Re: [R] Google, hard disc drives and R
Tim Churches tchur at optushome.com.au writes: A recent paper from Google Labs, interesting in many respects, not the least the exclusive use of R for data analysis and graphics (alas not cited in the approved manner): http://labs.google.com/papers/disk_failures.pdf ... For all of you who noted that the first author is E. Pinheiro: This is not the first half of D Bates, who's first name is José. Dieter __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Urgent: How to obtain the Consistent Standard Errors after apply 2SLS through tsls() from sem or systemfit(2SLS) without this error message !!!!!!!!!!!!!
Hi, I am trying to obtain the heteroskedasticity consitent standard errors (HCSE) after apply 2SLS. I obtain 2SLS through tsls from package sem or systemfit: tsls library (sem) Reg2SLS -tsls(LnP~Sc+Ag+Ag2+Var+R+D,~I2+Ag+Ag2+Var+R+D) summary (Reg2SLS) systemfit library (systemfit) RS - LnP~Sc+Ag+Ag2+Var+R+D Inst - ~I2+Ag+Ag2+Var+R+D labels -list(RS) system -list(RS) Reg2SLS - systemfit(2SLS, system, labels, Inst, saveMemory=TRUE) summary (Reg2SLS) If I try to obtain the HCSE with robcov I obtain the following error message in both cases: Error in rep.default(1, p) : rep() incorrect type for second argument If I tried to apply vcovHAC or vcovHC in the systemfit output of 2SLS I receive the following messages of errors respectively: Error in estfun(x) : no applicable method for estfun (for vcovHAC) Error in terms.default(object) : no terms component (for vcovHC) If somebody can help me to solve this problem I will thank you a lot. Best regards Guillermo [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Data frame: how to create list of row max?
Dear all, Can anyone please shed some light onto how to do this? This will give me all intensity columsn in my data frame: intensityindeces - grep(^Intensity,names(dataframe),value=TRUE) This will give me the maximum intensity for the first row: intensityone - max(dataframe[1,intensityindeces]) What I'm now looking for is how to dfo this for the whole data frame. Should yield a list of maximum intensities of all rows. Can't figure it out ... please nudge me where I need to go. Thanks, Joh __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Data frame: how to create list of row max?
Johannes Graumann wrote: Dear all, Can anyone please shed some light onto how to do this? This will give me all intensity columsn in my data frame: intensityindeces - grep(^Intensity,names(dataframe),value=TRUE) This will give me the maximum intensity for the first row: intensityone - max(dataframe[1,intensityindeces]) What I'm now looking for is how to dfo this for the whole data frame. Should yield a list of maximum intensities of all rows. Can't figure it out ... please nudge me where I need to go. If you want the values themselves: apply(dataframe[,intensityindeces], 1, max) If you want the column in which the max appears: apply(dataframe[,intensityindeces], 1, which.max) ?apply Thanks, Joh __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Data frame: how to create list of row max?
do.call(pmax, dataframe[,intensityindeces]) if I understand you aright. On Mon, 19 Feb 2007, Johannes Graumann wrote: Dear all, Can anyone please shed some light onto how to do this? This will give me all intensity columsn in my data frame: intensityindeces - grep(^Intensity,names(dataframe),value=TRUE) This will give me the maximum intensity for the first row: intensityone - max(dataframe[1,intensityindeces]) What I'm now looking for is how to dfo this for the whole data frame. Should yield a list of maximum intensities of all rows. Can't figure it out ... please nudge me where I need to go. -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] printing intermediate lines while in a function
I've read the Windows FAQ, I tried flush.console(), but then it continious with the calculations, while I didn't select a range for the graphics. Is there a possibility to wait for user input or something? Thanks Bart From: [EMAIL PROTECTED] To: [EMAIL PROTECTED] CC: r-help@stat.math.ethz.ch Subject: Re: [R] printing intermediate lines while in a function Date: Sun, 18 Feb 2007 17:04:21 -0400 (AST) You're using Windoze, aren't you? You didn't say. See the Windoze-specific FAQ, 7.1. cheers, Rolf Turner [EMAIL PROTECTED] ===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+=== Original message: snip But unfortunately R will do first the calculations and then afterwards return the strings. Is there a way around? __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help with loop over data frame
Try this: DF[c(FALSE, tail(DF$Open, -1) head(DF$High, -1)), ] or using zoo objects just compare the Open to the reverse lag of the High. Lines - Date Open HighLowClose 1/15/2000 10 11 8 10 1/16/2000 12 12 10 11 1/17/2000 12 12 10 11 library(zoo) z - read.zoo(textConnection(Lines), header = TRUE, format = %m/%d/%Y) z[ z[, Open] lag(z[, High],-1), ] On 2/18/07, Dr Remo Sammassimo [EMAIL PROTECTED] wrote: Dear List, This may be the fifth time Ive tried to send this to the list so apologies if there are multiple emails. I need some help getting started with this problem. I have a data frame containing a year of daily stock prices in the following format: Date Open HighLowClose 1/15/2000 10 11 8 10 1/16/2000 12 12 10 11 etc.. I want to create a new data frame which shows only the rows where the column value Open for 'today' is higher than the column value High for the previous day (previous row). How do I loop over each day accessing values from different rows and columns, as is needed here? I have tried 'if' statements but none have worked. Any help appreciated. Regards, Alf Sammassimo Melbourne,Australia __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Rcpp
Hello all,
using GNU WinGW under Windows, I have experimented with the Rcpp package.
Powerful package. Many thanks to Dominick Samperi.
Now I have tried to modify the RccpExample.cpp file in order to calculate two
different moving averages, a simple moving average and an exponential moving
average.
I call the function in R with:
params - list(nobs=10,matype=2)
tempC - .Call(Test_fun,x,params,PACKAGE = RcppTemplate)
where nobs are the number of observation to calculate the moving average and
matype could be 1 for a simple moving average and 2 for an exponential moving
average. x is a dataframe containing the relevant data in the column labeled
Close.
For matype=1 it works fine and the output looks like:
$mab
[1]0.0000.0000.0000.0000.0000.0000.0000.000
0.000 1450.710 1453.658 1459.822 1467.564
[14] 1477.226 1487.114 1495.231 1496.560 1499.667 1498.295 1488.754 1478.958
1469.565 1460.120 1445.006 1429.891 1417.258
[27] 1405.487 1393.141 1384.933 1382.347 1379.085 1370.778 1363.517 1359.175
1364.777 1365.676 1368.880 1370.997 1369.357
[40] 1368.533 1368.512 1374.000 1379.464 1387.269 1387.010 1389.155 1393.638
1400.011 1407.004 1413.114 1421.691 1432.297
[53] 1441.165 1450.033 1456.677 1467.145 1480.899 1495.727 1509.590 1522.596
1534.066 1545.307 1554.237 1561.848 1567.405
[66] 1565.960 1561.789 1557.102 1559.802 1561.216 1563.193 1559.656 1560.993
1558.660 1562.106 1567.487 1569.686 1570.313
[79] 1562.673 1556.586 1548.386 1543.358 1536.041 1532.702 1527.327 1524.134
1526.599 1529.143 1536.038 1542.074 1548.256
[92] 1552.895 1559.588 1567.022 1574.884 1581.358 1585.991 1590.170 1591.420
1590.616
$nobs
[1] 10
$n
[1] 100
But for matype=2 it seems not to work. The output is
$mab
[1] 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36
1483.36 1483.36 1483.36 1483.36 1483.36 1483.36
[16] 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36
1483.36 1483.36 1483.36 1483.36 1483.36 1483.36
[31] 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36
1483.36 1483.36 1483.36 1483.36 1483.36 1483.36
[46] 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36
1483.36 1483.36 1483.36 1483.36 1483.36 1483.36
[61] 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36
1483.36 1483.36 1483.36 1483.36 1483.36 1483.36
[76] 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36
1483.36 1483.36 1483.36 1483.36 1483.36 1483.36
[91] 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36 1483.36
1483.36
$nobs
[1] 10
$n
[1] 100
The modified RcppExpamle.cpp file looks like:
#include Rcpp.hpp
// simple moving average
vectordouble SMAVG(vectordouble data, int nobs, int n) {
int i,j;
double sum;
vectordouble mab(n);
for (i=0;i(n-nobs+1);i++)
{
sum=0.0;
for (j=i;j(i+nobs);j++)
{
sum += data[j];
}
mab[i+nobs-1]=sum/nobs;
}
return mab;
}
// exponential moving average
vectordouble EMAVG(vectordouble data, int nobs, int n) {
int i;
double optInK;
optInK=2/(nobs+1);
vectordouble mab(n);
mab[0] = data[0];
for (i=1;in;i++)
{
mab[i] = ((data[i]-mab[i-1])*optInK) + mab[i-1];
}
return mab;
}
// choose between simple and exponential moving average
RcppExport SEXP Test_fun(SEXP data, SEXP params) {
SEXP rl=R_NilValue;
char* exceptionMesg=NULL;
try{
int i=0;
RcppParams rparam(params);
int nobs = rparam.getIntValue(nobs);
int matype = rparam.getIntValue(matype);
RcppFrame datafm(data);
vectorvectorColDatum table = datafm.getTableData();
int nrow = table.size();
RcppVectordouble close(nrow);
for(int row=0; row nrow; row++) {
close(row)= table[row][4].getDoubleValue();
}
vectordouble stlvec(close.stlVector());
vectordouble res(nrow);
if (matype==1)
{
res = SMAVG(stlvec,nobs,nrow);
}
if (matype==2)
{
res = EMAVG(stlvec,nobs,nrow);
}
RcppVectordouble mab(nrow);
for (i=0; inrow; i++) {
mab(i)=res[i];
}
RcppResultSet rs;
rs.add(mab,mab);
rs.add(nobs,nobs);
rs.add(n,nrow);
rl = rs.getReturnList();
} catch(std::exception ex){
exceptionMesg = copyMessageToR(ex.what());
} catch(...){
exceptionMesg = copyMessageToR(unknown reason);
}
if(exceptionMesg != NULL)
error(exceptionMesg);
return rl;
}
It seems that the problem is in the EMAVG function. I am not an C++ expert,
perhapes I have made a mistake there. Could someone with stonger C++ skills
check this function? Or have I made a mistake by calling the function in the
Test_fun function, which is later called by R?
Besides, is there a more elegant way to access in the Test_fun the Close-Column
of the dataframe data which contains the columns (Date, Open, High, Low, Close,
Volume)?
Best regards
Jaci
--
Feel free - 10 GB Mailbox, 100 FreeSMS/Monat ...
Jetzt
[R] problem in reading TOMS observed ASCII data file
Hello R Users, I have two data sets i) TOMS aerosol optical depth(AOD) and ii) TOMS ozone(O3). AOD data is on 1x1 grid and O3 data is on 5x5 grid. First I want to read AOD and O3 as it is and then I want to regrid AOD on 5x5 grid as O3. Reading is first problem. FIRST PROBLEM READING AOD: AOD data is in following format: # Latitute: 89.5 167 0 0 0 0 0 182 0 0 0 0 0 0 0 0 0 0 0 0 200 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 155 0 0 0 0 0 156 0 0 0 0 0 0 ... Latitude: 88.5 . Lat. . ... .. Latitude: -88.5 180 0 0 0 0 0 182 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 655 0 0 0 0 0 156 0 0 0 0 0 0 .. . ## After each latitude header there is 360 AOD values (1x1 grid). This is monthly mean data. I have many years of data file. So the first problem is how to read the data by omiting latitude header, also data is written along row not along column ? SECOND PROBLEM READING O3: O3 data is in following format: ozone(72,12,324) 72: Longitude -177.5,-172.5,...,177.5' 12: Latitude -27.5,-22.5,...,27.5' 324: Month Jan79,Feb79,,Dec05' ### Month index:0 20.8 22.1 20.0 19.0 16.3 20.0 24.4 23.5 27.9 23.7 0.0 32.4 21.6 23.8 20.4 17.9 16.0 22.2 25.3 25.1 31.1 27.4 0.0 30.3 23.2 23.9 20.7 17.3 16.5 23.1 25.9 25.4 30.4 29.3 0.0 29.9 26.1 24.7 21.3 15.9 16.8 22.8 25.3 25.8 29.8 30.1 0.0 31.6 -- Month index: 323 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - - # 12 columns and 72 rows (latitudexlongitude) THIRD PROBLEM regriding AOD: How to regrid 1x1 AOD data on 5x5 grid as O3. Many thanks for yours help. Regards, Yogesh -- Dr. Yogesh K. Tiwari, Scientist, Indian Institute of Tropical Meteorology, Homi Bhabha Road, Pashan, Pune-411008 INDIA Phone: 0091-99 2273 9513 (Cell) : 0091-20-258 93 600 (O) (Ext.250) Fax: 0091-20-258 93 825 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Data frame: how to create list of row max?
On Monday 19 February 2007 11:53, Prof Brian Ripley wrote:
do.call(pmax, dataframe[,intensityindeces])
Thank you very much for your help!
Any idea why do.call(pmax,list(na.rm=TRUE),dataframe[,intensityindeces])
would give me
Error in if (quote) { : argument is not interpretable as logical
In addition: Warning message:
the condition has length 1 and only the first element will be used in: if
(quote) {
?
Thanks, Joh
pgpgfKKtY5smH.pgp
Description: PGP signature
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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] need help in reading TOMS observed ASCII data file
Hello R Users, I am new to R. I have two data sets i) TOMS aerosol optical depth(AOD) and ii) TOMS ozone(O3). AOD data is on 1x1 grid and O3 data is on 5x5 grid. First I want to read AOD and O3 as it is and then I want to regrid AOD on 5x5 grid as O3. Reading is first problem. FIRST PROBLEM READING AOD: AOD data is in following format: # Latitute: 89.5 167 0 0 0 0 0 182 0 0 0 0 0 0 0 0 0 0 0 0 200 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 155 0 0 0 0 0 156 0 0 0 0 0 0 ... Latitude: 88.5 . Lat. . ... .. Latitude: -88.5 180 0 0 0 0 0 182 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 655 0 0 0 0 0 156 0 0 0 0 0 0 .. . ## After each latitude header there is 360 AOD values (1x1 grid). This is monthly mean data. I have many years of data file. So the first problem is how to read the data by omiting latitude header, also data is written along row not along column ? SECOND PROBLEM READING O3: O3 data is in following format: ozone(72,12,324) 72: Longitude -177.5,-172.5,...,177.5' 12: Latitude -27.5,-22.5,...,27.5' 324: Month Jan79,Feb79,,Dec05' ### Month index:0 20.8 22.1 20.0 19.0 16.3 20.0 24.4 23.5 27.9 23.7 0.0 32.4 21.6 23.8 20.4 17.9 16.0 22.2 25.3 25.1 31.1 27.4 0.0 30.3 23.2 23.9 20.7 17.3 16.5 23.1 25.9 25.4 30.4 29.3 0.0 29.9 26.1 24.7 21.3 15.9 16.8 22.8 25.3 25.8 29.8 30.1 0.0 31.6 -- Month index: 323 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.00.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - - # 12 columns and 72 rows (latitudexlongitude) THIRD PROBLEM regriding AOD: How to regrid 1x1 AOD data on 5x5 grid as O3. Many thanks for yours help. Regards, Yogesh -- Dr. Yogesh K. Tiwari, Scientist, Indian Institute of Tropical Meteorology, Homi Bhabha Road, Pashan, Pune-411008 INDIA Phone: 0091-99 2273 9513 (Cell) : 0091-20-258 93 600 (O) ( Ext.250) Fax: 0091-20-258 93 825 -- Dr. Yogesh K. Tiwari, Scientist 'B', Indian Institute of Tropical Meteorology, Homi Bhabha Road, Pashan, Pune-411008 INDIA Phone: 0091-99 2273 9513 (Cell) : 0091-20-258 93 600 (O) (Ext.250) Fax: 0091-20-258 93 825 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Data frame: how to create list of row max?
On Mon, 19 Feb 2007, Johannes Graumann wrote:
On Monday 19 February 2007 11:53, Prof Brian Ripley wrote:
do.call(pmax, dataframe[,intensityindeces])
Thank you very much for your help!
Any idea why do.call(pmax,list(na.rm=TRUE),dataframe[,intensityindeces])
You want something like
do.call(pmax, c(dataframe[,intensityindeces], list(na.rm=TRUE)))
See ?do.call
would give me
Error in if (quote) { : argument is not interpretable as logical
In addition: Warning message:
the condition has length 1 and only the first element will be used in: if
(quote) {
?
Thanks, Joh
--
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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Data frame: how to create list of row max?
Try do.call(pmax,c(dataframe[,intensityindices],na.rm=TRUE))
This is like the second example in the help page for do.call
On 19/02/07, Johannes Graumann [EMAIL PROTECTED] wrote:
On Monday 19 February 2007 11:53, Prof Brian Ripley wrote:
do.call(pmax, dataframe[,intensityindeces])
Thank you very much for your help!
Any idea why do.call(pmax,list(na.rm=TRUE),dataframe[,intensityindeces])
would give me
Error in if (quote) { : argument is not interpretable as logical
In addition: Warning message:
the condition has length 1 and only the first element will be used in: if
(quote) {
?
Thanks, Joh
__
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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.
--
=
David Barron
Said Business School
University of Oxford
Park End Street
Oxford OX1 1HP
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Re: [R] Google, hard disc drives and R
Tim Churches tchur at optushome.com.au writes: A recent paper from Google Labs, interesting in many respects, not the least the exclusive use of R for data analysis and graphics (alas not cited in the approved manner): http://labs.google.com/papers/disk_failures.pdf Perhaps some of the eminences grises of the R Foundation could prevail upon Google to make some the data reported in the paper available for inclusion in an R library or two, for pedagogical purposes? Tim C After skimming the paper, I can't help wondering why they used barplots with error bars instead of boxplots, and why they broke the data into discrete age groups? Given that they had a relatively large data set (several percent of 100,000 disk drives), they could have done some cool visualization stuff ... Ben Bolker __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Google, hard disc drives and R
On Mon, 19 Feb 2007, Ben Bolker wrote: Tim Churches tchur at optushome.com.au writes: A recent paper from Google Labs, interesting in many respects, not the least the exclusive use of R for data analysis and graphics (alas not cited in the approved manner): http://labs.google.com/papers/disk_failures.pdf Perhaps some of the eminences grises of the R Foundation could prevail upon Google to make some the data reported in the paper available for inclusion in an R library or two, for pedagogical purposes? Tim C After skimming the paper, I can't help wondering why they used barplots with error bars instead of boxplots, and why they broke the data into discrete age groups? Given that they had a relatively large data set (several percent of 100,000 disk drives), they could have done some cool visualization stuff ... For example Mondrian via RServe? Ben Bolker __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Ubuntu Linux and X11
Oleg Sklyar wrote: The problem occurs after updating from Dapper to Edgy. Dapper had font paths: /usr/share/X11/fonts and Edgy, to make the whole font system unified, moved X11 fonts to /usr/share/fonts/X11. Oleg I think I changed the font path in the X config file *and* added a symlink of /usr/share/X11/fonts to point to /usr/share/fonts/X11 in case any other package had this coded into it. Barry __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Data frame: how to create list of row max?
Thanks to you and Brian Ripley. Quite confusing all this ...
Thanks again.
Joh
On Monday 19 February 2007 13:42, David Barron wrote:
Try do.call(pmax,c(dataframe[,intensityindices],na.rm=TRUE))
This is like the second example in the help page for do.call
On 19/02/07, Johannes Graumann [EMAIL PROTECTED] wrote:
On Monday 19 February 2007 11:53, Prof Brian Ripley wrote:
do.call(pmax, dataframe[,intensityindeces])
Thank you very much for your help!
Any idea why
do.call(pmax,list(na.rm=TRUE),dataframe[,intensityindeces]) would give
me
Error in if (quote) { : argument is not interpretable as logical
In addition: Warning message:
the condition has length 1 and only the first element will be used in:
if (quote) {
?
Thanks, Joh
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pgp4utFI3ZYyo.pgp
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[R] categorical column to numeric column
Hi R, Let 'dd' be a data frame given as: dd=data.frame(aa=c(a,a,b,a,b,b),bb=c(1,1,1,2,3,4)) Now I want to create a column 'g' such that if dd$aa=a then dd$g=1 else dd$g= -1 . So, I gave the below syntax: if((dd$aa)==a) dd$g=1 else dd$g= -1 But I get the error message as: Warning message: the condition has length 1 and only the first element will be used in: if ((dd$aa) == a) dd$g = 1 else dd$g = -1 and dd= dd aa bb g 1 a 1 1 2 a 1 1 3 b 1 1 4 a 2 1 5 b 3 1 6 b 4 1 Please let me know what is the error I am doing? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Calculating the Sharpe ratio
Hi useRs,
I am trying to calculate the Sharpe ratio with sharpe of the library
tseries.
The documentation requires the univariate time series to be a
portfolio's cumulated returns. In this case, the example given
data(EuStockMarkets)
dax - log(EuStockMarkets[,FTSE])
is however not the cumulated returns but rather the daily returns of the
FTSE stock index.
Is this way of calculating the Sharpe ratio correct?
Here are my own data:
yearIndexPercentReturns
19851170.091
1986129.90.11
1987149.90.154
1988184.80.233
1989223.10.208
1990223.20
1991220.5-0.012
1992208.1-0.056
1993202.1-0.029
1994203.10.005
1995199.6-0.017
1996208.60.045
1997221.70.063
1998233.70.054
1999250.50.072
2000275.10.098
2001298.60.085
2002350.60.174
2003429.10.224
2004507.60.183
2005536.60.057
2006581.30.083
I calculated the Sharpe ratio in two different ways:
(1) using natural logs as approximation of % returns, using sharpe of
tseries.
(2) using the % returns using a variation the sharpe function.
In both cases I used the risk free rate r=0 and scale=1 since I am using
annual data already.
My results:
METHOD 1: sharpe:
index - log(Index)
sharpe(index, scale=1)
[1] 0.9614212
METHOD 2: my own %-based formula:
mysharp
function(x, r=0, scale=sqrt(250))
{
if (NCOL(x) 1)
stop(x is not a vector or univariate time series)
if (any(is.na(x)))
stop(NAs in x)
if (NROW(x) ==1)
return(NA)
else{
return(scale * (mean(x) - r)/sd(x))
}
}
mysharp(PercentReturns, scale=1)
[1] 0.982531
Both Sharp ratios differ only slightly since logs approximate percentage
changes (returns).
Are both methods correct, esp. since I am NOT using cumulated returns as
the manual says?
If cumulated returns were supposed to be used, could I cumulate the
%-returns with cumsum(PercentReturns)?
Many thanks in advance!
Bernd
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[R] Start and Restart R over SSH
Hi, I have some big calculations in R to be done. Since I can use R on a server with ssh, i was wondering if I can reopen a R Shell after exiting ssh. I don't want to use the batch mode and nohup doesn't work. I want to use something like ssh [EMAIL PROTECTED] R ---do something in R and start calculation --- close ssh but let R remain on the server, doing the calculation ssh [EMAIL PROTECTED] open the existing R Shell / Process Has anyone done something similiar? Can you help me or suggest an other solution ? Thank you for your help Nils __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] categorical column to numeric column
Maybe this isn't the most elegant way, but it should work. dd$g - -1 dd$g[dd$aa == a] - 1 Cheers, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Reseach Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 [EMAIL PROTECTED] www.inbo.be Do not put your faith in what statistics say until you have carefully considered what they do not say. ~William W. Watt A statistical analysis, properly conducted, is a delicate dissection of uncertainties, a surgery of suppositions. ~M.J.Moroney -Oorspronkelijk bericht- Van: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Namens Shubha Vishwanath Karanth Verzonden: maandag 19 februari 2007 14:36 Aan: r-help Onderwerp: [R] categorical column to numeric column Hi R, Let 'dd' be a data frame given as: dd=data.frame(aa=c(a,a,b,a,b,b),bb=c(1,1,1,2,3,4)) Now I want to create a column 'g' such that if dd$aa=a then dd$g=1 else dd$g= -1 . So, I gave the below syntax: if((dd$aa)==a) dd$g=1 else dd$g= -1 But I get the error message as: Warning message: the condition has length 1 and only the first element will be used in: if ((dd$aa) == a) dd$g = 1 else dd$g = -1 and dd= dd aa bb g 1 a 1 1 2 a 1 1 3 b 1 1 4 a 2 1 5 b 3 1 6 b 4 1 Please let me know what is the error I am doing? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] categorical column to numeric column
On 2/19/2007 8:36 AM, Shubha Vishwanath Karanth wrote: Hi R, Let 'dd' be a data frame given as: dd=data.frame(aa=c(a,a,b,a,b,b),bb=c(1,1,1,2,3,4)) Now I want to create a column 'g' such that if dd$aa=a then dd$g=1 else dd$g= -1 . So, I gave the below syntax: if((dd$aa)==a) dd$g=1 else dd$g= -1 if() looks at just the first entry; it's designed for flow of control rather than vectorized calculations. You want ifelse(): ifelse( dd$aa == a, 1, -1) Duncan Murdoch But I get the error message as: Warning message: the condition has length 1 and only the first element will be used in: if ((dd$aa) == a) dd$g = 1 else dd$g = -1 and dd= dd aa bb g 1 a 1 1 2 a 1 1 3 b 1 1 4 a 2 1 5 b 3 1 6 b 4 1 Please let me know what is the error I am doing? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] categorical column to numeric column
try dd$g - ifelse(dd$aa==a,1,-1) and in general, you can convert categorical data (factors) into integers with as.integer(), though the values will be positive: dd$f - as.integer(factor(dd$aa)) --- Shubha Vishwanath Karanth [EMAIL PROTECTED] wrote: Hi R, Let 'dd' be a data frame given as: dd=data.frame(aa=c(a,a,b,a,b,b),bb=c(1,1,1,2,3,4)) Now I want to create a column 'g' such that if dd$aa=a then dd$g=1 else dd$g= -1 . So, I gave the below syntax: if((dd$aa)==a) dd$g=1 else dd$g= -1 But I get the error message as: Warning message: the condition has length 1 and only the first element will be used in: if ((dd$aa) == a) dd$g = 1 else dd$g = -1 and dd= dd aa bb g 1 a 1 1 2 a 1 1 3 b 1 1 4 a 2 1 5 b 3 1 6 b 4 1 Please let me know what is the error I am doing? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. TV dinner still cooling? Check out Tonight's Picks on Yahoo! TV. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Documenting options specific to a package.
If one specifies new options in a package, using the options() function, where does/should one document these new options? E.g. suppose that I put the line options(melvin=42) in a file zzz.R in the R directory of the package source, where the package contains functions foo(), bar(), clyde(), and irving() which all query options(melvin) and take some action based on the value of ``melvin''. The user can of course change the value of ``melvin'' from its default value by doing, e.g. options(melvin=99) Are there any conventions or standards as to how and where the option ``melvin'' should be documented? It seems somewhat redundant to include docmentation about melvin in the help on all 4 of foo(), bar(), clyde(), and irving(). Thanks for any insights. cheers, Rolf Turner [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] User defined split function in rpart
Maybe I should explain my Problem a little bit more detailed.
The rpart package allows for user defined split functions. An example is
given in the source/test directory of the package as usersplits.R.
The comments say that three functions have to be supplied:
1. The 'evaluation' function. Called once per node.
Produce a label (1 or more elements long) for labeling each node,
and a deviance.
2. The split function, where most of the work occurs.
Called once per split variable per node.
3. The init function:
fix up y to deal with offsets
return a dummy parms list
numresp is the number of values produced by the eval routine's label.
I have altered the evaluation function and the split function for my needs.
Within those functions, I need to fit a proportional odds model to the data
of the current node. I am using the polr() routine from the MASS package to
fit the model.
Now my problem is, how can I call the polr() function only with the data of
the current node. That's what I tried so far:
evalfunc - function(y,x,parms,data) {
pomnode-polr(data$y~data$x,data,weights=data$Freq)
parprobs-predict(pomnode,type=probs)
dev-0
K-dim(parprobs)[2]
N-dim(parprobs)[1]/K
for(i in 1:N){
tempsum-0
Ni-0
for(l in 1:K){
Ni-Ni+data$Freq[K*(i-1)+l]
}
for(j in 1:K){
tempsum-tempsum+data$Freq[K*(i-1)+j]/Ni*log(parprobs[i,j]*Ni/data$Freq[K*(i
-1)+j])
}
dev=dev+Ni*tempsum
}
dev=-2*dev
wmean-1
list(label= wmean, deviance=dev)
}
I get the error: Error in eval(expr, envir, enclos) : argument data is
missing, with no default
How can I use the data of the current node?
Thank you
Tobias Guennel
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Re: [R] Start and Restart R over SSH
On 2/19/07, Nils Höller [EMAIL PROTECTED] wrote: Hi, I have some big calculations in R to be done. Since I can use R on a server with ssh, i was wondering if I can reopen a R Shell after exiting ssh. I don't want to use the batch mode and nohup doesn't work. I want to use something like ssh [EMAIL PROTECTED] R ---do something in R and start calculation --- close ssh but let R remain on the server, doing the calculation ssh [EMAIL PROTECTED] open the existing R Shell / Process Has anyone done something similiar? Can you help me or suggest an other solution ? I don't think it is possible to reattach to a process started in one ssh session from another ssh session. However, you can put a session into the background with the -f flag to ssh. You haven't told us what operating system you are starting the ssh connection on and what system will run the R process. If I had an X server running on the local system and the remote system provided X clients like xterm I would do this by ssh -X -f [EMAIL PROTECTED] xterm This should spring up an autonomous xterm window on the local machine after which you can run R in it. I hope this helps. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Need to find most likely betas
Hello, I have a particular situation where a single wrong observation is impacting the results of a traditional regression to the point that betas become unreliable. I need a way to calculate the most likely betas. Here's an example: set.seed(1) unknownbeta - matrix(seq(100,500,100),25,5,byrow=TRUE) x -matrix(runif(25*5),25) y - rowSums(unknownbeta*x) summary(lm(y~0+x)) #gets back the unknown betas. #Now, let's introduce a single wrong data. unknownbeta[25,5] -100 y - rowSums(unknownbeta*x) summary(lm(y~0+x)) #every beta changes. I need to find out what are the most likely betas in the second example. There is no obvious way to know that row 25 has wrong input. I would even be happy if the conclusion was that x1:x4 are 100, 200, 300 and 400 and that x5 is zero. Thanks __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] categorical column to numeric column
Let 'dd' be a data frame given as: dd=data.frame(aa=c(a,a,b,a,b,b),bb=c(1,1,1,2,3,4)) Now I want to create a column 'g' such that if dd$aa=a then dd$g=1 else dd$g= -1 . You need to use ifelse instead of the if ... else construction: dd$g = ifelse(dd$a=='a', 1, -1) cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany and Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675 GSF - National Research Center Fax. +49-89-3187 3585 for Environment and Health Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Start and Restart R over SSH
Douglas Bates wrote: On 2/19/07, Nils Höller [EMAIL PROTECTED] wrote: Hi, I have some big calculations in R to be done. Since I can use R on a server with ssh, i was wondering if I can reopen a R Shell after exiting ssh. I don't want to use the batch mode and nohup doesn't work. I want to use something like ssh [EMAIL PROTECTED] R ---do something in R and start calculation --- close ssh but let R remain on the server, doing the calculation ssh [EMAIL PROTECTED] open the existing R Shell / Process Has anyone done something similiar? Can you help me or suggest an other solution ? I don't think it is possible to reattach to a process started in one ssh session from another ssh session. However, you can put a session No, it is. Check out the screen command - it is backgrounding your session, you can have several running at the same time and reattach and they persist between logouts (obviously, if you switch the computer of, it is gone...) Rainer into the background with the -f flag to ssh. You haven't told us what operating system you are starting the ssh connection on and what system will run the R process. If I had an X server running on the local system and the remote system provided X clients like xterm I would do this by ssh -X -f [EMAIL PROTECTED] xterm This should spring up an autonomous xterm window on the local machine after which you can run R in it. I hope this helps. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)86 516 2782 Fax:+27 - (0)21 808 3304 (w) Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Another subsetting enigma
Hello again, I'm trying to do the following: subset(dataframe,list %in% strsplit(dataframe[[Field]],,)) But This returns always the complete dataframe, since the strsplit(dataframe[[Field]],,) is evaluated as one big list for the whole data frame rather than one list per row. How can I have this evaluated on a per row basis? After 1.5 h hitting head against wall - begging for insights ... Joh __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Start and Restart R over SSH
Hi Nils, if the server you're using is *NIX, this is what you can do: example ssh [EMAIL PROTECTED] screen R do what you need in R close the terminal without quitting R ssh [EMAIL PROTECTED] screen -r continue working in R %% end example the problem is if you need X... it works until you quit the terminal, but screen -r doesn't reconnect the X11. b On Feb 19, 2007, at 9:40 AM, Douglas Bates wrote: On 2/19/07, Nils Höller [EMAIL PROTECTED] wrote: Hi, I have some big calculations in R to be done. Since I can use R on a server with ssh, i was wondering if I can reopen a R Shell after exiting ssh. I don't want to use the batch mode and nohup doesn't work. I want to use something like ssh [EMAIL PROTECTED] R ---do something in R and start calculation --- close ssh but let R remain on the server, doing the calculation ssh [EMAIL PROTECTED] open the existing R Shell / Process Has anyone done something similiar? Can you help me or suggest an other solution ? I don't think it is possible to reattach to a process started in one ssh session from another ssh session. However, you can put a session into the background with the -f flag to ssh. You haven't told us what operating system you are starting the ssh connection on and what system will run the R process. If I had an X server running on the local system and the remote system provided X clients like xterm I would do this by ssh -X -f [EMAIL PROTECTED] xterm This should spring up an autonomous xterm window on the local machine after which you can run R in it. I hope this helps. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Start and Restart R over SSH
Hi, You can take a look at GNU screen programm: http://www.gnu.org/software/screen/ Andris Jankevics On Pirmdiena, 19. Februāris 2007 15:56, Nils Höller wrote: Hi, I have some big calculations in R to be done. Since I can use R on a server with ssh, i was wondering if I can reopen a R Shell after exiting ssh. I don't want to use the batch mode and nohup doesn't work. I want to use something like ssh [EMAIL PROTECTED] R ---do something in R and start calculation --- close ssh but let R remain on the server, doing the calculation ssh [EMAIL PROTECTED] open the existing R Shell / Process Has anyone done something similiar? Can you help me or suggest an other solution ? Thank you for your help Nils __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Documenting options specific to a package.
(An R-devel topic, I believe.)
I would have documentation for options() in the package that documented
the additional options and linked to \code{\link[base]{options}}.
Users will be given a choice of which page to view on most systems, so
just make sure the title makes clear that this is options for the package.
On Mon, 19 Feb 2007, [EMAIL PROTECTED] wrote:
If one specifies new options in a package, using the options()
function, where does/should one document these new options?
E.g. suppose that I put the line
options(melvin=42)
in a file zzz.R in the R directory of the package source, where the
package contains functions foo(), bar(), clyde(), and irving() which
all query options(melvin) and take some action based on the value
of ``melvin''. The user can of course change the value of ``melvin''
from its default value by doing, e.g.
options(melvin=99)
Are there any conventions or standards as to how and where the option
``melvin'' should be documented? It seems somewhat redundant to
include docmentation about melvin in the help on all 4 of foo(),
bar(), clyde(), and irving().
Thanks for any insights.
cheers,
Rolf Turner
[EMAIL PROTECTED]
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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.
--
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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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Start and Restart R over SSH
Nils Höller wrote: Hi, I have some big calculations in R to be done. Since I can use R on a server with ssh, i was wondering if I can reopen a R Shell after exiting ssh. I don't want to use the batch mode and nohup doesn't work. I want to use something like ssh [EMAIL PROTECTED] R ---do something in R and start calculation --- close ssh but let R remain on the server, doing the calculation ssh [EMAIL PROTECTED] open the existing R Shell / Process Has anyone done something similiar? Can you help me or suggest an other solution ? Use screen http://www.gnu.org/software/screen/ 1. Login to remote server 2. Run screen 3. Run R, and the long calculation 4. Detach screen (Ctrl-A, Ctrl-D) 5. Logout Then you may login to server again, re-attach to the running screen and carry on! Best wishes, Mark -- Specialist Registrar and Clinical research fellow Department of Neurology Cardiff Vale NHS Trust and Cardiff University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] summary polr
Hi all, I have a problem to estimate Std. Error and t-value by “polr” in library Mass. They result from the summary of a polr object. I can obtain them working in the R environment with the following statements: temp - polr(formula = formula1, data = data1) coeff - summary(temp), but when the above statements are enclosed in a function, summary reports the following error: Error in eval(expr, envir, enclos) : object dat not found Someone knows how I can solve the problem? Thanks for any help. Paolo __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Start and Restart R over SSH
On Mon, 19 Feb 2007, Benilton Carvalho wrote: Hi Nils, if the server you're using is *NIX, this is what you can do: example ssh [EMAIL PROTECTED] screen R do what you need in R close the terminal without quitting R ssh [EMAIL PROTECTED] screen -r continue working in R %% end example the problem is if you need X... it works until you quit the terminal, but screen -r doesn't reconnect the X11. I find vnc sometimes helps with keeping a X active for an R session. Also, if you take care to close your x11 devices, and if when you re-ssh you happen to get the same forwarded X DISPLAY=localhost:11.0 or whatever, the R session in screen will use the new forwarded connection. It also seems like using Sys.putenv(DISPLAY='localhost:11.0') overrides the DISPLAY that screen's child R session inherits from the initial invocation of screen. Dave -- Dr. David Forrest [EMAIL PROTECTED](804)684-7900w [EMAIL PROTECTED] (804)642-0662h http://maplepark.com/~drf5n/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] need help in reading TOMS observed ASCII data file
Here is a script that will read in you O3 data. It assumes that the data is
perfect. You will have to either prescan the data for errors, or add code
to catch them.
# setup to read your file
# this procedure works if the data is 'perfect'; it does not catch errors
# 'result' is a list of matrices of the data
f.1 - file(/jph/r-help/TOMS_O3.txt, r)
result - list()
while(length(month - readLines(f.1, n=1))){
+ # read in 12*72 real numbers from the file after reading the 'month'
header
+ data.in - matrix(scan(f.1, what=0, n=12*72), ncol=12, byrow=TRUE)
+ # extract just the number and use it as the index into the list to
save the matrix
+ result[[gsub(.*(\\d file://d/+), \\1 file://0.0.0.1/, month,
perl=TRUE)]] - data.in
+ }
Read 864 items
Read 864 items
Read 864 items
Read 864 items
str(result)
List of 4
$ 0: num [1:72, 1:12] 20.8 21.6 23.2 26.1 26.2 29 22.2 18.5 19 20.5 ...
$ 1: num [1:72, 1:12] 22.7 22.4 20.4 19.7 16.9 20.8 24 25.1 24.7 24.7 ...
$ 2: num [1:72, 1:12] 25.4 24.6 27 28 29.9 33.3 32.4 28.2 24.5 21.6 ...
$ 3: num [1:72, 1:12] 31 31 31 30 30.1 27.4 20.5 19 18.8 19.2 ...
On 2/19/07, Yogesh Tiwari [EMAIL PROTECTED] wrote:
Hello R Users,
I am new to R.
I have two data sets i) TOMS aerosol optical depth(AOD) and ii) TOMS
ozone(O3).
AOD data is on 1x1 grid and O3 data is on 5x5 grid.
First I want to read AOD and O3 as it is and then I want to regrid AOD
on
5x5 grid as O3.
Reading is first problem.
FIRST PROBLEM READING AOD:
AOD data is in following format:
#
Latitute: 89.5
167 0 0 0 0 0 182 0 0 0 0 0 0 0 0 0 0 0 0 200 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 155 0 0 0 0 0 156 0 0 0 0 0 0
...
Latitude: 88.5
.
Lat.
.
...
..
Latitude: -88.5
180 0 0 0 0 0 182 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 655 0 0 0 0 0 156 0 0 0 0 0 0
..
.
##
After each latitude header there is 360 AOD values (1x1 grid). This is
monthly mean data. I have many years of data file.
So the first problem is how to read the data by omiting latitude header,
also data is written along row not along column ?
SECOND PROBLEM READING O3:
O3 data is in following format:
ozone(72,12,324)
72: Longitude -177.5,-172.5,...,177.5'
12: Latitude -27.5,-22.5,...,27.5'
324: Month Jan79,Feb79,,Dec05'
###
Month index:0
20.8 22.1 20.0 19.0 16.3 20.0 24.4 23.5 27.9 23.7 0.0 32.4
21.6 23.8 20.4 17.9 16.0 22.2 25.3 25.1 31.1 27.4 0.0 30.3
23.2 23.9 20.7 17.3 16.5 23.1 25.9 25.4 30.4 29.3 0.0
29.9
26.1 24.7 21.3 15.9 16.8 22.8 25.3 25.8 29.8 30.1 0.0 31.6
--
Month index: 323
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.00.0 0.0 0.0 0.0
0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
-
-
#
12 columns and 72 rows (latitudexlongitude)
THIRD PROBLEM regriding AOD:
How to regrid 1x1 AOD data on 5x5 grid as O3.
Many thanks for yours help.
Regards,
Yogesh
--
Dr. Yogesh K. Tiwari,
Scientist,
Indian Institute of Tropical Meteorology,
Homi Bhabha Road,
Pashan,
Pune-411008
INDIA
Phone: 0091-99 2273 9513 (Cell)
: 0091-20-258 93 600 (O) ( Ext.250)
Fax: 0091-20-258 93 825
--
Dr. Yogesh K. Tiwari,
Scientist 'B',
Indian Institute of Tropical Meteorology,
Homi Bhabha Road,
Pashan,
Pune-411008
INDIA
Phone: 0091-99 2273 9513 (Cell)
: 0091-20-258 93 600 (O) (Ext.250)
Fax: 0091-20-258 93 825
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--
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Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
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Re: [R] advanced plotting
try: plot(..., type='p',pch='.',...) you can also use the cex parameter to change the size of points. Also, look at the hexbin package for an alternative. Hope this helps, From: [EMAIL PROTECTED] on behalf of downunder Sent: Tue 11/21/2006 1:55 PM To: r-help@stat.math.ethz.ch Subject: [R] advanced plotting Hi all. I need some help. I have to plot so many observation in a coordinate system that you can't see really much. Is there any possiblilty in R to reduce the size of a plotted point? In the plot command i could find a solution. plot(,type = p ,..) thanks in advance lars -- View this message in context: http://www.nabble.com/-R--advanced-plotting-tf2681625.html#a7479700 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] advanced plotting
Also try the 'hexbin' package which is a good way of showing the 'density' of the points. On 2/19/07, Greg Snow [EMAIL PROTECTED] wrote: try: plot(..., type='p',pch='.',...) you can also use the cex parameter to change the size of points. Also, look at the hexbin package for an alternative. Hope this helps, From: [EMAIL PROTECTED] on behalf of downunder Sent: Tue 11/21/2006 1:55 PM To: r-help@stat.math.ethz.ch Subject: [R] advanced plotting Hi all. I need some help. I have to plot so many observation in a coordinate system that you can't see really much. Is there any possiblilty in R to reduce the size of a plotted point? In the plot command i could find a solution. plot(,type = p ,..) thanks in advance lars -- View this message in context: http://www.nabble.com/-R--advanced-plotting-tf2681625.html#a7479700 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html 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? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Help for constrained linear regression
Hello, I am trying to run a constrained linear regression of a dependent variable y on three explanatory variables x1, x2, and x3. However, I need to constrain the coefficients of the explanatory variables as follows: b10, b20, and b30. Does anyone know how to do this within the lm/glm framework so that one can still ask for statistics like the r-squared and t-ratios (I realize that in this case t-stats may be harder to compute than usual and may not be available from the lm/glm object)? Any help would be greatly appreciated Spyros __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Another subsetting enigma
On Mon, 2007-02-19 at 16:13 +0100, Johannes Graumann wrote: Hello again, I'm trying to do the following: subset(dataframe,list %in% strsplit(dataframe[[Field]],,)) But This returns always the complete dataframe, since the strsplit(dataframe[[Field]],,) is evaluated as one big list for the whole data frame rather than one list per row. How can I have this evaluated on a per row basis? After 1.5 h hitting head against wall - begging for insights ... Joh I may be misunderstanding your desired end result, but what about: subset(dataframe,list %in% strsplit(Field, ,)) This way 'Field' is evaluated within the data frame (default behavior for 'subset') on a row-wise basis, rather than passing the entire column. This entire process also presumes that 'Field' has embedded commas, delimiting component entries. If not, then strsplit() is not required. HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Need to find most likely betas
On Mon, 2007-02-19 at 09:58 -0500, Pierre Lapointe wrote: Hello, I have a particular situation where a single wrong observation is impacting the results of a traditional regression to the point that betas become unreliable. I need a way to calculate the most likely betas. Here's an example: set.seed(1) unknownbeta - matrix(seq(100,500,100),25,5,byrow=TRUE) x -matrix(runif(25*5),25) y - rowSums(unknownbeta*x) summary(lm(y~0+x)) #gets back the unknown betas. #Now, let's introduce a single wrong data. unknownbeta[25,5] -100 y - rowSums(unknownbeta*x) summary(lm(y~0+x)) #every beta changes. I need to find out what are the most likely betas in the second example. There is no obvious way to know that row 25 has wrong input. I would even be happy if the conclusion was that x1:x4 are 100, 200, 300 and 400 and that x5 is zero. Thanks It is not clear what you mean by a wrong observation. Is the data completely bad because it was improperly collected? Is this an observation that has correct data, but is an outlier relative to the other observations? Is the observation missing data, where values can be reasonably imputed? Are you in a setting where the observation MUST be included in the regression rather than be deleted? For example an Intent to Treat analysis in a clinical trial? Depending upon the context, your options may range from simply removing the single observation from the regression, considering some form of weighting of the observations, to perhaps considering a robust regression methodology and others. This is not strictly an R question, but one of methodology. Clarification of which is potentially impacted upon by community standards and prior work within your particular discipline. HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Another subsetting enigma
On Monday 19 February 2007 17:49, jim holtman wrote: have you tried 'unlist(strsplit())'?The 'unlist' will probably give you more values than you have rows, so it would be good if you could explain what it is you are trying to do. I want to isolate a data frame containing all rows of 'dataframe' which contain a member of 'list' in the field 'Field', which itself is a comma separated list of entries. Better this (know in brain ...)? Joh On 2/19/07, Johannes Graumann [EMAIL PROTECTED] wrote: Hello again, I'm trying to do the following: subset(dataframe,list %in% strsplit(dataframe[[Field]],,)) But This returns always the complete dataframe, since the strsplit(dataframe[[Field]],,) is evaluated as one big list for the whole data frame rather than one list per row. How can I have this evaluated on a per row basis? After 1.5 h hitting head against wall - begging for insights ... Joh __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. pgp7XFEEUi9oM.pgp Description: PGP signature __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] multiple comparisons
Dear R users, I need a professional help: i am a relatively new R user and I am just writing my diploma tesis where I have to conduct some multiple comparison. I am searching a method which include interaction between fixed factors. The following is my model: lmer(Leaf~water*region+(1|pop)+(1|pop:sib)+(1|block)+(1|block:pool),data=datx,method=ML) I want to compare: leaf dependent from water * region. I would prefer to make a comparision according to tukey or student newman keuls if this is possible. I am looking forward to your reply, sincerely Petra:-) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Another subsetting enigma
try this:
my.list - c(7,12,3)# set of matching numbers
set.seed(1)
result - character(40) # create empty vector
# create some comma separated data
for(i in 1:40) result[i] - paste(sample(1:20,6), collapse=',')
# just leave it as a character vector for testing == you can convert your
data frame
str(result)
chr [1:40] 6,8,11,16,4,14 19,13,12,2,4,3 14,8,20,9,12,15
8,15,17,4,11,2 ...
# find matching entries
matches - sapply(result, function(x){
+ .comma - strsplit(x, ',')[[1]] # get the fields
+ any(my.list %in% .comma)
+ })
# print matching entries
result[matches]
[1] 19,13,12,2,4,3 14,8,20,9,12,15 6,8,1,7,14,20
10,12,9,4,14,11 16,3,14,7,18,10
[6] 2,20,6,9,11,77,20,9,16,14,6 16,19,8,13,7,5
16,4,13,3,19,17 5,2,12,15,13,18
[11] 6,19,12,4,3,819,12,18,13,6,7 3,1,13,2,8,10
20,10,9,3,13,7 13,11,6,8,9,3
[16] 15,7,12,20,14,6 8,18,12,13,10,14 6,4,16,9,15,3
16,14,17,10,12,6 3,18,6,11,2,13
[21] 7,15,5,4,9,184,10,11,3,5,18 13,19,18,6,5,3
7,10,17,9,5,19,17,7,3,6,10
[26] 8,14,13,10,7,16
On 2/19/07, Johannes Graumann [EMAIL PROTECTED] wrote:
On Monday 19 February 2007 17:49, jim holtman wrote:
have you tried 'unlist(strsplit())'?The 'unlist' will probably
give
you more values than you have rows, so it would be good if you could
explain what it is you are trying to do.
I want to isolate a data frame containing all rows of 'dataframe' which
contain a member of 'list' in the field 'Field', which itself is a comma
separated list of entries.
Better this (know in brain ...)?
Joh
On 2/19/07, Johannes Graumann [EMAIL PROTECTED] wrote:
Hello again,
I'm trying to do the following:
subset(dataframe,list %in% strsplit(dataframe[[Field]],,))
But This returns always the complete dataframe, since the
strsplit(dataframe[[Field]],,) is evaluated as one big list for the
whole
data frame rather than one list per row. How can I have this evaluated
on
a
per row basis?
After 1.5 h hitting head against wall - begging for insights ...
Joh
__
R-help@stat.math.ethz.ch 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.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
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[R] Lengend function and moving average plot
Sir I am very new user of R. I am not understanding the how to write the plot description in box outside the plot. And how we can plot the moving averages on the plot having regression line and time series. Please guide me in this regard AMINA GC University, Lahore [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] memory management uestion
Hi All,
I would like to ask the following.
I have an array of data in an objetct, let's say X.
I need to use a for loop on the elements of one or more columns of X and I am
having a debate with a colleague about the best memory management.
I believe that if I do:
col1 = X[,1]
col2 = X[,2]
...
colx = X[,x]
and then
for(i in whatever){
do something using col1[i], col2[i] ... colx[i]
}
my memory management is better that doing:
for(i in whatever){
do something using X[i,1], X[i,2] ... X[,x]
}
BTW, here I *have to* use a for() loop an no nifty tapply, lapply and family.
Any comment is welcome.
Best,
Fede
--
Federico C. F. Calboli
Department of Epidemiology and Public Health
Imperial College, St Mary's Campus
Norfolk Place, London W2 1PG
Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193
f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com
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Re: [R] Need to find most likely betas
Hi Mark, In my example, there has been a regime change at time 25 and I'd like to find a way to discover 1- what has changed and 2- when it did. The problem is all that is observed are the x and y values. unknownbetas are... unknown. If you look at x and y, you can't really tell something has changed. It is not an outlier per se as it involves a change of one of the unknownbetas. In other words, I'm trying to single out which unknownbetas vs. x relationships still hold after time 25. I know it's complicated, but I you have any pointers, it will be appreciated. Thanks On 2/19/07, Marc Schwartz [EMAIL PROTECTED] wrote: On Mon, 2007-02-19 at 09:58 -0500, Pierre Lapointe wrote: Hello, I have a particular situation where a single wrong observation is impacting the results of a traditional regression to the point that betas become unreliable. I need a way to calculate the most likely betas. Here's an example: set.seed(1) unknownbeta - matrix(seq(100,500,100),25,5,byrow=TRUE) x -matrix(runif(25*5),25) y - rowSums(unknownbeta*x) summary(lm(y~0+x)) #gets back the unknown betas. #Now, let's introduce a single wrong data. unknownbeta[25,5] -100 y - rowSums(unknownbeta*x) summary(lm(y~0+x)) #every beta changes. I need to find out what are the most likely betas in the second example. There is no obvious way to know that row 25 has wrong input. I would even be happy if the conclusion was that x1:x4 are 100, 200, 300 and 400 and that x5 is zero. Thanks It is not clear what you mean by a wrong observation. Is the data completely bad because it was improperly collected? Is this an observation that has correct data, but is an outlier relative to the other observations? Is the observation missing data, where values can be reasonably imputed? Are you in a setting where the observation MUST be included in the regression rather than be deleted? For example an Intent to Treat analysis in a clinical trial? Depending upon the context, your options may range from simply removing the single observation from the regression, considering some form of weighting of the observations, to perhaps considering a robust regression methodology and others. This is not strictly an R question, but one of methodology. Clarification of which is potentially impacted upon by community standards and prior work within your particular discipline. HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Help on prediction intervals
I am trying to estimate prediction intervals for wind power production, it is a times series of wind power production. Im using neural networks for prediction, but I need to estimate the uncertainly in the prediction. How can I do this in R if I have a probability distribution that is right skewness. One tip is to use bootstrap but I dont know if is possible with this method to estimate those intervals. Any help would be greatly appreciated Ricardo Bessa __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Need to find most likely betas
Pierre, Unfortunately, I don't have much in the way of hands on experience with these, but conceptually, latent variable analysis/SEM methods seem like they might be apropos. If so, John Fox' SEM package might be of value here. More information here: http://socserv.mcmaster.ca/jfox/Misc/sem/index.html Since you mention time, if this is a repeated measures based approach, then you might want to look at lmer(), for which there is a recently created SIG list. More information is at: https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models Perhaps others will jump in with additional thoughts. HTH, Marc On Mon, 2007-02-19 at 13:32 -0500, Pierre Lapointe wrote: Hi Mark, In my example, there has been a regime change at time 25 and I'd like to find a way to discover 1- what has changed and 2- when it did. The problem is all that is observed are the x and y values. unknownbetas are... unknown. If you look at x and y, you can't really tell something has changed. It is not an outlier per se as it involves a change of one of the unknownbetas. In other words, I'm trying to single out which unknownbetas vs. x relationships still hold after time 25. I know it's complicated, but I you have any pointers, it will be appreciated. Thanks On 2/19/07, Marc Schwartz [EMAIL PROTECTED] wrote: On Mon, 2007-02-19 at 09:58 -0500, Pierre Lapointe wrote: Hello, I have a particular situation where a single wrong observation is impacting the results of a traditional regression to the point that betas become unreliable. I need a way to calculate the most likely betas. Here's an example: set.seed(1) unknownbeta - matrix(seq(100,500,100),25,5,byrow=TRUE) x -matrix(runif(25*5),25) y - rowSums(unknownbeta*x) summary(lm(y~0+x)) #gets back the unknown betas. #Now, let's introduce a single wrong data. unknownbeta[25,5] -100 y - rowSums(unknownbeta*x) summary(lm(y~0+x)) #every beta changes. I need to find out what are the most likely betas in the second example. There is no obvious way to know that row 25 has wrong input. I would even be happy if the conclusion was that x1:x4 are 100, 200, 300 and 400 and that x5 is zero. Thanks It is not clear what you mean by a wrong observation. Is the data completely bad because it was improperly collected? Is this an observation that has correct data, but is an outlier relative to the other observations? Is the observation missing data, where values can be reasonably imputed? Are you in a setting where the observation MUST be included in the regression rather than be deleted? For example an Intent to Treat analysis in a clinical trial? Depending upon the context, your options may range from simply removing the single observation from the regression, considering some form of weighting of the observations, to perhaps considering a robust regression methodology and others. This is not strictly an R question, but one of methodology. Clarification of which is potentially impacted upon by community standards and prior work within your particular discipline. HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Installing Package rgl - Compilation Fails
I'm running R 2.4.1 (with the latest versions of all packages) on an FC6 32-bit system. When I try to install the rgl package, compilation fails: install.packages(rgl) --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/rgl_0.70.tar.gz' Content type 'application/x-gzip' length 705556 bytes opened URL == downloaded 689Kb * Installing *source* package 'rgl' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking for X... libraries , headers checking for libpng-config... yes configure: using libpng-config configure: using libpng dynamic linkage configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -I/usr/lib/R/include -I/usr/lib/R/include -I -DHAVE_PNG_H -I/usr/include/libpng12 -Iext -I/usr/local/include-fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -c api.cpp -o api.o In file included from glgui.hpp:9, from gui.hpp:11, from rglview.h:10, from Device.hpp:11, from DeviceManager.hpp:9, from api.cpp:14: opengl.hpp:24:20: error: GL/glu.h: No such file or directory Disposable.hpp:13: warning: ‘struct IDisposeListener’ has virtual functions but non-virtual destructor types.h:77: warning: ‘class DestroyHandler’ has virtual functions but non-virtual destructor gui.hpp:56: warning: ‘class gui::WindowImpl’ has virtual functions but non-virtual destructor gui.hpp:90: warning: ‘class gui::GUIFactory’ has virtual functions but non-virtual destructor pixmap.h:39: warning: ‘class PixmapFormat’ has virtual functions but non-virtual destructor api.cpp: In function ‘void rgl_user2window(int*, int*, double*, double*, double*, double*, int*)’: api.cpp:764: error: ‘gluProject’ was not declared in this scope api.cpp: In function ‘void rgl_window2user(int*, int*, double*, double*, double*, double*, int*)’: api.cpp:792: error: ‘gluUnProject’ was not declared in this scope make: *** [api.o] Error 1 chmod: cannot access `/usr/lib/R/library/rgl/libs/*': No such file or directory ERROR: compilation failed for package 'rgl' ** Removing '/usr/lib/R/library/rgl' The downloaded packages are in /tmp/RtmpJY8uNp/downloaded_packages Warning message: installation of package 'rgl' had non-zero exit status in: install.packages(rgl) I was able to install this on an 64-bit system running FC4 and R 2.4.1. Any ideas on why it fails on FC6? Rick B. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing Package rgl - Compilation Fails
Check again your error message: opengl.hpp:24:20: error: GL/glu.h: No such file or directory you need to install mesa-libGLU-devel FC6 version is 6.5.1-7 which will provide development files for glut3. Needless to say the above will probably pool some dependencies and (-devel) means it will install *.h files as well. Start your FC package manager and search for GLU, install the above and try again. Best, Oleg Rick Bilonick wrote: I'm running R 2.4.1 (with the latest versions of all packages) on an FC6 32-bit system. When I try to install the rgl package, compilation fails: install.packages(rgl) --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/rgl_0.70.tar.gz' Content type 'application/x-gzip' length 705556 bytes opened URL == downloaded 689Kb * Installing *source* package 'rgl' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking for X... libraries , headers checking for libpng-config... yes configure: using libpng-config configure: using libpng dynamic linkage configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -I/usr/lib/R/include -I/usr/lib/R/include -I -DHAVE_PNG_H -I/usr/include/libpng12 -Iext -I/usr/local/include-fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -c api.cpp -o api.o In file included from glgui.hpp:9, from gui.hpp:11, from rglview.h:10, from Device.hpp:11, from DeviceManager.hpp:9, from api.cpp:14: opengl.hpp:24:20: error: GL/glu.h: No such file or directory Disposable.hpp:13: warning: ‘struct IDisposeListener’ has virtual functions but non-virtual destructor types.h:77: warning: ‘class DestroyHandler’ has virtual functions but non-virtual destructor gui.hpp:56: warning: ‘class gui::WindowImpl’ has virtual functions but non-virtual destructor gui.hpp:90: warning: ‘class gui::GUIFactory’ has virtual functions but non-virtual destructor pixmap.h:39: warning: ‘class PixmapFormat’ has virtual functions but non-virtual destructor api.cpp: In function ‘void rgl_user2window(int*, int*, double*, double*, double*, double*, int*)’: api.cpp:764: error: ‘gluProject’ was not declared in this scope api.cpp: In function ‘void rgl_window2user(int*, int*, double*, double*, double*, double*, int*)’: api.cpp:792: error: ‘gluUnProject’ was not declared in this scope make: *** [api.o] Error 1 chmod: cannot access `/usr/lib/R/library/rgl/libs/*': No such file or directory ERROR: compilation failed for package 'rgl' ** Removing '/usr/lib/R/library/rgl' The downloaded packages are in /tmp/RtmpJY8uNp/downloaded_packages Warning message: installation of package 'rgl' had non-zero exit status in: install.packages(rgl) I was able to install this on an 64-bit system running FC4 and R 2.4.1. Any ideas on why it fails on FC6? Rick B. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing Package rgl - Compilation Fails
As the error message indicates, there is no GL/glu.h file installed in the system. If it is, the path is not properly set. % yum provides GL/glu.h on FC6 should give you some clues and tell you what to install, and also whether it should be installed. Ranjan On Mon, 19 Feb 2007 14:35:29 -0500 Rick Bilonick [EMAIL PROTECTED] wrote: I'm running R 2.4.1 (with the latest versions of all packages) on an FC6 32-bit system. When I try to install the rgl package, compilation fails: install.packages(rgl) --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/rgl_0.70.tar.gz' Content type 'application/x-gzip' length 705556 bytes opened URL == downloaded 689Kb * Installing *source* package 'rgl' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking for X... libraries , headers checking for libpng-config... yes configure: using libpng-config configure: using libpng dynamic linkage configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -I/usr/lib/R/include -I/usr/lib/R/include -I -DHAVE_PNG_H -I/usr/include/libpng12 -Iext -I/usr/local/include-fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -c api.cpp -o api.o In file included from glgui.hpp:9, from gui.hpp:11, from rglview.h:10, from Device.hpp:11, from DeviceManager.hpp:9, from api.cpp:14: opengl.hpp:24:20: error: GL/glu.h: No such file or directory Disposable.hpp:13: warning: ___struct IDisposeListener___ has virtual functions but non-virtual destructor types.h:77: warning: ___class DestroyHandler___ has virtual functions but non-virtual destructor gui.hpp:56: warning: ___class gui::WindowImpl___ has virtual functions but non-virtual destructor gui.hpp:90: warning: ___class gui::GUIFactory___ has virtual functions but non-virtual destructor pixmap.h:39: warning: ___class PixmapFormat___ has virtual functions but non-virtual destructor api.cpp: In function ___void rgl_user2window(int*, int*, double*, double*, double*, double*, int*)___: api.cpp:764: error: ___gluProject___ was not declared in this scope api.cpp: In function ___void rgl_window2user(int*, int*, double*, double*, double*, double*, int*)___: api.cpp:792: error: ___gluUnProject___ was not declared in this scope make: *** [api.o] Error 1 chmod: cannot access `/usr/lib/R/library/rgl/libs/*': No such file or directory ERROR: compilation failed for package 'rgl' ** Removing '/usr/lib/R/library/rgl' The downloaded packages are in /tmp/RtmpJY8uNp/downloaded_packages Warning message: installation of package 'rgl' had non-zero exit status in: install.packages(rgl) I was able to install this on an 64-bit system running FC4 and R 2.4.1. Any ideas on why it fails on FC6? Rick B. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing Package rgl - Compilation Fails
You are missing the OpenGLU headers. On FC5 they are in mesa-libGLU-devel From the README: REQUIREMENTS Windowing System (osx/carbon, unix/x11 or win32) OpenGL Library OpenGL Utility Library (GLU) On Mon, 19 Feb 2007, Rick Bilonick wrote: I'm running R 2.4.1 (with the latest versions of all packages) on an FC6 32-bit system. When I try to install the rgl package, compilation fails: install.packages(rgl) --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/rgl_0.70.tar.gz' Content type 'application/x-gzip' length 705556 bytes opened URL == downloaded 689Kb * Installing *source* package 'rgl' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking for X... libraries , headers checking for libpng-config... yes configure: using libpng-config configure: using libpng dynamic linkage configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -I/usr/lib/R/include -I/usr/lib/R/include -I -DHAVE_PNG_H -I/usr/include/libpng12 -Iext -I/usr/local/include-fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -c api.cpp -o api.o In file included from glgui.hpp:9, from gui.hpp:11, from rglview.h:10, from Device.hpp:11, from DeviceManager.hpp:9, from api.cpp:14: opengl.hpp:24:20: error: GL/glu.h: No such file or directory Disposable.hpp:13: warning: ÿÿstruct IDisposeListenerÿÿ has virtual functions but non-virtual destructor types.h:77: warning: ÿÿclass DestroyHandlerÿÿ has virtual functions but non-virtual destructor gui.hpp:56: warning: ÿÿclass gui::WindowImplÿÿ has virtual functions but non-virtual destructor gui.hpp:90: warning: ÿÿclass gui::GUIFactoryÿÿ has virtual functions but non-virtual destructor pixmap.h:39: warning: ÿÿclass PixmapFormatÿÿ has virtual functions but non-virtual destructor api.cpp: In function ÿÿvoid rgl_user2window(int*, int*, double*, double*, double*, double*, int*)ÿÿ: api.cpp:764: error: ÿÿgluProjectÿÿ was not declared in this scope api.cpp: In function ÿÿvoid rgl_window2user(int*, int*, double*, double*, double*, double*, int*)ÿÿ: api.cpp:792: error: ÿÿgluUnProjectÿÿ was not declared in this scope make: *** [api.o] Error 1 chmod: cannot access `/usr/lib/R/library/rgl/libs/*': No such file or directory ERROR: compilation failed for package 'rgl' ** Removing '/usr/lib/R/library/rgl' The downloaded packages are in /tmp/RtmpJY8uNp/downloaded_packages Warning message: installation of package 'rgl' had non-zero exit status in: install.packages(rgl) I was able to install this on an 64-bit system running FC4 and R 2.4.1. Any ideas on why it fails on FC6? Rick B. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] memory management uestion
On Mon, 19 Feb 2007, Federico Calboli wrote:
Hi All,
I would like to ask the following.
I have an array of data in an objetct, let's say X.
I need to use a for loop on the elements of one or more columns of X and I am
having a debate with a colleague about the best memory management.
Yez guys should take this fight out into the parking lot. ;-)
Armed with gc(), system.time(), and whatever memory monitoring tools your
OS'es provide you can pound each other with memory usage and timing stats
till one of you screams 'uncle' or you both have had enough and decide to
shake hands and come back inside.
I believe that if I do:
col1 = X[,1]
col2 = X[,2]
...
colx = X[,x]
and then
for(i in whatever){
do something using col1[i], col2[i] ... colx[i]
}
my memory management is better that doing:
for(i in whatever){
do something using X[i,1], X[i,2] ... X[,x]
}
Whoa! You are accessing one ROW at a time.
Either way this will tangle up your cache if you have many rows and
columns in your orignal data.
You might do better to do
Y - t( X ) ### use '-' !
for (i in whatever ){
do something using Y[ , i ]
}
BTW, here I *have to* use a for() loop an no nifty tapply, lapply and family.
Any comment is welcome.
Best,
Fede
--
Federico C. F. Calboli
Department of Epidemiology and Public Health
Imperial College, St Mary's Campus
Norfolk Place, London W2 1PG
Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193
f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:[EMAIL PROTECTED] UC San Diego
http://biostat.ucsd.edu/~cberry/ La Jolla, San Diego 92093-0901
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing Package rgl - Compilation Fails
On Mon, 2007-02-19 at 19:56 +, Oleg Sklyar wrote: Check again your error message: opengl.hpp:24:20: error: GL/glu.h: No such file or directory you need to install mesa-libGLU-devel FC6 version is 6.5.1-7 which will provide development files for glut3. Needless to say the above will probably pool some dependencies and (-devel) means it will install *.h files as well. Start your FC package manager and search for GLU, install the above and try again. Best, Oleg I installed a slightly newer version (the one that yum found): mesa-libGLU-devel-6.5.1-9.fc6 but it still fails (I'm installing as root): install.packages(rgl) --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/rgl_0.70.tar.gz' Content type 'application/x-gzip' length 705556 bytes opened URL Deleted a bunch of lines Disposable.hpp:13: warning: ‘struct IDisposeListener’ has virtual functions but non-virtual destructor gui.hpp:56: warning: ‘class gui::WindowImpl’ has virtual functions but non-virtual destructor gui.hpp:90: warning: ‘class gui::GUIFactory’ has virtual functions but non-virtual destructor g++ -shared -L/usr/local/lib -o rgl.so api.o Background.o BBoxDeco.o Color.o device.o devicemanager.o Disposable.o FaceSet.o fps.o geom.o gl2ps.o glgui.o gui.o Light.o LineSet.o LineStripSet.o Material.o math.o osxgui.o osxlib.o par3d.o pixmap.o PointSet.o PrimitiveSet.o QuadSet.o RenderContext.o render.o rglview.o scene.o select.o Shape.o SphereMesh.o SphereSet.o SpriteSet.o String.o Surface.o TextSet.o Texture.o TriangleSet.o Viewpoint.o win32gui.o win32lib.o x11gui.o x11lib.o -L -lX11 -lXext -lGL -lGLU -L/usr/lib -lpng12 -L/usr/lib/R/lib -lR /usr/bin/ld: cannot find -lXext collect2: ld returned 1 exit status make: *** [rgl.so] Error 1 chmod: cannot access `/usr/lib/R/library/rgl/libs/*': No such file or directory ERROR: compilation failed for package 'rgl' ** Removing '/usr/lib/R/library/rgl' The downloaded packages are in /tmp/RtmpMc94yC/downloaded_packages Warning message: installation of package 'rgl' had non-zero exit status in: install.packages(rgl) Rick B. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] memory management uestion
Charles C. Berry wrote:
Whoa! You are accessing one ROW at a time.
Either way this will tangle up your cache if you have many rows and
columns in your orignal data.
You might do better to do
Y - t( X ) ### use '-' !
for (i in whatever ){
do something using Y[ , i ]
}
My question is NOT how to write the fastest code, it is whether dummy variables
(for lack of better words) make the memory management better, i.e. faster, or
not.
Best,
Fede
--
Federico C. F. Calboli
Department of Epidemiology and Public Health
Imperial College, St Mary's Campus
Norfolk Place, London W2 1PG
Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193
f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing Package rgl - Compilation Fails
The error is different now. It now cannot find Xext library. Do a yum search on this and install that. yum provides libXext which will give you the package Xext which needs to be installed. You may also need to install the libXext-devel.i386 package. HTH. Ranjan On Mon, 19 Feb 2007 16:02:09 -0500 Rick Bilonick [EMAIL PROTECTED] wrote: On Mon, 2007-02-19 at 19:56 +, Oleg Sklyar wrote: Check again your error message: opengl.hpp:24:20: error: GL/glu.h: No such file or directory you need to install mesa-libGLU-devel FC6 version is 6.5.1-7 which will provide development files for glut3. Needless to say the above will probably pool some dependencies and (-devel) means it will install *.h files as well. Start your FC package manager and search for GLU, install the above and try again. Best, Oleg I installed a slightly newer version (the one that yum found): mesa-libGLU-devel-6.5.1-9.fc6 but it still fails (I'm installing as root): install.packages(rgl) --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/rgl_0.70.tar.gz' Content type 'application/x-gzip' length 705556 bytes opened URL Deleted a bunch of lines Disposable.hpp:13: warning: ___struct IDisposeListener___ has virtual functions but non-virtual destructor gui.hpp:56: warning: ___class gui::WindowImpl___ has virtual functions but non-virtual destructor gui.hpp:90: warning: ___class gui::GUIFactory___ has virtual functions but non-virtual destructor g++ -shared -L/usr/local/lib -o rgl.so api.o Background.o BBoxDeco.o Color.o device.o devicemanager.o Disposable.o FaceSet.o fps.o geom.o gl2ps.o glgui.o gui.o Light.o LineSet.o LineStripSet.o Material.o math.o osxgui.o osxlib.o par3d.o pixmap.o PointSet.o PrimitiveSet.o QuadSet.o RenderContext.o render.o rglview.o scene.o select.o Shape.o SphereMesh.o SphereSet.o SpriteSet.o String.o Surface.o TextSet.o Texture.o TriangleSet.o Viewpoint.o win32gui.o win32lib.o x11gui.o x11lib.o -L -lX11 -lXext -lGL -lGLU -L/usr/lib -lpng12 -L/usr/lib/R/lib -lR /usr/bin/ld: cannot find -lXext collect2: ld returned 1 exit status make: *** [rgl.so] Error 1 chmod: cannot access `/usr/lib/R/library/rgl/libs/*': No such file or directory ERROR: compilation failed for package 'rgl' ** Removing '/usr/lib/R/library/rgl' The downloaded packages are in /tmp/RtmpMc94yC/downloaded_packages Warning message: installation of package 'rgl' had non-zero exit status in: install.packages(rgl) Rick B. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Installing Rmpi on FC5 with lam
After several trial and error attempts, I managed to install the Rmpi package without error on my Linux machine, running Fedora 5. I installed lam-7.1.2, lam-devel-7.1.2 and R-2.4.1, R-devel-2.4.1 The Package Rmpi_5.0-3.tar.gz, I installed once from within R and once from the command line to make sure, I link the right libraries: R CMD INSTALL Rmpi_5.0-3.tar.gz --configure-args=--with-mpi=/usr/lib/lam Rmpi is correctly installed in $R_HOME/library/Rmpi. However on compiling, I get strange warnings: internal.c: In function ‘mystrcpy’: internal.c:64: warning: operation on ‘i’ may be undefined internal.c: In function ‘mpitype’: internal.c:43: warning: ‘datatype’ may be used uninitialized in this function Rmpi.c: In function ‘mpi_testany’: Rmpi.c:1315: warning: unused variable ‘index’ Rmpi.c: In function ‘mpi_get_count’: Rmpi.c:768: warning: ‘datatype’ may be used uninitialized in this function Rmpi.c: In function ‘mpi_allreduce’: Rmpi.c:672: warning: ‘op’ may be used uninitialized in this function Rmpi.c:673: warning: ‘sexp_recv’ may be used uninitialized in this function Rmpi.c: In function ‘mpi_reduce’: Rmpi.c:586: warning: ‘op’ may be used uninitialized in this function Rmpi.c:587: warning: ‘sexp_recv’ may be used uninitialized in this function Rmpi.c: In function ‘mpi_scatterv’: Rmpi.c:320: warning: ‘displs’ may be used uninitialized in this function Rmpi.c: In function ‘mpi_gatherv’: Rmpi.c:225: warning: ‘displs’ may be used uninitialized in this function On loading the library occurs the following error: library(Rmpi) Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/usr/lib/R/library/Rmpi/libs/Rmpi.so': /usr/lib/R/library/Rmpi/libs/Rmpi.so: undefined symbol: lam_mpi_double Error in library(Rmpi) : .First.lib failed for 'Rmpi' Error in dyn.unload(x) : dynamic/shared library '/usr/lib/R/library/Rmpi/libs/Rmpi.so' was not loaded I'm running kernel 2.6.18-1.2257.fc5smp on a i686 machine Thank you for any ideas. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] random effect nested within fixed effects (binomial lmer)
I have a large dataset where each Subject answered seven similar Items, which are binary yes/no questions. So I've always used Subject and Item random effects in my models, fit with lmer(), e.g.: model-lmer(Response~Race+Gender+...+(1|Subject_ID)+(1| Item_ID),data,binomial) But I recently realized something. Most of the variables that I've tested as fixed effects are properties of the subject (e.g. Race, Gender, etc.). Is it correct to be using a random effect Subject that is nested within (partially-crossed) fixed effects like Gender and Race? - I hope I'm using the terminology correctly. So today, I accidentally ran a model without the Subject random effect, and the fixed effect of Race was significant for the first time. With the Subject effect included, Race is not significant. This also happens if Race is treated as random, though the effect is smaller then. The following table shows the various pairs of model fits, from somers2(), and the p-values given by anova(). Somers' Dxy p from anova() random Subject term no Subject term Somers' Dxy no Race term0.8487 0.4096 vs. 0.300.00064 fixed Race term 0.8483 0.4332 no Race term0.8487 0.4096 vs. 0.960.0047 random Race term0.8486 0.4334 Adding the Subject effect always highly improves the fit of the model, so I would certainly want to keep it. But if there is a real effect of Race, why does adding the Subject effect make it go away? I thought the Subject random effect would be a sort of residual subject effect, once everything else was accounted for by other subject properties (some of which do remain significant with Subject in there as well). This must be a common scenario, since people are interested in inherent properties of subjects, yet also try to model and 'factor out' the random individual variation between people. I'm simply not very familiar with the relevant literature, and I hope someone here can help. Thank you, Daniel P.S. Also, why does treating Race as a random factor have (very slightly) more of an effect on the Somers' Dxy, while judging by anova () it's more significant as a fixed factor? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing Rmpi on FC5 with lam
Is /usr/lib/lam in your ld search path? This sort of message usually means a shared library cannot be found. You do need lam-libs as well according to yum. R CMD ldd /usr/lib/R/library/Rmpi/libs/Rmpi.so /sbin/ldconfig -p | grep /usr/lib/lam might be illuminating. There are various problems with the configure scripts in Rmpi for Fedora layouts that the maintainer is looking into: it fails completely on x86_64 systems. I don't understand how your line worked: that looks for -lmpi in /usr/lib/lam/lib/libmpi.a and that is not where FC5 puts the libraries. On Mon, 19 Feb 2007, Thomas Mangold wrote: After several trial and error attempts, I managed to install the Rmpi package without error on my Linux machine, running Fedora 5. I installed lam-7.1.2, lam-devel-7.1.2 and R-2.4.1, R-devel-2.4.1 The Package Rmpi_5.0-3.tar.gz, I installed once from within R and once from the command line to make sure, I link the right libraries: R CMD INSTALL Rmpi_5.0-3.tar.gz --configure-args=--with-mpi=/usr/lib/lam Rmpi is correctly installed in $R_HOME/library/Rmpi. However on compiling, I get strange warnings: internal.c: In function ?mystrcpy?: internal.c:64: warning: operation on ?i? may be undefined internal.c: In function ?mpitype?: internal.c:43: warning: ?datatype? may be used uninitialized in this function Rmpi.c: In function ?mpi_testany?: Rmpi.c:1315: warning: unused variable ?index? Rmpi.c: In function ?mpi_get_count?: Rmpi.c:768: warning: ?datatype? may be used uninitialized in this function Rmpi.c: In function ?mpi_allreduce?: Rmpi.c:672: warning: ?op? may be used uninitialized in this function Rmpi.c:673: warning: ?sexp_recv? may be used uninitialized in this function Rmpi.c: In function ?mpi_reduce?: Rmpi.c:586: warning: ?op? may be used uninitialized in this function Rmpi.c:587: warning: ?sexp_recv? may be used uninitialized in this function Rmpi.c: In function ?mpi_scatterv?: Rmpi.c:320: warning: ?displs? may be used uninitialized in this function Rmpi.c: In function ?mpi_gatherv?: Rmpi.c:225: warning: ?displs? may be used uninitialized in this function On loading the library occurs the following error: library(Rmpi) Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/usr/lib/R/library/Rmpi/libs/Rmpi.so': /usr/lib/R/library/Rmpi/libs/Rmpi.so: undefined symbol: lam_mpi_double Error in library(Rmpi) : .First.lib failed for 'Rmpi' Error in dyn.unload(x) : dynamic/shared library '/usr/lib/R/library/Rmpi/libs/Rmpi.so' was not loaded I'm running kernel 2.6.18-1.2257.fc5smp on a i686 machine Thank you for any ideas. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RSNPper SNPinfo and making it handle a vector
Farrel Buchinsky [EMAIL PROTECTED] wrote: I tried biomaRt library(biomaRt) ensnp = useMart(snp, dataset = hsapiens_snp) snp = getSNP(chromosome = 17, start = 73649033, end = 73679033, mart = ensnp) show(snp) Gave me a nice table but it did not seem to permit starting from the point of knowing the SNP and entering a list of rs##. I guess I could always fudge around. But it does not provide the one-stop I was looking for. Try, for example, getBM(attributes=c(refsnp_id,chr_name,chrom_start, ensembl_external_gene_id,allele, validated), filter=refsnp, values=(refsnp=c(rs17166282,rs3897937)), mart=ensnp) -- | David Duffy (MBBS PhD) ,-_|\ | email: [EMAIL PROTECTED] ph: INT+61+7+3362-0217 fax: -0101 / * | Epidemiology Unit, Queensland Institute of Medical Research \_,-._/ | 300 Herston Rd, Brisbane, Queensland 4029, Australia GPG 4D0B994A v __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] bootstrapping Levene's test
Hello all,
I am low down on the learning curve of R but so far I have had little
trouble using most of the packages. However, recently I have run into
a wall when it comes to bootstrapping a Levene's test (from the car
package) and thought you might be able to help. I have not been able
to find R examples for the boot package where the test statistic
specifically uses a grouping variable (or at least a simple example
with this condition). I would like to do a non-parametric bootstrap
to eventually get 95% confidence intervals using the boot.ci command.
I have included the coding I have tried on a simple data set below. If
anyone could provide some help, specifically with regards to how the
statistic arguement should be set up in the boot package, it would
be greatly appreciated.
library(boot)
library(car)
data-c(2,45,555,1,77,1,2,1,2,1)
group-c(1,1,1,1,1,2,2,2,2,2)
levene.test(data,group)
Levene's Test for Homogeneity of Variance
Df F value Pr(F)
group 1 1.6929 0.2294
8
stat-function(a){levene.test(a,group)}
trial1-boot(data,statistic,100)
Error in statistic(data, original, ...) : unused argument(s) ( ...)
Best regards,
Kevin
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and provide commented, minimal, self-contained, reproducible code.
[R] tree()
Hi I am trying to use tree() to classify movements in a futures contract. My data is like this: diff dip dim adx 1 0100.08650.100.0 2 0 93.185402044.5455 93.18540 3 0 90.309951549.1169 90.30995 4 1 85.22030 927.0419 85.22030 5 1 85.36084 785.6480 85.36084 6 0 85.72627 663.3814 85.72627 7 0 78.06721 500.1113 78.06721 8 1 69.59398 376.7558 69.59398 9 1 71.15429 307.4533 71.15429 10 1 71.81023 280.6238 71.81023 plus another 6000 lines The cpus example works fine and I am trying this: tree.model - tree(as.factor(indi$diff) ~ indi$dim + indi$dip + indi$adx, indi[1:4000,]) tree.model summary(tree.model) plot(tree.model); text(tree.model) but I get this: tree.model - tree(as.factor(indi$diff) ~ indi$dim + indi$dip + indi$adx, indi[1:4000,]) tree.model node), split, n, deviance, yval, (yprob) * denotes terminal node 1) root 6023 8346 0 ( 0.513 0.487 ) * summary(tree.model) Classification tree: tree(formula = as.factor(indi$diff) ~ indi$dim + indi$dip + indi$adx, data = indi[1:4000, ]) Variables actually used in tree construction: character(0) Number of terminal nodes: 1 Residual mean deviance: 1.386 = 8346 / 6022 Misclassification error rate: 0.487 = 2933 / 6023 plot(tree.model); text(tree.model) Error in plot.tree(tree.model) : cannot plot singlenode tree I'm not getting any sort of tree formed. I wondered if anyone could point me in the right direction. Thanks. Stephen Choularton [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to avoid sort of x values in dotplot?
I am trying to avoid that dotplot sorts my x-values. They are in the correct order in the data.frame and the connections between the x-y values follows this order, but the placement of the x-values on the x-axis is re-ordered. In the following example, the order should be d1, d8 and d15. However, this script places d8 at the highest x position. Any help is appreciated. Subj - rep(1:4,each=3) Time - rep(c(d1,d8,d15),4) Conc - 1:12 df - data.frame(Subj,Time,Conc) dotplot(Conc ~ Time | Subj, data = df, layout = c(2,2), type=b) Thanks, -Rene Irvine, CA, USA __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to avoid sort of x values in dotplot?
Am 19 Feb 2007 um 20:28 hat Rene Braeckman geschrieben: From: Rene Braeckman [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Date sent: Mon, 19 Feb 2007 20:28:01 -0800 Subject:[R] How to avoid sort of x values in dotplot? I am trying to avoid that dotplot sorts my x-values. They are in the correct order in the data.frame and the connections between the x-y values follows this order, but the placement of the x-values on the x-axis is re-ordered. In the following example, the order should be d1, d8 and d15. However, this script places d8 at the highest x position. Any help is appreciated. Subj - rep(1:4,each=3) Time - rep(c(d1,d8,d15),4) Conc - 1:12 df - data.frame(Subj,Time,Conc) dotplot(Conc ~ Time | Subj, data = df, layout = c(2,2), type=b) library(lattice) Subj - rep(1:4,each=3) Time - rep(c(d1,d8,d15),4) Conc - 1:12 df - data.frame(Subj,Time,Conc) df$Time - factor(df$Time,levels=df$Time) dotplot(Conc ~ Time | Subj, data = df, layout = c(2,2), type=b) HTH, Bernd __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] categorical column to numeric column
Hi On 19 Feb 2007 at 9:11, Duncan Murdoch wrote: Date sent: Mon, 19 Feb 2007 09:11:52 -0500 From: Duncan Murdoch [EMAIL PROTECTED] To: Shubha Vishwanath Karanth [EMAIL PROTECTED] Copies to: r-help R-help@stat.math.ethz.ch Subject:Re: [R] categorical column to numeric column On 2/19/2007 8:36 AM, Shubha Vishwanath Karanth wrote: Hi R, Let 'dd' be a data frame given as: dd=data.frame(aa=c(a,a,b,a,b,b),bb=c(1,1,1,2,3,4)) Now I want to create a column 'g' such that if dd$aa=a then dd$g=1 else dd$g= -1 . So, I gave the below syntax: if((dd$aa)==a) dd$g=1 else dd$g= -1 if() looks at just the first entry; it's designed for flow of control rather than vectorized calculations. You want ifelse(): ifelse( dd$aa == a, 1, -1) Another approach is to use the fact that logical vector can be interpreted as 1 and 0 vector (dd$a==a)*2-1 HTH Petr Duncan Murdoch But I get the error message as: Warning message: the condition has length 1 and only the first element will be used in: if ((dd$aa) == a) dd$g = 1 else dd$g = -1 and dd= dd aa bb g 1 a 1 1 2 a 1 1 3 b 1 1 4 a 2 1 5 b 3 1 6 b 4 1 Please let me know what is the error I am doing? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Petr Pikal [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Any packages for conducting AHP( Analytic Hierarchy Process) data
I have so far had the only return to my query from Steve Dutky. I am familir with matrix eigen value and vector manipulation. If you have anything to share with me, it would be good chance for me to follow up the AHP-related thing. Furthermore, I am good at statistics fairely. Thanks for your comments, Kum-Hoe Hwang, Ph.D. On 2/19/07, Steve Dutky [EMAIL PROTECTED] wrote: Hi, Kum-Hoe Hwang, Did you get any help for your query? I have used R/Splus for a number of years, primarily for isolating anomalies with TCP/IP network traffic. I have become somewhat adept at importing data from a variety of sources and formats into R. I first became interested in AHP some time back, but have never gotten around to working with it under R. I probably cannot help you much with the analysis of AHP data. If your main problem involves casting your AHP data into a data.frame, I will be happy to assist you as far my time and understanding allow. Have you reviewed the packages for handling eigen values/vectors? Thanks, Steve Dutky 400 Domer Ave Takoma Park, MD 20912 US Message: 101 Date: Wed, 14 Feb 2007 16:56:11 +0900 From: Kum-Hoe Hwang [EMAIL PROTECTED] Subject: [R] Any packages for conducting AHP( Analytic Hierarchy Process) data To: R Help mail address r-help@stat.math.ethz.ch Message-ID: [EMAIL PROTECTED] Content-Type: text/plain Hi, R Lovers! I have some survey data. I'd like to run R or R packages for processing data inputted from AHP(Analytic Hierarchy Process) survey. Are there any R packages or subsititues for running data from AHP survey. Thanks in advance, -- Kum-Hoe Hwang, Ph.D.Phone : 82-31-250-3516Email : [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
