,seatpos)
plot(lm.ridge(hipcenter ~ .,seatpos, lambda =
seq(0,0.1,0.001)))
select(lm.ridge(hipcenter ~ ., seatpos,lambda =
seq(0,0.1,0.001)))

Any advice will be appreaciated. Rodrigo B.

__
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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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reproducible code.






--
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__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] use of sequence on ridge regression

[Prof Brian Ripley]

What do you mean by 'the sequence option'?

The authot of lm.ridge

On Wed, 7 May 2008, Rodrigo Briceño wrote:


Dear R users. I have a doubt about the use of the sequence option on
Ridge regression. I'm trying to understand the use of this option when
variables are highly linear correlated. I'm running a model where the
variables HtShoes and Ht have high VIF values. My program is written
below, but I'm not sure about the correct way of using the sequence
option:

library (faraway)
data (seatpos)
attach (seatpos)
spos.mod <- lm(hipcenter ~ .,seatpos) summary (spos.mod)
library(MASS)
lm.ridge(hipcenter ~ .,seatpos)
plot(lm.ridge(hipcenter ~ .,seatpos, lambda = seq(0,0.1,0.001)))
select(lm.ridge(hipcenter ~ ., seatpos,lambda = seq(0,0.1,0.001)))

Any advice will be appreaciated. Rodrigo B.

__
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https://stat.ethz.ch/mailman/listinfo/r-help
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and provide commented, minimal, self-contained, reproducible code.



--
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__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Installing A2R in Windows

[Kate]

Thank you very much for your help. This should take care of my problem.

@Romain: it would be greatly appreciated if you could release A2R on CRAN.

On Wed, May 7, 2008 at 5:31 AM, Romain Francois <
[EMAIL PROTECTED]> wrote:

> Hello Kate,
>
> Sorry I've only seen that thread. I've not been using A2R for some time,
> and never really found the time to release it properly, in CRAN for example.
> I'll try to allocate some time to that.
>
> If you have the sufficient tools installed (
> http://www.murdoch-sutherland.com/Rtools/), installing the package on
> windows is very similar to installing it on linux.
>
> Cheers,
>
> Romain
>
> Prof Brian Ripley wrote:
>
> > On Tue, 6 May 2008, Kate wrote:
> >
> >  Thanks. I used the command you mention and it works fine in Linux. But
> > > I
> > > need to get it to work for Windows XP as well (currently running
> > > R-2.7.0). Any idea if it's possible?
> > >
> >
> > Yes, same commmand works -- I've just tested it.  You need the tools
> > installed, or to submit to Uwe Ligges' win-builder (mentioned in the
> > manual).
> >
> >
> > > On Tue, May 6, 2008 at 5:18 PM, Prof Brian Ripley <
> > > [EMAIL PROTECTED]>
> > > wrote:
> > >  How did you install it?
> > >
> > >  You need to get A2R_0.0-4.tar.gz and do R CMD INSTALL
> > >  A2R_0.0-4.tar.gz, after reading the 'R Installation and
> > >  Administration manual, especially the sections for your OS.
> > >
> > >  The package in A2R/lastVersion/ was built for Unix on R
> > >  2.2.1. An expert might be able to get it working, but we
> > >  don't even know your OS and R version.
> > >
> > >
> > >
> > > On Tue, 6 May 2008, Kate wrote:
> > >
> > > Hi there,
> > >
> > > I've tried to install the A2R package using the files from
> > > http://addictedtor.free.fr/packages/A2R/lastVersion/
> > >
> > > This is the error I get when trying to load the library:
> > > library(A2R)
> > > Error in library(A2R) :
> > >  'A2R' is not a valid package -- installed < 2.0.0?
> > >
> > > Can anyone please help? Thanks.
> > > Kate
> > >
> > >   [[alternative HTML version deleted]]
> > >
> > > __
> > > R-help@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible
> > > code.
> > >
> > >
> > > PLEASE do read it.
> > >
> > > --
> > > 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
> > >
> > >
> > >
> > >
> > >
> > 
> >
> > __
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
> >
>
>
> --
> Mango Solutions
> data analysis that delivers
>
> Tel:  +44(0) 1249 76 77 00
> Fax:  +44(0) 1249 76 77 07
> Mob:  +44(0) 7813 52 61 23
>
>

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] use of sequence on ridge regression

[Rodrigo Briceño]

Dear R users. I have a doubt about the use of the sequence option on
Ridge regression. I'm trying to understand the use of this option when
variables are highly linear correlated. I'm running a model where the
variables HtShoes and Ht have high VIF values. My program is written
below, but I'm not sure about the correct way of using the sequence
option:

library (faraway)
data (seatpos)
attach (seatpos)
spos.mod <- lm(hipcenter ~ .,seatpos) summary (spos.mod)
library(MASS)
lm.ridge(hipcenter ~ .,seatpos)
plot(lm.ridge(hipcenter ~ .,seatpos, lambda = seq(0,0.1,0.001)))
select(lm.ridge(hipcenter ~ ., seatpos,lambda = seq(0,0.1,0.001)))

Any advice will be appreaciated. Rodrigo B.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Importing data

[Wensui Liu]

import stata data should be straight. take a look at foreign package


On Wed, May 7, 2008 at 9:30 AM, Yemi Oyeyemi <[EMAIL PROTECTED]> wrote:
> Hi everyone, please I'm having problem importing data from Stata and excel. 
> Help me out.
>   Thanks
>
>
>  -
>  [[elided Yahoo spam]]
> [[alternative HTML version deleted]]
>
>  __
>  R-help@r-project.org mailing list
>  https://stat.ethz.ch/mailman/listinfo/r-help
>  PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>  and provide commented, minimal, self-contained, reproducible code.
>



-- 
===
WenSui Liu
ChoicePoint Precision Marketing
Phone: 678-893-9457
Email : [EMAIL PROTECTED]
Blog : statcompute.spaces.live.com

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Re: [R] Importing data

[Neil Shephard]

Yemi Oyeyemi wrote:
> 
> Hi everyone, please I'm having problem importing data from Stata and
> excel. Help me out.
>   Thanks
> 
> 

You don't provide...

a) the code that you've tried

b) the error message that relates to the problem you are having

...without these people have little information on what _exactly_  your
problem is.  Please read the R-help posting guide as advised in the
signature of every mail that appears on the list.  For clarity its...
 
"PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code. "

In this instance you would also do well to read the "R Data Import/Export"
manual at http://cran.r-project.org/doc/manuals/R-data.html and pay
particular attention to section 3 titled "Importing from other Statistical
Systems"
(http://cran.r-project.org/doc/manuals/R-data.html#Importing-from-other-statistical-systems).

This would lead you to the read.dta() and write.dta() functions for
respectively reading and writing Stata formatted data sets.

Neil
-- 
View this message in context: 
http://www.nabble.com/Importing-data-tp17104951p17106184.html
Sent from the R help mailing list archive at Nabble.com.

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] CRAN and Multiple Linear Regression

[Peter Dalgaard]

Abhijit Dasgupta wrote:
> Multiple linear regression is handled by the function lm() in the
> default installation of R. This takes inputs as lm(y~x1+x2+x3).
>
> If you're going to be using R regularly, there are several books which
> cover the basic statistical analyses available in R (and then some),
> including those by Peter Daalgard and by Brian Ripley, who are very
> regular contributors to this list.
Thanks for saving me a shameless plug (notice that the double a comes
last, though...).

For people just out to get their feet wet, there's also a collection of
shorter and longer documents in the contributed section on CRAN,
http://cran.r-project.org/other-docs.html . I particularly like Jason
Owen's "The R Guide" as a kickstart document. As far as I can tell, you
can just skip things that rely on math that you haven't heard of (such
as matrix algebra) without getting lost.

-pd

>
> Abhijit
>
> Anja und Th. Sponsel wrote:
>> Hello
>>
>> I have to solve a multiple linear regression. Most programs like Excel
>> or Mathlab only support 5-10 dimensions. Now I have installed CRAN and
>> I have no clue what to do next. At the moment I am entering my data
>> into an excelsheet (for quick copy- paste). The Y-array will be 20
>> columns (=dimensions) and 128 rows (=variables). The X-array may also
>> be 128 rows in Excel.
>>
>> Which package do I need - or does it work without any package?
>>
>> What commands do I have to enter? I'm not familiar with CRAN and I
>> didn't find any example.
>>
>> Best regards,
>>  Thomas
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


-- 
   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] Importing data

[Juan Manuel Barreneche]

i usually import data from exel, using read.table or read.csv (which implies 
that i have to save exel files as .txt or .csv)

JM

El Miércoles, 7 de Mayo de 2008 11:25, John Kane escribió:
> First step would be to read the manual on the R site
> "R Data Import/Export" describes the import and export
> facilities available either in R itself or via
> packages which are available from CRAN
>
> Then if that does not solve the problem you need to
> explain in detail what the problems are, preferably
> with the code that you are using.  See the
> instructions at the bottom of the post.
>
> --- Yemi Oyeyemi <[EMAIL PROTECTED]> wrote:
> > Hi everyone, please I'm having problem importing
> > data from Stata and excel. Help me out.
> >   Thanks
> >
> >
> > -
> > [[elided Yahoo spam]]
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained,
> > reproducible code.
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html and provide commented, minimal,
> self-contained, reproducible code.

__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] categorical data analysis

[David Winsemius]

"Greg Snow" <[EMAIL PROTECTED]> wrote in
news:[EMAIL PROTECTED]:

> The last example in ?fisher.test is not a 2x2 table, in fact it uses
> levels with a natural ordering similar to the original question. 
> Why would this not be applicable to the situation? 

Apologies. Clearly I misunderstood the R implementation. My parsing of 
the fisher.test code (influenced by having just read the Campbell 
article) lead me to erroneously conclude that it was only applicable to 
2x2 tables. I see now that the error message says "_at_least_ 2 rows 
and columns" and that the error check is an inquality. 

-- 
David Winsemius
> 
> 
> From: [EMAIL PROTECTED] [EMAIL PROTECTED] On
> Behalf Of David Winsemius [EMAIL PROTECTED] Sent: Wednesday,
> May 07, 2008 7:34 AM To: [EMAIL PROTECTED]
> Subject: Re: [R] categorical data analysis
> 
> Simon Blomberg <[EMAIL PROTECTED]> wrote in
> news:[EMAIL PROTECTED]:
> 
>> But see these posts:
>>
>> http://finzi.psych.upenn.edu/R/Rhelp02a/archive/119079.html
>>
>> http://finzi.psych.upenn.edu/R/Rhelp02a/archive/119080.html
>>
>> Simon.
> 
> Interesting reading, but the OP specifically said he was not dealing
> with 2x2 tables, so neither fisher.test nor the suggested
> alternatives would be applicable to his data situation.
> 
> --
> David Winsemius
> 
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html and provide commented,
> minimal, self-contained, reproducible code. 
> 
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html and provide commented,
> minimal, self-contained, reproducible code. 
> 
>

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[R] p values for polychor

[andrew collier]

hello,

i have been using cor.test() for calculating the correlation coefficient  and p 
values for some data. however, since the data consist of two dichotomous 
sequences (actually just binary data), i understand that simply using the 
pearson correlation is not sufficient. however, having done a bit of research i 
found that the 
tetrachoric correlation is what i am after. found the polycor package and the 
polychor routine, which seem to do precisely what i want. however, i don't get 
p values out of polychor, just the standard deviation.

so, in a rather naive way i have tried to write a function which will return a 
list with similar fields as what one gets from cor.test(). not being terribly 
strong with statistics though, i am not sure whether this is entirely correct. 
could someone tell me if i am on the right track... or point out where i am 
going wrong?

tetrachoric.test <- function(x, y) {
p <- polychor(x, y, std.err = TRUE)
#
p$statistic <- p$rho / sqrt(c(p$var))
#
p$estimate <- p$rho
p$p.value = 2 * (1 - pnorm(abs(p$statistic)))

p
}

the assumption is that the p value is the integration of the two tails of the 
distribution?

> x <- as.integer(runif(20) > 0.5)
> y <- as.integer(runif(20) > 0.5)
> p <- tetrachoric.test(x, y)   
> p$statistic
[1] -0.2616866
> p$p.value
[1] 0.7935631
> p$var
  [,1]
[1,] 0.1452105

thanks for any help!

best regards,
andrew.

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Re: [R] Importing data

[John Kane]

First step would be to read the manual on the R site
"R Data Import/Export" describes the import and export
facilities available either in R itself or via
packages which are available from CRAN

Then if that does not solve the problem you need to
explain in detail what the problems are, preferably
with the code that you are using.  See the
instructions at the bottom of the post.
--- Yemi Oyeyemi <[EMAIL PROTECTED]> wrote:

> Hi everyone, please I'm having problem importing
> data from Stata and excel. Help me out.
>   Thanks
> 
>
> -
> [[elided Yahoo spam]]
>   [[alternative HTML version deleted]]
> 
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained,
> reproducible code.
>

__
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and provide commented, minimal, self-contained, reproducible code.

Re: [R] ggplo2: x_discrete labels size/direction

[hadley wickham]

>  PS Perhaps it'd still be really useful to be able to change text direction
>  in labels.
>  Hadley, what do you think?

Agreed.  I've added it to my ggplot2 customisation to do list.

Thanks,

Hadley


-- 
http://had.co.nz/

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Re: [R] CRAN and Multiple Linear Regression

[Abhijit Dasgupta]

Multiple linear regression is handled by the function lm() in the 
default installation of R. This takes inputs as lm(y~x1+x2+x3).


If you're going to be using R regularly, there are several books which 
cover the basic statistical analyses available in R (and then some), 
including those by Peter Daalgard and by Brian Ripley, who are very 
regular contributors to this list.


Abhijit

Anja und Th. Sponsel wrote:

Hello

I have to solve a multiple linear regression. Most programs like Excel
or Mathlab only support 5-10 dimensions. Now I have installed CRAN and
I have no clue what to do next. At the moment I am entering my data
into an excelsheet (for quick copy- paste). The Y-array will be 20
columns (=dimensions) and 128 rows (=variables). The X-array may also
be 128 rows in Excel.

Which package do I need - or does it work without any package?

What commands do I have to enter? I'm not familiar with CRAN and I
didn't find any example.

Best regards,
 Thomas

__
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Re: [R] Solution of function

[Peter Dalgaard]

Megh Dal wrote:
> Hi,
>
>   I want to find solution of function :  f(x,y) = x'Cx - a under constraints :
>
>   0 < x,y < p
>   0 < x-y< q
>
>   where a, p,q are given constants and x = (x, y) and C is a 2X2 matrix 
> (given)
>
>   Can anyone suggest me any R function to do that?
>
>   
Not likely. What you have (if C is  positive definite) is the
intersection between the boundary of an ellipse and the interior of a
parallelepiped, where the center of the ellipse and one corner of the
parallelepiped is at (0,0).

This is the union of between zero and three curve segments (hmm, maybe
only two) and I don't think any of the standard solvers and minimizers
can come up with that kind of result.

-- 
   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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] categorical data analysis

[Greg Snow]

The last example in ?fisher.test is not a 2x2 table, in fact it uses levels 
with a natural ordering similar to the original question.  Why would this not 
be applicable to the situation?


From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of David Winsemius [EMAIL 
PROTECTED]
Sent: Wednesday, May 07, 2008 7:34 AM
To: [EMAIL PROTECTED]
Subject: Re: [R] categorical data analysis

Simon Blomberg <[EMAIL PROTECTED]> wrote in
news:[EMAIL PROTECTED]:

> But see these posts:
>
> http://finzi.psych.upenn.edu/R/Rhelp02a/archive/119079.html
>
> http://finzi.psych.upenn.edu/R/Rhelp02a/archive/119080.html
>
> Simon.

Interesting reading, but the OP specifically said he was not dealing with
2x2 tables, so neither fisher.test nor the suggested alternatives would
be applicable to his data situation.

--
David Winsemius

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Re: [R] Not to draw the xaxis ticks in ggplot2

[hadley wickham]

On Tue, May 6, 2008 at 11:44 PM, ronggui <[EMAIL PROTECTED]> wrote:
> >library(ggplot2)
>  >(p<- qplot(mpg, wt, data=mtcars))
>  What I am doing is to set color of the ticks to hide them.
>  >grid.gedit(gPath("xaxis", "ticks"), gp=gpar(col="white"))
>
>  It should be a better way to achieve the purpose. Thanks.

Agreed.  I've added it to my ggplot2 customisation to do list.

Thanks,

Hadley

-- 
http://had.co.nz/

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[R] CRAN and Multiple Linear Regression

[Anja und Th. Sponsel]

Hello

I have to solve a multiple linear regression. Most programs like Excel
or Mathlab only support 5-10 dimensions. Now I have installed CRAN and
I have no clue what to do next. At the moment I am entering my data
into an excelsheet (for quick copy- paste). The Y-array will be 20
columns (=dimensions) and 128 rows (=variables). The X-array may also
be 128 rows in Excel.

Which package do I need - or does it work without any package?

What commands do I have to enter? I'm not familiar with CRAN and I
didn't find any example.

Best regards,
 Thomas

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Re: [R] categorical data analysis

[David Winsemius]

Simon Blomberg <[EMAIL PROTECTED]> wrote in
news:[EMAIL PROTECTED]: 

> But see these posts:
> 
> http://finzi.psych.upenn.edu/R/Rhelp02a/archive/119079.html
> 
> http://finzi.psych.upenn.edu/R/Rhelp02a/archive/119080.html
> 
> Simon.

Interesting reading, but the OP specifically said he was not dealing with 
2x2 tables, so neither fisher.test nor the suggested alternatives would 
be applicable to his data situation.

-- 
David Winsemius

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[R] Importing data

[Yemi Oyeyemi]

Hi everyone, please I'm having problem importing data from Stata and excel. 
Help me out.
  Thanks

   
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Re: [R] fft: characteristic function to distribution

[Thomas Steiner]

Thank you Prof Ripley for your answer.

> > The characteristic function is the inverse Fourier transform of the
> > distribution function. The characteristic function of a normaly
> > distributed random variable is exp(-t^2/2).
> >
>
> The fft is a discrete Fourier transforn, not a continuous one.

This is correct. I try to approximate the continous normal
distribution with infinite support by a set of discrete and bounded
points. A real discrete baby example would be the bernoulli
distribution:

p=0.4
t=seq(-0.01,1.001,length=100)
char=1-p+p*exp(1i*t)
cdf=stepfun(c(0,1),c(0,1-p,1))
plot(t,cdf(t),type="l",col="red",ylim=range(cdf(t),Re(fft(char)[2:99])))
lines(t,fft(char),col="blue")

This is more or less like the normal example.

> Further in each case where the normalizing constants are placed and the
> units of frequecy differ from source to source.
>
> ?fft has references to exactly what it computes: please consult them.

I read the documentation/help page. More details there would be
helpful. For example an example (it says "example*s*") something where
explicit expressions are known (as I tried it here).
Another possible improvement could be to make for example the
following sentence nicer/clearer: "(the inverse has a + in the
exponent of e, but here, we do not divide by 1/length(x))."
I did not consult the two given references (two old but surely valuable books).

Enough prattled. Can you give a working example where the cummulative
distribution function and the fourier transform are explicitly known?

I cannot add any value neither to wonderful R nor to this helpful
function. But perhaps my question isn't that stupid and you can give a
hint to proceed. Thank you very much in advance,
Thomas

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Re: [R] Citation in the literature

[Marc Schwartz]

Sébastien wrote:

Hello everyone,

Very quick question: How should I cite the use of R in a publication ?

Thanks in advance.

Sebastien


See the FAQs:

  http://cran.r-project.org/doc/FAQ/R-FAQ.html#Citing-R


This is also referenced in the startup banner in an R console:

...

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

...


HTH,

Marc Schwartz

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Re: [R] Citation in the literature

[ronggui]

> citation()

To cite R in publications use:

  R Development Core Team (2008). R: A language and environment for
  statistical computing. R Foundation for Statistical Computing,
  Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org.

A BibTeX entry for LaTeX users is

  @Manual{,
title = {R: A Language and Environment for Statistical Computing},
author = {{R Development Core Team}},
organization = {R Foundation for Statistical Computing},
address = {Vienna, Austria},
year = {2008},
note = {{ISBN} 3-900051-07-0},
url = {http://www.R-project.org},
  }

We have invested a lot of time and effort in creating R, please cite
it when using it for data analysis. See also 'citation("pkgname")'
for citing R packages.



On Wed, May 7, 2008 at 9:03 PM, Sébastien <[EMAIL PROTECTED]> wrote:
> Hello everyone,
>
>  Very quick question: How should I cite the use of R in a publication ?
>
>  Thanks in advance.
>
>  Sebastien
>
>  __
>  R-help@r-project.org mailing list
>  https://stat.ethz.ch/mailman/listinfo/r-help
>  PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
>  and provide commented, minimal, self-contained, reproducible code.
>



-- 
HUANG Ronggui, Wincent

Bachelor of Social Work, Fudan University, China

Master of sociology, Fudan University, China

Ph.D. Candidate, CityU of HK,
http://www.cityu.edu.hk/sa/psa_web2006/students/rdegree/huangronggui.html

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[R] Citation in the literature

[Sébastien]

Hello everyone,

Very quick question: How should I cite the use of R in a publication ?

Thanks in advance.

Sebastien

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Re: [R] list manipulation

[Thompson, David (MNR)]

 Beautiful! Thanks Jim.

DaveT.
>-Original Message-
>From: jim holtman [mailto:[EMAIL PROTECTED] 
>Sent: May 6, 2008 07:33 PM
>To: Thompson, David (MNR)
>Subject: Re: [R] list manipulation
>
>The reason for the NULLs is that is the output of the lapply you are
>executing.  If you don't want to see the value, then use 'invisible'
>or assign to an object since you are executing this at the command
>level, the default is to print the value.
>
>invisible(lapply(...))
>
>On Tue, May 6, 2008 at 2:35 PM, Thompson, David (MNR)
><[EMAIL PROTECTED]> wrote:
>> Hello,
>>
>> I have a set of one-liners (many thanks to previous 
>responses from this
>> list) that I use to look at newly imported data sets with 
>functions like
>> dim(), names(), str(), etc. within lapply(). Generally, 
>these commands
>> work for me but, I am apparently still missing some aspect of list
>> manipulation. I don't understand why I get a set of NULL 
>list elements
>> at the end of each output as demonstrated below. How can I 
>generate this
>> (and similar) result(s) without all the trailing NULLs?
>>
>> > lapply(ls(pattern='bn'), function(x) cat(x, dim(get(x)), "\t",
>> names(get(x)), "\n"))
>> bn1993 2885 11   oplt rplt rsiz tree bd ht oaz odst raz rdst spr
>> bn1994 3158 7oplt tree bd ht spr stat dam
>> bn1995 734 7 oplt tree bd ht spr stat dam
>> bn1996 293 7 oplt tree bd ht spr stat dam
>> bn1997 264 7 oplt tree bd ht spr stat dam
>> bn1998 768 7 oplt tree bd ht spr stat dam
>> bn1999 654 7 oplt tree bd ht dbh stat dam
>> bn2003 1407 9oplt tree bd94 ht94 ht99 ht02 ht03 stat dam
>> [[1]]
>> NULL
>>
>> [[2]]
>> NULL
>>
>> [[3]]
>> NULL
>>
>> [[4]]
>> NULL
>>
>> [[5]]
>> NULL
>>
>> [[6]]
>> NULL
>>
>> [[7]]
>> NULL
>>
>> [[8]]
>> NULL
>>
>> Thanx, DaveT.
>> *
>> Silviculture Data Analyst
>> Ontario Forest Research Institute
>> Ontario Ministry of Natural Resources
>> [EMAIL PROTECTED]
>> http://ofri.mnr.gov.on.ca
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide 
>http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
>
>-- 
>Jim Holtman
>Cincinnati, OH
>+1 513 646 9390
>
>What is the problem you are trying to solve?
>

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Re: [R] i-best, grep function

[Peter Dalgaard]

[EMAIL PROTECTED] wrote:
>> T1 <- read.delim(file="S://SEDIM//Yvonne//2_5//T1.txt",col.names= 
>> c("Dye/Sample_Peak", "Sample_File_Name", "Size", "Height", 
>> "Area_in_Point", "Area_in_BP", "Data_Point", "Begin_Point", 
>> "Begin_BP", "End_Point", "End_BP", "Width_in_Point", "Width_in_BP", 
>> "User_Comments", "User_Edit"))
>> T1 <- subset(T1, Size < 1000 & Size > 50)
>> T1.B <- cbind(T1[grep("^B", as.character(T1$Color),perl=T),3],
>> T1[grep("^B", as.character(T1$Color),perl=T),5])
>> T1.B <- cbind(T1.B, T1.B[,2]/sum(T1.B[,2]))
>>
>>
>> It works alright until the last two lines.  I try to grep the 
>> columns 3 and 5, but the outcome is 
>>  T1.B
>>  [,1] [,2]. 
>> I don´t quite understand the code of as.character(t1$Color), perl=T.
>> 
>
> T1 is a data frame, and T1$Color is one of the columns.
>   
With all due respect: I think you missed the point: T1$Color is NOT one
of the columns (look at the col.names).

So T1$Color is NULL and things go downhill from there.

But what is "i-best" This looks like a plain R issue.

-p
> as.character converts the column T1$Color from type factor to type 
> character (i.e. a vector of strings).
>
> grep("^B", as.character(T1$Color),perl=T) means 'find all strings in the 
> vector T1$Color that begin with the letter (capital) B'.  "^B" is an 
> example of a regular expression.  There is a very good guide to them here: 
> http://www.regular-expressions.info/quickstart.html
>
> The relevant help pages in R are ?grep and ?regexp.  Don't worry about the 
> parameter perl=TRUE; there are subtle variations on regular expression 
> syntax, and it just means that you follow PERL-style syntax.
>
> Regards,
> Richie.
>
> Mathematical Sciences Unit
> HSL
>   


-- 
   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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[R] Aling elmentos into Windows with TK

[ermimi]

Hello!!

I would like create a window that has diferent element as:

http://bioinf.wehi.edu.au/~wettenhall/RTclTkExamples/checkboxes.html
http://bioinf.wehi.edu.au/~wettenhall/RTclTkExamples/radiobuttons.html

I know as make it, but I don´t know as I could (align the diferent elemnts
to left, right, top, bottom) or (put in a coordinates into windows).

If anybody know as I could make it, I would like you say me.

Thank you very much, Luismi
A greetings
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[R] How do I write a power of matrices?? [was: How do I write a sum of matrixes??]

[Alberto Monteiro]

Jorge Ivan Velez wrote:
> 
> I think the function could be better but try this:
> 
> # Function: M is your matrix and n MUST be an integer>0
> mat.pow<-function(M,n) {
>   result<-M
> if(n>1){
>for ( iter in 2:n) result<-M%*%result
>result
>}
> else {result}
>   result
>  }
> 
There are much more efficient ways to compute a power,
just check:
http://en.wikipedia.org/wiki/Exponentiation_by_squaring

Or, translating the pseudo-code to R:

mat.pow <- function(M, n) {
  result <- diag(1, ncol(M))
  while (n > 0) {
if (n %% 2 == 1) {  
  result <- result %*% M
  n <- n - 1
}
M <- M %*% M
n <- n / 2
  }
  return(result)
}

# The matrix
m <-  rbind(c(1,1,0), c(0,1,1), c(0,0,1))
 
# Goal m^6 = m x m x m x m x m x m
goal=  m %*% m %*% m %*% m %*% m %*% m
 
# matpow
res=mat.pow(m,6)
 
# Check point
all.equal(goal,res)

This algorithm would be fast, unless n is a _very_ big number.

Alberto Monteiro

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[R] Problem with help system on linux

[Agustin Lobo]

Hi!

When I start the help system from within JGR,
I get a page stating that I have some
Packages in /usr/local/lib/R/site-library
and others in
/usr/lib/R/library

The problem is while I can have access to the help
info for the ones in /usr/local/lib/R/site-library,
when I try to access any pages of the ones
in /usr/lib/R/library (for example, base)
I get an error:
java.io.FileNotFoundException: 
/tmp/RtmpIwDHQD/.R/library/base/html/00Index.html (No such file or 
directory)

with lots of lines suach are:
at java.io.FileInputStream.open(Native Method)

Actually, the same happens if I start R without JGR and use
help.start(): I get a "file not found" at
file:///tmp/RtmpxKozFe/.R/library/base/html/00Index.html
if I select base,

while pages for rjava, for example, can be accessed on
file:///tmp/RtmpxKozFe/.R/library/rJava.1/html/00Index.html

I'm using:
platform   i486-pc-linux-gnu
arch   i486
os linux-gnu
system i486, linux-gnu
status
major  2
minor  7.0
year   2008
month  04
day22
svn rev45424
language   R
version.string R version 2.7.0 (2008-04-22)

I'd appreciate your help.

Agus
--
Dr. Agustin Lobo
Institut de Ciencies de la Terra "Jaume Almera" (CSIC)
LLuis Sole Sabaris s/n
08028 Barcelona
Spain
Tel. 34 934095410
Fax. 34 934110012
email: [EMAIL PROTECTED]
http://www.ija.csic.es/gt/obster

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Re: [R] i-best, grep function

[Richard . Cotton]

> T1 <- read.delim(file="S://SEDIM//Yvonne//2_5//T1.txt",col.names= 
> c("Dye/Sample_Peak", "Sample_File_Name", "Size", "Height", 
> "Area_in_Point", "Area_in_BP", "Data_Point", "Begin_Point", 
> "Begin_BP", "End_Point", "End_BP", "Width_in_Point", "Width_in_BP", 
> "User_Comments", "User_Edit"))
> T1 <- subset(T1, Size < 1000 & Size > 50)
> T1.B <- cbind(T1[grep("^B", as.character(T1$Color),perl=T),3],
> T1[grep("^B", as.character(T1$Color),perl=T),5])
> T1.B <- cbind(T1.B, T1.B[,2]/sum(T1.B[,2]))
> 
> 
> It works alright until the last two lines.  I try to grep the 
> columns 3 and 5, but the outcome is 
>  T1.B
>  [,1] [,2]. 
> I don´t quite understand the code of as.character(t1$Color), perl=T.

T1 is a data frame, and T1$Color is one of the columns.

as.character converts the column T1$Color from type factor to type 
character (i.e. a vector of strings).

grep("^B", as.character(T1$Color),perl=T) means 'find all strings in the 
vector T1$Color that begin with the letter (capital) B'.  "^B" is an 
example of a regular expression.  There is a very good guide to them here: 
http://www.regular-expressions.info/quickstart.html

The relevant help pages in R are ?grep and ?regexp.  Don't worry about the 
parameter perl=TRUE; there are subtle variations on regular expression 
syntax, and it just means that you follow PERL-style syntax.

Regards,
Richie.

Mathematical Sciences Unit
HSL


ATTENTION:

This message contains privileged and confidential inform...{{dropped:21}}

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Re: [R] unable to use functions require DLL from package "base"

[A.N.]

Thanks, I had indeed several versions of R and removed the older ones and it
worked.







I suspect you have more than one version of R installed and are mixing 
them up.  Those symbols have been in package stats for quite a while.

Try starting R with --vanilla, and if that works, clean out your startup 
files (see ?Startup).  If not, remove all your R installations and 
reinstall R 2.7.0 (or R-patched).

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[R] Fwd: Re: Solution of function

[Megh Dal]

Forgot to send one copy to R help. Sorry

Megh Dal <[EMAIL PROTECTED]> wrote:  Date: Wed, 7 May 2008 02:45:09 -0700 (PDT)
From: Megh Dal <[EMAIL PROTECTED]>
Subject: Re: [R] Solution of function
To: Berwin A Turlach <[EMAIL PROTECTED]>

  Hi Berwin,
   
  Thanks for having look on my problem. However on ipop() function I see 
following:
   
  ipop solves the quadratic programming problem :
min(c'*x + 1/2 * x' * H * x)
subject to: 
b <= A * x <= b + r
l <= x <= u 
   
  But my problem is not to find maxima or minima rather to get solution at that 
defined region. How to modify that function for my problem?

Berwin A Turlach <[EMAIL PROTECTED]> wrote:
  G'day Megh,

On Wed, 7 May 2008 01:11:34 -0700 (PDT)
Megh Dal wrote:

> I want to find solution of function : f(x,y) = x'Cx - a under
> constraints : 
> 0 < x,y < p
> 0 < x-y< q
> 
> where a, p,q are given constants and x = (x, y) and C is a 2X2
> matrix (given) 
> Can anyone suggest me any R function to do that?

ipop() in package kernlab
solve.QP in package quadprog
Depending on the form of C, package LowRankQP could also be of interest.

HTH.

Cheers,

Berwin

=== Full address =
Berwin A Turlach Tel.: +65 6515 4416 (secr)
Dept of Statistics and Applied Probability +65 6515 6650 (self)
Faculty of Science FAX : +65 6872 3919 
National University of Singapore 
6 Science Drive 2, Blk S16, Level 7 e-mail: [EMAIL PROTECTED]
Singapore 117546 http://www.stat.nus.edu.sg/~statba


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Re: [R] use list elements to subtract values from the dataframe

[jim holtman]

What you want is:

wf[[fl[1]]]

'fl' is a vector, so you should only be using a single '[' for indexing.

On Wed, May 7, 2008 at 3:20 AM, Dirkheld <[EMAIL PROTECTED]> wrote:
>
> Hi,
>
> I have a dataframe wf existing of a header with different labels and beneath
> the values of those labels :
> wf:
> label1  label2  ...
> 0,450,21
> 0,100,45
>   
>
> I have a list
> fl <- c("label2","label3",..)
>
> Isn't possible to use the list elements in the list in order to subtract
> values from the dataframe? like :
> wf$fl[[1]]
> When I do in R I get :NULL
> fl[[1]] gives  "label2"  so no problem here...
>
> While wf$label1 works fine.
>
>
>
> --
> View this message in context: 
> http://www.nabble.com/use-list-elements-to-subtract-values-from-the-dataframe-tp17098923p17098923.html
> Sent from the R help mailing list archive at Nabble.com.
>
> __
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> and provide commented, minimal, self-contained, reproducible code.
>



-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem you are trying to solve?

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Re: [R] Installing A2R in Windows

[Romain Francois]

Hello Kate,

Sorry I've only seen that thread. I've not been using A2R for some time, 
and never really found the time to release it properly, in CRAN for 
example. I'll try to allocate some time to that.


If you have the sufficient tools installed 
(http://www.murdoch-sutherland.com/Rtools/), installing the package on 
windows is very similar to installing it on linux.


Cheers,

Romain

Prof Brian Ripley wrote:

On Tue, 6 May 2008, Kate wrote:


Thanks. I used the command you mention and it works fine in Linux. But I
need to get it to work for Windows XP as well (currently running
R-2.7.0). Any idea if it's possible?


Yes, same commmand works -- I've just tested it.  You need the tools 
installed, or to submit to Uwe Ligges' win-builder (mentioned in the 
manual).




On Tue, May 6, 2008 at 5:18 PM, Prof Brian Ripley 
<[EMAIL PROTECTED]>

wrote:
  How did you install it?

  You need to get A2R_0.0-4.tar.gz and do R CMD INSTALL
  A2R_0.0-4.tar.gz, after reading the 'R Installation and
  Administration manual, especially the sections for your OS.

  The package in A2R/lastVersion/ was built for Unix on R
  2.2.1. An expert might be able to get it working, but we
  don't even know your OS and R version.



On Tue, 6 May 2008, Kate wrote:

Hi there,

I've tried to install the A2R package using the files from
http://addictedtor.free.fr/packages/A2R/lastVersion/

This is the error I get when trying to load the library:
library(A2R)
Error in library(A2R) :
 'A2R' is not a valid package -- installed < 2.0.0?

Can anyone please help? Thanks.
Kate

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PLEASE do read it.

--
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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--
Mango Solutions
data analysis that delivers

Tel:  +44(0) 1249 76 77 00
Fax:  +44(0) 1249 76 77 07
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Re: [R] Regarding nls()

[Karl Ove Hufthammer]

Spencer Graves:

> Bates' condemnation of R^2 has merit, but I would not go as far as
> he did in the comment cited below (dated 13 Aug 2000).  A standard
> definition of R^2 is as follows:
> 
> R^2 = (1 - var(prediction error) / var(obs)).
> 
> I can name several different ways of getting a negative R^2 in
> this case.  When that happens, it says the model is worse than useless,
> and you would be better off using the training set mean.
> 
> If I have an audience who wants an R^2 in an application where it
> is not clear what it even means, I try to briefly explain some of the
> difficulties while asking what question they are trying to solve using
> R^2.  Their answers will help me make a recommendation, which may
> include selecting which of the possible generalizations of R^2 to use.

I would like to recommend the following two articles on R²:

Model Comparisons and R²
Richard Anderson-Sprecher 
The American Statistician, Vol. 48, No. 2. (May, 1994), pp. 113-117. 
http://www.jstor.org/stable/2684259

Cautionary Note about R²
Tarald O. Kvalseth 
The American Statistician, Vol. 39, No. 4, (Nov., 1985), pp. 279-285. 
http://www.jstor.org/stable/2683704

-- 
Karl Ove Hufthammer

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Re: [R] use list elements to subtract values from the dataframe

[Ashish Ranpura]

Dirkheld  soc.kuleuven.be> writes:
> I have a dataframe wf existing of a header with different labels and beneath
> the values of those labels :
> wf:
> label1  label2  ...
> 0,450,21
> 0,100,45 
>   
> 
> I have a list
> fl <- c("label2","label3",..)
> 
> Isn't possible to use the list elements in the list in order to subtract
> values from the dataframe? like :
> wf$fl[[1]] 
> When I do in R I get :NULL
> fl[[1]] gives  "label2"  so no problem here...
> 
> While wf$label1 works fine.
> 


Dirk, possibly not the most elegant solution, but I would use:

f1.indices = match(f1, names(wf))
wf[f1.indices[1]]

Good luck,

-Ash.

---

-
Ashish Ranpura
Institute of Cognitive Neuroscience
University College London
17 Queen Square
London WC1N 3AR

tel: +44 (20) 7679 1126
web: http://www.icn.ucl.ac.uk

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[R] i-best, grep function

[Monna Nygård]

Hi,

I'm trying to use the i-best software. Does anyone have experience from this, I 
can't get it to work with my data.

Here is the code: 

T1 <- read.delim(file="S://SEDIM//Yvonne//2_5//T1.txt",col.names= 
c("Dye/Sample_Peak", "Sample_File_Name", "Size", "Height", "Area_in_Point", 
"Area_in_BP", "Data_Point", "Begin_Point","Begin_BP", "End_Point", 
"End_BP", "Width_in_Point", "Width_in_BP", "User_Comments", "User_Edit"))
T1 <- subset(T1, Size < 1000 & Size > 50)
T1.B <- cbind(T1[grep("^B", as.character(T1$Color),perl=T),3],T1[grep("^B", 
as.character(T1$Color),perl=T),5])
T1.B <- cbind(T1.B, T1.B[,2]/sum(T1.B[,2]))


It works alright until the last two lines.  I try to grep the columns 3 and 5, 
but the outcome is 
 T1.B
 [,1] [,2]. 
I don´t quite understand the code of as.character(t1$Color), perl=T. Could 
anyone please explane what this does, I havn´t found it anyware and I am so 
stuck. Maybe I'm doing something else wrong as well..

I would really appreciate some help, thank you.

Yvonne


_


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Re: [R] rggobi is crashing R-2.7.0

[Michael Lawrence]

On Tue, May 6, 2008 at 11:11 PM, Mark Kimpel <[EMAIL PROTECTED]> wrote:

> Hard as it is for me to imagine, the ggobi windows stay open and
> functional while R (in emacs) has crashed in the background after throwing
> the error messages. As a perhaps naive Linux user, I thought that if a
> parent process crashed any processes it spawned would crash too. I guess not
> in this case.
>

Well running it within Emacs may explain it. We actually aren't spawning a
new GGobi process - just dynamically linking the GGobi library and starting
it that way.



> Ubuntu currently is distributing graphviz 2.16.1
>

Do you have libgvc.so.3 on your system?

Michael


> Thanks,
> Mark
>
>
> On Wed, May 7, 2008 at 12:14 AM, Michael Lawrence <[EMAIL PROTECTED]>
> wrote:
>
> >
> >
> > On Tue, May 6, 2008 at 6:06 PM, Mark Kimpel <[EMAIL PROTECTED]> wrote:
> >
> > > R crashed just after the warnings were issued, but ggobi kept running
> > > (if that makes sense).
> >
> >
> > I am not sure if that makes sense; GGobi should exit when the R process
> > does.
> >
> >  I have Graphviz and Rgraphiz installed and use Rgraphviz regularly
> > > without a problem, so I'm not sure why it didn't load. Mark
> > >
> >
> > Which version of graphviz? I am not sure which version the Ubuntu binary
> > expects, but this may be a binary compatibility issue.
> >
> > That said, I am not sure if the GraphLayout plugin is the reason for R
> > crashing...
> >
> >
> > >
> > >
> > > On Tue, May 6, 2008 at 4:37 PM, Michael Lawrence <[EMAIL PROTECTED]>
> > > wrote:
> > >
> > > >
> > > >
> > > > On Tue, May 6, 2008 at 10:32 AM, Mark Kimpel <[EMAIL PROTECTED]>
> > > > wrote:
> > > >
> > > > > I am running 64-bit Ubuntu 8.04 and when I invoke rggobi the
> > > > > interactive
> > > > > graph displays but R crashes. See my sessionInfo() and a short
> > > > > example
> > > > > below. Ggobi and rggobi installed without complaints. Mark
> > > > >
> > > > > > sessionInfo()
> > > > > R version 2.7.0 Patched (2008-05-04 r45620)
> > > > > x86_64-unknown-linux-gnu
> > > > >
> > > > > locale:
> > > > >
> > > > > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> > > > >
> > > > > attached base packages:
> > > > > [1] stats graphics  grDevices utils datasets  methods
> > > > > base
> > > > >
> > > > > other attached packages:
> > > > > [1] rggobi_2.1.9   RGtk2_2.12.5-3 graph_1.18.0
> > > > >
> > > > > loaded via a namespace (and not attached):
> > > > > [1] cluster_1.11.10 tools_2.7.0
> > > > >
> > > > >
> > > > > > a <- matrix(rnorm(1000), nrow = 10)
> > > > >
> > > > > > g <- ggobi(a)
> > > > >
> > > > > ** (R:25146): CRITICAL **: Error on loading plugin library
> > > > > plugins/GraphLayout/plugin.la: libgvc.so.3: cannot open shared
> > > > > object file:
> > > > > No such file or directory
> > > > >
> > > > > ** (R:25146): CRITICAL **: Error on loading plugin library
> > > > > plugins/GraphLayout/plugin.la: libgvc.so.3: cannot open shared
> > > > > object file:
> > > > > No such file or directory
> > > > >
> > > > > ** (R:25146): CRITICAL **: can't locate required plugin routine
> > > > > addToToolsMenu in GraphLayout
> > > > > >
> > > > >
> > > >
> > > > It's not clear to me - did R crash or did you just receive these
> > > > warnings? These warnings are due to a missing graphviz, so the 
> > > > GraphLayout
> > > > plugin fails to load.
> > > >
> > > >
> > > > >
> > > > > --
> > > > > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
> > > > > Indiana University School of Medicine
> > > > >
> > > > > 15032 Hunter Court, Westfield, IN 46074
> > > > >
> > > > > (317) 490-5129 Work, & Mobile & VoiceMail
> > > > > (317) 663-0513 Home (no voice mail please)
> > > > >
> > > > > **
> > > > >
> > > > >[[alternative HTML version deleted]]
> > > > >
> > > > > __
> > > > > R-help@r-project.org mailing list
> > > > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > > > PLEASE do read the posting guide
> > > > > http://www.R-project.org/posting-guide.html
> > > > > and provide commented, minimal, self-contained, reproducible code.
> > > > >
> > > >
> > > >
> > >
> > >
> > > --
> > > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
> > > Indiana University School of Medicine
> > >
> > > 15032 Hunter Court, Westfield, IN 46074
> > >
> > > (317) 490-5129 Work, & Mobile & VoiceMail
> > > (317) 663-0513 Home (no voice mail please)
> > >
> > > **
> > >
> >
> >
>
>
> --
> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
> Indiana University School of Medicine
>
> 15032 Hunter Court, Westfield, IN 46074
>
> (317) 490-5129 Work, & Mobile & VoiceMail
> (317) 663-0513 Home (no voice mail please)
>
>

[R] Solution of function

[Megh Dal]

Hi,
   
  I want to find solution of function :  f(x,y) = x'Cx - a under constraints :
   
  0 < x,y < p
  0 < x-y< q
   
  where a, p,q are given constants and x = (x, y) and C is a 2X2 matrix (given)
   
  Can anyone suggest me any R function to do that?
   
   

   
-
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Re: [R] Significance analysis of Microarrays (SAM)

[Eleni Christodoulou]

Thanks Martin,

I also posted the question on the bioconductor list but I have no reply yet.
In the meanwhile I found out that instead of saying
d=list(data.matrix2,y,censored)

I should specify the arguments:
d=list(x=data.matrix2,y=y,censoring.status=censored)

Strange, huh? Anyway, it solves the problem.

Thanks once again,
Eleni



On Tue, May 6, 2008 at 6:43 PM, Martin Morgan <[EMAIL PROTECTED]> wrote:

> Hi Eleni --
>
> Although samr is not a Bioconductor package, you might have more luck
> asking on the Bioconductor mailing list, http://bioconductor.org. The
> obvious place to start, and probably you have already done this, is to
> ensure that the class of the objects passed to the function agree with
> the classes described on the function help page.
>
> Martin
>
> "Eleni Christodoulou" <[EMAIL PROTECTED]> writes:
>
> > Dear list,
> >
> > I am trying to perform a significance analysis of a microarray
> experiment
> > with survival data using the {samr} package. I have a matrix containing
> my
> > data which has 17816 rows corresponding to genes, and 286 columns
> > corresponding to samples. The name of this matrix is data.matrix2. Some
> of
> > the first values of this matrix are:
> > data.matrix2[1:3,1:5]
> >  GSM36777  GSM36778 GSM36779 GSM36780 GSM36781
> > [1,] 1.009274 1.0740659 1.048540 1.015946 1.022650
> > [2,] 1.007992 0.8768410 0.962442 1.111742 1.121150
> > [3,] 0.981853 0.9606492 1.024987 1.053302 1.063408
> >
> >  I also have the time in which each patient-sample is examined for
> relapse.
> > This information is in vector y, which has length 286, and is declared
> in
> > months. Indicatively:
> > y[1:5]
> > [1] 101 118   9 106  37
> >
> > Finally, I have a variable censored, which is 1 if the patient has
> relapsed
> > when examined at the examined time and 0 if not. Indicatively:
> > censored[1:5]
> > [1] 0 0 1 0 1
> >
> >
> > I am trying to perform the following sam analysis:
> > d=list(data.matrix2,y,censored)
> > samr.obj=samr(d,resp.type="Survival", nperms=20)
> >
> > When I am running the above commands I  get the error:
> > Error in check.format(y, resp.type = resp.type, censoring.status =
> > censoring.status) :
> >   Error in input response data: response type  Survival  specified;
> error in
> > censoring indicator
> > In addition: Warning message:
> > In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
> >
> >
> > I really cannot understand what  is wrong with my code.  Could anyone
> please
> > help me with this?
> >
> > Thank you all,
> > Eleni
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M2 B169
> Phone: (206) 667-2793
>

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