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    <title>gmane.comp.lang.r.general</title>
    <link>http://blog.gmane.org/gmane.comp.lang.r.general</link>
    <description/>
    <syn:updatePeriod>hourly</syn:updatePeriod>
    <syn:updateFrequency>1</syn:updateFrequency>
    <syn:updateBase>1901-01-01T00:00+00:00</syn:updateBase>
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      <rdf:Seq>
        <rdf:li rdf:resource="http://comments.gmane.org/gmane.comp.lang.r.general/133303"/>
        <rdf:li rdf:resource="http://comments.gmane.org/gmane.comp.lang.r.general/133301"/>
        <rdf:li rdf:resource="http://comments.gmane.org/gmane.comp.lang.r.general/133299"/>
        <rdf:li rdf:resource="http://comments.gmane.org/gmane.comp.lang.r.general/133296"/>
        <rdf:li rdf:resource="http://comments.gmane.org/gmane.comp.lang.r.general/133295"/>
        <rdf:li rdf:resource="http://comments.gmane.org/gmane.comp.lang.r.general/133289"/>
        <rdf:li rdf:resource="http://comments.gmane.org/gmane.comp.lang.r.general/133288"/>
        <rdf:li rdf:resource="http://comments.gmane.org/gmane.comp.lang.r.general/133287"/>
        <rdf:li rdf:resource="http://comments.gmane.org/gmane.comp.lang.r.general/133280"/>
        <rdf:li rdf:resource="http://comments.gmane.org/gmane.comp.lang.r.general/133277"/>
        <rdf:li rdf:resource="http://comments.gmane.org/gmane.comp.lang.r.general/133276"/>
        <rdf:li rdf:resource="http://comments.gmane.org/gmane.comp.lang.r.general/133274"/>
        <rdf:li rdf:resource="http://comments.gmane.org/gmane.comp.lang.r.general/133271"/>
        <rdf:li rdf:resource="http://comments.gmane.org/gmane.comp.lang.r.general/133268"/>
        <rdf:li rdf:resource="http://comments.gmane.org/gmane.comp.lang.r.general/133265"/>
        <rdf:li rdf:resource="http://comments.gmane.org/gmane.comp.lang.r.general/133259"/>
        <rdf:li rdf:resource="http://comments.gmane.org/gmane.comp.lang.r.general/133258"/>
        <rdf:li rdf:resource="http://comments.gmane.org/gmane.comp.lang.r.general/133253"/>
        <rdf:li rdf:resource="http://comments.gmane.org/gmane.comp.lang.r.general/133251"/>
        <rdf:li rdf:resource="http://comments.gmane.org/gmane.comp.lang.r.general/133241"/>
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    <title>Gmane</title>
    <url>http://gmane.org/img/gmane-25t.png</url>
    <link>http://gmane.org</link>
  </image>
  <item rdf:about="http://comments.gmane.org/gmane.comp.lang.r.general/133303">
    <title>Help with reading code</title>
    <link>http://comments.gmane.org/gmane.comp.lang.r.general/133303</link>
    <description>
I would like to give out the equation for calculating the maximum likelihood.
Below is the code, but I still have problems with it.  After I read the
code, I found there are two cases for "w(weights)".  If  "w" is not zero,
then the equation is given as "val &lt;- 0.5 * (sum(log(w)) - N * (log(2 * pi)
+ 1 - log(N) + 
        log(sum(w * res^2))))". However, if "w" is zero, then I do not know
what equation it should be since it does not make any sense for "log0". Hope
someone can help me to figure this out. Thanks!




function (object, REML = FALSE, ...) 
{
    res &lt;- object$residuals
    p &lt;- object$rank
    N &lt;- length(res)
    if (is.null(w &lt;- object$weights)) {
        w &lt;- rep.int(1, N)
    }
    else {
        excl &lt;- w == 0  #####I can not understand the following lines after
this. 
        if (any(excl)) {
            res &lt;- res[!excl]
            N &lt;- length(res)
            w &lt;- w[!excl]        }
    }
    N0 &lt;- N
    if (REML) 
        N &lt;- N - p
    val &lt;- 0.5 * (sum(log(w)) - N * (log(2 * pi) + 1 - log(N) + 
        log(sum(w * res^2))))
    if (REML) 
        val &lt;- val - sum(log(abs(diag(object$qr$qr)[1:p])))
    attr(val, "nall") &lt;- N0
    attr(val, "nobs") &lt;- N
    attr(val, "df") &lt;- p + 1
    class(val) &lt;- "logLik"
    val
}


Best,

Dana
</description>
    <dc:creator>Dana77</dc:creator>
    <dc:date>2008-12-03T23:24:17</dc:date>
  </item>
  <item rdf:about="http://comments.gmane.org/gmane.comp.lang.r.general/133301">
    <title>Static random numbers</title>
    <link>http://comments.gmane.org/gmane.comp.lang.r.general/133301</link>
    <description>Hello,

can anybody help me out saving random numbers? What I am doing is to 
generate a series of random numbers and keep it as a zoo object.

z &lt;- 1000

rn1 &lt;- as.zoo(rnorm(z))

The random numbers will be analyzed and described in a LaTeX document, 
so I have to keep them static somehow. The fact that they are kept
as a zoo object should not be of too much concern here. Thanks in advance.

Regards

Bastian Offermann


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

</description>
    <dc:creator>Bastian Offermann</dc:creator>
    <dc:date>2008-12-04T00:10:06</dc:date>
  </item>
  <item rdf:about="http://comments.gmane.org/gmane.comp.lang.r.general/133299">
    <title>Random Forest weighting</title>
    <link>http://comments.gmane.org/gmane.comp.lang.r.general/133299</link>
    <description>Folks,

I have a query around weighting in Random Forest (RF). I know that several
earlier emails in this group have raised this issue, but I did not find an
answer to my query.

I am working on a dataset (dataset1) that consists of 4 million records that
can be reduced to a dataset (dataset2) of approximately 1500 unique records
with frequency counts that add up to the 4 million records number as above.
Because of size issues, I cannot work with dataset1 in R and therefore, I am
working with dataset2 .

Each record consists of whether or not a patient chose a particular drug
based on 14 comorbidity (Yes / No) variables; I am using RF to understand
the comorbidity drivers of drug adoption (yes/no) classification.

At full dataset level (dataset1), the drug adoption incidence is ~11%. At
the reduced dataset dataset2 level, the drug adoption incidence increases to
~38%.

My question is that, if am using the reduced dataset (dataset2), how should
I inform RF that the adoption incidence at the full dataset level was 11%.
Should that be used as a classwt prior with classwt=c(Yes=.11, No=.89)? My
understanding is that RF does not allow case weighting.
Or can this be handled with the sampsize arguement through oversampling?
What proportions should one use for this (e.g., sampsize=c(Yes=100,
No=100))?



I would appreciate any feedback or pointers to any earlier thread that I may
have overlooked.

Regards,

Raghu
______________________________________________
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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.

</description>
    <dc:creator>Raghu Naik</dc:creator>
    <dc:date>2008-12-03T22:24:28</dc:date>
  </item>
  <item rdf:about="http://comments.gmane.org/gmane.comp.lang.r.general/133296">
    <title>applying a function to another function</title>
    <link>http://comments.gmane.org/gmane.comp.lang.r.general/133296</link>
    <description>Hello,
I did a function (sec_conop) whose arguments are syndic,
well and wellconop. 
 
sec_conop(syndic='01syndic.txt',well='well-1.csv',wellconop='well-1.dat');closeAllConnections()
 
This function takes “well” and “syndic”, matching between
them and then it does some transformations. The result is exported to
“wellconop”.
I will apply this function to one hundred different “wells”.
Therefore, for each well I use, the “wellconop argument will change too.
For intance if “well” is now well-2.csv, the function will be 

sec_conop(syndic='01syndic.txt',well='well-2.csv',wellconop='well-2.dat');closeAllConnections()
 
I am trying to apply this function automatically to all
“well” I have, but I do not find the way.
The last I tried, for three different “wells”, was :

wells&lt;-data.frame(funct=rep('sec_conop(',3),syndic=c('01syndic.txt','01syndic.txt','01syndic.txt'),well=c('well-1.csv','well-2.csv','well-3-1.csv'),wellconop=c('well-1.dat','well-2.dat','well-3.dat'))
 
funct_3wells&lt;-paste(wells$funct,"'",wells$syndic,"'", ","
,"'", wells$well,"'",
"," , "'" ,wells$wellconop,"'",")",";","closeAllConnections()",sep='')
 
lapply(funct_3wells,as.formula)
 
This way works partially because the results in “wellconop”
are truncated. 
Has anyone any suggestion?

Thanks in advance

Carlos


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

</description>
    <dc:creator>Carlos Cuartas</dc:creator>
    <dc:date>2008-12-03T20:51:52</dc:date>
  </item>
  <item rdf:about="http://comments.gmane.org/gmane.comp.lang.r.general/133295">
    <title>reading version 9 SAS datasets in R</title>
    <link>http://comments.gmane.org/gmane.comp.lang.r.general/133295</link>
    <description>Hi,

 

I am trying to read a SAS version 9.1.3 SAS dataset into R (to preserve
the SAS labels), but am unable to do so (I have read in a CSV version).
I first created a transport file using the SAS code:

 

libname ces2 'D:\CES Analysis\Data';

filename transp 'D:\CES Analysis\Data\fadata.xpt';

 

/* create a transport file - R cannot read file created by proc cport */

proc cport data=ces2.fadata file=transp;

run;

 

I then tried to read it in R using:

 




Error in lookup.xport(file) : file not in SAS transfer format

 

Next I tried using the libname statement and the xport engine to create
a transport file. The problem with this method is that variable names
cannot be more than 8 characters as this method creates a SAS version 6
transport file. 

 

libname to_r xport 'D:\CES Analysis\Data\fadata2.xpt';

 

data to_r.fadata2;

  set ces2.fadata;

run;

 

But I get an error message in the SAS log:

 

493  libname to_r xport 'D:\CES Analysis\Data\fadata2.xpt';

NOTE: Libref TO_R was successfully assigned as follows:

      Engine:        XPORT

      Physical Name: D:\CES Analysis\Data\fadata2.xpt

494

495  data to_r.fadata2;

496    set ces2.fadata;

497  run;

 

ERROR: The variable name BUS_TEL_N is illegal for the version 6 file
TO_R.FADATA2.DATA.

NOTE: The SAS System stopped processing this step because of errors.

WARNING: The data set TO_R.FADATA2 was only partially opened and will
not be saved.

 

Next I tried other ways of reading a SAS dataset in R, as shown below:

 

fadata2 &lt;- sas.get("D:\\CES Analysis\\Data", mem=fadata)

Error in sas.get("D:\\CES Analysis\\Data", mem = fadata) : 

  Unix file, "D:\CES Analysis\Data/c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, .sd2 D:\CES Analysis\Data/c(NA, 64716,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 64716, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 

In addition: Warning message:

In sas.get("D:\\CES Analysis\\Data", mem = fadata) :

  D:\CES Analysis\Data/formats.sc? or formats.sas7bcat  not found.
Formatting ignored. 

 


[1] "fadata"



Error in lookup.xport(file) : file not in SAS transfer format



SAS failed.  SAS program at
D:\DOCUME~1\re06572\LOCALS~1\Temp\RtmpLqCVUx\file72ae2cd6.sas 

The log file will be file72ae2cd6.log in the current directory

Warning messages:

1: In system(paste(sascmd, tmpProg)) : "sas" not found

2: In read.ssd("D:\\CES Analysis\\Data", "fadata") :

  SAS return code was -1


sascmd=file.path(sashome, "sas.exe"))

SAS failed.  SAS program at
D:\DOCUME~1\re06572\LOCALS~1\Temp\RtmpLqCVUx\file6df11649.sas 

The log file will be file6df11649.log in the current directory

Warning message:

In read.ssd(file.path(sashome, "core", "sashelp"), "fadata", sascmd =
file.path(sashome,  :

  SAS return code was 2


 

Is there any way I can read in a SAS version 9 dataset in R, so that I
can preserve the SAS labels?

If I have to change the SAS variable names to be 8 characters or less,
to create a SAS version 6 transport file, I could probably do without
the SAS labels as I have already read in the data into R from a CSV
file.

 

Thanks in advance for any help.

 

Jude

 

___________________________________________
Jude Ryan
Director, Client Analytic Services
Strategy &amp; Business Development
UBS Financial Services Inc.
1200 Harbor Boulevard, 4th Floor
Weehawken, NJ 07086-6791
Tel. 201-352-1935
Fax 201-272-2914
Email: jude.ryan&lt; at &gt;ubs.com

 


























Please do not transmit orders or instructions regarding a UBS account by e-mail. The information provided in this e-mail or any attachments is not an official transaction confirmation or account statement. For your protection, do not include account numbers, Social Security numbers, credit card numbers, passwords or other non-public information in your e-mail. Because the information contained in this message may be privileged, confidential, proprietary or otherwise protected from disclosure, please notify us immediately by replying to this message and deleting it from your computer if you have received this communication in error. Thank you.



UBS Financial Services Inc.

UBS International Inc.

UBS Financial Services Incorporated of Puerto Rico

UBS AG
______________________________________________
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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.

</description>
    <dc:creator>jude.ryan&lt; at &gt;ubs.com</dc:creator>
    <dc:date>2008-12-03T21:40:12</dc:date>
  </item>
  <item rdf:about="http://comments.gmane.org/gmane.comp.lang.r.general/133289">
    <title>Strplit code</title>
    <link>http://comments.gmane.org/gmane.comp.lang.r.general/133289</link>
    <description>
Dear R-users,

The strsplit function does not exist in S-plus and I would like to use it. How
could I reproduce the function in Splus or access to its source code?

Thank you in advance,

Sebastien

______________________________________________
R-help&lt; at &gt;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.

</description>
    <dc:creator>pomchip&lt; at &gt;free.fr</dc:creator>
    <dc:date>2008-12-03T19:52:21</dc:date>
  </item>
  <item rdf:about="http://comments.gmane.org/gmane.comp.lang.r.general/133288">
    <title>Hmisc latex() and Rcmdr numSummary() percentage issues</title>
    <link>http://comments.gmane.org/gmane.comp.lang.r.general/133288</link>
    <description>Dear R users,
I have issues regarding latex() from Hmisc and numSummary() from
Rcmdr. Here's an example:

The resulting LaTeX code (see below) is not compilable, because of the
`%' signs present in the column headers, and that are not escaped by
latex() (contrary to the behaviour of xtable()). I can solve the issue
manually by escaping the percentage signs `\%'.

Would there be a way to automatise this?
Thank you,
Liviu


######## Uncompilable LaTeX ########
% latex.default(as.table(.numSummary$table), cdec = c(2), file = "",
   title = "")
%
\begin{table}[!tbp]
 \begin{center}
 \begin{tabular}{lrrrrrrr}\hline\hline
\multicolumn{1}{l}{}&amp;
\multicolumn{1}{c}{mean}&amp;
\multicolumn{1}{c}{sd}&amp;
\multicolumn{1}{c}{0%}&amp;
\multicolumn{1}{c}{25%}&amp;
\multicolumn{1}{c}{50%}&amp;
\multicolumn{1}{c}{75%}&amp;
\multicolumn{1}{c}{100%}
\\ \hline
&amp;$31.37$&amp;$20.41$&amp;$10.6$&amp;$16.9$&amp;$23.7$&amp;$39$&amp;$84.5$\\
\hline
\end{tabular}

\end{center}

\end{table}
######## End of LaTeX ########


######## Compilable LaTeX ########
% latex.default(as.table(.numSummary$table), cdec = c(2), file = "",
   title = "")
%
\begin{table}[!tbp]
 \begin{center}
 \begin{tabular}{lrrrrrrr}\hline\hline
\multicolumn{1}{l}{}&amp;
\multicolumn{1}{c}{mean}&amp;
\multicolumn{1}{c}{sd}&amp;
\multicolumn{1}{c}{0\%}&amp;
\multicolumn{1}{c}{25\%}&amp;
\multicolumn{1}{c}{50\%}&amp;
\multicolumn{1}{c}{75\%}&amp;
\multicolumn{1}{c}{100\%}
\\ \hline
&amp;$31.37$&amp;$20.41$&amp;$10.6$&amp;$16.9$&amp;$23.7$&amp;$39$&amp;$84.5$\\
\hline
\end{tabular}

\end{center}

\end{table}
######## End of LaTeX ########


</description>
    <dc:creator>Liviu Andronic</dc:creator>
    <dc:date>2008-12-03T19:44:27</dc:date>
  </item>
  <item rdf:about="http://comments.gmane.org/gmane.comp.lang.r.general/133287">
    <title>changing colnames in dataframes</title>
    <link>http://comments.gmane.org/gmane.comp.lang.r.general/133287</link>
    <description>dear all,

I'm building new dataframes from bigger one's using e.g. columns F76, F83,
F90:

JJ&lt;-data.frame( c( as.character(rep( gender,3))) , c( F76,6- F83, F90) )

Looking into JJ one has:

    c.as.character.rep.gender..8...
c.6...F73..F78..F79..F82..6...F84..F94..F106..F109
1                                     w                   2
2                                     w                   3
3                                     m                  1
etc.

Instead of the automatic colnames 'c.as.character.rep.gender..8' I like to
have the colnames 'gender' and 'J.value'.
I tried levels, labels etc but without success.

OK, I can fix(FF) manually, but this is bad, because it has to be done again
and again ..
OK, I can do

gender.J&lt;-c( as.character(rep( gender,3)))
Jvalue&lt;-c( F76,6- F83, F90)
JJ&lt;-data.frame(gender.J, J.value)

but this is not optimal because 'gender' is depending on rep(.., n) and I
have many dataframes KK, LL, .. using 'gender' with different size.

Question: is it possible to do something like

JJ&lt;-data.frame(c( as.character(rep( gender,3))),c( F76,6- F83, F90),  ??
col.names=c("gender","Jvalue") ?? )

Sorry, if my question is elementary, but I could not find a fix.

Thank your for your advice.

hth

Wolfgang

______________________________________________
R-help&lt; at &gt;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.

</description>
    <dc:creator>Wolfgang Lindner</dc:creator>
    <dc:date>2008-12-03T19:30:56</dc:date>
  </item>
  <item rdf:about="http://comments.gmane.org/gmane.comp.lang.r.general/133280">
    <title>how do I eliminate excess levels in lattice contourplot key /legend?</title>
    <link>http://comments.gmane.org/gmane.comp.lang.r.general/133280</link>
    <description>I'm working on a contourplot( ) graph, the subject of several previous 
posts to this list. The contours express probabilities from 0 - 1, but the 
key that is automatically generated by contourplot pads the probability 
scale with values that are impossible (i.e, range goes from -0.2 to 1.2), 
which will be confusing to those who view the plot. How can I get the 
scale to just run from 0 - 1?

I have toiled mightily in the depths of the Murrell &amp; Sarkar graphics 
books. Any pointers will be gratefully received.

--Seth

Minimal, commented code:

library(lattice)

model &lt;- function(a,b,c,d,e, f, X1,X2)          # model function for 
contour plot
{J &lt;- a + (b*X1) + (c*X2) + (d*X1*X2) + e*(X1^2) + f*(X2^2)
  pp &lt;- exp(J)/(1+exp(J))
  return(pp)}

g &lt;- expand.grid(X1= seq(0.3,0.9,0.01), X2 = seq(0.3,1, 0.01)) 
## create x and y data matrix

g$z &lt;- model(-29, -14, 52, 80, -3, -56, g$X1, g$X2) 
## Create variable z using model and g data frame

contourplot(z ~ X1 * X2,
data = g,
region = TRUE,         # Add color to background
cuts = 5            # Number of contour/color intervals. 
)


Dr. Seth  W. Bigelow
Sierra Nevada Research Center
USFS - PSW.
______________________________________________
R-help&lt; at &gt;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.

</description>
    <dc:creator>Seth W Bigelow</dc:creator>
    <dc:date>2008-12-03T17:13:57</dc:date>
  </item>
  <item rdf:about="http://comments.gmane.org/gmane.comp.lang.r.general/133277">
    <title>SARIMA Model</title>
    <link>http://comments.gmane.org/gmane.comp.lang.r.general/133277</link>
    <description>Hi,
I'm looking to use R to find p,d,q, P,D,Q coefficients in SARIMA
(p,d,q,P,D,Q) model. However I'm new to R and am having below difficulties.

(1) unable to read the data into R. while I save the .csv file into R
workspace and try to load the same I run into the following error:
"Error: bad restore file magic number (file may be corrupted) -- no data
loaded
In addition: Warning message:
file 'Default.csv' has magic number '4/9/2'
   Use of save versions prior to 2 is deprecated".
Default.csv has two columns viz. date column and numerical value column.

(2) second I'm unaware of the acf and pacf functions in R which need to be
used to calculate p,d,q, P,D,Q coefficients in SARIMA (p,d,q,P,D,Q) model.
Would appreciate if someone could send me pointers for the same? Thanks.

Regards,
Rahul
______________________________________________
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</description>
    <dc:creator>rahul chandola</dc:creator>
    <dc:date>2008-12-03T16:25:52</dc:date>
  </item>
  <item rdf:about="http://comments.gmane.org/gmane.comp.lang.r.general/133276">
    <title>GLMM using lme4</title>
    <link>http://comments.gmane.org/gmane.comp.lang.r.general/133276</link>
    <description>Dear R-experts, 

I am running R version 2.7.1 on Windows Vista. I have a small dataset which consists of “chick ID”, “year (0, 1)”, “hatching order [HO, defined as first, second and third-hatched chick]”, and the binary outcome of interest “death (0, 1)”. So a subset of my dataset looks like this on a txt file: 

y ID Yr HO
1 1 1 First
0 2 1 First
0 3 1 Second
0 4 1 First
1 5 1 First
0 6 1 Third
0 7 1 First
0 8 1 Third
0 9 1 First
0 10 1 First
1 11 1 Third
0 12 1 First
0 13 1 First
0 14 1 First
0 15 1 First
0 17 1 First
1 19 1 First
1 20 1 First
............
n ni nj nk 

I need to run a GLMM using Year (Yr) and chick ID (ID) as random effects in order to account for lack of independence at the nest level (many chicks are siblings) and eliminate “year effect” incase a significant difference exists between years.

Using lmer, I specified my model as follows: 

model1 &lt;- lmer(y~HO+(Yr|ID),family=binomial,1)
summary(model1) 

Output: 

Error en model.frame.default(data = 1, formula = y ~ HO + (Yr + ID), drop.unused.levels = TRUE) : 
las longitudes de las variables son diferentes (encontrada para 'HO') 

Q1: What does this error message mean and how can I solve the problema? 

Q2: Is my model correctly specified? 

I look forward to hearing from you guys, always so helpful. 

Lucho 



      

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and provide commented, minimal, self-contained, reproducible code.
</description>
    <dc:creator>Luciano La Sala</dc:creator>
    <dc:date>2008-12-03T16:21:54</dc:date>
  </item>
  <item rdf:about="http://comments.gmane.org/gmane.comp.lang.r.general/133274">
    <title>weighted standard deviation</title>
    <link>http://comments.gmane.org/gmane.comp.lang.r.general/133274</link>
    <description>Please assist, how do you find the weighted standard deviation?

______________________________________________
R-help&lt; at &gt;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.

</description>
    <dc:creator>Humphrey Kaunda</dc:creator>
    <dc:date>2008-12-03T10:43:25</dc:date>
  </item>
  <item rdf:about="http://comments.gmane.org/gmane.comp.lang.r.general/133271">
    <title>Function output difficulties</title>
    <link>http://comments.gmane.org/gmane.comp.lang.r.general/133271</link>
    <description>
is there anyway for some parts of the function output to not be returned,
even if the output has been used to calculate a further part of the
function? i have tried invisible() to no avail.

Thanks Emma
</description>
    <dc:creator>emj83</dc:creator>
    <dc:date>2008-12-03T13:41:53</dc:date>
  </item>
  <item rdf:about="http://comments.gmane.org/gmane.comp.lang.r.general/133268">
    <title>Spectral Analysis of Time Series in R</title>
    <link>http://comments.gmane.org/gmane.comp.lang.r.general/133268</link>
    <description>Dear R Community,

I am currently student at the Vienna University of Technology writing my 
Diploma thesis on causality in time series and doing some analyses of 
time series in R. I have the following questions:

(1) Is there a function in R to estimate the PARTIAL spectral coherence 
of a multivariate time series? If yes, how does this work? Is there an 
test in R if the partial spectral coherence between two variables is 
zero? The functions I know (spectrum, etc.) only work to estimate the 
spectral coherence.

(2) For some causality analysis I need an estimate of the inverse of the 
spectral density matrix of a multivariate time series. Is there any 
possibility in R to get this? Actually, I would be happy if I could at 
least get a functional estimate of the spectral density matrix. I guess 
this should work because R can plot the kernel density estimator of the 
spectral density, so it should be possible to extract the underlying 
function estimate.

(3) Is there any possibility to do Granger Causality in R? That means 
fitting an VAR model and testing if some coefficients are zero.

Thank you very much in advance!

Best Regards,
Alexander
T

______________________________________________
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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.

</description>
    <dc:creator>Alexander Schnebel</dc:creator>
    <dc:date>2008-12-03T14:41:58</dc:date>
  </item>
  <item rdf:about="http://comments.gmane.org/gmane.comp.lang.r.general/133265">
    <title>Creating Tabel for Mean, Deviance</title>
    <link>http://comments.gmane.org/gmane.comp.lang.r.general/133265</link>
    <description>Hi,

Can someone help me how to create a table for Min, Max, Mean, Deviance.

I have input data like this:

Person Age Child
1  517   2
2  517   0 
3  517   1 
4  520    2 
5  520   3
6  710   1
7  721   4
8  721   5
9  721   1


Now i want to create a table for the Min, Max, Deviance, and Mean. from the 
Child Value.

It should  look like this:

  Person  Age Min Max Mean Deviance 

1  517  0  1  0.610.62
2  518  1  2 1.611.62
3  519  1  4  1.612.62
4  520  2  4 2.631.42
5  521  1  5  2.610.22
6  717  0  1 0.610.52
7  718  1 2 1.610.72
8  719  1  4  1.610.82
9  720 1 4 2.630.12



-----------------------------------------------------------------


what i can do is only manually:

data&lt;- read.table("test.data")

Min(data$Child), Max(data$Child), Mean(data$Child), Deviance(data$Child)

I only know how to calculate. But i dont know how to buiild the tabell like 
this.


I would appreciate if someone can help me. Thanks in advance.

______________________________________________
R-help&lt; at &gt;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.

</description>
    <dc:creator>Edwin Sendjaja</dc:creator>
    <dc:date>2008-12-03T13:27:02</dc:date>
  </item>
  <item rdf:about="http://comments.gmane.org/gmane.comp.lang.r.general/133259">
    <title>intersection of two matrices(updated)</title>
    <link>http://comments.gmane.org/gmane.comp.lang.r.general/133259</link>
    <description>Hi,

I have two matrices as follow:
matrix A =

a=matrix(c(c("abc","abc","bcd","bcd","bce","bce"),c("a1","d2","d1","d2","a1","a2")),6,2)

and matrix B which contains pair of values :
 b=matrix(c(c("a1","a1"),c("a2","d2")),2,2)


 In short, I wish to find out pairs of values in matrix a[,2] having
same value in a[,1], which occur as a row in matrix b, so that the
output becomes :
abc
bce, or

even better
abc a1 d2
bce a1 a2

 How can I do that?
cheers,
Joshi

______________________________________________
R-help&lt; at &gt;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.

</description>
    <dc:creator>T Joshi</dc:creator>
    <dc:date>2008-12-03T12:18:31</dc:date>
  </item>
  <item rdf:about="http://comments.gmane.org/gmane.comp.lang.r.general/133258">
    <title>intersection of two matrices</title>
    <link>http://comments.gmane.org/gmane.comp.lang.r.general/133258</link>
    <description>Hi,
I have two matrices as follow:
matrix A =

a=matrix(c(c("abc","abc","bcd","bcd","bce","bce"),c("a1","d2","d1","d2","a1","a2")),6,2)

and matrix B which contains pair of values :
 b=matrix(c(c("a1","a2"),c("a1","d2")),2,2)

 In short, I wish to find out pairs of values in matrix a[,2] having
same value in a[,1], which occur as a row in matrix b, so that the
output becomes :
abc
bce, or

even better
abc a1 d2
bce a1 a2

 How can I do that?
cheers,
Joshi

_________________________________

Ms Tejal Joshi

Researcher
Center for Biological Sequence Analysis
Technical University of Denmark
Kemitorvet, Building 208
DK-2800 Kgs. Lyngby, Denmark
Phone: +45 4525 6148
tejal&lt; at &gt;cbs.dtu.dk
www.cbs.dtu.dk

______________________________________________
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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.

</description>
    <dc:creator>T Joshi</dc:creator>
    <dc:date>2008-12-03T12:11:10</dc:date>
  </item>
  <item rdf:about="http://comments.gmane.org/gmane.comp.lang.r.general/133253">
    <title>stuck with repeated values</title>
    <link>http://comments.gmane.org/gmane.comp.lang.r.general/133253</link>
    <description>R Gurus,I have a vector of nearly 90,000 characters from which I have to
extract the index of the characters which are repeated. So suppose if
x&lt;-c("a","a","b","a","b","c","d") then my output would be a vector having
the index where the values are repeated i.e (1,2,3,4,5). I have been able to
isolate out the values that are repeated from the unique list of characters
in x (i.e. y&lt;-c("a","b")). One method can be to use a loop on the which
function but that would be too time consuming. Any hint on using the apply
function effectively would be useful
Thanks and Regards
Souvik Bandyopadhyay
Lecturer,
Dept of Biostatistics,
Indian Institute of Public Health,
Hyderabad

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

</description>
    <dc:creator>SOUVIK BANDYOPADHYAY</dc:creator>
    <dc:date>2008-12-03T11:32:21</dc:date>
  </item>
  <item rdf:about="http://comments.gmane.org/gmane.comp.lang.r.general/133251">
    <title>adding a new dataset to the default R distribution</title>
    <link>http://comments.gmane.org/gmane.comp.lang.r.general/133251</link>
    <description>Hi,
I am a student in archaeology with some interest in statistics and R.

Recently I've obtained the permission to distribute in the public domain
a small dataset (named "spearheads" with 40 obs. of  14 variables) that
was used in an introductory statistics book for archaeologists
(published in 1994).

I've rewritten most of the exercises of that book in R and made them
available at http://wiki.iosa.it/diggingnumbers:start along with the
original dataset, but I was wondering if there is a standard procedure
for getting a new dataset included in the default R distribution, like
"cars" and others.

Please add me to CC if replying because I'm not subscribed to the list.

Best regards,
Stefano

</description>
    <dc:creator>Stefano Costa</dc:creator>
    <dc:date>2008-12-03T10:29:13</dc:date>
  </item>
  <item rdf:about="http://comments.gmane.org/gmane.comp.lang.r.general/133241">
    <title>Buchinsky estimator</title>
    <link>http://comments.gmane.org/gmane.comp.lang.r.general/133241</link>
    <description>Is there a R package available that facilitates estimation of
Buchinsky's two step procedure in order to correct for sample selection
in a quantile regression setting? Thanks in advance for any help.

 

Reference:

 

Moshe Bushinsky (2001) Quantile regression with sample selection:
estimating women's return to education in the US, Empirical Economics,
26, 87-113 .

 

 

Geraint Johnes 
Professor of Economics 
Lancaster University Management School 
Lancaster LA1 4YX 
United Kingdom 
Tel: +44 1524 594215 
Mob: +44 7753 826342 
Fax: +44 1524 594244 
Skype: geraintjohnes 
WWW: http://www.lancs.ac.uk/people/ecagj/ 

 


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

</description>
    <dc:creator>Johnes, Geraint</dc:creator>
    <dc:date>2008-12-03T09:50:31</dc:date>
  </item>
  <item rdf:about="http://comments.gmane.org/gmane.comp.lang.r.general/133240">
    <title>ggplot2 - suggestion for facet_wrap/grid</title>
    <link>http://comments.gmane.org/gmane.comp.lang.r.general/133240</link>
    <description>Hello R users (and Hadley),

facet_wrap and facet_grid function are both very usefull. But they are
perhaps a bit redundant.

I probably don't see the advantage of two separate functions, but what do
you think of this suggestion : add 'nrow' and 'ncol arguments to facet_grid.
These arguments would have an effect only if user draws a 1d ribbon of
panels (~ var1+ ...).

Thank you very much for this wonderfull package.

Best regards.

david

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

</description>
    <dc:creator>David Hajage</dc:creator>
    <dc:date>2008-12-03T09:56:49</dc:date>
  </item>
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    <title>Search Engine</title>
    <description>Search the mailing list at Gmane</description>
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