Re: [R] Antialiasing plots and text on different devices
Update: The font situation on Macs with cairo and Cairo is a little worse
that I initially thought. I re-generated the images on a different Mac. The
previous Mac had OS 10.4 and this one has 10.5. The fonts from cairo and
Cairo have changed. Now there are italics and bold italics where there
should be normal and bold text.
http://stdout.org/~winston/X/r-antialias/pch.htmlhttp://stdout.org/%7Ewinston/X/r-antialias/pch.html
On Thu, Jun 4, 2009 at 7:30 PM, Winston Chang
winstonchang2...@u.northwestern.edu wrote:
I have a question about antialiasing when R generates bitmaps. (This
follows a thread on the ggplot2 mailing list.)
I mostly use R on Linux, although I sometimes use it in Mac and Windows as
well. On Linux, I've found that plotting shapes 15-18 via cairo results in
bad-looking output. The points are not antialiased, and they are jagged and
misshapen. Plots generated in Windows also aren't antialiased, but at least
the vector shapes seem to be aligned to pixel boundaries so that the raster
images look consistent.
You can see this in the scatterplots I've posted here:
http://stdout.org/~winston/X/r-antialias/pch.htmlhttp://stdout.org/%7Ewinston/X/r-antialias/pch.html
Also on that page are pch symbol charts from a modified version of
pchShow() from the pch help page. I rendered PNG's of the chart on Mac,
Linux, and Windows, using png() and setting type to Xlib, cairo, quartz,
if available on the given platform. In Windows, I did it without the type
argument (in Windows, the flag wasn't available). Finally, I also installed
the Cairo package and used CairoPNG. Please note the distinction between
cairo, which is built-in, and Cairo, which is an installed package.
(Side note: there's no Mac-Xlib image, but only because I had some X server
issues on that computer.)
Here are some observations and questions that hopefully someone can answer:
- With cairo, all shapes are antialiased except 15-18. Why do cairo and
Cairo give different results for shapes 15-18?
- With CairoPNG, all shapes are antialiased. Title text looks different
between the platforms, though. On Mac, it's normal text; on Linux, it's
bold; and on Windows, it's italic. I believe that font.main was set to 2, so
it should be bold. Why does Cairo render text so differently on different
platforms?
It would be nice not to have to tailor scripts to fit the quirks of
whatever platform I happen to be at. For example, to have the title render
properly in bold and have all shapes be anti-aliased, here's what I would
need to do:
- Mac: png(type=quartz)
- Linux: CairoPNG()
- Windows: not possible
Ideally, I would like to use the same command on all platforms to generate
good antialiased graphs with similar-looking fonts. Is such a thing
possible?
-Winston
This is the code that I used to generate all the images for each platform:
pchShow -
function(extras = c(*,., o,O,0,+,-,|,%,#),
cex = 3, ## good for both .Device==postscript and x11
col = red3, bg = gold, coltext = brown, cextext = 1.2,
main = paste(plot symbols : points (... pch = *, cex =,
cex,)))
{
nex - length(extras)
np - 26 + nex
ipch - 0:(np-1)
k - floor(sqrt(np))
dd - c(-1,1)/2
rx - dd + range(ix - ipch %/% k)
ry - dd + range(iy - 3 + (k-1)- ipch %% k)
pch - as.list(ipch) # list with integers strings
if(nex 0) pch[26+ 1:nex] - as.list(extras)
plot(rx, ry, type=n, axes = FALSE,
xlab = x-axis label, ylab = y-axis label,
main = main)
abline(v = ix, h = iy, col = lightgray, lty = dotted)
for(i in 1:np) {
pc - pch[[i]]
## 'col' symbols with a 'bg'-colored interior (where available) :
points(ix[i], iy[i], pch = pc, col = col, bg = bg, cex = cex)
if(cextext 0)
text(ix[i] - 0.3, iy[i], pc, col = coltext, cex = cextext)
}
}
sysname - paste(version$platform, _, version$major, ., version$minor,
sep=)
# Make the scatterplot
set.seed(123)
png(paste(sysname, -default_png_scatterplot.png, sep=), width=300,
height=300)
plot(rnorm(20),rnorm(20), pch=16, main=paste(sysname,pch=16))
dev.off()
# Get the possible types on this computer (cairo, Xlib, etc)
types - NULL
if (capabilities()[cairo])types - c(types, cairo)
if (capabilities()[X11]) types - c(types, Xlib)
if (capabilities()[aqua]) types - c(types, quartz)
# Generate the images
if (is.null(types)) {
# If no types available
png(paste(sysname, -default_png.png, sep=), width=300,
height=300)
pchShow(cex=.9, cextext=.8, main=paste(sysname, default PNG
output))
dev.off()
} else {
for (i in 1:length(types)) {
# If types are available, use them
png(paste(sysname, -, types[i], .png, sep=), width=300,
height=300,
type=types[i])
pchShow(cex=.9, cextext=.8,
[R] Odp: Plot and lm
Hi r-help-boun...@r-project.org napsal dne 04.06.2009 16:11:29: I want to make a log-log plot with a regression line, but I can't figure out what I'm doing wrong. What I'm trying is: plot(mass,area, log=xy, pch=as.numeric(food)) abline(lm(mass~area)) abline(lm(area~mass)) or plot(mass,area, log=xy, pch=as.numeric(food)) islands$logmass - log(mass) islands$logarea - log(area) attach(islands) abline(lm(logmass~logarea)) abline(lm(logarea~logmass)) But that does not show a line. Where am I going wrong? plot(x,y) but lm(y~x) Regards Petr data: island, area,species,food,mass Ibiza , 577 , Anser n. sp., herb, 2.0 Ibiza , 577 ,Haliaeetus albicilla, carn, 4.8 Mauritius , 1874 , Raphus cucullatus, herb, 19 Mauritius , 1874 , Circus alphonsi, carn, 0.63 Mallorca , 3667 , Myotragus balearicus, herb, 40 Mallorca , 3667 , Aquila chrysaetos, carn, 4.2 Kreta , 8259 , Elephas creutzburgi, herb, 3200 ... /Par -- Par Leijonhufvud p...@hunter-gatherer.org I don't believe in reincarnation. I used to, but that was in another life. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Done: Fast way of finding top-n values of a long vector
I'm all done now. The max2 version below is what I went with in the
end for my proposed change to caret::nearZeroVar (which used the sort
method). Max Kuhn will make it available on CRAN soon. It speeds up
that routine by a factor 2-5 on my test cases and uses much less
memory. For what it is worth, I also made a C version (cmax below)
which of course is faster yet again and scales nicely for returning the
top n values of the array:
cmax - function (v) {max - vector(double,2); max - .C(test,
as.double(v), as.integer(length(v)), max, NAOK=TRUE)[[3]];
return(max[1]/max[2]);}
library(rbenchmark)
set.seed(1); x - runif(1e7, max=1e8); x[1] - NA;
benchmark(
replications=20,
columns=c(test,elapsed),
order=elapsed
, sort = {a-sort(x, decreasing=TRUE, na.last=NA)[1:2]; a[1]/a[2];}
, qsrt = {a-sort(x, decreasing=TRUE, na.last=NA, method=quick)[1:2];
a[1]/a[2];}
, part = {a-sort.int(-x, partial=1:2, na.last=NA)[1:2]; a[1]/a[2];}
, max1 = {m-max(x, na.rm=TRUE); w-which(x==m)[1];
m/max(x[-w],na.rm=TRUE);}
, max2 = {w-which.max(x); max(x, na.rm=TRUE)/max(x[-w], na.rm=TRUE);}
, cmax = {cmax(x);}
)
# test elapsed
# 6 cmax 4.394
# 5 max2 8.954
# 4 max1 18.835
# 3 part 21.749
# 2 qsrt 46.692
# 1 sort 77.679
Thanks for all the suggestions and comments.
Allan.
PS: Slightly off-topic but is there a way within the syntax of R to set
up things so that 'sort' (or any function) would know it is called in a
partial list context in sort(x)[1:2] and it therefore could choose to
use the partial argument automatically for small [] lists? The R
interpreter of course knows full well that it is going to drop all but
the first two values of the result before it calls 'sort'. Perl has
'use Want' where howmany() and want(n) provides a subset of this
functionality (essentially for [] lists of the form 1:n).
__
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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] EM Algorithm
Dear R expert I am a student and I am currently conducting a research project on the Modeling Loss Index Triggers to price Cat Bonds: Application of the risk of hurricanes in USA. I need to solve with R (especially with EM algorithm) this specific problem below. CRAN Package archive doesn't seem to have it also the statistical modeling journal didn't contain a paper that implements this: I have two data samples. The first sample contains 64 depths for historical hurricanes happened in Florida between 1950 - 2008. The second sample contains only 48 losses associated to these hurricanes. This second data is missing 16 values of losses. Since 48 out 64 observations have information about hurricanes losses, it is necessary to treat the missing data of losses for a further analysis. So, I chose to make an EM-algorithm: 1- Experts in climatology describe that hurricanes losses are directly proportional to the depths of the hurricanes. Besides, statistically we observe a relationship between the two vectors (depths of hurricanes and losses). So the approach is to estimate the missing losses by means of the linear regression model x= á+ â yi + åi, where x (n x 1) is a vector of observations on the response variable and y (n x p) is the p explanatory variables. 2- An approach to deal with the missing data is the expectation -Maximum algorithm (EM) The expectation step: This algorithm consists of omitting the cases with missing data and running a regression on what remains. The regression coefficient will be used to estimate the missing data. The maximization step: After this estimation step, a new regression will be done over the complete data (including estimated values). With the new regression coefficients, the missing data is re-estimated. This process will continue until the estimates are adjusted to give model sampling error, ie it will not be a longer noticeable change. Does anyone have any ideas how to make this in R algorithm? Can you guide me to something already done? Or please help me to find the true code. Thank you in advance to consider my request Best regards Souad _ [[elided Hotmail spam]] [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Import ARIMA coefficients
On Thu, 2009-06-04 at 15:21 +0100, Daniel Mail wrote: snip / Hello, I need to know how to import ARIMA coefficients. I already determined the coefficients of the model with other software, but now i need to do the forecast in R. snip/ fit - arima(x, order=c(1, 0, 1), fixed=c(-.172295, .960043, 0)) fit Call: arima(x = x, order = c(1, 0, 1), fixed = c(-0.172295, 0.960043, 0)) Coefficients: Error in se nrow(x$var.coef) : invalid 'y' type in 'x y' Looks like this is a bug in print.Arima, as it assumes that x$var.coef is a matrix or similar. In this case, it is actually mod2$var.coef numeric(0) nrow(mod2$var.coef) NULL And the NULL is causing the error: [note 'se' is TRUE here] TRUE NULL Error in TRUE NULL : invalid 'y' type in 'x y' The simple work around is just to call the print method explicitly and set argument 'se' to be FALSE. This only seems to affect the print method - you can use the predict method (?predict.Arima) to do your forecasts. Here is an example using dummy data so it is reproducible: set.seed(123) x - cumsum(rnorm(1000)) x - as.ts(x) mod - arima(x, order=c(1, 1, 1)) mod Call: arima(x = x, order = c(1, 1, 1)) Coefficients: ar1 ma1 0.6000 -0.6362 s.e. 0.2963 0.2855 sigma^2 estimated as 0.9814: log likelihood = -1408.14, aic = 2822.28 ## note coefs - use them in a new fit as you were doing mod2 - arima(x, order=c(1, 1, 1), fixed = c(0.6000,-0.6362)) print(mod2, se = FALSE) Call: arima(x = x, order = c(1, 1, 1), fixed = c(0.6, -0.6362)) Coefficients: ar1 ma1 0.6000 -0.6362 sigma^2 estimated as 0.9814: log likelihood = -1408.14, aic = 2818.28 ## Now do a prediction - default is the 1-step ahead forecast: predict(mod2) $pred Time Series: Start = 1001 End = 1001 Frequency = 1 [1] 16.15804 $se Time Series: Start = 1001 End = 1001 Frequency = 1 [1] 0.9906526 Although, you'd probably be better off doing the fit in R directly... G I will be very pleased if someone help me. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% signature.asc Description: This is a digitally signed message part __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem with using subset from two different tables
venkata kirankumar wrote: Hi all, I am new to R-project my problem is I tried to get subset from two different tables its giving error but if i m tring for geting results from one table its working actually i have to take values from two tables with applying different conditions on two tables like kk- is an object of one table and fk- is an object of another table here i have to get values from these tables like subset(kk fk,kk$Rmaxtgavcg 1.256 fk$rmaxtgavcg 3.25,select=c(uniqueid)) my doubt is, that if any thing like this expression is there in R-project or i have to go for two different subsets and then adding those two one after another with checking the common uniqueid's Hi Kiran, I assume that your tables are data frames and have the same first dimension. If not, subsetvector-kk$Rmaxygavcg 1.256 fk$rmaxtgavcg 3.25 will recycle the shorter of the two logical vectors, which is almost certainly not what you want. If they have the same first dimension, you could then combine the tables and get your result: dupnames-which(names(fk)%in%names(kk)) subset(cbind(kk,fk[,-dupnames]),subsetvector) Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Odp: Plot and lm
A mix of Petr and William's answers will sort you out. You had two problems: the base 10/e problem and the axes swapping problem. ?dput I didn't know about that one either - very useful! andydol...@gmail.com 2009/6/5 Petr PIKAL petr.pi...@precheza.cz Hi r-help-boun...@r-project.org napsal dne 04.06.2009 16:11:29: I want to make a log-log plot with a regression line, but I can't figure out what I'm doing wrong. What I'm trying is: plot(mass,area, log=xy, pch=as.numeric(food)) abline(lm(mass~area)) abline(lm(area~mass)) or plot(mass,area, log=xy, pch=as.numeric(food)) islands$logmass - log(mass) islands$logarea - log(area) attach(islands) abline(lm(logmass~logarea)) abline(lm(logarea~logmass)) But that does not show a line. Where am I going wrong? plot(x,y) but lm(y~x) Regards Petr data: island, area,species,food,mass Ibiza , 577 , Anser n. sp., herb, 2.0 Ibiza , 577 ,Haliaeetus albicilla, carn, 4.8 Mauritius , 1874 , Raphus cucullatus, herb, 19 Mauritius , 1874 , Circus alphonsi, carn, 0.63 Mallorca , 3667 , Myotragus balearicus, herb, 40 Mallorca , 3667 , Aquila chrysaetos, carn, 4.2 Kreta , 8259 , Elephas creutzburgi, herb, 3200 ... /Par -- Par Leijonhufvud p...@hunter-gatherer.org I don't believe in reincarnation. I used to, but that was in another life. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R 2.9.0 on AIX 5.3: Error: Invalid DESCRIPTION file
Hi, I am trying to install R 2.9.0 on AIX 5.3. During the 'make' run I get the following error: Error: Invalid DESCRIPTION file Invalid Priority field. Packages with priorities 'base' or 'recommended' or 'defunct-base' must already be known to R. See the information on DESCRIPTION files in section 'Creating R packages' of the 'Writing R Extensions' manual. Execution halted Any ideas? Full output below. Thanks Loris Here is the full output of 'make': Target R is up to date. Target R is up to date. Target R is up to date. Target R is up to date. Target Makedeps is up to date. Target libbz2.a is up to date. Target all is up to date. Target Makedeps is up to date. Target libpcre.a is up to date. Target all is up to date. Target Makedeps is up to date. Target libz.a is up to date. Target all is up to date. Target R is up to date. Target Makedeps is up to date. Target libappl.a is up to date. Target Makedeps is up to date. Target libnmath.a is up to date. Target Makedeps is up to date. Target libunix.a is up to date. xlc_r -q64 -I. -I../../src/include -I../../src/include -I/usr/lpp/X11/include/X11 -DHAVE_CONFIG_H -O -qstrict -DR_HOME='/opt/sw/install/R-2.9.0' -o Rscript ./Rscript.c Target Makedeps is up to date. /opt/sw/install/R-2.9.0/bin/exec/R is unchanged Target Makedeps is up to date. Target internet.so is up to date. Target all is up to date. Target Makedeps is up to date. Target libRlapack.so is up to date. /opt/sw/install/R-2.9.0/lib/libRlapack.so is unchanged Target lapack.so is up to date. Target all is up to date. Target Makedeps is up to date. Target vfonts.so is up to date. Target all is up to date. Target Makedeps is up to date. Target R_X11.so is up to date. building system startup profile building package 'base' all.R is unchanged building package 'tools' all.R is unchanged Target Makedeps is up to date. ../../../../library/tools/libs/tools.so is unchanged Error: Invalid DESCRIPTION file Invalid Priority field. Packages with priorities 'base' or 'recommended' or 'defunct-base' must already be known to R. See the information on DESCRIPTION files in section 'Creating R packages' of the 'Writing R Extensions' manual. Execution halted make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 1. Stop. -- Dr. Loris Bennett Computer Centre Freie Universität Berlin Berlin, Germany __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] SSOAP failing
Duncan Temple Lang a écrit : Olivier Cailloux wrote: Dear list, I am trying to use the SSOAP package to access a very simple SOAP service, included as a demonstrator in the axis2 Apache package: Version (takes no input parameters and should return a string with the version number). The web service itself seems to be working as I could access it using an other client (eclipse Web Server tester). You will find the service wsdl here: http://smg8.ulb.ac.be:8080/axis2/services/Version?wsdl, and informations on the other services I tried here: http://smg8.ulb.ac.be:8080/axis2/services/listServices. I used the following commands: library(SSOAP) smg8Version - SOAPServer(smg8.ulb.ac.be, axis2/services/Version, 8080) .SOAP(smg8Version, getVersion, action=I(VersionHttpSoap11Endpoint)) The first command seems to give a proper smg8Version object, but the second one fails with Error: evaluation nested too deeply: infinite recursion / options(expressions=)?. The best thing to do is find where the error is occurring. You can step through the .SOAP call and see where the problem arises. The issue is in fromXML when converting the result. In the separation of the code in the SSOAP package into SSOAP and XMLSchema, I overlooked some methods for the fromXML() function for cases where no type information is available. There is now a new version (0.1-1) of XMLSchema on the Omegahat web site. When reporting problems such as these, it is important to provide information about what OS, version of R, and the different packages you are using. The code above involves the SSOAP, XML, RCurl and XMLSchema packages. Sorry about that, my e-mail has been sent too soon by mistake (also from an incorrect exp. address). I was planning to add further details. So I'm running Debian Lenny. sessionInfo() gives: R version 2.7.1 (2008-06-23) i486-pc-linux-gnu locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base Package: SSOAP Version: 0.5-0 Date: 2009/05/04 Package: XML Version: 2.3-0 Date: 2009/03/04 Package: RCurl Version: 0.97-3 Package: XMLSchema Version: 0.1-0 I must be stupid but I can't find XMLSchema on the omegahat website. (I just installed the 0.1-0 version a few days ago when trying to use SSOAP.) Google gives nothing useful for XMLSchema site:omegahat.org. I'm beginner in both web services and R programming (my knowledge is more in desktop CORBA Java programming). I am simply trying to make Java and R communicate (call Java code from R remotely), for use by someone else who works in R. I'd like to provide him with a fully functional example. I must recognize that having to step through SSOAP code to find where the problem lies might be too difficult considering my current knowledge (knowing I don't intend to become an expert R programmer). Please don't take it as rude or implying that I'm simply expecting someone to solve the problem for me: I am ready to investigate but I'd simply like to have an idea of how difficult it will be. If I have to patch part of SSOAP or if you think that the functions I need are not implemented yet, then I'd better not insist and try to communicate from R to Java using an other way. If on the other hand you think it should be working and is simply a matter of using the right version of the right package, or using an other web services platform on the Java side, or configuring something differently, etc., then I'll happily dig into it. More generally, if someone has a suggestion on what to use to call Java over TCP/IP from R, I'd be interested. I am currently considering OSS as well as SSOAP. I'd prefer learning an approach that I can reuse for other languages, so possibly a standard like SOAP or CORBA would be best. Thanks for any pointer. Olivier D. I tried different action values, because I don't know what I should put there. But I always get the same error. Also, FYI, the following command produces the following output: smg8Def - processWSDL(http://smg8.ulb.ac.be:8080/axis2/services/Version?wsdl;, verbose=TRUE) processing (sub) schema http://axisversion.sample 1 ) Exception 2 ) Exception 3 ) getVersionResponse Warning message: In processWSDL(http://smg8.ulb.ac.be:8080/axis2/services/Version?wsdl;, : Ignoring additional serviceport ... elements and then I also tried a simpler service (WSDL manually created myself, but I am not sure it is correct although it validates): smg8EchoDef - processWSDL(http://smg8.ulb.ac.be:8080/axis2/services/EchoService?wsdl;, verbose=TRUE) processing (sub) schema http://smg8.ulb.ac.be/echoSvc/ 1 ) TheString genSOAPClientInterface(def = smg8EchoDef) Error in d...@operations[[1]] : subscript out of bounds Indeed: length(smg8echo...@operations) [1] 0 __
[R] New Meta-Analysis Package (metafor)
A new package is now available via CRAN, called metafor. The metafor package consists of a collection of functions for conducting meta-analyses in R. Fixed- and random-effects models (with and without moderators) can be fitted via the general linear (mixed-effects) model. For 2x2 table data, the Mantel-Haenszel and Peto's method are also implemented. The package also provides various plot functions (for example, for forest, funnel, and radial plots) and functions for assessing the model fit and obtaining case diagnostics. Best, -- Wolfgang Viechtbauer Department of Methodology and Statistics University of Maastricht, The Netherlands http://www.wvbauer.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Morlet wavelet analysis
Irina Foss wrote: Dear, I am using cwt function from Rwave package to perform Morlet wavelet analysis. d1-ts(d1deltat=1,start=c(1960,1)) library(Rwave) D1-cwt(d1,noctave=8,nvoice=1) After I did Morlet wavelet analysis by using function wavelet from dplR package. library(dplR) D2-wavelet(d1,Dt=1) But the wavelets from two tests are very different. What is the reason?? Try D2-wavelet(d1, 1, s0=2, dj=1, J=7, siglvl=0.95) plot(abs(D1)) plot(abs(D2$wave)) This at least gives the shape of the other one for each frequency analysed, but unfortunately the magnitudes are different. Differences are probably due to the energy normalisation constants and the size of the gaussian envelope. You'll have to look at the code to find out. I have a Morlet Wavelet script in Scilab if you're interested in checking that out. I wrote it so that I could customise everything I was interested in easily and as a learning process. Matt Albrecht __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ADF test
Hi, While doing the ADF test in R using the following command I am getting the error and the result.. x.ct=ur.df(rev$REVENUE,start=1,end=length(rev$REVENUE),frequency=1) Error in ur.df(rev$REVENUE, start = 1, end = length(rev$REVENUE), frequency = 1) : unused argument(s) (start = 1, end = 4, frequency = 1) rev$REVENUE.ct=ur.df(rev$REVENUE,start=1,end=length(rev$REVENUE),frequency=1) Error in ur.df(rev$REVENUE, start = 1, end = length(rev$REVENUE), frequency = 1) : unused argument(s) (start = 1, end = 4, frequency = 1) plot(rev$REVENUE.ct) Error in plot.window(...) : need finite 'xlim' values In addition: Warning messages: 1: In min(x) : no non-missing arguments to min; returning Inf 2: In max(x) : no non-missing arguments to max; returning -Inf 3: In min(x) : no non-missing arguments to min; returning Inf 4: In max(x) : no non-missing arguments to max; returning -Inf library(tseries) adf.test(REVENUE,alternative=explosive,k=0) Error in NCOL(x) : object 'REVENUE' not found adf.test(rev$REVENUE,alternative=explosive,k=0) Error in if (interpol == min(tablep)) warning(p-value smaller than printed p-value) else warning(p-value greater than printed p-value) : missing value where TRUE/FALSE needed summary(ur.df(rev$REVENUE,lags=0,type=trend) + ) ### # Augmented Dickey-Fuller Test Unit Root Test # ### Test regression trend Call: lm(formula = z.diff ~ z.lag.1 + 1 + tt) Residuals: ALL 3 residuals are 0: no residual degrees of freedom! Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 171.522 NA NA NA z.lag.1 -5.579 NA NA NA tt 3.459 NA NA NA Residual standard error: NaN on 0 degrees of freedom Multiple R-squared: 1, Adjusted R-squared: NaN F-statistic: NaN on 2 and 0 DF, p-value: NA Value of test-statistic is: NaN NaN NaN Critical values for test statistics: 1pct 5pct 10pct tau3 -4.38 -3.60 -3.24 phi2 8.21 5.68 4.67 phi3 10.61 7.24 5.91 Can anyone tell me what is wrong with the codes???The code used is given below. Thanx t=1:length(x) plot(t,x) trend = lm(x~t) abline(lm(x~t)) summary(trend) library(urca) x = ts(x, start=1, end = length(x), frequency=1) x.ct = ur.df(x,lags=0,type='trend') plot(x.ct) library(tseries) adf.test(x,alternative = explosive , k=0) summary(ur.df(x,lags=0,type='trend') [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Regular expression \ String Extraction help
Thanks guys, that's information if very much appreciated. Both
solution are better than mine which was to use capture.output after
using the cat function.
re: collapse argument in paste() -- I've always wondered what that
argument was for, i thought it was basically doing what the sep
argument does, but i can now see that it can do something else that is
very useful which sep does not do
txt - c('Doctor', 'Who', 'For', 'The', 'Win!')
paste(txt, sep=' ')
[1] Doctor WhoForTheWin!
paste(txt, collapse=' ')
[1] Doctor Who For The Win!
re: regulare expression by Gabor - mate, that line of code is a thing
of beauty, i can honestly say i would never have come up with that.
Cheers,
Tony
2009/6/3 Greg Snow greg.s...@imail.org:
Ted,
Try using paste with the collapse argument.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of Ted Harding
Sent: Wednesday, June 03, 2009 7:56 AM
To: Tony Breyal; r-help@r-project.org
Subject: Re: [R] Regular expression \ String Extraction help
On 03-Jun-09 11:34:16, Tony Breyal wrote:
Dear all,
Is there a good way of doing the following conversion:
[]-[MM]-[DD] [Time] [Day] [Name][Integer].[Extention]
to become
C:\test\[Name]\[]-[MM]-[DD] [Time] [Day]\[]-[MM]-[DD] [Time]
[Day] [Name][Integer].[Extention]
i.e. these
2009-04-10 1400 Fri Foo1.txt
2009-04-10 1400 Fri Universities2.txt
2009-04-10 1400 Fri Hitchhikers Guide To The Galaxy42.txt
will become
C:\test\Foo\2009-04-10 1400 Fri Foo1.txt
C:\test\Universities\2009-04-10 1400 Fri Universities2.txt
C:\test\Hitchhikers Guide To The Galaxy\2009-04-10 1400 Fri
Hitchhikers Guide To The Galaxy42.txt
My main issue is the conversion for 'Hitchkikers Guide To The
Galaxy54' because of the spaces in the Name. So far this is what i
have:
txt - '2009-04-10 1400 Fri Universities1.txt'
step1 - unlist(strsplit(txt, '\\.'))
step2 - unlist(strsplit(step1[1], ' '))
Name - gsub('[0-9]',replacement='', step2[4])
step3 - paste(step2[1], step2[2], step2[3], sep=' ')
paste('C:\\test\\', Name, '\\', step3, '\\', txt, sep='' )
[1] C:\\test\\Universities\\2009-04-10 1400 Fri\\2009-04-10 1400 Fri
Universities1.txt
Cheers,
Tony Breyal
I can get as far as the following (using the Hitchhikers one):
txt - '2009-04-10 1400 Fri Hitchhikers Guide To The Galaxy42.txt'
step1 - unlist(strsplit(txt, '\\.'))
step2 - unlist(strsplit(step1[1], ' '))
step2
# [1] Hitchhikers Guide To The Galaxy42
What is now needed is to join all the separate elements of step2
into a single character string. paste() won't do it, because it
produces a separate character string for each element of step2.
cat() won't do it because it has no value (so cannot be assigned).
You could loop over step2:
Name1 - step2[4]
for(i in (5:length(step2))) Name1 - paste(Name1,step2[i])
Name1
# [1] Hitchhikers Guide To The Galaxy42
Then do your gsub:
Name - gsub('[0-9]',replacement='', Name1)
step3 - paste(step2[1], step2[2], step2[3], sep=' ')
paste('C:\\test\\', Name, '\\', step3, '\\', txt, sep='' )
[1] C:\\test\\Hitchhikers Guide To The Galaxy\\2009-04-10 1400
Fri\\2009-04-10 1400 Fri Hitchhikers Guide To The Galaxy42.txt
So that works; but it would be nice to be able to avoid the loop!
Ted.
E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 03-Jun-09 Time: 14:55:28
-- XFMail --
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[R] find a sequence of characters in a vector
Hello, I'm just looking for an easy way to find the positions of a complete sequence in a bigger vector. For example : c(a,z,e) in c(a,z,e,r,t,a,z,a,z,e,c) and the result should be 1 8 that is the positions of the beginning of the complete sequence. I tried with %in%, match, is.element but all I get is, for example which(c(a,z,e) in c(a,z,e,r,t,a,z,a,z,e,c)) 1 2 3 meaning that each character is in the bigger vector. It must be easy, except for me. Sorry. If you have a solution, thanks in advance to share it. Have a good week-end, Ptit Bleu. -- View this message in context: http://www.nabble.com/find-a-sequence-of-characters-in-a-vector-tp23888063p23888063.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] find a sequence of characters in a vector
use gregexpr and paste aze - paste(c(a, z, e), collapse = ) sequence - paste(c(a,z,e,r,t,a,z,a,z,e,c), collapse = ) gregexpr(aze, sequence, fixed = TRUE) [[1]] [1] 1 8 attr(,match.length) [1] 3 3 HTH, --sundar On Fri, Jun 5, 2009 at 6:22 AM, Ptit_Bleuptit_b...@yahoo.fr wrote: Hello, I'm just looking for an easy way to find the positions of a complete sequence in a bigger vector. For example : c(a,z,e) in c(a,z,e,r,t,a,z,a,z,e,c) and the result should be 1 8 that is the positions of the beginning of the complete sequence. I tried with %in%, match, is.element but all I get is, for example which(c(a,z,e) in c(a,z,e,r,t,a,z,a,z,e,c)) 1 2 3 meaning that each character is in the bigger vector. It must be easy, except for me. Sorry. If you have a solution, thanks in advance to share it. Have a good week-end, Ptit Bleu. -- View this message in context: http://www.nabble.com/find-a-sequence-of-characters-in-a-vector-tp23888063p23888063.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] read.table, row.names arg
Dear R users, I had somehow expected that read.table() would treat the column specified by the row.names argument as of class character. That seems to be the only sensible class allowed for a column containing row names. However, that does not seem to be the case, as the following example shows: x - cbind.data.frame(ID = c(010007787048271871, 1007109516820319, 10094843652996959, 010145176274075487), X1 = 1:4, X2 = 4:1); write.table(x, tmp.txt, quote = FALSE, row.names = FALSE); y - read.table(tmp.txt, header= TRUE, row.names=1) y X1 X2 10007787048271872 1 4 1007109516820319 2 3 10094843652996960 3 2 10145176274075488 4 1 x ID X1 X2 1 010007787048271871 1 4 2 1007109516820319 2 3 3 10094843652996959 3 2 4 010145176274075487 4 1 The first column was not read in as a string, which mangled the IDs. I could use colClasses explicitly, but then I would need to know the number and classes of the remaining columns in advance. Is this a bug or expected behavior ? Any advice would be most helpful. Thanks, Markus [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] React on sigterm
Dear all, is there any possibility to react on a process termination signal in R? In a cluster (using RMPI and snow) if the main R process is aborted due to runtime limitations I want to properly shutdown all spawned node processes, e.g. via mpi.close.Rslaves. Any hints are welcome, Christian __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] EM Algorithm
Look into the R packages for missing data by Joe Schafer. These missing data routines use EM. See here for starters. He also wrote a book: http://www.stat.psu.edu/~jls/misoftwa.html Janet __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] RWeka write.arff: set @relation
Dear all, I am using the RWeka package to append several arff files. Although it works the resulting arff files always have @relation R_data_frame, and I have to change this manually to my desired relation name. Can the package accomplish this for me instead? Thank you, Wil Koetsier __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] theta.mod in mda()
Hello, Does someone know what are theta.mod coefficients in the output of mda() function in the mda package? Thanks for your help Amélie Vaniscotte, Department of Chrono-environment, UMR UFC/CNRS 6249 aff. INRA University of Franche-Comté amelie.vanisco...@univ-fcomte.fr __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Linear model with coefficient restriction
Hi every one I perform a simple linear regression lm(a b + c + d , data = data1) How to say to R to perform and print the regression with restricting the coefficient of the variable c to be equal to 0.1. In the model print, I want to show the p-values of all my coefficients. Thank you in advance. Axel [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Linear model with coefficient restriction
On Jun 5, 2009, at 11:10 AM, Axel Leroix wrote: Hi every one I perform a simple linear regression lm(a b + c + d , data = data1) How to say to R to perform and print the regression with restricting the coefficient of the variable c to be equal to 0.1. ?lm Examine material on specifying an offset ... in your case 0.1 * c. In the model print, I want to show the p-values of all my coefficients. ?anova David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ADF test
koyel chakrabartti wrote: While doing the ADF test in R using the following command I am getting the error and the result.. x.ct=ur.df(rev$REVENUE,start=1,end=length(rev$REVENUE),frequency=1) Error in ur.df(rev$REVENUE, start = 1, end = length(rev$REVENUE), frequency = 1) : unused argument(s) (start = 1, end = 4, frequency = 1) The error and code above does not fit to the code below. The arguments start, end and frequency belong to the ts command which you probably forgot in the code above. Btw. it seems you have a time series of only 4 dates, so either there is another mistake or you don't know what you do... t=1:length(x) plot(t,x) trend = lm(x~t) abline(lm(x~t)) summary(trend) library(urca) x = ts(x, start=1, end = length(x), frequency=1) x.ct = ur.df(x,lags=0,type='trend') plot(x.ct) library(tseries) adf.test(x,alternative = explosive , k=0) summary(ur.df(x,lags=0,type='trend') __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] S4: Initialization method called during setClass??
Dear UseRs,
A simple class inheritance example:
setClass(test,representation(a=numeric))
setMethod(initialize,test,
function(.Object,x,...){
print(Initialization!!!)
callNextMethod(.Object,a=x,...)
})
new(test,x=23)
[1] Initialization!!!
An object of class test
Slot a:
[1] 23
setClass(test2,contains=test,representation(b=integer))
[1] Initialization!!!
Error in .nextMethod(.Object, a = x, ...) :
argument x is missing, with no default
When trying to define a new class test2 above, initialize method for test is called (??? looks like a bug to me) and naturally argument x is not found. Thus I can not create a subclass for test.
I could not find anything in documentation.
Thanks,
Vitalie.
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Re: [R] S4: Initialization method called during setClass??
Hi Vitalie --
Vitalie S. wrote:
Dear UseRs,
A simple class inheritance example:
setClass(test,representation(a=numeric))
setMethod(initialize,test,
function(.Object,x,...){
print(Initialization!!!)
callNextMethod(.Object,a=x,...)
})
new(test,x=23)
[1] Initialization!!!
An object of class test
Slot a:
[1] 23
the implicit contract is that the initialize method is written so that
new(test) works. This contract comes up at several points during class
definition and instantiation. You've identified one of those points.
setClass(test2,contains=test,representation(b=integer))
[1] Initialization!!!
Error in .nextMethod(.Object, a = x, ...) : argument x is missing,
with no default
I'm not sure of the details, but part of the class definition is a
coercion method, and in defining this new() is called, without
arguments, on the contained classes.
Martin
When trying to define a new class test2 above, initialize method for
test is called (??? looks like a bug to me) and naturally argument x
is not found. Thus I can not create a subclass for test.
I could not find anything in documentation.
Thanks,
Vitalie.
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http://www.R-project.org/posting-guide.html
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Re: [R] read.table, row.names arg
Markus Loecher markus.loecher at gmail.com writes: [...] x ID X1 X2 1 010007787048271871 1 4 2 1007109516820319 2 3 3 10094843652996959 3 2 4 010145176274075487 4 1 The first column was not read in as a string, which mangled the IDs. I could use colClasses explicitly, but then I would need to know the number and classes of the remaining columns in advance. Is this a bug or expected behavior ? Any advice would be most helpful. You could use a generic colClasses for all columns, like: y - read.table(tmp.txt, header= TRUE, row.names=1, colClasses=character) y X1 X2 010007787048271871 1 4 10071095168203192 3 10094843652996959 3 2 010145176274075487 4 1 In this case, all columns are read as character and need to be converted manually, but your row names are appropriate. Hoping this helps, Adrian __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] New Meta-Analysis Package (metafor)
Le vendredi 05 juin 2009 à 14:03 +0200, Viechtbauer Wolfgang (STAT) a écrit : A new package is now available via CRAN, called metafor. The metafor package consists of a collection of functions for conducting meta-analyses in R. Fixed- and random-effects models (with and without moderators) can be fitted via the general linear (mixed-effects) model. For 2x2 table data, the Mantel-Haenszel and Peto's method are also implemented. The package also provides various plot functions (for example, for forest, funnel, and radial plots) and functions for assessing the model fit and obtaining case diagnostics. Thank you very much ! I think that this package was expected ... Emmanuel Charpentier __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] find a sequence of characters in a vector
Here is one approach (this could be wrapped into a function if you are applying it repeatedly): one - c(a,z,e) two - c(a,z,e,r,t,a,z,a,z,e,c) which( sapply( 1:(length(two)-length(one)+1), + function(i) isTRUE( all.equal( one, two[ i + 0:(length(one)-1) ] ) ) ) ) [1] 1 8 Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Ptit_Bleu Sent: Friday, June 05, 2009 7:22 AM To: r-help@r-project.org Subject: [R] find a sequence of characters in a vector Hello, I'm just looking for an easy way to find the positions of a complete sequence in a bigger vector. For example : c(a,z,e) in c(a,z,e,r,t,a,z,a,z,e,c) and the result should be 1 8 that is the positions of the beginning of the complete sequence. I tried with %in%, match, is.element but all I get is, for example which(c(a,z,e) in c(a,z,e,r,t,a,z,a,z,e,c)) 1 2 3 meaning that each character is in the bigger vector. It must be easy, except for me. Sorry. If you have a solution, thanks in advance to share it. Have a good week-end, Ptit Bleu. -- View this message in context: http://www.nabble.com/find-a-sequence-of- characters-in-a-vector-tp23888063p23888063.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] help with duplicates
I have a large dataset that contain duplicate records. How do I identify and remove duplicate records? Chris Anderson 707.315.8486 www.sassydeals4u.com Free info for small business owners. Click here to find great products geared for your business. http://thirdpartyoffers.netzero.net/TGL2241/fc/BLSrjpYWIQYSqjUJ0P8Kjx22OUKmSdbeF2JnHh5X1EZsmlucvn6niiClhHS/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Mixed Latin, Greek and subscript characters in axis label
Dear R-helpers,
I have been trying to figure out how to plot a graph with an axis label
consisting of a mixture of Latin, Greek and subscript characters.
Specifically, I need to write A[beta]{1-42}, where A is Latin script A,
[beta] is Greek lower case beta and {1-42} is subscript '1-42'.
I can use xlab=expression(beta[1-42]) and obtain the [beta]{1-42} part of
the label. But, I can't add the preceding Latin character A to this
expression.
I have tried xlab=expression(A,beta[1-42]), which simply prints 'A'. I have
tried xlab=paste('A',expression(beta[1-42])), but this prints A
(beta[1-42]).
Anything else that I try returns an error (e.g. xlab=expression(A
beta[1]42]) returns 'Error: unexpected symbol').
So, I would be very grateful if someone can tell me how to write my label.
Thanks,
Jonathan Williams
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Re: [R] help with duplicates
Try this: d - data.frame(a = c(1, 1, 2, 3), b = c(10, 10, 9, 8)) unique(d) On Fri, Jun 5, 2009 at 1:38 PM, Chris Anderson chris6...@netzero.netwrote: I have a large dataset that contain duplicate records. How do I identify and remove duplicate records? Chris Anderson 707.315.8486 www.sassydeals4u.com Free info for small business owners. Click here to find great products geared for your business. http://thirdpartyoffers.netzero.net/TGL2241/fc/BLSrjpYWIQYSqjUJ0P8Kjx22OUKmSdbeF2JnHh5X1EZsmlucvn6niiClhHS/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help with duplicates
Chris, How large is large? How may columns? Duplicate across all columns of just some? Henrique gave you simple R answer. Perhaps doing in SQL is more efficient? eg SELECT DISTINCT stuff FROM somewhere; HTH, Jim Porzak TGN.com San Francisco, CA www.linkedin.com/in/jimporzak use R! Group SF: www.meetup.com/R-Users/ On Fri, Jun 5, 2009 at 9:38 AM, Chris Anderson chris6...@netzero.netwrote: I have a large dataset that contain duplicate records. How do I identify and remove duplicate records? Chris Anderson 707.315.8486 www.sassydeals4u.com Free info for small business owners. Click here to find great products geared for your business. http://thirdpartyoffers.netzero.net/TGL2241/fc/BLSrjpYWIQYSqjUJ0P8Kjx22OUKmSdbeF2JnHh5X1EZsmlucvn6niiClhHS/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] question about read.xls
I am woking on Windows and using read.xls to read Excel.xls file. But it needs to install perl on my machine first, and then give the following until it can work: read.xls(file,sheet=i,perl=E:\\Perl\\bin\\bin\\perl.exe); I am wondering if there is other way to read Excel.xls file without needing do this? jlm [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] find a sequence of characters in a vector
I think I would use Sundar's solution but here are a couple more just in case: x - c(a, z, e) y - c(a, z, e, r, t, a, z, a, z, e, c) #1 which(apply(embed(y, 3), 1, identical, rev(x))) [1] 1 8 #2 library(zoo) which(rollapply(zoo(y), 3, identical, x, align = left)) [1] 1 8 On Fri, Jun 5, 2009 at 9:30 AM, Sundar Dorai-Rajsdorai...@gmail.com wrote: use gregexpr and paste aze - paste(c(a, z, e), collapse = ) sequence - paste(c(a,z,e,r,t,a,z,a,z,e,c), collapse = ) gregexpr(aze, sequence, fixed = TRUE) [[1]] [1] 1 8 attr(,match.length) [1] 3 3 HTH, --sundar On Fri, Jun 5, 2009 at 6:22 AM, Ptit_Bleuptit_b...@yahoo.fr wrote: Hello, I'm just looking for an easy way to find the positions of a complete sequence in a bigger vector. For example : c(a,z,e) in c(a,z,e,r,t,a,z,a,z,e,c) and the result should be 1 8 that is the positions of the beginning of the complete sequence. I tried with %in%, match, is.element but all I get is, for example which(c(a,z,e) in c(a,z,e,r,t,a,z,a,z,e,c)) 1 2 3 meaning that each character is in the bigger vector. It must be easy, except for me. Sorry. If you have a solution, thanks in advance to share it. Have a good week-end, Ptit Bleu. -- View this message in context: http://www.nabble.com/find-a-sequence-of-characters-in-a-vector-tp23888063p23888063.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list 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] question about read.xls
Check out: http://wiki.r-project.org/rwiki/doku.php?id=tips:data-io:ms_windows On Fri, Jun 5, 2009 at 1:37 PM, jlfmssmjlfm...@gmail.com wrote: I am woking on Windows and using read.xls to read Excel.xls file. But it needs to install perl on my machine first, and then give the following until it can work: read.xls(file,sheet=i,perl=E:\\Perl\\bin\\bin\\perl.exe); I am wondering if there is other way to read Excel.xls file without needing do this? jlm [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] re ad.table, row.names arg
Markus Loecher-4 wrote: Dear R users, I had somehow expected that read.table() would treat the column specified by the row.names argument as of class character. That seems to be the only sensible class allowed for a column containing row names. However, that does not seem to be the case, as the following example shows: x - cbind.data.frame(ID = c(010007787048271871, 1007109516820319, 10094843652996959, 010145176274075487), X1 = 1:4, X2 = 4:1) [...snip...] As a better alternative, why not move directly the first column in the rownames? rownames(x) - x$ID write.table(x[, -1], tmp.txt) y - read.table(tmp.txt, header=T) y X1 X2 010007787048271871 1 4 10071095168203192 3 10094843652996959 3 2 010145176274075487 4 1 In this case, X1 and X2 variables are read as numeric, while the first column is read as character and assigned directly to the rownames. HTH, Adrian -- View this message in context: http://www.nabble.com/read.table%2C-row.names-arg-tp23888975p23892826.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help with duplicates
Chris Anderson wrote: I have a large dataset that contain duplicate records. How do I identify and remove duplicate records? Here's one way: aq - airquality[sample(NROW(airquality), replace=TRUE),] any(duplicated(aq)) [1] TRUE which(duplicated(aq)) [1] 2 15 34 44 45 47 49 50 52 53 65 75 76 78 83 86 88 90 91 [20] 94 96 98 99 100 103 104 107 108 110 111 112 114 117 119 120 121 122 124 [39] 125 126 127 129 130 132 133 135 137 140 141 143 145 146 147 151 152 aqs - subset(aq,!duplicated(aq)) any(duplicated(aqs)) [1] FALSE dim(aqs) [1] 98 6 dim(aq) [1] 153 6 For data frames wit many columns you might want to think more carefully about how you recognize duplicates and maybe uses a subset of columns. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Mixed Latin, Greek and subscript characters in axis label
Jonathan Williams wrote:
Dear R-helpers,
I have been trying to figure out how to plot a graph with an axis label
consisting of a mixture of Latin, Greek and subscript characters.
Specifically, I need to write A[beta]{1-42}, where A is Latin script A,
[beta] is Greek lower case beta and {1-42} is subscript '1-42'.
I can use xlab=expression(beta[1-42]) and obtain the [beta]{1-42} part of
the label. But, I can't add the preceding Latin character A to this
expression.
I have tried xlab=expression(A,beta[1-42]), which simply prints 'A'. I have
tried xlab=paste('A',expression(beta[1-42])), but this prints A
(beta[1-42]).
Anything else that I try returns an error (e.g. xlab=expression(A
beta[1]42]) returns 'Error: unexpected symbol').
So, I would be very grateful if someone can tell me how to write my label.
Thanks,
Jonathan Williams
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try xlab=expression(A*beta[1-42])
?plotmath entry *
x*y juxtapose x and y
HTH,
baptiste
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[R] Problem with generic methods
Hi I want to create a new generic method, but I end up with an error (evaluation nested too deeply). see the transcript below. The function beginYear.Fun() works, but not beginYear. I have no idea why. Any ideas welcome, Rainer setClass(fun, representation(x = numeric)) [1] fun new(fun) An object of class “fun” Slot x: numeric(0) setGeneric( beginYear, function(object, ...) standardGeneric(beginYear) ) setGeneric( +beginYear, +function(object, ...) standardGeneric(beginYear) + ) [1] beginYear beginYear.Fun = function(x) x^2 beginYear.Fun(4) [1] 16 setMethod( beginYear, signature( object = numeric ), beginYear ) setMethod( + beginYear, + signature( object = numeric ), + beginYear + ) [1] beginYear beginYear.Fun(4) [1] 16 beginYear(4) Error: evaluation nested too deeply: infinite recursion / options(expressions=)? -- Rainer M. Krug, Centre of Excellence for Invasion Biology, Stellenbosch University, South Africa __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] p-values from VGAM function vglm
Anyone know how to get p-values for the t-values from the coefficients produced in vglm? Attached is the code and output — see comment added to output to show where I need p-values + print(paste(** Using VGAM function gamma2 **)) + modl2- vglm(MidPoint~Count,gamma2,data=modl.subset,trace=TRUE,crit=c) + print(coef(modl2,matrix=TRUE)) + print(summary(modl2)) [1] ** Using VGAM function gamma2 ** VGLMlinear loop 1 : coefficients = 0.408464609241, 3.255887520104, -0.000220585671 VGLMlinear loop 2 : coefficients = 2.34723239e-01, 1.28969691e+00, -4.52393778e-05 VGLMlinear loop 3 : coefficients = 2.19500481e-01, 1.92534895e+00, -3.02160949e-05 VGLMlinear loop 4 : coefficients = 2.19383151e-01, 2.26845910e+00, -3.00838664e-05 VGLMlinear loop 5 : coefficients = 2.19383045e-01, 2.34645688e+00, -3.00836087e-05 VGLMlinear loop 6 : coefficients = 2.19383045e-01, 2.34977070e+00, -3.00836082e-05 VGLMlinear loop 7 : coefficients = 2.19383045e-01, 2.34977637e+00, -3.00836082e-05 VGLMlinear loop 8 : coefficients = 2.19383045e-01, 2.34977637e+00, -3.00836082e-05 log(mu) log(shape) (Intercept) 2.193830e-01 2.349776 Count -3.008361e-05 0.00 Call: vglm(formula = MidPoint ~ Count, family = gamma2, data = modl.subset, trace = TRUE, crit = c) Pearson Residuals: Min 1Q Median 3Q Max log(mu)-1.7037 -0.82997 0.072275 0.78520 1.72834 log(shape) -2.5152 -0.32448 0.254698 0.58772 0.70678 # NEED P-VALUES HERE # Coefficients: Value Std. Error t value (Intercept):1 2.1938e-01 5.2679e-02 4.16455 (Intercept):2 2.3498e+00 1.7541e-01 13.39574 Count -3.0084e-05 8.9484e-05 -0.33619 Number of linear predictors: 2 Names of linear predictors: log(mu), log(shape) Dispersion Parameter for gamma2 family: 1 Log-likelihood: -26.39268 on 123 degrees of freedom Number of Iterations: 8 Steven Matthew Anderson Anderson Research, LLC Statistical Programming and Analysis SAS (R) Certified Professional adastr...@mac.com Ad Astra per Aspera שָׁלוֹם __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] error installing RCurl in SUSE SLES10-SP2
Hi Robert As Brian Ripley wrote in a message to the list earlier today, you will want a more recent version of libcurl. RCurl can be easily made to check the availability of all the different options to handle old versions of libcurl, but this slows down the installation for everyone. But more importantly, it is advisable to update curl to avoid some security issues in older versions and to access the improvements. D. Robert Castelo wrote: dear list, i'm trying to install the package RCurl into a linux system running SUSE Linux Enterprise Server 10 SP2 but i get compilation errors which i guess should be due to some missing additional software. i've been searching about the R-help archives without success so i hope somebody can point me out to this missing piece. in principle, i have the necessary curl software installed: $ rpm -qa | grep curl curl-7.15.1-19.11 curl-devel-7.15.1-19.11 curl-32bit-7.15.1-19.11 however as you'll see below, when i try to install it from R the compilation breaks. i've included at the end also the sessionInfo() output (it's R-2.9.0). i've also tried to install a newer version of RCurl (0.98) which i found in http://www.omegahat.org/RCurl but it gives the same errors. thanks! robert. install.packages(RCurl, repos=http://cran.r-project.org;) trying URL 'http://cran.r-project.org/src/contrib/RCurl_0.97-3.tar.gz' Content type 'application/x-gzip' length 1437829 bytes (1.4 Mb) opened URL == downloaded 1.4 Mb * Installing *source* package 'RCurl' ... checking for curl-config... /usr/bin/curl-config 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 Version has a libidn field Version has CURLOPT_URL No CURLOPT_NOPROXY enumeration value. No CURLINFO_CONDITION_UNMET enumeration value. No CURLINFO_REDIRECT_URL enumeration value. No CURLINFO_CERTINFO enumeration value. No CURLINFO_PRIMARY_IP enumeration value. No CURLINFO_APPCONNECT_TIME enumeration value. No CURLOPT_KEYPASSWD enumeration value. No CURLOPT_DIRLISTONLY enumeration value. No CURLOPT_APPEND enumeration value. No CURLOPT_KRBLEVEL enumeration value. No CURLOPT_USE_SSL enumeration value. No CURLOPT_TIMEOUT_MS enumeration value. No CURLOPT_CONNECTTIMEOUT_MS enumeration value. No CURLOPT_HTTP_TRANSFER_DECODING enumeration value. No CURLOPT_HTTP_CONTENT_DECODING enumeration value. No CURLOPT_NEW_FILE_PERMS enumeration value. No CURLOPT_NEW_DIRECTORY_PERMS enumeration value. No CURLOPT_POSTREDIR enumeration value. No CURLOPT_SSH_HOST_PUBLIC_KEY_MD enumeration value. No CURLOPT_OPENSOCKETFUNCTION enumeration value. No CURLOPT_OPENSOCKETDATA enumeration value. No CURLOPT_COPYPOSTFIELDS enumeration value. No CURLOPT_PROXY_TRANSFER_MODE enumeration value. No CURLOPT_SEEKFUNCTION enumeration value. No CURLOPT_SEEKDATA enumeration value. No CURLOPT_CRLFILE enumeration value. No CURLOPT_ISSUERCERT enumeration value. No CURLOPT_ADDRESS_SCOPE enumeration value. No CURLOPT_CERTINFO enumeration value. No CURLOPT_USERNAME enumeration value. No CURLOPT_PASSWORD enumeration value. No CURLOPT_PROXYUSERNAME enumeration value. No CURLOPT_PROXYPASSWORD enumeration value. No CURLOPT_SSH_HOST_PUBLIC_KEY_MD5 enumeration value. No CURLOPT_NOPROXY enumeration value. No CURLOPT_TFTP_BLKSIZE enumeration value. No CURLOPT_SOCKS5_GSSAPI_SERVICE enumeration value. No CURLOPT_SOCKS5_GSSAPI_NEC enumeration value. Version has CURLOPT_PROTOCOLS Version has CURLOPT_REDIR_PROTOCOLS configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -std=gnu99 -I/cursos/MBI/soft/R/R-2.9.0/lib64/R/include -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -I/usr/local/include-fpic -g -O2 -c base64.c -o base64.o gcc -std=gnu99 -I/cursos/MBI/soft/R/R-2.9.0/lib64/R/include -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -I/usr/local/include-fpic -g -O2 -c curl.c -o curl.o curl.c:553: warning: 'struct curl_certinfo' declared inside parameter list curl.c:553: warning: its scope is only this definition or declaration, which is probably not what you want gcc -std=gnu99 -I/cursos/MBI/soft/R/R-2.9.0/lib64/R/include -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -I/usr/local/include-fpic -g -O2 -c curlInit.c -o curlInit.o gcc -std=gnu99 -I/cursos/MBI/soft/R/R-2.9.0/lib64/R/include -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -I/usr/local/include-fpic -g -O2 -c
[R] from 3 numeric variables to a string
Hi there, I have 3 numeric variables: day (e.g., 05), month (e.g., 06), year (e.g., 2009). I would like to create a (string) variable of the following form: month/day/year (e.g., 06/05/2009). I would be grateful to anyone who could point me toward a solution. Sincerely, Marc === Marc Bélisle Professeur agrégé Chaire de recherche du Canada en écologie spatiale et en écologie du paysage Département de biologie Université de Sherbrooke 2500 Boul. de l'Université Sherbrooke, Québec J1K 2R1 Canada Tél: +1-819-821-8000 poste 61313 Fax: +1-819-821-8049 Courriél: marc.m.beli...@usherbrooke.ca __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] from 3 numeric variables to a string
?paste paste(month,day,year, sep=/) On Jun 5, 2009, at 4:56 PM, Marc Belisle wrote: Hi there, I have 3 numeric variables: day (e.g., 05), month (e.g., 06), year (e.g., 2009). I would like to create a (string) variable of the following form: month/day/year (e.g., 06/05/2009). I would be grateful to anyone who could point me toward a solution. Sincerely, Marc David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Chi plot and Kendall plot
Dear R users, I was trying to find a library for the Chi-plot and Kendall plot, as described in the paper Everything you always wanted to know about Copula Modeling but you were afraid to ask, but unsuccessfully. I was wondering if anyone have already implemented these 2 functions in R? Many thanks in advance, Nan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Dependency modeling - chi-plot and kendall-plot
Dear R users, I was trying to find a library for the Chi-plot and Kendall plot, as described in the paper Everything you always wanted to know about Copula Modeling but you were afraid to ask, but unsuccessfully. I was wondering if anyone have already implemented these 2 functions in R and could kindly help me out? Many thanks in advance, Nan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] S4: When is validObject issued? (or why S4 is killing me:( ..
Dear UseRs,
Does anyone know when exactly the validity is checked in S4? Documentation is silent:(.
Here is a small example:
setClass(test1,representation(a=numeric))
setMethod(initialize,test1,
function(.Object,...){
a-runif(1) ## here slot a is initialized ##
callNextMethod(.Object,a=a,...)
})
new(test1)
An object of class test1
Slot a:
[1] 0.755
#next new subclass is created with an additional slot b:
setClass(test2,contains=test1,representation(b=numeric)
## validity to test a==b ##
,validity=function(object){
if(obj...@a!=object@b) print(values must be equal!!)
else TRUE
})
setMethod(initialize,test2,
function(.Object,...){
.Object-callNextMethod(.Object,...)
.obj...@b-.obj...@a ## here b is initialized ##
.Object
})
new(test2)
Error in if (obj...@a != obj...@b) print(values must be equal!!) else TRUE :
argument is of length zero
This could mean only one thing, validity of test2 is checked before it gets to point when b is initialized (i.e. in callNextMethod). But this is absurd (at leas from my point): callNextMethod constructs object of type test and should have nothing to do with validity of test2.
Shouldn't validity be checked only after the object is created?
Second my slot a is initialized in test1's constructor and b must be
assigned only after the callNextMethod as in above code. Seemingly unsolvable paradox? How to be?
Many thanks.
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[R] time series, longitudinal data or trajectories
Hi the list Strictly speaking, this is not a R question, but I need the information for the creation of a package. My question is about vocabulary: What is the difference between time series, longitudinal data and trajectories? Sincerely Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] SSOAP failing
Olivier Cailloux wrote: Duncan Temple Lang a écrit : Olivier Cailloux wrote: Dear list, Sorry about that, my e-mail has been sent too soon by mistake (also from an incorrect exp. address). I was planning to add further details. So I'm running Debian Lenny. sessionInfo() gives: R version 2.7.1 (2008-06-23) i486-pc-linux-gnu locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base Package: SSOAP Version: 0.5-0 Date: 2009/05/04 Package: XML Version: 2.3-0 Date: 2009/03/04 Package: RCurl Version: 0.97-3 Package: XMLSchema Version: 0.1-0 I must be stupid but I can't find XMLSchema on the omegahat website. (I just installed the 0.1-0 version a few days ago when trying to use SSOAP.) Google gives nothing useful for XMLSchema site:omegahat.org. http://www.omegahat.org/XMLSchema/XMLSchema_0.1-1.tar.gz or from a link in http://www.omegahat.org/XMLSchema/ or via the repository using install.packages(XMLSchema, repos = http://www.omegahat.org/R;) I'm beginner in both web services and R programming (my knowledge is more in desktop CORBA Java programming). I am simply trying to make Java and R communicate (call Java code from R remotely), for use by someone else who works in R. I'd like to provide him with a fully functional example. I must recognize that having to step through SSOAP code to find where the problem lies might be too difficult considering my current knowledge (knowing I don't intend to become an expert R programmer). Please don't take it as rude or implying that I'm simply expecting someone to solve the problem for me: I am ready to investigate but I'd simply like to have an idea of how difficult it will be. If I have to patch part of SSOAP or if you think that the functions I need are not implemented yet, then I'd better not insist and try to communicate from R to Java using an other way. If on the other hand you think it should be working and is simply a matter of using the right version of the right package, or using an other web services platform on the Java side, or configuring something differently, etc., then I'll happily dig into it. Either of Simon Urbanek's rJava or Rserve packages are worth investigating. More generally, if someone has a suggestion on what to use to call Java over TCP/IP from R, I'd be interested. I am currently considering OSS as well as SSOAP. I'd prefer learning an approach that I can reuse for other languages, so possibly a standard like SOAP or CORBA would be best. Thanks for any pointer. Olivier D. I tried different action values, because I don't know what I should put there. But I always get the same error. Also, FYI, the following command produces the following output: smg8Def - processWSDL(http://smg8.ulb.ac.be:8080/axis2/services/Version?wsdl;, verbose=TRUE) processing (sub) schema http://axisversion.sample 1 ) Exception 2 ) Exception 3 ) getVersionResponse Warning message: In processWSDL(http://smg8.ulb.ac.be:8080/axis2/services/Version?wsdl;, : Ignoring additional serviceport ... elements and then I also tried a simpler service (WSDL manually created myself, but I am not sure it is correct although it validates): smg8EchoDef - processWSDL(http://smg8.ulb.ac.be:8080/axis2/services/EchoService?wsdl;, verbose=TRUE) processing (sub) schema http://smg8.ulb.ac.be/echoSvc/ 1 ) TheString genSOAPClientInterface(def = smg8EchoDef) Error in d...@operations[[1]] : subscript out of bounds Indeed: length(smg8echo...@operations) [1] 0 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list 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] p-values from VGAM function vglm
On Jun 5, 2009, at 3:15 PM, Steven Matthew Anderson wrote: Anyone know how to get p-values for the t-values from the coefficients produced in vglm? Attached is the code and output — see comment added to output to show where I need p-values + print(paste(** Using VGAM function gamma2 **)) + modl2- vglm(MidPoint~Count,gamma2,data=modl.subset,trace=TRUE,crit=c) + print(coef(modl2,matrix=TRUE)) + print(summary(modl2)) [1] ** Using VGAM function gamma2 ** VGLMlinear loop 1 : coefficients = 0.408464609241, 3.255887520104, -0.000220585671 VGLMlinear loop 2 : coefficients = 2.34723239e-01, 1.28969691e+00, -4.52393778e-05 VGLMlinear loop 3 : coefficients = 2.19500481e-01, 1.92534895e+00, -3.02160949e-05 VGLMlinear loop 4 : coefficients = 2.19383151e-01, 2.26845910e+00, -3.00838664e-05 VGLMlinear loop 5 : coefficients = 2.19383045e-01, 2.34645688e+00, -3.00836087e-05 VGLMlinear loop 6 : coefficients = 2.19383045e-01, 2.34977070e+00, -3.00836082e-05 VGLMlinear loop 7 : coefficients = 2.19383045e-01, 2.34977637e+00, -3.00836082e-05 VGLMlinear loop 8 : coefficients = 2.19383045e-01, 2.34977637e+00, -3.00836082e-05 log(mu) log(shape) (Intercept) 2.193830e-01 2.349776 Count -3.008361e-05 0.00 Call: vglm(formula = MidPoint ~ Count, family = gamma2, data = modl.subset, trace = TRUE, crit = c) Pearson Residuals: Min 1Q Median 3Q Max log(mu)-1.7037 -0.82997 0.072275 0.78520 1.72834 log(shape) -2.5152 -0.32448 0.254698 0.58772 0.70678 # NEED P-VALUES HERE # Perhaps: dt(summary( modl2 )@coef3[ , 3], 1) Coefficients: Value Std. Error t value (Intercept):1 2.1938e-01 5.2679e-02 4.16455 (Intercept):2 2.3498e+00 1.7541e-01 13.39574 Count -3.0084e-05 8.9484e-05 -0.33619 Number of linear predictors: 2 Names of linear predictors: log(mu), log(shape) Dispersion Parameter for gamma2 family: 1 Log-likelihood: -26.39268 on 123 degrees of freedom Number of Iterations: 8 Steven Matthew Anderson Anderson Research, LLC Statistical Programming and Analysis SAS (R) Certified Professional adastr...@mac.com -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Done: Fast way of finding top-n values of a long vector
On Fri, Jun 5, 2009 at 4:09 AM, Allan Engelhardt all...@cybaea.com wrote:
I'm all done now. The max2 version below is what I went with in the end
for my proposed change to caret::nearZeroVar (which used the sort method).
Max Kuhn will make it available on CRAN soon. It speeds up that routine by
a factor 2-5 on my test cases and uses much less memory.
You can save a little in max2 like this:
max2a = {w-which.max(x); x[w]/max(x[-w], na.rm=TRUE);}
If you don't need to handle NA's (or if you know a priori how many there
are), you can also speed up part:
parta = {sel - length(x)+c(-1,0); a-sort.int(x, partial=sel,
na.last=NA)[2:1]; a[1]/a[2];}
which becomes about as fast as max2.
library(rbenchmark)
set.seed(1); x - runif(1e7, max=1e8);
benchmark(
replications=20,
columns=c(test,elapsed),
order=elapsed
, sort = {a-sort(x, decreasing=TRUE, na.last=NA)[1:2];
a[1]/a[2];}
, qsrt = {a-sort(x, decreasing=TRUE, na.last=NA, method=quick)[1:2];
a[1]/a[2];}
, part = {a-sort.int(-x, partial=1:2, na.last=NA)[1:2];
a[1]/a[2];}
, parta = {end-length(x)+c(-1,0);
a-sort.int(x, partial=end, na.last=FALSE)[end];
a[1]/a[2]; }
, max1 = {m-max(x, na.rm=TRUE);
w-which(x==m)[1];
m/max(x[-w],na.rm=TRUE);}
, max2 = {w-which.max(x);
max(x, na.rm=TRUE)/max(x[-w], na.rm=TRUE);}
, max2a = {w-which.max(x);
x[w]/max(x[-w], na.rm=TRUE);}
)
test elapsed
7 max2a7.80
6 max28.94
4 parta9.05
3 part 10.72
5 max1 20.21
2 qsrt 49.33
1 sort 94.18
For what it is worth, I also made a C version (cmax below) which of
course is faster yet again and scales nicely for returning the top n values
of the array:
cmax - function (v) {max - vector(double,2); max - .C(test,
as.double(v), as.integer(length(v)), max, NAOK=TRUE)[[3]];
return(max[1]/max[2]);}
library(rbenchmark)
set.seed(1); x - runif(1e7, max=1e8); x[1] - NA;
benchmark(
replications=20,
columns=c(test,elapsed),
order=elapsed
, sort = {a-sort(x, decreasing=TRUE, na.last=NA)[1:2]; a[1]/a[2];}
, qsrt = {a-sort(x, decreasing=TRUE, na.last=NA, method=quick)[1:2];
a[1]/a[2];}
, part = {a-sort.int(-x, partial=1:2, na.last=NA)[1:2]; a[1]/a[2];}
, max1 = {m-max(x, na.rm=TRUE); w-which(x==m)[1];
m/max(x[-w],na.rm=TRUE);}
, max2 = {w-which.max(x); max(x, na.rm=TRUE)/max(x[-w], na.rm=TRUE);}
, cmax = {cmax(x);}
)
# test elapsed
# 6 cmax 4.394
# 5 max2 8.954
# 4 max1 18.835
# 3 part 21.749
# 2 qsrt 46.692
# 1 sort 77.679
Thanks for all the suggestions and comments.
Allan.
PS: Slightly off-topic but is there a way within the syntax of R to set up
things so that 'sort' (or any function) would know it is called in a partial
list context in sort(x)[1:2] and it therefore could choose to use the
partial argument automatically for small [] lists? The R interpreter of
course knows full well that it is going to drop all but the first two values
of the result before it calls 'sort'. Perl has 'use Want' where howmany()
and want(n) provides a subset of this functionality (essentially for []
lists of the form 1:n).
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Re: [R] from 3 numeric variables to a string
On Jun 5, 2009, at 3:56 PM, Marc Belisle wrote: Hi there, I have 3 numeric variables: day (e.g., 05), month (e.g., 06), year (e.g., 2009). I would like to create a (string) variable of the following form: month/day/year (e.g., 06/05/2009). I would be grateful to anyone who could point me toward a solution. Sincerely, Marc If you want the result just as text: day - 5 month - 6 year - 2009 sprintf(%02d/%02d/%4d, day, month, year) [1] 05/06/2009 Note that the day/month integers will of course not have the leading zeros, so using sprintf() allows you to specify that the results should include them (the '%02d' in the format string). See ?sprintf for more information. If you further want to use them as actual date objects, you can use as.Date() on the result: as.Date(sprintf(%02d/%02d/%4d, day, month, year), format = %d/%m/ %Y) [1] 2009-06-05 Note that the above is now of Class 'Date': str(as.Date(sprintf(%02d/%02d/%4d, day, month, year), format = %d/%m/%Y)) Class 'Date' num 14400 which then enables you to perform date based operations on the results. See ?as.Date for more information on converting text to dates. HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] S4: Initialization method called during setClass??
Martin Morgan wrote:
Hi Vitalie --
Vitalie S. wrote:
Dear UseRs,
A simple class inheritance example:
setClass(test,representation(a=numeric))
setMethod(initialize,test,
function(.Object,x,...){
print(Initialization!!!)
callNextMethod(.Object,a=x,...)
})
new(test,x=23)
[1] Initialization!!!
An object of class test
Slot a:
[1] 23
the implicit contract is that the initialize method is written so that
new(test) works. This contract comes up at several points during class
definition and instantiation. You've identified one of those points.
setClass(test2,contains=test,representation(b=integer))
[1] Initialization!!!
Error in .nextMethod(.Object, a = x, ...) : argument x is missing,
with no default
I'm not sure of the details, but part of the class definition is a
coercion method, and in defining this new() is called, without
arguments, on the contained classes.
it sounds approximately ok that defining a subclass fails if its
initalizer does not provide a value required by the initializer of the
superclass. pardon me my ignorance, but here's an obvious question:
what if i *do* want to extend a class that has an initializer with an
argument without a default? (it does not seem to be a particularly
extravagant idea, does it?) i can't define the subclass with setClass,
because it fails, as above, due to a violation of the contract. but i
can't define an appropriate initializer for the subclass that would
fulfil the contract before i define the subclass itself. deadlock?
there is another quirk here, or -- in case the above is not a quirk --
there is a quirk here. imagine i want to implement a class that counts
its instances as they are created, assigning to each a unique identifier
from a contiguous sequence of integers, starting at 1 (this doesn't seem
to be a particularly extravagant idea either):
setClass('foo', representation(id='integer'))
setMethod('initialize', 'foo', local({
id=0L
function(.Object, ...) {
id - id+1L
.obj...@id = id
return(.Object) } }))
foos = replicate(3, new('foo'))
sapply(foos, slot, 'id')
# 1 2 3
setClass('bar', contains='foo', representation(name='character'))
setMethod('initialize', 'bar', function(.Object, name='bar', ...) {
.obj...@name = name
callNextMethod() })
bars = replicate(3, new('bar'))
sapply(bars, slot, 'id')
# 6 7 8
what?? why on earth creating a subclass *calls* (twice!) the
superclass's initializer? is there no other way for checking the
contract without actually calling the initializer, as if an instance
(two!) was created? suppose one creates a package defining a hierarchy
of classes with something like 'foo' at the top, and a user of the
package loads it and creates a new -- the first -- instance which
suddenly has 17 as the id -- just imagine the curses.
pardon me for the usual harshness, but this is seems irrational, plain
and simple. i can imagine that this is a well-documented behaviour
(even if that's only in fine print), but the motivation...?
btw.,
sapply(foos, `...@`, 'id')
# Error in lapply(X, FUN, ...) :
# no slot of name ... for this object of class foo
even though
`...@`(foos[[1]], 'id')
# 1
`slot`(foos[[1]], 'id')
# 1
and sapply works fine with slot. what's wrong here?
deeply confused,
vQ
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Re: [R] Install RCurl in Linux
Thanks Prof. Ripley, I installed the current version curl-7.19.2, still got the same problem. I am installing RCurl_0.97-3 and my system is x86_64/CentOS 5. Looking forward to more suggestions/ideas. --- On Fri, 6/5/09, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: From: Prof Brian Ripley rip...@stats.ox.ac.uk Subject: Re: [R] Install RCurl in Linux To: heyi xiao xiaohey...@yahoo.com Cc: r-help@r-project.org, dun...@wald.ucdavis.edu Date: Friday, June 5, 2009, 1:50 AM It seems you need a later curl -- 7.15 is rather old (and I think incomplete as a version number) and 7.19.5 is current. It is helpful to tell us what version of packages (here RCurl) you are trying to use, as well as your precise OS. On Thu, 4 Jun 2009, heyi xiao wrote: Hello all, I had both curl and curl-devel (both 7.15) installed on my x86_64/CentOS machine. However, I still got problem when I do R CMD INSTALL RCurl ?? Error message below, since library and/or include path is missing. I tried R CMD INSTALL RCurl --configure-args='--libdir=/usr/lib64/?? --includedir=/usr/include/' That should be part of the default paths. Same result. Any hint/suggestion would be appreciated. ... No CURLOPT_NOPROXY enumeration value. No CURLINFO_CONDITION_UNMET enumeration value. No CURLINFO_REDIRECT_URL enumeration value. No CURLINFO_CERTINFO enumeration value. No CURLINFO_PRIMARY_IP enumeration value. No CURLINFO_APPCONNECT_TIME enumeration value. No CURLOPT_KEYPASSWD enumeration value. No CURLOPT_DIRLISTONLY enumeration value. No CURLOPT_APPEND enumeration value. No CURLOPT_KRBLEVEL enumeration value. ... Version has CURLOPT_PROTOCOLS Version has CURLOPT_REDIR_PROTOCOLS configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -std=gnu99 -I/usr/local/lib64/R/include?? -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -I/usr/local/include?? -fpic?? -g -O2 -c enums.c -o enums.o In file included from CurlOptEnums.h:10, from enums.c:79: CURLOptTable.h:145: error: ??CURLOPT_SOCKOPTFUNCTION?? undeclared here (not in a function) CURLOptTable.h:146: error: ??CURLOPT_SOCKOPTDATA?? undeclared here (not in a function) CURLOptTable.h:147: error: ??CURLOPT_SSL_SESSIONID_CACHE?? undeclared here (not in a function) CURLOptTable.h:148: error: ??CURLOPT_SSH_AUTH_TYPES?? undeclared here (not in a function) CURLOptTable.h:149: error: ??CURLOPT_SSH_PUBLIC_KEYFILE?? undeclared here (not in a function) CURLOptTable.h:150: error: ??CURLOPT_SSH_PRIVATE_KEYFILE?? undeclared here (not in a function) CURLOptTable.h:151: error: ??CURLOPT_FTP_SSL_CCC?? undeclared here (not in a function) make: *** [enums.o] Error 1 ERROR: compilation failed for package ??RCurl?? * Removing ??/usr/local/lib64/R/library/RCurl??    [[alternative HTML version deleted]] -- Brian D. Ripley,         rip...@stats.ox.ac.uk 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, UK        Fax: +44 1865 272595 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] from 3 numeric variables to a string
Marc Belisle wrote: Hi there, I have 3 numeric variables: day (e.g., 05), month (e.g., 06), year (e.g., 2009). I would like to create a (string) variable of the following form: month/day/year (e.g., 06/05/2009). I would be grateful to anyone who could point me toward a solution. ?sprintf vQ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Looking for R software consultant
My apologies if this is not the correct venue for this type of question. I am looking for a software consultant to assist in our project to integrate R with an existing Java data collection application. So far, I have not been able to find a directory of software consultants who have R experience. Ideally, the consultant would be located in the New York area, but it is not necessary. Would appreciate if anyone could point me in the right direction. Thank You, Eric Hernaez __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with generic methods
Rainer M Krug wrote: Hi I want to create a new generic method, but I end up with an error (evaluation nested too deeply). see the transcript below. The function beginYear.Fun() works, but not beginYear. I have no idea why. Any ideas welcome, Rainer setClass(fun, representation(x = numeric)) [1] fun new(fun) An object of class “fun” Slot x: numeric(0) setGeneric( beginYear, function(object, ...) standardGeneric(beginYear) ) setGeneric( +beginYear, +function(object, ...) standardGeneric(beginYear) + ) [1] beginYear beginYear.Fun = function(x) x^2 beginYear.Fun(4) [1] 16 setMethod( beginYear, signature( object = numeric ), beginYear ) setMethod( + beginYear, + signature( object = numeric ), + beginYear + ) [1] beginYear because the method function you want to call is beginYear.Fun rather than beginYear as declared in the method specification? Uwe Ligges beginYear.Fun(4) [1] 16 beginYear(4) Error: evaluation nested too deeply: infinite recursion / options(expressions=)? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Dependency modeling - chi-plot and kendall-plot
At least for chi-plot: http://lmgtfy.com/?q=genest+%20copula+r-project+%22chi-plot%22 Genest and Favre cite R in that article. Have you contacted them? On Jun 5, 2009, at 5:29 PM, Zhao Nan wrote: Dear R users, I was trying to find a library for the Chi-plot and Kendall plot, as described in the paper Everything you always wanted to know about Copula Modeling but you were afraid to ask, but unsuccessfully. I was wondering if anyone have already implemented these 2 functions in R and could kindly help me out? Many thanks in advance, Nan -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with generic methods
Rainer M Krug r.m.k...@gmail.com writes: Hi I want to create a new generic method, but I end up with an error (evaluation nested too deeply). see the transcript below. The function beginYear.Fun() works, but not beginYear. I have no idea why. Any ideas welcome, Rainer setClass(fun, representation(x = numeric)) [1] fun new(fun) An object of class “fun” Slot x: numeric(0) setGeneric( beginYear, function(object, ...) standardGeneric(beginYear) ) setGeneric( +beginYear, +function(object, ...) standardGeneric(beginYear) + ) [1] beginYear beginYear.Fun = function(x) x^2 beginYear.Fun(4) [1] 16 Are you confusing S3 and S4 method systems? The .Fun has no special meaning in S4 setMethod( beginYear, signature( object = numeric ), beginYear ) here the beginYear,numeric-method is defined to invoke the beginYear generic, so you end up calling yourself. You might have meant setMethod(beginYear, signature(object=numeric), beginYear.Fun) but I would have written setMethod(beginYear, signature(object=numeric), function(object, ...) object^2) Martin setMethod( + beginYear, + signature( object = numeric ), + beginYear + ) [1] beginYear beginYear.Fun(4) [1] 16 beginYear(4) Error: evaluation nested too deeply: infinite recursion / options(expressions=)? -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Fitting a Weibull Distribution
How do you fit a Weibull distribution in R? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] OT: a weighted rank-based, non-paired test statistic ?
Hi, Is anyone aware of a rank-based, non-paired test such as the Krustal-Wallis, that can accommodate weights? Alternatively, would it make sense to simulate a dataset by duplicating observations in proportion to their weight, and then using the Krustal-Wallis test? thanks! Dylan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] S4: When is validObject issued? (or why S4 is killing me:( ..
Vitalie S. vitosm...@rambler.ru writes:
Dear UseRs,
Does anyone know when exactly the validity is checked in S4?
Documentation is silent:(.
It gets called as part of initialize,ANY-method, i.e., at the bottom
of your 'callNextMethod'. It is NOT called when there are no arguments
in addition to .Object, e.g., in a call like new(test).
Here is a small example:
setClass(test1,representation(a=numeric))
setMethod(initialize,test1,
function(.Object,...){
a-runif(1) ## here slot a is initialized ##
callNextMethod(.Object,a=a,...) })
new(test1)
An object of class test1
Slot a:
[1] 0.755
#next new subclass is created with an additional slot b:
setClass(test2,contains=test1,representation(b=numeric)
## validity to test a==b ##
,validity=function(object){
if(obj...@a!=object@b) print(values must be equal!!)
else TRUE
})
setMethod(initialize,test2,
function(.Object,...){
.Object-callNextMethod(.Object,...)
validity is checked in the preceeding line
.obj...@b-.obj...@a ## here b is initialized ##
.Object
})
new(test2)
Error in if (obj...@a != obj...@b) print(values must be equal!!)
else TRUE : argument is of length zero
This could mean only one thing, validity of test2 is checked before
it gets to point when b is initialized (i.e. in callNextMethod). But
this is absurd (at leas from my point): callNextMethod constructs
object of type test and should have nothing to do with validity of
test2. Shouldn't validity be checked only after the object is
created?
The class of .Object is test2, and initialize should return a (valid)
instance of test2, right? So the validity check on test2 has to have
been performed before returning from callNextMethod.
Second my slot a is initialized in test1's constructor and b
must be assigned only after the callNextMethod as in above
code. Seemingly unsolvable paradox? How to be?
My own solution would avoid using initialize (because as you're
discovering the contract is hard to satisfy in general) and instead
use constructors
test2 - function(a=runif(1), b=a, ...) new(test2, a=a, b=b, ...)
or similar, which I think helps to provide a bit of an interface
between the class and it's implementation.
One could think of additional solutions (creating a new 'test' inside
'test2', and not using callNextMethod(), for instance) but this is
unlikely to be robust (e.g., when derived classes are relying on
initialize,ANY-method to fill in slots with supplied arguments).
Martin
Many thanks.
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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Re: [R] time series, longitudinal data or trajectories
At 04:02 PM 6/5/2009, Christophe Genolini wrote: Hi the list Strictly speaking, this is not a R question, but I need the information for the creation of a package. My question is about vocabulary: What is the difference between time series, longitudinal data and trajectories? Sincerely Christophe Longitudinal data are measurements over long periods of time, often at irregular periods, but consistent across subjects. Repeated measures data are replicates at the same point in time, or over a short period of time (e.g., laboratory experiments). Time series typically have constant increments of time and typically a stochastic character, although this term might be considered all-encompassing for all measurements at different times. Trajectory implies a continuous curve in time, as opposed to discrete times. Trajectory also implies an underlying causal model, as it is a term from kinematics. I hope this helps. Robert A. LaBudde, PhD, PAS, Dpl. ACAFS e-mail: r...@lcfltd.com Least Cost Formulations, Ltd.URL: http://lcfltd.com/ 824 Timberlake Drive Tel: 757-467-0954 Virginia Beach, VA 23464-3239Fax: 757-467-2947 Vere scire est per causas scire __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] S4: Initialization method called during setClass??
Wacek Kusnierczyk waclaw.marcin.kusnierc...@idi.ntnu.no writes:
Martin Morgan wrote:
Hi Vitalie --
Vitalie S. wrote:
Dear UseRs,
A simple class inheritance example:
setClass(test,representation(a=numeric))
setMethod(initialize,test,
function(.Object,x,...){
print(Initialization!!!)
callNextMethod(.Object,a=x,...)
})
new(test,x=23)
[1] Initialization!!!
An object of class test
Slot a:
[1] 23
the implicit contract is that the initialize method is written so that
new(test) works. This contract comes up at several points during class
definition and instantiation. You've identified one of those points.
setClass(test2,contains=test,representation(b=integer))
[1] Initialization!!!
Error in .nextMethod(.Object, a = x, ...) : argument x is missing,
with no default
I'm not sure of the details, but part of the class definition is a
coercion method, and in defining this new() is called, without
arguments, on the contained classes.
it sounds approximately ok that defining a subclass fails if its
initalizer does not provide a value required by the initializer of the
superclass. pardon me my ignorance, but here's an obvious question:
what if i *do* want to extend a class that has an initializer with an
argument without a default? (it does not seem to be a particularly
extravagant idea, does it?) i can't define the subclass with setClass,
because it fails, as above, due to a violation of the contract. but i
I'm speaking as a user, so my understanding is not meant to be
definitive. I'd say the class with the intializer with an argument
without a default is broken, and you should not want to extend it.
can't define an appropriate initializer for the subclass that would
fulfil the contract before i define the subclass itself. deadlock?
there is another quirk here, or -- in case the above is not a quirk --
there is a quirk here. imagine i want to implement a class that counts
its instances as they are created, assigning to each a unique identifier
remembering that R has copy-on-change semantics that are only
approximately adhered to (e.g., some copying even without change),
this objective would not likely be useful, e.g., it would not be a
good identifier to know that you were dealing with the 'same'
instance, and it would not be the way you'd want to track references
for garbage collection or other clean-up, for instance.
from a contiguous sequence of integers, starting at 1 (this doesn't seem
to be a particularly extravagant idea either):
setClass('foo', representation(id='integer'))
setMethod('initialize', 'foo', local({
id=0L
function(.Object, ...) {
id - id+1L
.obj...@id = id
return(.Object) } }))
foos = replicate(3, new('foo'))
sapply(foos, slot, 'id')
# 1 2 3
setClass('bar', contains='foo', representation(name='character'))
setMethod('initialize', 'bar', function(.Object, name='bar', ...) {
.obj...@name = name
callNextMethod() })
bars = replicate(3, new('bar'))
sapply(bars, slot, 'id')
# 6 7 8
what?? why on earth creating a subclass *calls* (twice!) the
superclass's initializer? is there no other way for checking the
once when the superclass is instantiated (fair enough!) and once when
the validity of the subclass is checked -- the way that valildity
checking works is that subclass is validated according to the subclass
validity method, then the subclass is coerced to the superclass, and
the superclass is checked for validity. The user can define the coerce
method, but the default, for class hierarchies where it is
appropriate, involves a call to new(), and hence to initialize and
validObject.
setClass(A)
[1] A
setClass(B, contains=A, representation(y=numeric))
[1] B
b - as(new(B), A)
showMethods(coerce, class=B, includeDef=TRUE)
Function: coerce (package methods)
from=B, to=A
function (from, to = A, strict = TRUE)
if (strict) {
value - new(A)
for (what in x) slot(value, what) - slot(from, what)
value
} else from
Martin
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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Re: [R] OT: a weighted rank-based, non-paired test statistic ?
On Fri, 5 Jun 2009, Dylan Beaudette wrote: Is anyone aware of a rank-based, non-paired test such as the Krustal-Wallis, that can accommodate weights? You don't say what sort of weights, but basically, no. Whether you have precision weights or sampling weights, the test will no longer be distribution-free. Alternatively, would it make sense to simulate a dataset by duplicating observations in proportion to their weight, and then using the Krustal-Wallis test? No. -thomas Thomas Lumley Assoc. Professor, Biostatistics tlum...@u.washington.eduUniversity of Washington, Seattle __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Circular shift function?
Is there a circular shift function in R similar to the shift function in Octave? From my reading of the manual there does not appear to be one, but if I am mistaken, can someone point out the relevant section? -- View this message in context: http://www.nabble.com/Circular-shift-function--tp23896972p23896972.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fitting a Weibull Distribution
http://lmgtfy.com/?q=fit+weibull+distribution+R Hit #8: http://cran.r-project.org/doc/contrib/Ricci-distributions-en.pdf On Fri, Jun 5, 2009 at 7:21 PM, r...@rstatx.com wrote: How do you fit a Weibull distribution in R? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mike Lawrence Graduate Student Department of Psychology Dalhousie University Looking to arrange a meeting? Check my public calendar: http://tr.im/mikes_public_calendar ~ Certainty is folly... I think. ~ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] OT: a weighted rank-based, non-paired test statistic ?
On Friday 05 June 2009, Thomas Lumley wrote:
On Fri, 5 Jun 2009, Dylan Beaudette wrote:
Is anyone aware of a rank-based, non-paired test such as the
Krustal-Wallis, that can accommodate weights?
You don't say what sort of weights, but basically, no.
Whether you have precision weights or sampling weights, the test will no
longer be distribution-free.
Alternatively, would it make sense to simulate a dataset by duplicating
observations in proportion to their weight, and then using the
Krustal-Wallis test?
No.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.edu University of Washington, Seattle
Thanks,
Perhaps I am thinking about the problem incorrectly. Here are some more
details.
I have a series of values, each associated with a polygon that represents an
area on the ground. A sample is made by collecting the polygons (i.e. the
values associated with each polygon) and the area fraction of each polygon
(i.e. the observation's weight). In this past I have used this method to
compute a weighted average, or weighted standard deviation.
However, I now have a case where a subset of individuals from the region are
selected, and re-assigned an area fraction. I would like to evaluate if the
subsets are representative of the original data-- so far I have been
comparing weighted means.
Unfortunately, the data are prone to having highly skewed distributions--
possibly making my comparisons of weighted-means invalid.
I posted a question about this a while back, but just in case here are some
data that approximately resemble the problem at hand:
# generate some data
# note lack of balance
x.1 - rnorm(n=100, mean=0, sd=1)
x.2 - rnorm(n=10, mean=4, sd=3)
x.3 - rnorm(n=10, mean=0, sd=1.5)
# generate some weights that sum to 1 for each treatment
# c/o this post:
# https://stat.ethz.ch/pipermail/r-help/2008-July/167044.html
#
w.1 - diff(c(0,sort(sample(seq(1,99,1),99,replace=T)),100)) / 100
w.2 - diff(c(0,sort(sample(seq(1,99,1),9,replace=T)),100)) / 100
w.3 - diff(c(0,sort(sample(seq(1,99,1),9,replace=T)),100)) / 100
# generate treatment labels:
trt - factor(c(rep('baseline', 100), rep(c('data1','data2'), each=10)))
# combine into dataframe
d - data.frame(values=c(x.1,x.2,x.3), wts=c(w.1,w.2,w.3), treatment=trt)
# compute means and wt.means
d.means - sapply(by(d, d$treatment, function(i) mean(i$value)), '[')
d.wt.means - sapply(by(d, d$treatment, function(i) weighted.mean(i$value,
w=i$wts)), '[')
# quick check:
boxplot(values~ treatment, data=d, varwidth=TRUE, border=grey(0.5),
main='symbol size is proportional to observation weight')
points(1:3, d.means, col='green', pch=15, cex=1.2)
points(1:3, d.wt.means, col='blue', pch=15, cex=1.2)
points(jitter(as.numeric(d$treatment)), d$values, col='red',
cex=sqrt(d$wts*100))
legend('topleft', legend=c('original data','mean','wt.mean'), pch=c(1,15,15),
col=c('red','green','blue'))
# another way of looking at the data:
library(lattice)
densityplot(~ values, groups=treatment, data=d, auto.key=list(columns=3),
pch='|')
# comparison of means (without weights):
# effects are equal to treatment means
summary(lm(values ~ treatment, data=d))
# comparison with means
# effects are equal to treatment weighted-means
summary(lm(values ~ treatment, data=d, weights=wts))
Cheers,
Dylan
--
Dylan Beaudette
Soil Resource Laboratory
http://casoilresource.lawr.ucdavis.edu/
University of California at Davis
530.754.7341
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Re: [R] S4: Initialization method called during setClass??
Martin Morgan wrote:
[...]
it sounds approximately ok that defining a subclass fails if its
initalizer does not provide a value required by the initializer of the
superclass. pardon me my ignorance, but here's an obvious question:
what if i *do* want to extend a class that has an initializer with an
argument without a default? (it does not seem to be a particularly
extravagant idea, does it?) i can't define the subclass with setClass,
because it fails, as above, due to a violation of the contract. but i
I'm speaking as a user, so my understanding is not meant to be
definitive. I'd say the class with the intializer with an argument
without a default is broken, and you should not want to extend it.
broken? in which sense? do you want to say that it is essential, in an
oo system, to provide a default for each parameter in a
constructor/initializer for the respective class not to be broken?
there is another quirk here, or -- in case the above is not a quirk --
there is a quirk here. imagine i want to implement a class that counts
its instances as they are created, assigning to each a unique identifier
remembering that R has copy-on-change semantics that are only
approximately adhered to (e.g., some copying even without change),
this objective would not likely be useful, e.g., it would not be a
good identifier to know that you were dealing with the 'same'
instance, and it would not be the way you'd want to track references
for garbage collection or other clean-up, for instance.
yes, i've visited this issue it in one of my earlier examples posted
here. to me, the fact that you can clone an instance of a class without
the class's constructor/initializer being called (and without using
low-level memory copy operations) is a candidate to be considered a flaw
in the language. the fact that it breaks the simple instance-counting
pattern (or any similar pattern) is a problem with the language, not the
pattern.
in c++, for example, you can obtain a copy of the representation of an
object, but not without a constructor being called at some point --
either before the copy operation or during it (where the copy
constructor is called):
class Foo {
private:
static int count;
int id;
public:
Foo() { id = ++count; }
Foo(const Foo foo) { id = ++count; } };
Foo foo; // foo.id is 1
Foo bar = foo; // bar.id is 2
Foo yee(bar); // yee.id is 3
Foo daa; // daa.id is 4
Foo.daa = foo; // daa.id is 1
i find the r way, where you can create a copy of an instance without the
object system being involved, potentially confusing for users.
from a contiguous sequence of integers, starting at 1 (this doesn't seem
to be a particularly extravagant idea either):
setClass('foo', representation(id='integer'))
setMethod('initialize', 'foo', local({
id=0L
function(.Object, ...) {
id - id+1L
.obj...@id = id
return(.Object) } }))
foos = replicate(3, new('foo'))
sapply(foos, slot, 'id')
# 1 2 3
setClass('bar', contains='foo', representation(name='character'))
setMethod('initialize', 'bar', function(.Object, name='bar', ...) {
.obj...@name = name
callNextMethod() })
bars = replicate(3, new('bar'))
sapply(bars, slot, 'id')
# 6 7 8
what?? why on earth creating a subclass *calls* (twice!) the
superclass's initializer? is there no other way for checking the
once when the superclass is instantiated (fair enough!)
fair? what's fair here? that just creating a subclass involves
instantiation of the superclass? makes little sense to me.
and once when
the validity of the subclass is checked -- the way that valildity
checking works is that subclass is validated according to the subclass
validity method, then the subclass is coerced to the superclass, and
the superclass is checked for validity.
but you're talking classes here; is coercing a *class* to another
*class* implying instantiation? makes little sense to me.
The user can define the coerce
method, but the default, for class hierarchies where it is
appropriate, involves a call to new(), and hence to initialize and
validObject.
i consider this a flaw in the object system. if subclass validation
goes on at the instance level, why couldn't it be postponed until the
user actually creates a new instance? otherwise, why couldn't it be
done without creating two dummy instances just for the purpose of
validation?
setClass(A)
[1] A
setClass(B, contains=A, representation(y=numeric))
[1] B
b - as(new(B), A)
showMethods(coerce, class=B, includeDef=TRUE)
Function: coerce (package methods)
from=B, to=A
function (from, to = A, strict = TRUE)
if (strict) {
value - new(A)
for (what in x) slot(value, what) - slot(from, what)
value
} else from
well, i see i can define a coerce on my own, and that's fine, but (a)
Re: [R] p-values from VGAM function vglm
?str It's a pretty fundamental function for understanding R objects. str(summary(vglm.D93)) Formal class 'summary.vglm' [package VGAM] with 43 slots ..@ coef3 : num [1:5, 1:3] 3.04 -4.54e-01 -2.93e-01 1.00e-15 9.33e-16 ... .. ..- attr(*, dimnames)=List of 2 .. .. ..$ : chr [1:5] (Intercept) outcome2 outcome3 treatment2 ... .. .. ..$ : chr [1:3] Value Std. Error t value ..@ cov.unscaled: num [1:5, 1:5] 0.0292 -0.0159 -0.0159 -0.02 -0.02 ... .. ..- attr(*, dimnames)=List of 2 .. .. ..$ : chr [1:5] (Intercept) outcome2 outcome3 treatment2 ... .. .. ..$ : chr [1:5] (Intercept) outcome2 outcome3 treatment2 ... snipped about three pages of further output On Jun 5, 2009, at 7:28 PM, Steven Matthew Anderson wrote: Thank you for your reply. Related question ... how do you know the matrix of values in the summary(modl2) was called coef3? Is there a function for extracting that information? dt(summary( modl2 )@coef3[ , 3], 1) Thank you, Steve On Jun 5, 2009, at 2:18 PM, David Winsemius wrote: On Jun 5, 2009, at 3:15 PM, Steven Matthew Anderson wrote: Anyone know how to get p-values for the t-values from the coefficients produced in vglm? Attached is the code and output — see comment added to output to show where I need p-values + print(paste(** Using VGAM function gamma2 **)) + modl2- vglm(MidPoint~Count,gamma2,data=modl.subset,trace=TRUE,crit=c) + print(coef(modl2,matrix=TRUE)) + print(summary(modl2)) [1] ** Using VGAM function gamma2 ** VGLMlinear loop 1 : coefficients = 0.408464609241, 3.255887520104, -0.000220585671 VGLMlinear loop 2 : coefficients = 2.34723239e-01, 1.28969691e+00, -4.52393778e-05 VGLMlinear loop 3 : coefficients = 2.19500481e-01, 1.92534895e+00, -3.02160949e-05 VGLMlinear loop 4 : coefficients = 2.19383151e-01, 2.26845910e+00, -3.00838664e-05 VGLMlinear loop 5 : coefficients = 2.19383045e-01, 2.34645688e+00, -3.00836087e-05 VGLMlinear loop 6 : coefficients = 2.19383045e-01, 2.34977070e+00, -3.00836082e-05 VGLMlinear loop 7 : coefficients = 2.19383045e-01, 2.34977637e+00, -3.00836082e-05 VGLMlinear loop 8 : coefficients = 2.19383045e-01, 2.34977637e+00, -3.00836082e-05 log(mu) log(shape) (Intercept) 2.193830e-01 2.349776 Count -3.008361e-05 0.00 Call: vglm(formula = MidPoint ~ Count, family = gamma2, data = modl.subset, trace = TRUE, crit = c) Pearson Residuals: Min 1Q Median 3Q Max log(mu)-1.7037 -0.82997 0.072275 0.78520 1.72834 log(shape) -2.5152 -0.32448 0.254698 0.58772 0.70678 # NEED P-VALUES HERE # Perhaps: dt(summary( modl2 )@coef3[ , 3], 1) Coefficients: Value Std. Error t value (Intercept):1 2.1938e-01 5.2679e-02 4.16455 (Intercept):2 2.3498e+00 1.7541e-01 13.39574 Count -3.0084e-05 8.9484e-05 -0.33619 Number of linear predictors: 2 Names of linear predictors: log(mu), log(shape) Dispersion Parameter for gamma2 family: 1 Log-likelihood: -26.39268 on 123 degrees of freedom Number of Iterations: 8 Steven Matthew Anderson Anderson Research, LLC Statistical Programming and Analysis SAS (R) Certified Professional adastr...@mac.com -- David Winsemius, MD Heritage Laboratories West Hartford, CT Steven Matthew Anderson Anderson Research, LLC Statistical Programming and Analysis SAS (R) Certified Professional adastr...@mac.com Ad Astra per Aspera שָׁלוֹם David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] S4: Initialization method called during setClass??
Wacek Kusnierczyk wrote:
Martin Morgan wrote:
[...]
from a contiguous sequence of integers, starting at 1 (this doesn't seem
to be a particularly extravagant idea either):
setClass('foo', representation(id='integer'))
setMethod('initialize', 'foo', local({
id=0L
function(.Object, ...) {
id - id+1L
.obj...@id = id
return(.Object) } }))
foos = replicate(3, new('foo'))
sapply(foos, slot, 'id')
# 1 2 3
setClass('bar', contains='foo', representation(name='character'))
setMethod('initialize', 'bar', function(.Object, name='bar', ...) {
.obj...@name = name
callNextMethod() })
bars = replicate(3, new('bar'))
sapply(bars, slot, 'id')
# 6 7 8
what?? why on earth creating a subclass *calls* (twice!) the
superclass's initializer? is there no other way for checking the
once when the superclass is instantiated (fair enough!)
fair? what's fair here? that just creating a subclass involves
instantiation of the superclass? makes little sense to me.
I completely misread your post, sorry. Martin
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[R] SAS CMO and SVP Jim Davis on Open Source, BI , competition, leadership succession others
An interview with Chief Marketing Officer of SAS Institute, Jim Davis. Here is an extract- http://www.decisionstats.com/2009/06/05/interview-jim-davis-sas-institute/ *Ajay -It is rare to find a major software company that has zero involvement with open source movement (or as I call it with peer-reviewed code). Could you name some of SAS Instituteâs contribution to open source? What could be further plans to enhance this position with the global community of scientists?* * Jim -* SAS does support open source and open standards too. Open standards typically guide open source implementations (e.g., the OASIS work is guiding some of the work in Eclipse Cosmos, some of the JCP standards guide the Tomcat implementation, etc.). Some examples of SASâs contributions to open source and open standards include: * Apache Software Foundation* â a senior SAS developer has been a committer on multiple releases of the Apache Tomcat project, and has also acted as Release Coordinator. *Eclipse Foundation* â SAS developers were among the early adopters of Eclipse. One senior SAS developer wrote a tutorial whitepaper on using Eclipse RCP, and was named âTop Ambassadorâ in the 2006 Eclipse Community Awards. Another is a committer on the Eclipse Web Tools project. A third proposed and led Eclipseâs Albireo project. SAS is a participant in the Eclipse Cosmos project, with three RD employees as committers. Finally, SASâ Rich Main served on the board of directors of the Eclipse Foundation from 2003 to 2006, helping write the Eclipse Bylaws, Development Process, Membership Agreement, Intellectual Property Policy and Public License. *Java Community Process *â SAS has been a Java licensee partner since 1997 and has been active in the Java Community Process. SAS has participated in approximately 25 Java Specification Requests spanning both J2SE and J2EE technology. Rich Main of SAS also served on the JCP Executive Committee from 2005 through 2008. *OASIS* â A senior SAS developer serves as secretary of the OASIS Solution Deployment Descriptor (SDD) Technical Committee. In total, six SAS employees serve on this committee. *XML for Analysis* â SAS co-sponsored XML for Analysis standard with Microsoft and Hyperion. *Others *â A small SAS team developed Cobertura, an open source coverage analysis tool for Java. SAS (through our database access team) is one of the top corporate contributors to Firebird, an open source relational database. Another developer contributes to Slide WebDav. Weâve had people work on HtmlUnit (another testing framework) and FreeBSD. In addition, there are dozens if not hundreds of contributed bug reports, fixes/patches from SAS developers using open source software. SAS will continue to expand our work with and contribute to open-source tools and communities. For example, we know a number of our customers use R as well as SAS. So we decided to make it easier for them to access R by . http://www.decisionstats.com/2009/06/05/interview-jim-davis-sas-institute/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fitting a Weibull Distribution
Dear ryan, See the third example in require(survival) ?survreg HTH, Jorge On Fri, Jun 5, 2009 at 6:21 PM, r...@rstatx.com wrote: How do you fit a Weibull distribution in R? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Installation of R in Redhat Linux (64 bit)
Dear R experts.. I would highly appreciate your help in troubleshooting errors as shown below.. When I type R at shell prompt, I get the following error: The version of R in 64bit Linux is: R version 2.9.0 (2009-04-17) *** Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/usr/lib64/R/library/stats/libs/stats.so': /usr/lib64/R/library/stats/libs/stats.so: undefined symbol: _gfortran_copy_string During startup - Warning message: package stats in options(defaultPackages) was not found When I run the following: nm /usr/lib64/R/library/stats/libs/stats.so | grep _gfortran_copy_string gives the result: U _gfortran_copy_string Thanks so much in advance.. Regards, Santosh [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installation of R in Redhat Linux (64 bit)
On Fri, Jun 05, 2009 at 08:27:45PM -0700, Santosh wrote: When I run the following: nm /usr/lib64/R/library/stats/libs/stats.so | grep _gfortran_copy_string You probably need to install libraries related to gfortran. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
