Re: [R] sorting a data.frame by mean values of grouped data
Thanks Mark,
I see that I made an error in my original request for help. I got my
labels and groups mixed up (see below). Nonetheless, your code has been
a good pointer in the direction of a solution. I'll post it up when I
have it working.
Thanks again,
Stephen Barry.
I should have written it more like this:
Given data.frame:
Value Group Label
55 D Small
33 D Small
11 D Small
55 D Small
66 D Small
11 D Small
19 A Big
29 A Big
39 A Big
3 B Small
2 B Small
5 B Small
6 B Small
5 B Small
6 B Small
2 C Big
3 C Big
3 C Big
3 C Big
3 C Big
3 C Big
3 C Big
end up with:
Value Group Label
19 A Big
29 A Big
39 A Big
2 C Big
3 C Big
3 C Big
3 C Big
3 C Big
3 C Big
3 C Big
55 D Small
33 D Small
11 D Small
55 D Small
66 D Small
11 D Small
3 B Small
2 B Small
5 B Small
6 B Small
5 B Small
6 B Small
Mark W Kimpel wrote:
Stephen,
I am sure someone will have a more elegant solution, but the following
works. Mark
d.lst - split(x = d, f = as.factor(d$Group), drop = FALSE)
d.lst.mn - sapply(d.lst, FUN =
function(x){mean(as.numeric(as.character(x$Value)))})
o - order(d.lst.mn, decreasing = TRUE)
d.lst.mn - d.lst.mn[o]
e - NULL
for (i in 1:length(d.lst.mn)){
if (i == 1){
e - d[d$Group == names(d.lst.mn)[i],]
} else {
e - rbind(e, d[as.character(d$Group) == names(d.lst.mn)[i],])
}
}
e
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, Mobile VoiceMail
(317) 204-4202 Home (no voice mail please)
mwkimpelatgmaildotcom
**
sjbarry wrote:
Hi,
I have what I think is a fairly straightforward problem. I've looked
through the FAQ's and mailing lists but have been unable to identify
a solution, probably because I don't understand the language well
enough.
I have a set of data d, with 3 columns as shown,
I want to sort the data Group, mean(Value by Label). I know that this
can be done for one level, say Label, using factor() but I cannot see
how to extend that. I have included the code to create the data.frame
below and would greatly appreciate a solution or a link to a similar
problem that has already been solved in the mailing list.
Value Label Group
19 Big A
29 Big A
39 Big A
55 Small D
33 Small D
11 Small D
55 Small D
66 Small D
11 Small D
2 Big C
3 Big C
3 Big C
3 Big C
3 Big C
3 Big C
3 Big C
3 Small B
2 Small B
5 Small B
6 Small B
5 Small B
6 Small B
Value - c(19,29,39,55,33,11,55,66,11,2,3,3,3,3,3,3,3,2,5,6,5,6)
Group - c(A,A,A,D,D,D,D,D,D,
C,C,C,C,C,C,C,B,B,B,B,B,B)
Label - c(Big,Big,Big,
Small,Small,Small,Small,Small,Small,
Big,Big,Big,Big,Big,Big,Big,
Small,Small,Small,Small,Small,Small)
d - as.data.frame(cbind(Value, Label, Group))
Thanks
Stephen Barry
--
Stephen Barry
School of Earth and Environmental Sciences
University of Wollongong
Northfields Ave.
Wollongong, NSW. 2522
Australia
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[R] use bootstrap to get MLE of lamda from the exp model
the data are 3,5,7,18,43,85,91,98,100,130,230,487, it follows an exp(lamda) model, how to use bootstrap to obtain MLE of lamda, bias, sd. Thanks a lot so far my code is obj-boot(data,statistic,R=2000) here statistic should call a function to get an estimate of lamda I think, anyone can help ?I am new to bootstrap:) -- View this message in context: http://www.nabble.com/use-bootstrap-to-get-MLE-of-lamda-from-the-exp-model-tp16021176p16021176.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] survival curve for only certain values of a factor
Chang Liu changisme at hotmail.com writes: data(aml) If I use instead dummy variables: aml$x1 = (aml$x==maintained)aml$x2 = (aml$x==unmaintained) and I want to plot the survival curve using x1, x2, and I just want the 2 levels, rather than 4 curves from: I don's understand what you want, but the first step is definitively incorrect apart from the missint line break. The levels of aml are Maintained,Nonmaintained so both your == lead to all-false levels. Dieter __ 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] Bessel functions of complex argument
Many thanks for this information! I'm pretty sure Matlab can handle complex argument in besselj, although i haven't checked myself, http://www.mathworks.com/access/helpdesk/help/techdoc/index.html?/ access/helpdesk/help/techdoc/ref/besselj.html After some more thinking, it turns out my code doesn't need a complex argument at the moment, i can live with the simplest case where it is real. Good to know where to go if this is to change in the future, though. Thanks again, baptiste On 10 Mar 2008, at 08:49, Robin Hankin wrote: Hello Baptiste Bessel functions with complex arguments are not supported in R. Neither matlab nor the Gnu Scientific Library support them either. . . . but . . . the pari/gp system (released on the GPL) does: ? besselj(1+I,3) %3 = 0.6919067491368555819808728680 + 0.4484268613977010268818252591*I ? You can access some pari/gp functionality from within R by using the elliptic package, although unfortunately its wrapper function, P.pari(), is not quite flexible enough to deal with besselj(). I'd be happy to discuss this offline; P.pari() will need only minor changes to accommodate besselj(). HTH Robin On 9 Mar 2008, at 13:44, baptiste Auguié wrote: Dear R users, I'm porting a piece of Matlab code to R, but I'm now stuck with the following: I need an equivalent of besselJ(x, nu) that can handle a complex argument x. I couldn't find any R implementation. I did find a possible fortran solution in SLATEC ( http://www.netlib.org/ slatec/ , CBESJ-C), however I've never tried to use external C or Fortran code together with my R code, so I'm not sure where to go for a simple solution. Any advice welcome, Best regards baptiste _ Baptiste Auguié Physics Department University of Exeter Stocker Road, Exeter, Devon, EX4 4QL, UK Phone: +44 1392 264187 http://newton.ex.ac.uk/research/emag http://projects.ex.ac.uk/atto __ 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. -- Robin Hankin Uncertainty Analyst and Neutral Theorist, National Oceanography Centre, Southampton European Way, Southampton SO14 3ZH, UK tel 023-8059-7743 _ Baptiste Auguié Physics Department University of Exeter Stocker Road, Exeter, Devon, EX4 4QL, UK Phone: +44 1392 264187 http://newton.ex.ac.uk/research/emag http://projects.ex.ac.uk/atto __ 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] incomplete final line by readTableHeader?
Dear everyone I tried reading my own Excel spreadsheet data in R, but kept getting an warning message 'incomplete final line by readTableHeader'F:\mm1data.xls'. On viewing its rows and columns, only 'NA's were returned. Having difficult time with this problem for too long, any solution would be greatly appreciated. Thank you in advance Dai Nishikawa (PhD candidate) Biomechanics Laboratory Tamaki Campus, University of Auckland (0)9 373 7599 ext 82560 Mobile: 0212144873 [[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] Spatially Lagged Predictor Variable Models
ArunPrasad wrote: Hi Everyone, I am doing a project based on Spatially Lagged Predictor Variable Models, I would like to know which package in R would execute this model. Also, I am new to this field of spatial statistics. Any suggestions for a good book on spatial regression analysis would be appreciated. Thanks Again. Cheers Arun Hi, you may have a look at lag.listw in the package 'spdep' by R Bivand, which computes a lag vector given a variable and a list of spatial weights. There is a nice review of spatial methods in ecology, already mentioned on this list I think: Carsten F. Dormann, Jana M. McPherson, Miguel B. Araújo, Roger Bivand, Janine Bolliger, Gudrun Carl, Richard G. Davies, Alexandre Hirzel, Walter Jetz, W. Daniel Kissling, Ingolf Kühn, Ralf Ohlemüller, Pedro R. Peres-Neto, Björn Reineking, Boris Schröder, Frank M. Schurr and Robert Wilson,. (2007) Methods to account for spatial autocorrelation in the analysis of species distributional data: a review. /Ecography/ 30:5, 609–628 This may be a good starting point. Cheers, Thibaut. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en http://adegenet.r-forge.r-project.org/ __ 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] Sealed for setGeneric
Hi the list When two setGeneric occurs on the same function, the second erage the first and erase all the function previously define. Is it possible to prevent that ? Is it possible to declare a setGeneric that can not be erased later ? Something like the |sealed for setMethod...| || |Thanks| || 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.
[R] How to set type of censored data in coxph regression
Dear R users, I tried to analysis the hazard function of some data by coxph function in survival package. The type of the data include left-censored, right-censored, both right-censored and left-censored (btw, does this has a technical term?), and complete ones. I noticed that event (one parameter in Surv()) might be an indicator for the censored type. However, whenever I set event to 2 or 3, the Surv() function always returns error msg. Take the following code segment for example, state = c(0, 0, 1, 1, 2, 2, 3, 3, 0, 1) begin = c(0, 0, 1, 1, 1, 2, 2, 1, 0, 1) end = c(8, 8, 9, 7, 8, 6, 9, 8, 8, 9) Surv(begin, end, state) will get err msg: Surv(begin, end, state) : Invalid status value When trying the following code segment: state = c(0, 0, 1, 1, 0, 1, 0, 1, 0, 1) Surv(begin, end, state) will get [1] (0,8+] (0,8+] (1,9 ] (1,7 ] (1,8+] (2,6 ] (2,9+] (1,8 ] (0,8+] (1,9 ] I can understand the second code segment, but I cannot understand why the first code segments failed. Can anyone give me some examples or suggestions? Thanks a lot. __ 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] howto find corresponding values in datasource?
The x coordinate of the max y value: x[which.max(mydiff$y)] Jonas Stein wrote: Hi, i am sure, that this is a noob-question, but i have searched for hours without any good result. I want to draw a vertical line through the maximum of the first derivation. Here is a small example. --8-[mydata.csv] HM 115 222 323 417 510 --8-[myquestion.R]-- mydata - read.table(mydata.csv, header=TRUE, sep=\t) attach(mydata) # make a smooth fit through the points and calculate the first derivation d/dx myspl - smooth.spline(H, M, all.knots = FALSE, nknots = 10, spar=0.5) mydiff - predict(myspl, 0:max(H), deriv=1) # find the maximum peak max(y) y1=y2= max(mydiff$y) # now i want to plot a line through the maximum of the derivation # how can i get the x-coordinate? # segments(x1,y1,x2,y2) detach() --8- Thank you, -- Jonas Stein __ 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. -- View this message in context: http://www.nabble.com/howto-find-corresponding-values-in-datasource--tp16016130p16023738.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] Specifying relative position of text in a plot
On Thu, 13 Mar 2008, Tom La Bone wrote: Thanks for all of the suggestions. The key key here seems to be using the par function to change the coordinate system like so plot(rnorm(100), rnorm(100)) op - par(usr) par(usr = c(0, 1, 0, 1)) text(0.5,0.5,TEST) par(usr = op) Prof Ripley commented that this approach will also work on log plots, but I don't think I completely understand what is going on because this does not work for me plot(rlnorm(100), rlnorm(100),log=xy) op - par(usr) par(usr = c(0, 1, 0, 1)) text(0.5,0.5,TEST) par(usr = op) Any hints on what I am doing wrong with the log plots? Thanks again for the help. You need par(usr = c(0, 1, 0, 1), xlog=FALSE, ylog=FALSE) to set up a non-log coordinate system. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Specifying relative position of text in a plot
Thanks for all of the suggestions. The key key here seems to be using the par function to change the coordinate system like so plot(rnorm(100), rnorm(100)) op - par(usr) par(usr = c(0, 1, 0, 1)) text(0.5,0.5,TEST) par(usr = op) Prof Ripley commented that this approach will also work on log plots, but I don't think I completely understand what is going on because this does not work for me plot(rlnorm(100), rlnorm(100),log=xy) op - par(usr) par(usr = c(0, 1, 0, 1)) text(0.5,0.5,TEST) par(usr = op) Any hints on what I am doing wrong with the log plots? Thanks again for the help. Tom -- View this message in context: http://www.nabble.com/Specifying-relative-position-of-text-in-a-plot-tp16002549p16024549.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] recover masked functions?
Werner Wernersen wrote: Hi, I have loaded the packages car, memisc, Hmisc and all of these implement the function recode. The order in which the packages are loaded depends on the order I execute my scripts and thus is not always the same and the syntax of the recode function changes with the package. Is there any way to call specificly the memisc recode function? Or maybe it's better to detach all packages first and then load the required once in each script. Is there a way to detach all non-standard packages with a single line of code? This is my first larger project in R and I see there is a lot to learn about how to manage the pieces. You can specify the package in which to find the function in by using pkgname::recode. Duncan Murdoch __ 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] Compare two correlations matrices
Hi there, When I make two correlations matrices of the same size from a - cor(el[1:20]) b - cor(fl[1:20]) how can I compare if this matrices are equal? Thanks, Martin -- Ihr Partner für Webdesign, Webapplikationen und Webspace. http://www.roomandspace.com/ Martin Kaffanke +43 650 4514224 signature.asc Description: Dies ist ein digital signierter Nachrichtenteil __ 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] recover masked functions?
Use: memisc::recode() car::recode() Hmisc::recode() On 13/03/2008, Werner Wernersen [EMAIL PROTECTED] wrote: Hi, I have loaded the packages car, memisc, Hmisc and all of these implement the function recode. The order in which the packages are loaded depends on the order I execute my scripts and thus is not always the same and the syntax of the recode function changes with the package. Is there any way to call specificly the memisc recode function? Or maybe it's better to detach all packages first and then load the required once in each script. Is there a way to detach all non-standard packages with a single line of code? This is my first larger project in R and I see there is a lot to learn about how to manage the pieces. Thanks a million, Werner E-Mails jetzt auf Ihrem Handy. __ 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 __ 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] Sealed for setGeneric
On Mar 13, 2008, at 5:04 AM, Christophe Genolini wrote: Hi the list When two setGeneric occurs on the same function, the second erage the first and erase all the function previously define. Is it possible to prevent that ? Is it possible to declare a setGeneric that can not be erased later ? Something like the |sealed for setMethod...| || |Thanks| || Christophe Does this answer your questions? http://www1.maths.lth.se/help/R/setGenericS3/ Haris Skiadas Department of Mathematics and Computer Science Hanover College __ 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 Finance
Hi, I am an R novice working with financial data. I am developing a portfolio strategy evaluation technique to back-test the performance of our screens; checking how the screened stock would've performed over the period in question. I am using quantmod in R to download the historical data from yahoo and then analyzing it using PerformanceAnalytics. My problem is that, as our screens are done using Bloomberg, my list of screened stocks only has Bloomberg tickers and ISINs. Does anybody know of a method which could convert ISINs to yahoo tickers/symbols?? Or a method of accessing yahoo historical data from an ISIN (instead of a symbol call)? I would prefer not to use RBloomberg to download the data as the data calls would be extensive in testing. Thank you!! __ 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] internet proxy settings (win)
Thank you Philipp for your suggestions. In Rprofile.site every line is commented out and I could not find any .Rprofile. I even tried starting R with additional cmdline arguments --no-environ and --no-init-file. Still update.packages(ask='graphics') --- Please select a CRAN mirror for use in this session --- Fehler: Indizierung außerhalb der Grenzen Zusätzlich: Warning messages: 1: In read.dcf(file = tmpf) : Line starting 'html ...' is malformed! 2: In read.dcf(file = tmpf) : Line starting ' head ...' is malformed! 3: In read.dcf(file = tmpf) : Line starting '/html ...' is malformed! This is as far as I allready have been - or not? Thomas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Compare two correlations matrices
Try: all.equal(cor(d), cor(e)) identical(cor(d), cor(e)) cor(d) == cor(e) On 13/03/2008, Martin Kaffanke [EMAIL PROTECTED] wrote: Hi there, When I make two correlations matrices of the same size from a - cor(el[1:20]) b - cor(fl[1:20]) how can I compare if this matrices are equal? Thanks, Martin -- Ihr Partner für Webdesign, Webapplikationen und Webspace. http://www.roomandspace.com/ Martin Kaffanke +43 650 4514224 __ 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 __ 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] cumsum list..
Hi all, i have the following.. a - data.frame(data = seq(1,10)) i have indices: x - c(1, 5, 3, 9) y - c(2, 7, 4, 10) I want the cumsum of a[1:2], a[5:7], a[3:4]... is there an elegant way to do it without any loop? Thanks! -- View this message in context: http://www.nabble.com/cumsum-list..-tp16025202p16025202.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] cumsum list..
cumsum( mapply(function(i,j) sum(a$data[i:j]), x, y) ) Is this what you want? Gabor On Thu, Mar 13, 2008 at 06:02:13AM -0700, yoo wrote: Hi all, i have the following.. a - data.frame(data = seq(1,10)) i have indices: x - c(1, 5, 3, 9) y - c(2, 7, 4, 10) I want the cumsum of a[1:2], a[5:7], a[3:4]... is there an elegant way to do it without any loop? Thanks! -- View this message in context: http://www.nabble.com/cumsum-list..-tp16025202p16025202.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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] R Finance
I guess I would create a mapping table to convert between the symbols from Bloomberg and from Yahoo. You should be able to just create it once and add to it as new symbols appear on your screens. Most of the symbols should be the same so you could omit those. If it all has to be automated, you could use RBloomberg to get the tickers from the ISINs in one call, but there may still be other transformations needed, such as XYZ/A to XYZA or whatever. HTH, David L. Reiner, PhD Head Quant Rho Trading Securities, LLC -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ruby Sent: Thursday, March 13, 2008 6:44 AM To: r-help@r-project.org Subject: [R] R Finance Hi, I am an R novice working with financial data. I am developing a portfolio strategy evaluation technique to back-test the performance of our screens; checking how the screened stock would've performed over the period in question. I am using quantmod in R to download the historical data from yahoo and then analyzing it using PerformanceAnalytics. My problem is that, as our screens are done using Bloomberg, my list of screened stocks only has Bloomberg tickers and ISINs. Does anybody know of a method which could convert ISINs to yahoo tickers/symbols?? Or a method of accessing yahoo historical data from an ISIN (instead of a symbol call)? I would prefer not to use RBloomberg to download the data as the data calls would be extensive in testing. Thank you!! __ 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] joining matrices, vectors, scalars in one object
Hi, I have: a - matrix(c(0,1,0,1),nrow=2) b - matrix(c(1,1,1,0,0,0),nrow=3) c - 1 d - c(1,0,1) And I would like to join them in an object 'thing' so that I can access a, b, c, or d through an index in a for loop. For example: thing[4] would return [1] 1 0 1 Note however, that I have many of these 'thing' components. So many that a command like thing - list(a = matrix(c(0,1,0,1),nrow=2), b = matrix(c (1,1,1,0,0,0),nrow=3), c = 1, d = c(1,0,1)) would become long and awkward. Is there a way of declaring an empty 'thing' of a given length and then assigning its elements from a for loop? I need to allow elements a, b, c... that can be scalars, vectors or matrices with varying dimensions. Thanks! Gonçalo [[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] joining matrices, vectors, scalars in one object
You want to do
thing - list()# empty thing
for ( i in 1:100 ) {
thing[[i]] - ?
}
But where is ? coming from? If you can index it with an integer
then it is exactly coming from the kind of object you want to create.
Chicken-egg problem. No?
G.
On Thu, Mar 13, 2008 at 09:04:11AM -0400, Gonçalo Ferraz wrote:
Hi,
I have:
a - matrix(c(0,1,0,1),nrow=2)
b - matrix(c(1,1,1,0,0,0),nrow=3)
c - 1
d - c(1,0,1)
And I would like to join them in an object 'thing' so that I can
access a, b, c, or d through an index in a for loop.
For example:
thing[4]
would return
[1] 1 0 1
Note however, that I have many of these 'thing' components. So many
that a command like
thing - list(a = matrix(c(0,1,0,1),nrow=2), b = matrix(c
(1,1,1,0,0,0),nrow=3), c = 1, d = c(1,0,1))
would become long and awkward.
Is there a way of declaring an empty 'thing' of a given length and
then assigning its elements from a for loop? I need to allow elements
a, b, c... that can be scalars, vectors or matrices with varying
dimensions.
Thanks!
Gon?alo
[[alternative HTML version deleted]]
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--
Csardi Gabor [EMAIL PROTECTED]UNIL DGM
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Re: [R] type of object of a variable in a data frame
Chang Liu [EMAIL PROTECTED] wrote in news:[EMAIL PROTECTED]: 3. The reason I want it to be a list or vector, is that I want to fill in some blank values, i can't seem to do things like: data$V1[1] = 3 Is it because these variables are pointers? Is there a better way to do this? You have not given reproducible code, so it is difficult to know why that does not succeed. I have a data.frame with a similar name left over from another problem. When I enter DATA$V1[1] = -.5 , it has the desired effect. Although it is not the source of the error, you should learn to use - rather than =. You should also learn to post questions with reproducible code. -- David Winsemius __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] a more elegant way to get percentages?
Hi,
I am trying to get percentages in a more elegant way. I have a data.frame with
locations and values (counts) of species at that location. Each location is
repeated for each species i have values for and i would like to get percentages
of each species at that location. I am not sure if i am clear in my
explanations so i will paste my code below:
#
x
locat val
1 a 5
2 b 5
3 b 15
4 c 5
5 c 20
6 c 5
7 c 10
8 d 5
9 d 15
10 d 10
loc1 - x$locat
n - length(loc1)
locuniq1 - unique(loc1)
m - length(locuniq1)
counts - seq(1:m)
for (i in 1:m) {
+ count - 0
+ for (j in 1:n) {
+ if (loc1[j]==locuniq1[i]) count - count+1
+ counts[i] - count
+ }
+ }
percent1 - rep(0,n)
j - 0
for (i in 1:m) {
+
+ b - x[(j+1):(j+counts[i]),]
+ total - sum(b$val)
+ percent1[(j+1):(j+counts[i])] - round(apply(as.matrix(b$val), 1, function(x)
{x*100/total}),2)
+ j = j+counts[i]
+ }
x1 - cbind(x, percent1)# this is the result i want
x1
locat val percent1
1 a 5 100.00
2 b 525.00
3 b 1575.00
4 c 512.50
5 c 2050.00
6 c 512.50
7 c 1025.00
8 d 516.67
9 d 1550.00
10 d 1033.33
I am wondering if there is any way to do it more efficiently, much more that
the first loop which gives how many times each location is present in the
data.frame is slow if you have a larger data.frame and not only 10 rows.
Thanks for any input and sorry if the email is on the long side,
Monica
_
[[elided Hotmail spam]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] joining matrices, vectors, scalars in one object
I think you need:
thing - vector(list, 4)
for (i in seq_along(thing)) {
thing[[i]] - # what you want to put here
}
Best,
Dimitris
Dimitris Rizopoulos
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://med.kuleuven.be/biostat/
http://www.student.kuleuven.be/~m0390867/dimitris.htm
- Original Message -
From: Gonçalo Ferraz [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Thursday, March 13, 2008 2:04 PM
Subject: [R] joining matrices, vectors, scalars in one object
Hi,
I have:
a - matrix(c(0,1,0,1),nrow=2)
b - matrix(c(1,1,1,0,0,0),nrow=3)
c - 1
d - c(1,0,1)
And I would like to join them in an object 'thing' so that I can
access a, b, c, or d through an index in a for loop.
For example:
thing[4]
would return
[1] 1 0 1
Note however, that I have many of these 'thing' components. So many
that a command like
thing - list(a = matrix(c(0,1,0,1),nrow=2), b = matrix(c
(1,1,1,0,0,0),nrow=3), c = 1, d = c(1,0,1))
would become long and awkward.
Is there a way of declaring an empty 'thing' of a given length and
then assigning its elements from a for loop? I need to allow elements
a, b, c... that can be scalars, vectors or matrices with varying
dimensions.
Thanks!
Gonçalo
[[alternative HTML version deleted]]
__
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http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
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and provide commented, minimal, self-contained, reproducible code.
[R] lmer and correlation
Hello list, I've been reading through the archives and it seems as though, as of right now, there is no way to specify the correlation structure in lmer. I was wondering if anyone knows if this is going to be implemented? I'm using mixed-effects models within a tree structure, so I make a lot of calls to lme to get the resulting deviance, and lmer2 is almost 5 times faster than lme on my test data, so if it may be implemented later I'd be willing to wait, otherwise I might look into trying to hack it myself. Sam Stewart __ 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] a more elegant way to get percentages?
try the following:
x - read.table(textConnection(locat val
1 a 5
2 b 5
3 b 15
4 c 5
5 c 20
6 c 5
7 c 10
8 d 5
9 d 15
10 d 10), header = TRUE)
x$percent1 - unlist(tapply(x$val, x$locat, function(x){
round(100 * x / sum(x), 2)
}))
x
however, check whether the levels of the factor 'x$locat' are
appropriately ordered.
I hope it helps.
Best,
Dimitris
Dimitris Rizopoulos
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://med.kuleuven.be/biostat/
http://www.student.kuleuven.be/~m0390867/dimitris.htm
- Original Message -
From: Monica Pisica [EMAIL PROTECTED]
To: r-help@r-project.org
Sent: Thursday, March 13, 2008 2:36 PM
Subject: [R] a more elegant way to get percentages?
Hi,
I am trying to get percentages in a more elegant way. I have a
data.frame with locations and values (counts) of species at that
location. Each location is repeated for each species i have values
for and i would like to get percentages of each species at that
location. I am not sure if i am clear in my explanations so i will
paste my code below:
#
x
locat val
1 a 5
2 b 5
3 b 15
4 c 5
5 c 20
6 c 5
7 c 10
8 d 5
9 d 15
10 d 10
loc1 - x$locat
n - length(loc1)
locuniq1 - unique(loc1)
m - length(locuniq1)
counts - seq(1:m)
for (i in 1:m) {
+ count - 0
+ for (j in 1:n) {
+ if (loc1[j]==locuniq1[i]) count - count+1
+ counts[i] - count
+ }
+ }
percent1 - rep(0,n)
j - 0
for (i in 1:m) {
+
+ b - x[(j+1):(j+counts[i]),]
+ total - sum(b$val)
+ percent1[(j+1):(j+counts[i])] - round(apply(as.matrix(b$val), 1,
function(x) {x*100/total}),2)
+ j = j+counts[i]
+ }
x1 - cbind(x, percent1)# this is the result i want
x1
locat val percent1
1 a 5 100.00
2 b 525.00
3 b 1575.00
4 c 512.50
5 c 2050.00
6 c 512.50
7 c 1025.00
8 d 516.67
9 d 1550.00
10 d 1033.33
I am wondering if there is any way to do it more efficiently, much
more that the first loop which gives how many times each location is
present in the data.frame is slow if you have a larger data.frame
and not only 10 rows.
Thanks for any input and sorry if the email is on the long side,
Monica
_
[[elided Hotmail spam]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] a more elegant way to get percentages?
Assuming your x is as follows:
x - data.frame(locat = c(a, b, b, c, c, c, c, d, d, d),
val = c(5, 5, 15, 5, 20, 5, 10, 5, 15, 10))
Try this:
x$percent1 - ave(x$val, x$locat, FUN = function(x) 100*x/sum(x))
On Thu, Mar 13, 2008 at 9:36 AM, Monica Pisica [EMAIL PROTECTED] wrote:
Hi,
I am trying to get percentages in a more elegant way. I have a data.frame
with locations and values (counts) of species at that location. Each location
is repeated for each species i have values for and i would like to get
percentages of each species at that location. I am not sure if i am clear in
my explanations so i will paste my code below:
#
x
locat val
1 a 5
2 b 5
3 b 15
4 c 5
5 c 20
6 c 5
7 c 10
8 d 5
9 d 15
10 d 10
loc1 - x$locat
n - length(loc1)
locuniq1 - unique(loc1)
m - length(locuniq1)
counts - seq(1:m)
for (i in 1:m) {
+ count - 0
+ for (j in 1:n) {
+ if (loc1[j]==locuniq1[i]) count - count+1
+ counts[i] - count
+ }
+ }
percent1 - rep(0,n)
j - 0
for (i in 1:m) {
+
+ b - x[(j+1):(j+counts[i]),]
+ total - sum(b$val)
+ percent1[(j+1):(j+counts[i])] - round(apply(as.matrix(b$val), 1,
function(x) {x*100/total}),2)
+ j = j+counts[i]
+ }
x1 - cbind(x, percent1)# this is the result i want
x1
locat val percent1
1 a 5 100.00
2 b 525.00
3 b 1575.00
4 c 512.50
5 c 2050.00
6 c 512.50
7 c 1025.00
8 d 516.67
9 d 1550.00
10 d 1033.33
I am wondering if there is any way to do it more efficiently, much more that
the first loop which gives how many times each location is present in the
data.frame is slow if you have a larger data.frame and not only 10 rows.
Thanks for any input and sorry if the email is on the long side,
Monica
_
[[elided Hotmail spam]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] a more elegant way to get percentages?
Monica,
You can try the following:
x.tot - aggregate(x$val, by=list(total=x$locat), 'sum')
x.tot
total x
1 a 5
2 b 20
3 c 40
4 d 30
cbind(x, perc=x$val/rep(x.tot$x, table(x$locat)) * 100)
locat val perc
1 a 5 100.0
2 b 5 25.0
3 b 15 75.0
4 c 5 12.5
5 c 20 50.0
6 c 5 12.5
7 c 10 25.0
8 d 5 16.7
9 d 15 50.0
10 d 10 33.3
-Christos
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Monica Pisica
Sent: Thursday, March 13, 2008 9:36 AM
To: r-help@r-project.org
Subject: [R] a more elegant way to get percentages?
Hi,
I am trying to get percentages in a more elegant way. I have
a data.frame with locations and values (counts) of species at
that location. Each location is repeated for each species i
have values for and i would like to get percentages of each
species at that location. I am not sure if i am clear in my
explanations so i will paste my code below:
#
x
locat val
1 a 5
2 b 5
3 b 15
4 c 5
5 c 20
6 c 5
7 c 10
8 d 5
9 d 15
10 d 10
loc1 - x$locat
n - length(loc1)
locuniq1 - unique(loc1)
m - length(locuniq1)
counts - seq(1:m)
for (i in 1:m) {
+ count - 0
+ for (j in 1:n) {
+ if (loc1[j]==locuniq1[i]) count - count+1 counts[i] - count } }
percent1 - rep(0,n)
j - 0
for (i in 1:m) {
+
+ b - x[(j+1):(j+counts[i]),]
+ total - sum(b$val)
+ percent1[(j+1):(j+counts[i])] - round(apply(as.matrix(b$val), 1,
+ function(x) {x*100/total}),2) j = j+counts[i] }
x1 - cbind(x, percent1)# this is the result i want
x1
locat val percent1
1 a 5 100.00
2 b 525.00
3 b 1575.00
4 c 512.50
5 c 2050.00
6 c 512.50
7 c 1025.00
8 d 516.67
9 d 1550.00
10 d 1033.33
I am wondering if there is any way to do it more efficiently,
much more that the first loop which gives how many times each
location is present in the data.frame is slow if you have a
larger data.frame and not only 10 rows.
Thanks for any input and sorry if the email is on the long side,
Monica
_
[[elided Hotmail spam]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Negative/ positive rolling correlation
Rthoughts [EMAIL PROTECTED] wrote in news:[EMAIL PROTECTED]: There is one question I have though. I can see that worksheets and history can be saved, however I am beat as to exactly what they save? Do they save the command lines and associated data sheets and graphs? There is no datasheet but the R objects defined and saved in the last session will automatically be loaded into the workspace from the .Rdata file when a new session begins. It is also possible to save named .Rdata files and reload them under user control. If you look at an .Rdata file with a text editor, it is pretty much meaningless. On the other hand, if you look at .Rhistory, you will see a text file that is simply a sequential listing of the commands of earlier saved sessions. Oh, I'm using Rcmdr. In my case it is an excellent software that cuts hours off my progamming work freeing up time for other parts of the project and breaks, lol! The other, I want to do a correlation to highlight matching patterns between two columns of radon levels (96 lines each) divided by the hour they were recorded in the two machines. A scattergraph is similar but I want to produce visualtisations for negative/ positive correlation against time. Can anyone suggest anything? Thanks. You need to investigate time series analyses methods. I am assuming that the radon levels are ordered and associated with times, rather than mathematically divided by them. There are extensive capabilities for analyzing and displaying such information in R. See for instance: http://cran.r-project.org/doc/contrib/Ricci-refcard-ts.pdf -- David Winsemius __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to set type of censored data in coxph regression
Dear R users, I tried to analysis the hazard function of some data by coxph function in survival package. The type of the data include left-censored, right-censored, both right-censored and left-censored (btw, does this has a technical term?), and complete ones. The coxph function is only defined for right-censored data. That is why you get an error when you include left and interval censored observations. Terry Therneau __ 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] a more elegant way to get percentages?
Hi everybody,
I am amazed how quick i got my answer ;-) I have to recognize that Gabor's code
really puts to shame my skills in doing any programming in R. Is there any book
or documentation which really explains in details all these neat tricks from
{stats} like ave (i even didn't know this function existed), apply and all its
friends (sapply, tapply, etc) ? To be honest it took me quite a while to come
up with the fancy subscripting to get my persantages ;-))
thank you so much, i really appreciate your help,
Monica
Date: Thu, 13 Mar 2008 09:45:05 -0400
From: [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Subject: Re: [R] a more elegant way to get percentages?
CC: r-help@r-project.org
Assuming your x is as follows:
x - data.frame(locat = c(a, b, b, c, c, c, c, d, d, d),
val = c(5, 5, 15, 5, 20, 5, 10, 5, 15, 10))
Try this:
x$percent1 - ave(x$val, x$locat, FUN = function(x) 100*x/sum(x))
On Thu, Mar 13, 2008 at 9:36 AM, Monica Pisica wrote:
Hi,
I am trying to get percentages in a more elegant way. I have a data.frame
with locations and values (counts) of species at that location. Each
location is repeated for each species i have values for and i would like to
get percentages of each species at that location. I am not sure if i am
clear in my explanations so i will paste my code below:
#
x
locat val
1 a 5
2 b 5
3 b 15
4 c 5
5 c 20
6 c 5
7 c 10
8 d 5
9 d 15
10 d 10
loc1 - x$locat
n - length(loc1)
locuniq1 - unique(loc1)
m - length(locuniq1)
counts - seq(1:m)
for (i in 1:m) {
+ count - 0
+ for (j in 1:n) {
+ if (loc1[j]==locuniq1[i]) count - count+1
+ counts[i] - count
+ }
+ }
percent1 - rep(0,n)
j - 0
for (i in 1:m) {
+
+ b - x[(j+1):(j+counts[i]),]
+ total - sum(b$val)
+ percent1[(j+1):(j+counts[i])] - round(apply(as.matrix(b$val), 1,
function(x) {x*100/total}),2)
+ j = j+counts[i]
+ }
x1 - cbind(x, percent1) # this is the result i want
x1
locat val percent1
1 a 5 100.00
2 b 5 25.00
3 b 15 75.00
4 c 5 12.50
5 c 20 50.00
6 c 5 12.50
7 c 10 25.00
8 d 5 16.67
9 d 15 50.00
10 d 10 33.33
I am wondering if there is any way to do it more efficiently, much more that
the first loop which gives how many times each location is present in the
data.frame is slow if you have a larger data.frame and not only 10 rows.
Thanks for any input and sorry if the email is on the long side,
Monica
_
[[elided Hotmail spam]]
__
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.
_
08
__
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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] How to cbind or rbind different lengths vectors/arrays without repeating the elements of the shorter vectors/arrays ?
Hi, How to cbind or rbind different lengths vectors/arrays without repeating the elements of the shorter vectors/arrays ? cbind(1:2, 1:10) [,1] [,2] [1,]11 [2,]22 [3,]13 [4,]24 [5,]15 [6,]26 [7,]17 [8,]28 [9,]19 [10,]2 10 [[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] Sealed for setGeneric
Christophe Genolini [EMAIL PROTECTED] writes: Hi the list When two setGeneric occurs on the same function, the second erage the first and erase all the function previously define. 'erase' is only true if you attempt to define the generic in the same name space (e.g., in the global environment, as occurs from the command line, or in a single package). Is it possible to prevent that ? Is it possible to declare a setGeneric that can not be erased later ? Generics defined in different name spaces are not 'erased', but the name space occuring earlier in the search path is 'masked' by generics occuring later in the search path. getGeneric(show) standardGeneric for show defined from package methods function (object) standardGeneric(show) environment: 0x16b8b40 Methods may be defined for arguments: object Use showMethods(show) for currently available ones. show(1:10) [1] 1 2 3 4 5 6 7 8 9 10 setGeneric(show, function(object) standardGeneric(show)) [1] show setMethod(show, numeric, function(object) oops) [1] show show(1:10) [1] oops methods::show(1:10) [1] 1 2 3 4 5 6 7 8 9 10 removeGeneric(show) [1] TRUE show(1:10) [1] 1 2 3 4 5 6 7 8 9 10 Something like the |sealed for setMethod...| an unusual strategy would be to use lockBinding to make the symbol associated with the generic unchangeable. setGeneric(show, function(object) standardGeneric(show)) [1] show lockBinding(show, .GlobalEnv) NULL setGeneric(show, function(object) standardGeneric(show)) Error in assign(name, fdef, where) : cannot change value of locked binding for 'show' unlockBinding(show, .GlobalEnv) NULL setGeneric(show, function(object) standardGeneric(show)) [1] show Martin || |Thanks| || 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. -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793 __ 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] [PS] Re: a more elegant way to get percentages? (now R books)
Monica --
There has been a virtual population explosion of R books in recent years
and we all have our favorites. You may wish to pick one oriented toward
your specialty, but the absolute minimum lowest common denominator (by
which I mean that it has the ground zero essential information that all
users must share, not that it is minimal or incomplete) is the manual
An Introduction to R, available by download from the Cran website.
Beyond that, my favorite introduction is Peter Dalgaard's Introductory
Statistics with R. He has an elegance and clarity of style, as well as
a feel for what is necessary to include in an introduction, that some
others lack. Others may disagree, but I find myself returning to
Dalgaard again and again.
Ben
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Monica Pisica
Sent: Thursday, March 13, 2008 9:05 AM
To: Gabor Grothendieck; [EMAIL PROTECTED];
[EMAIL PROTECTED]
Cc: r-help@r-project.org
Subject: [PS] Re: [R] a more elegant way to get percentages?
Hi everybody,
I am amazed how quick i got my answer ;-) I have to recognize that
Gabor's code really puts to shame my skills in doing any programming in
R. Is there any book or documentation which really explains in details
all these neat tricks from {stats} like ave (i even didn't know this
function existed), apply and all its friends (sapply, tapply, etc) ? To
be honest it took me quite a while to come up with the fancy
subscripting to get my persantages ;-))
thank you so much, i really appreciate your help,
Monica
Date: Thu, 13 Mar 2008 09:45:05 -0400
From: [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Subject: Re: [R] a more elegant way to get percentages?
CC: r-help@r-project.org
Assuming your x is as follows:
x - data.frame(locat = c(a, b, b, c, c, c, c, d, d,
d),
val = c(5, 5, 15, 5, 20, 5, 10, 5, 15, 10))
Try this:
x$percent1 - ave(x$val, x$locat, FUN = function(x) 100*x/sum(x))
On Thu, Mar 13, 2008 at 9:36 AM, Monica Pisica wrote:
Hi,
I am trying to get percentages in a more elegant way. I have a
data.frame with locations and values (counts) of species at that
location. Each location is repeated for each species i have values for
and i would like to get percentages of each species at that location. I
am not sure if i am clear in my explanations so i will paste my code
below:
#
x
locat val
1 a 5
2 b 5
3 b 15
4 c 5
5 c 20
6 c 5
7 c 10
8 d 5
9 d 15
10 d 10
loc1 - x$locat
n - length(loc1)
locuniq1 - unique(loc1)
m - length(locuniq1)
counts - seq(1:m)
for (i in 1:m) {
+ count - 0
+ for (j in 1:n) {
+ if (loc1[j]==locuniq1[i]) count - count+1
+ counts[i] - count
+ }
+ }
percent1 - rep(0,n)
j - 0
for (i in 1:m) {
+
+ b - x[(j+1):(j+counts[i]),]
+ total - sum(b$val)
+ percent1[(j+1):(j+counts[i])] - round(apply(as.matrix(b$val), 1,
function(x) {x*100/total}),2)
+ j = j+counts[i]
+ }
x1 - cbind(x, percent1) # this is the result i want
x1
locat val percent1
1 a 5 100.00
2 b 5 25.00
3 b 15 75.00
4 c 5 12.50
5 c 20 50.00
6 c 5 12.50
7 c 10 25.00
8 d 5 16.67
9 d 15 50.00
10 d 10 33.33
I am wondering if there is any way to do it more efficiently, much
more that the first loop which gives how many times each location is
present in the data.frame is slow if you have a larger data.frame and
not only 10 rows.
Thanks for any input and sorry if the email is on the long side,
Monica
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[R] How to manipulate data according to groups ?
Hi, I have a two columns data, the first column are values, and second column are the groups. For this example, there are 3 groups 1,2,3. How can I manipulate the values in the first column according to groups, say I would like to find mean, sum, and standard deviation for the different groups ? How do I plot data according to groups ? t - matrix(c(rnorm(10), 1,1,2,2,1,3,3,3,3,2), ncol=2) [[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] how to generate bar charts with the standard deviation
Hi, I have the two vectors mean and sd of individual columns, but I am unsure how to generate bar charts with the standard deviation, even after looking the help of barplot and barplot.2. [[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] [PS] How to manipulate data according to groups ?
Look at ?tapply, based on your description, it is what you want. Ben -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ng Stanley Sent: Thursday, March 13, 2008 9:25 AM To: r-help Subject: [PS] [R] How to manipulate data according to groups ? Hi, I have a two columns data, the first column are values, and second column are the groups. For this example, there are 3 groups 1,2,3. How can I manipulate the values in the first column according to groups, say I would like to find mean, sum, and standard deviation for the different groups ? How do I plot data according to groups ? t - matrix(c(rnorm(10), 1,1,2,2,1,3,3,3,3,2), ncol=2) [[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] a more elegant way to get percentages?
From: [EMAIL PROTECTED]
Now that people have answered Monica's query, can someone help me?!!
See below.
On 13-Mar-08 13:36:03, Monica Pisica wrote:
Hi,
I am trying to get percentages in a more elegant way. I have a
data.frame with locations and values (counts) of species at that
location. Each location is repeated for each species i have
values for
and i would like to get percentages of each species at that
location. I
am not sure if i am clear in my explanations so i will paste my code
below:
#
x
locat val
1 a 5
2 b 5
3 b 15
4 c 5
5 c 20
6 c 5
7 c 10
8 d 5
9 d 15
10 d 10
With Monica's dataframe as above, the answer would be 100*x[,1]/z
where we want z to be c(5,20,20,40,40,40,40,30,30,30).
So, intending to give Monica a helpful answer, I tried
apply(x,1,function(y) sum(x[x[,1]==y,2]))
1 2 3 4 5 6 7 8 9 10
5 15 15 30 30 30 30 15 15 15
and similarly
apply(x,1,function(y) sum(x$val[x$locat==y]))
1 2 3 4 5 6 7 8 9 10
5 15 15 30 30 30 30 15 15 15
So why didn't this work? Where's my blind spot? Indeed, why
did it gives the results it did?
One strategy is similar to what the piano teacher ask my son to try:
break it into small pieces.
apply() works on slices of the data, so take a slice where the answer
wasn't what you expected; e.g., the last row of x. What gets passed
into the anonymous function is the 10th row of x, namely c(4, 10) (note
that apply() converts its first argument to a matrix or array). so what
would you get when you test for equality to that?
Andy
With thanks,
Ted.
E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 13-Mar-08 Time: 14:15:34
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Re: [R] a more elegant way to get percentages?
Now that people have answered Monica's query, can someone help me?!! See below. On 13-Mar-08 13:36:03, Monica Pisica wrote: Hi, I am trying to get percentages in a more elegant way. I have a data.frame with locations and values (counts) of species at that location. Each location is repeated for each species i have values for and i would like to get percentages of each species at that location. I am not sure if i am clear in my explanations so i will paste my code below: # x locat val 1 a 5 2 b 5 3 b 15 4 c 5 5 c 20 6 c 5 7 c 10 8 d 5 9 d 15 10 d 10 With Monica's dataframe as above, the answer would be 100*x[,1]/z where we want z to be c(5,20,20,40,40,40,40,30,30,30). So, intending to give Monica a helpful answer, I tried apply(x,1,function(y) sum(x[x[,1]==y,2])) 1 2 3 4 5 6 7 8 9 10 5 15 15 30 30 30 30 15 15 15 and similarly apply(x,1,function(y) sum(x$val[x$locat==y])) 1 2 3 4 5 6 7 8 9 10 5 15 15 30 30 30 30 15 15 15 So why didn't this work? Where's my blind spot? Indeed, why did it gives the results it did? With thanks, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 13-Mar-08 Time: 14:15:34 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to cbind or rbind different lengths vectors/arrays without repeating the elements of the shorter vectors/arrays ?
Try converting them to time series, cbinding and unconverting: cbind(x = ts(x), y = ts(y))[TRUE, ] On Thu, Mar 13, 2008 at 10:13 AM, Ng Stanley [EMAIL PROTECTED] wrote: Hi, How to cbind or rbind different lengths vectors/arrays without repeating the elements of the shorter vectors/arrays ? cbind(1:2, 1:10) [,1] [,2] [1,]11 [2,]22 [3,]13 [4,]24 [5,]15 [6,]26 [7,]17 [8,]28 [9,]19 [10,]2 10 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] a more elegant way to get percentages?
well, check what the apply() gives for each row of 'x', i.e., x - read.table(textConnection(locat val 1 a 5 2 b 5 3 b 15 4 c 5 5 c 20 6 c 5 7 c 10 8 d 5 9 d 15 10 d 10), header = TRUE) # apply() uses as.matrix() for data frames # 1st row of 'x' y - as.matrix(x)[1, ] x$val[x$locat == y] # 2nd row of 'x' y - as.matrix(x)[2, ] x$val[x$locat == y] # 3rd row of 'x' y - as.matrix(x)[3, ] x$val[x$locat == y] # 4th row of 'x' y - as.matrix(x)[4, ] x$val[x$locat == y] in which 'y' is auto-replicated to match the length of 'x$locat' each time. Best, Dimitris Dimitris Rizopoulos Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/337015 Web: http://med.kuleuven.be/biostat/ http://www.student.kuleuven.be/~m0390867/dimitris.htm - Original Message - From: Ted Harding [EMAIL PROTECTED] To: r-help@r-project.org Sent: Thursday, March 13, 2008 3:15 PM Subject: Re: [R] a more elegant way to get percentages? Now that people have answered Monica's query, can someone help me?!! See below. On 13-Mar-08 13:36:03, Monica Pisica wrote: Hi, I am trying to get percentages in a more elegant way. I have a data.frame with locations and values (counts) of species at that location. Each location is repeated for each species i have values for and i would like to get percentages of each species at that location. I am not sure if i am clear in my explanations so i will paste my code below: # x locat val 1 a 5 2 b 5 3 b 15 4 c 5 5 c 20 6 c 5 7 c 10 8 d 5 9 d 15 10 d 10 With Monica's dataframe as above, the answer would be 100*x[,1]/z where we want z to be c(5,20,20,40,40,40,40,30,30,30). So, intending to give Monica a helpful answer, I tried apply(x,1,function(y) sum(x[x[,1]==y,2])) 1 2 3 4 5 6 7 8 9 10 5 15 15 30 30 30 30 15 15 15 and similarly apply(x,1,function(y) sum(x$val[x$locat==y])) 1 2 3 4 5 6 7 8 9 10 5 15 15 30 30 30 30 15 15 15 So why didn't this work? Where's my blind spot? Indeed, why did it gives the results it did? With thanks, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 13-Mar-08 Time: 14:15:34 -- XFMail -- __ 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. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ 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] need automake/autoconf help to build RnetCDF and ncdf packages
Greetings all,
I recently tried to install RNetCDF from within R (install.packages)
on Fedora Core 8 (with netcdf 3.6.2 and netcdf-devel 3.6.2 already
installed). This resulted in an error because the netcdf header files
are installed in /usr/include/netcdf-3 rather than /usr/include which
is where RNetCDF looks for them. This problem was described in a 2006
post (see below), but no satisfactory resolution was posted.
For the benefit of Fedora users that run into this problem and search
the R-help archives, I am posting a solution. The command is
actually quite simple:
install.packages(RNetCDF,configure.args=--with-netcdf-include=/usr/include/netcdf-3)
If this does not work, check RnetCDF's configure.ac file for the line
that points to something like /usr/include/... and change the
netcdf-include to the name of the new variable. This will only be
necessary if the RNetCDF folks change the name of this variable (which
they did between the time of Paul's post below and yesterday).
As an aside, I've found netcdf extractions run much faster under
(64-bit) linux than (32-bit) windows xp.
Good luck!
Adam
[R] need automake/autoconf help to build RnetCDF and ncdf packages
Paul Johnson pauljohn32 at gmail.com
Tue Apr 25 22:46:26 CEST 2006
I imagine this where are your header files problem comes up in other
packages, so I'm asking this as a general R question. How should
configure scripts be re-written so they look in more places?
Briefly, the problem is that Fedora-Extras installs the header files
in a subdirectory /usr/include/netcdf-3 rather than /usr/include:
# rpm -ql netcdf-devel
/usr/include/netcdf-3
/usr/include/netcdf-3/ncvalues.h
/usr/include/netcdf-3/netcdf.h
/usr/lib/netcdf-3/libnetcdf.a
/usr/lib/netcdf-3/libnetcdf_c++.a
/usr/lib/netcdf-3/libnetcdf_g77.a
Last week I posted in this list that I re-built the Fedora-Extras
netcdf rpm so that it would have more standard installation, and then
I was able to make RNetCDF work.
In the meanwhile, I posted in bugzilla.redhat.com asking if they
might use the standard packaging, but their response is an adamant
refusal:
https://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=189734
When netcdf updates are issued in the Fedora-Extras network, the
special hacks I put in to un-do their special hacks are lost, and
netcdf programs don't work anymore.
The attempt to build ncdf fails inside R or on the command line, but
it gives a GOOD HINT about a command line work around:
# R CMD INSTALL ncdf_1.5.tar.gz
[...]
checking /sw/include/netcdf.h presence... no
checking for /sw/include/netcdf.h... no
Fatal error: I cannot find the directory that holds the netcdf include
file netcdf.h!
You can specify it as follows:
./configure --with-netcdf_incdir=directory_with_file_netcdf.h
*** Special note for R CMD INSTALL users: *
The syntax for specifying multiple --configure-args does not seem to be
well documented in R. If you have installed the netcdf include and library
directories in some non-standard location, you can specify BOTH these
during the R CMD INSTALL process using the following syntax:
R CMD INSTALL
--configure-args=-with-netcdf_incdir=/path/to/netcdf/incdir
-with-netcdf_libdir=/path/to/netcdf/libdir ncdf_1.1.tar.gz
where you should, of course, specify your own netcdf include and library
directories, and the actual package name.
***
I found that the following did work!
# R CMD INSTALL
--configure-args=-with-netcdf_incdir=/usr/include/netcdf-3
-with-netcdf_libdir=/usr/lib/netcdf-3 ncdf_1.5.tar.gz
It is not the best solution, because special administrative effort is
required. And the install.packages approach inside R won't work.
However, with RNetCDF, the problem is slightly worse, and no such
helpful message appears:
# R CMD INSTALL RNetCDF_1.1-3.tar.gz
* Installing *source* package 'RNetCDF' ...
checking for gcc... gcc
checking for C compiler default output... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for executable suffix...
checking for object suffix... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for main in -lnetcdf... no
configure: error: netcdf library not found
ERROR: configuration failed for package 'RNetCDF'
** Removing '/usr/lib/R/library/RNetCDF'
I have no reason to doubt that the Fedora-Extras authors are right,
and that some changes in the configure scripts for these packages are
required.
In RnetCDF's configure.ac file, I see the place where it specifies the
NETCDF_INCDIR
if test -z ${NETCDF_PATH}; then
AC_CHECK_FILE(/usr/local/include/netcdf.h,
[USR_LOCAL_NETCDF_H=TRUE], [USR_LOCAL_NETCDF_H=FALSE])
if test ${USR_LOCAL_NETCDF_H} = TRUE; then
NETCDF_INCDIR=/usr/local/include
NETCDF_LIBDIR=/usr/local/lib
NETCDF_LIBNAME=netcdf
HAVE_NETCDF_H=TRUE
elif test ${HAVE_NETCDF_H} = FALSE;
[R] [R-pkgs] new version of minpack.lm
The package minpack.lm allows nonlinear regression problems to be addressed with a modification of the Levenberg-Marquardt algorithm based on the implementation of 'lmder' and 'lmdif' in MINPACK. Version 1.0-8 of the package is now available on CRAN. Changes in version 1.0-8 include: o possibility to obtain standard error estimates on the parameters via new methods for the generic functions 'summary' and 'vcov' o possibility to extract other information via new methods for the generic functions 'coef', 'deviance', 'df.residual', 'print', and 'residuals' o the argument 'control' of 'nls.lm' now defaults to 'nls.lm.control()'; 'nls.control.lm' allows a maximum number of iterations to be specified; when the element 'nprint' of the 'control' argument of a call to 'nls.lm' is an integer greater than 0, the residual sum of squares is now included in the information printed every 'nprint' iterations ` o the list returned by 'nls.lm' includes elements 'niter' and 'deviance' that represent the number of iterations performed and the residual sum of squares, respectively side-note on Levenberg-Marquardt (LM) versus Gauss-Newton (GN): There was some discussion (http://finzi.psych.upenn.edu/R/Rhelp02a/archive/108758.html) on Rhelp regarding whether one comes across real-world problems in which LM performs better than GN. I have been seeing such problems recently in some applications where GN as implemented in 'nls' reduces the step to a very small value, resulting in little change in the residual sum of squares from the starting values, whereas both NL2SOL applied via 'nls' called with 'algorithm=port' or LM as implemented in 'minpack.lm::nls.lm' significantly reduce the RSS. The implementation of NL2SOL is slower by a significant factor on these problems as compared to either the GN or LM implementations, making use of 'minpack.lm::nls.lm' attractive. Note that these problems may be considered pathological; there are issues with near collinearity of columns of the Jacobian and with the assumption that the residuals are Gaussian. Kate Mullen Timur Elzhov ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ 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] factanal and plotting?
Hi there! To make a good choice for the estimation of the number of usefull factors. And I'd like to plot a graph like: http://de.wikipedia.org/wiki/Bild:Parallelanalyse.jpg where I don't need the green line (random values). But with str(factanal(data, factors=10)) I cannot figure out where I can find the values for plotting. Can you please help me in this question? Thanks, Martin -- Ihr Partner für Webdesign, Webapplikationen und Webspace. http://www.roomandspace.com/ Martin Kaffanke +43 650 4514224 signature.asc Description: Dies ist ein digital signierter Nachrichtenteil __ 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] how to generate bar charts with the standard deviation
Ng Stanley wrote: Hi, I have the two vectors mean and sd of individual columns, but I am unsure how to generate bar charts with the standard deviation, even after looking the help of barplot and barplot.2. Barplots are not well suited for presenting continuous data and many would argue that even for proportions, they should not be used to present CI's. You are better off using: 1. plotCI() in the gplots package: http://cged.genes.nig.ac.jp/RGM2/R_current/library/gplots/man/plotCI.html 2. plotmeans() in the same, which is a wrapper to the above: http://cged.genes.nig.ac.jp/RGM2/R_current/library/gplots/man/plotmeans.html 3. errbar() in the Hmisc package: http://cged.genes.nig.ac.jp/RGM2/R_current/library/Hmisc/man/errbar.html 4. arrows() and/or segments() in the default R installation, which can be used like errbar() to add CI's to points. 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.
[R] lars with weights - unshrunk coef do not match with lm with weights
I have been looking at 'lars' pkg and got puzzled by the behavior of function 'lars'. I want to do weighted lasso regression and can't get a match from lars output with lm output. Here is an example: y = rnorm(10) x = matrix(runif(50),nrow=10) X = data.frame(y,x) z = runif(10) X = data.frame(y,x,z) X$z = X$z / sum(X$z) # this is not necessary. fit1 = lars(as.matrix(X[,2:6])*matrix(sqrt(X[,7]),10,5),as.matrix (X[,1])*sqrt(X[,7])) fit2 = lm(y~.-z,data=X,weights=z) coef(fit1,mode='fraction',s=1) fit2 I got this: coef(fit1,mode='fraction',s=1) X1 X2 X3 X4 X5 -2.8603082 -0.8303739 0.1064474 3.6563283 2.8342368 fit2 Call: lm(formula = y ~ . - z, data = X, weights = z) Coefficients: (Intercept) X1 X2 X3 X4 X5 -0.4227 -2.4817 -0.7105 -0.2611 2.6908 2.0295 Shouldn't they match? If not, what did I do wrong and how to correctly do lasso with weights? Thanks a lot. Young [[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] lars with weights do not match with lm output
I got my posting bounced and sorry if I accidentally post twice. I have been looking at 'lars' pkg and got puzzled by the behavior of function 'lars'. I want to do weighted lasso regression and can't get a match from lars output with lm output. Here is an example: y = rnorm(10) x = matrix(runif(50),nrow=10) X = data.frame(y,x) z = runif(10) X = data.frame(y,x,z) X$z = X$z / sum(X$z) # this is not necessary. fit1 = lars(as.matrix(X[,2:6])*matrix(sqrt(X[,7]),10,5),as.matrix (X[,1])*sqrt(X[,7])) fit2 = lm(y~.-z,data=X,weights=z) coef(fit1,mode='fraction',s=1) fit2 I got this: coef(fit1,mode='fraction',s=1) X1 X2 X3 X4 X5 -2.8603082 -0.8303739 0.1064474 3.6563283 2.8342368 fit2 Call: lm(formula = y ~ . - z, data = X, weights = z) Coefficients: (Intercept) X1 X2 X3 X4 X5 -0.4227 -2.4817 -0.7105 -0.2611 2.6908 2.0295 Shouldn't they match? If not, what did I miss and how to correctly do lasso with weights? Thanks a lot for any advice. Young [[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] Use of ellipses ... in argument list of optim(), integrate(), etc.
Hi, I have noticed that there is a change in the use of ellipses or . in R versions 2.6.1 and later. In versions 2.5.1 and earlier, the . were always at the end of the argument list, but in 2.6.1 they are placed after the main arguments and before method control arguments. This results in the user having to specify the exact (complete) names of the control arguments, i.e. partial matching is not allowed. An example with integrate() : integrate(function(x) exp(-x^2), lower=-Inf, upper=L, subdiv=1000) Error in f(x, ...) : unused argument(s) (subdiv = 1000) integrate(function(x) exp(-x^2), lower=-Inf, upper=L, subdivisions=1000) 1.633051 with absolute error 1.6e-06 Here is an example with optim(): res - optim(50, fw, meth=BFGS, control=list(maxit=2, temp=20, parscale=20)) Error in fn(par, ...) : unused argument(s) (meth = BFGS) FYI, I am using R version 2.6.1 on Windows XP. May I ask what the rationale behind this change is and also about the pros and cons of the two different ways of specifying (.)? Thank you very much. Best, Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: [EMAIL PROTECTED] Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html [[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] fast way to compare two matrices of combinations
I have a list (length 750), each element containing a vector of unique
strings (unique gene ids), with length up to ~40 (median 15). I want to
compile a matrix of all possible triplets and their frequency within
gene elements. Using combn and a lot of looping, I am accomplishing this
but it is VERY slow.
I've tried to figure out a way to vectorize this, using match and
%in%, but can't get my mind around it.
Below is my code. sig.tf.pairs is the list. Suggestions?
Mark
M - 3 # 3 for triplets, etc.
##
# count all triplets
all.triplets - NULL
all.count.vec - NULL
for (i in 1:length(sig.tf.pairs)){
if (length(sig.tf.pairs[[i]] = M)){
triplets - combn(sig.tf.pairs[[i]], M, simplify = TRUE)
for (j in 1:ncol(triplets)){
o - order(triplets[,j])
triplets[,j] - triplets[o,j]
count.vec - rep(1, ncol(triplets))
}
if (is.null(all.count.vec)){
all.count.vec - count.vec
all.triplets - triplets
} else {
redundant.vec - NULL
for (k in 1:ncol(all.triplets)){
for (m in 1:ncol(triplets)){
if (length(intersect(triplets[,m], all.triplets[,k] == M))){
all.count.vec[k] - all.count.vec[k] + 1
redundant.vec - c(redundant.vec, m)
}
}
}
if(!is.null(redundant.vec)){
triplets - triplets[,-redundant.vec]
count.vec - count.vec[,-redundant.vec]
}
all.triplets - cbind(all.triplets, triplets)
all.count.vec - c(all.count.vec, count.vec)
}
}
}
###
--
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, Mobile VoiceMail
(317) 204-4202 Home (no voice mail please)
mwkimpelatgmaildotcom
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Re: [R] fast way to compare two matrices of combinations
Hello Mark -
It may help if you provide a (small) set of example input and what you'd
like as your output.
Best,
Erik Iverson
Mark W Kimpel wrote:
I have a list (length 750), each element containing a vector of unique
strings (unique gene ids), with length up to ~40 (median 15). I want to
compile a matrix of all possible triplets and their frequency within
gene elements. Using combn and a lot of looping, I am accomplishing this
but it is VERY slow.
I've tried to figure out a way to vectorize this, using match and
%in%, but can't get my mind around it.
Below is my code. sig.tf.pairs is the list. Suggestions?
Mark
M - 3 # 3 for triplets, etc.
##
# count all triplets
all.triplets - NULL
all.count.vec - NULL
for (i in 1:length(sig.tf.pairs)){
if (length(sig.tf.pairs[[i]] = M)){
triplets - combn(sig.tf.pairs[[i]], M, simplify = TRUE)
for (j in 1:ncol(triplets)){
o - order(triplets[,j])
triplets[,j] - triplets[o,j]
count.vec - rep(1, ncol(triplets))
}
if (is.null(all.count.vec)){
all.count.vec - count.vec
all.triplets - triplets
} else {
redundant.vec - NULL
for (k in 1:ncol(all.triplets)){
for (m in 1:ncol(triplets)){
if (length(intersect(triplets[,m], all.triplets[,k] == M))){
all.count.vec[k] - all.count.vec[k] + 1
redundant.vec - c(redundant.vec, m)
}
}
}
if(!is.null(redundant.vec)){
triplets - triplets[,-redundant.vec]
count.vec - count.vec[,-redundant.vec]
}
all.triplets - cbind(all.triplets, triplets)
all.count.vec - c(all.count.vec, count.vec)
}
}
}
###
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Re: [R] Types of quadrature
David,
The problem is with 1 - pghyp(.). Here is a better way to compute your
omega - I first compute a complementary pghyp, which is 1 - pghyp, and
then use this to compute the numerator. The denominator is okay as it is.
pghyp.c - function(x) sapply(x, function(x){integrate(function(x)dghyp(x),
lower=x, upper=Inf, subdivisions=1000, rel.tol=1.e-07)$val})
L - 1
int.num - integrate(function(x)pghyp.c(x), lower=L, upper=Inf)$val
int.denom - integrate(pghyp, lower = -Inf, upper = L)$val
int.num
[1] 0.08397642
int.denom
[1] 1.083976
You should contact the package developer to provide an option for computing
1 - pghyp by specifying an option such as lower.tail=FALSE, as it is done
with pnorm(). This would also solve your problem.
Hope this helps,
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: Lüthi David (luda) [mailto:[EMAIL PROTECTED]
Sent: Thursday, March 13, 2008 12:16 PM
To: Ravi Varadhan
Subject: AW: [R] Types of quadrature
Hi Ravi
Thanks again. The integral exists because the ghyp density decays
exponentially for x - \infty. The problem is that pghyp (which performs
numerical integration of the density dghyp) gives 0 for large x (e.g. 2)
which results in (1 - pghyp) = 1 for large x and this of course diverges. I
know that there is a package rjacobi and also cwhmisc with function
adaptsim, however, both of them seem to be inappropriate.
Adaptsim does not accept infinite boundaries and rjacobi does need
quadrature nodes...
Best regards,
David
-Ursprüngliche Nachricht-
Von: Ravi Varadhan [mailto:[EMAIL PROTECTED]
Gesendet: Donnerstag, 13. März 2008 16:53
An: Lüthi David (luda)
Betreff: RE: [R] Types of quadrature
Hi David,
As integrate() says, your integrals for ghyp are probably divergent. Do you
know any theoretical result that says that the ratio you are computing for
ghyp actually exists?
Here is how you would integrate in your pnorm() example:
integrate(function(x) pnorm(x, lower.tail=FALSE), lower=1, upper=Inf)
0.08331547 with absolute error 1.5e-07
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: Lüthi David (luda) [mailto:[EMAIL PROTECTED]
Sent: Thursday, March 13, 2008 4:41 AM
To: Ravi Varadhan
Subject: AW: [R] Types of quadrature
Dear Prof. Ripley, Dear Prof. Varadhan
Forgive me for being unprecise. Let me demonstrate my problem in an example:
Assume the cumulative distribution function has to be integrated
numerically:
scalar.pnorm - function(x){
return(integrate(dnorm, -Inf, x)$value)
}
.pnorm - Vectorize(scalar.pnorm)
integrate(function(x)1 - .pnorm(x), lower = 1, upper = Inf)$value
The final usage would be:
library(ghyp)
omega.ghyp - function(L, object = ghyp(), ...){
int.num - integrate(function(x, object, ...)1 - pghyp(x, object, ...),
object = object, lower = L, upper = Inf, ...)
int.denom - integrate(pghyp, object = object, lower = -Inf, upper = L,
...)
return(int.num$value / int.denom$value)
}
object - ghyp()
omega.ghyp(1, object)
I do not see a way to avoid this or reformulate those expressions!?
Many thanks and best regards,
David
-Ursprüngliche Nachricht-
Von: Ravi Varadhan [mailto:[EMAIL PROTECTED]
Gesendet: Mittwoch, 12. März 2008 19:21
An: Lüthi David (luda); r-help@r-project.org
Betreff: RE: [R] Types of quadrature
Hi,
Why do you need an extension of integrate()? integrate() is adaptive - it
uses an adaptive Gauss-Kronrod quadrature.
You can specify Inf and -Inf as upper and lower limits, resp., in
integrate(). In fact, this is what the help page recommends, and it also
discourages the use of a large number as a surrogate for Inf.
What is the specific problem or distribution that you are having trouble
with in using integrate()?
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage:
[R] smoothest way to upgrade R, say from 2.6.1 to 2.6.2?
Like many software assemblies, R is updated frequently. Also, it creates its own release-numbered directory when it is installed. Packages get dumped into the subdirectory library. I have a personal habit of storing documents related to R packages in the doc subdirectory. Here are my questions. (1) How do people manage an upgrade, from 2.6.1, say, to 2.6.2? 2.6.2 will create its own subdirectory, obliging a copy of library contents to the new spot. The documents are easier. (2) The problem with simply copying library contents is a fear of upward incompatibilities. Am I worrying for naught here? Are packages upward compatible but possibly not downwardly so? (3) What about changing shortcuts, places for .Rprofile and the like? Do people have scripts that do all these things at once? It would be nice to have a single control file where R binaries and libraries and the like could be specified. That way, all that would need to be done is edit one file with an uptick on a point release number, say, and things would be fine. I suggest this because R is so rich and deep that there may well be such a thing I just don't know about. Or there may be a way of arranging things so they are done this way. Ideas? -- Jan [[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] Use of ellipses ... in argument list of optim(), integrate(), etc.
From the NEWS file: CHANGES IN R VERSION 2.6.0 SIGNIFICANT USER-VISIBLE CHANGES o integrate(), nlm(), nlminb(), optim(), optimize() and uniroot() now have '...' much earlier in their argument list. This reduces the chances of unintentional partial matching but means that the later arguments must be named in full. --- Vincent Goulet, Associate Professor École d'actuariat Université Laval, Québec [EMAIL PROTECTED] http://vgoulet.act.ulaval.ca Le jeu. 13 mars à 12:05, Ravi Varadhan a écrit : Hi, I have noticed that there is a change in the use of ellipses or . in R versions 2.6.1 and later. In versions 2.5.1 and earlier, the . were always at the end of the argument list, but in 2.6.1 they are placed after the main arguments and before method control arguments. This results in the user having to specify the exact (complete) names of the control arguments, i.e. partial matching is not allowed. An example with integrate() : integrate(function(x) exp(-x^2), lower=-Inf, upper=L, subdiv=1000) Error in f(x, ...) : unused argument(s) (subdiv = 1000) integrate(function(x) exp(-x^2), lower=-Inf, upper=L, subdivisions=1000) 1.633051 with absolute error 1.6e-06 Here is an example with optim(): res - optim(50, fw, meth=BFGS, control=list(maxit=2, temp=20, parscale=20)) Error in fn(par, ...) : unused argument(s) (meth = BFGS) FYI, I am using R version 2.6.1 on Windows XP. May I ask what the rationale behind this change is and also about the pros and cons of the two different ways of specifying (.)? Thank you very much. Best, Ravi. Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: [EMAIL PROTECTED] Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html __ 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] Using loop numbers in write.csv
This is a question I have wanted to ask for a while but hesitated
because I was sut sure I would find the answer on my own, but as of
yet...no dice.
1) Is there a way to use the loop number in naming things in R.
Specifically I have a simulation that has two loops. I would like to
be able to write out the results to a csv file after each iteration.
something like:
for (i in 1:10){
exampleMatrix - matrix(runif(25, 0, 1),5, 5)
write.csv(exampleMatrix, file = resultsMatrix_i.csv)
}
Where I would get 10 csv files named resultsMatrix_1, resultsMatrix_2
... resultsMatrix_10.
2) On a similar note is there a way to use the loop number when naming things.
something like:
for (i in 1:10){
exampleMatrix_i - matrix(runif(25, 0, 1),5, 5)
}
Where I would then have 10 matrices in memory with the names
exampleMatrix_1, exampleMatrix_2 ... exampleMatrix_10.
Thanks,
EG
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[R] label each bar by value
I want to label each bar on the top of bars when using barplot. anyone know how to do this? thanks __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Use of ellipses ... in argument list of optim(), integrate(), etc.
Thank you, Vince. Best, Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: [EMAIL PROTECTED] Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html -Original Message- From: Vincent Goulet [mailto:[EMAIL PROTECTED] Sent: Thursday, March 13, 2008 1:09 PM To: Ravi Varadhan Cc: r-help@r-project.org Subject: Re: [R] Use of ellipses ... in argument list of optim(), integrate(), etc. From the NEWS file: CHANGES IN R VERSION 2.6.0 SIGNIFICANT USER-VISIBLE CHANGES o integrate(), nlm(), nlminb(), optim(), optimize() and uniroot() now have '...' much earlier in their argument list. This reduces the chances of unintentional partial matching but means that the later arguments must be named in full. --- Vincent Goulet, Associate Professor École d'actuariat Université Laval, Québec [EMAIL PROTECTED] http://vgoulet.act.ulaval.ca Le jeu. 13 mars à 12:05, Ravi Varadhan a écrit : Hi, I have noticed that there is a change in the use of ellipses or . in R versions 2.6.1 and later. In versions 2.5.1 and earlier, the . were always at the end of the argument list, but in 2.6.1 they are placed after the main arguments and before method control arguments. This results in the user having to specify the exact (complete) names of the control arguments, i.e. partial matching is not allowed. An example with integrate() : integrate(function(x) exp(-x^2), lower=-Inf, upper=L, subdiv=1000) Error in f(x, ...) : unused argument(s) (subdiv = 1000) integrate(function(x) exp(-x^2), lower=-Inf, upper=L, subdivisions=1000) 1.633051 with absolute error 1.6e-06 Here is an example with optim(): res - optim(50, fw, meth=BFGS, control=list(maxit=2, temp=20, parscale=20)) Error in fn(par, ...) : unused argument(s) (meth = BFGS) FYI, I am using R version 2.6.1 on Windows XP. May I ask what the rationale behind this change is and also about the pros and cons of the two different ways of specifying (.)? Thank you very much. Best, Ravi. Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: [EMAIL PROTECTED] Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Use of ellipses ... in argument list of optim(), integrate(), etc.
Ravi Varadhan wrote: Hi, I have noticed that there is a change in the use of ellipses or . in R versions 2.6.1 and later. In versions 2.5.1 and earlier, the . were always at the end of the argument list, but in 2.6.1 they are placed after the main arguments and before method control arguments. This results in the user having to specify the exact (complete) names of the control arguments, i.e. partial matching is not allowed. An example with integrate() : integrate(function(x) exp(-x^2), lower=-Inf, upper=L, subdiv=1000) Error in f(x, ...) : unused argument(s) (subdiv = 1000) integrate(function(x) exp(-x^2), lower=-Inf, upper=L, subdivisions=1000) 1.633051 with absolute error 1.6e-06 Here is an example with optim(): res - optim(50, fw, meth=BFGS, control=list(maxit=2, temp=20, parscale=20)) Error in fn(par, ...) : unused argument(s) (meth = BFGS) FYI, I am using R version 2.6.1 on Windows XP. May I ask what the rationale behind this change is and also about the pros and cons of the two different ways of specifying (.)? Putting optim() arguments after the ... disallows the use of abbreviated actual arguments for optim(). This is generally a good thing, because prior to this change, it was impossible to supply, via the '...' arguments of optim(), an argument to fn() whose name was a prefix of one of the arguments of optim(). E.g., if your function had a argument named 'm', you could not previously supply it via the '...' argument of optim(), because if you did something like optim(x, fun, m=240), intending 'm' to be passed to 'fun', the 'm' would instead match the 'method' argument of optim(). The cons of the new argument structure are that abbreviations for names of arguments of optim() can't be used (a minor and debatable con), and that previous code that used abbreviations might break, but it will likely break quickly and noisily, so it's not too bad (the only case where it wouldn't break is when fn has a '...' argument itself, and it ignores unrecognized components, or where the are other argument name collisions). -- Tony Plate Thank you very much. Best, Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: [EMAIL PROTECTED] Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html [[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] smoothest way to upgrade R, say from 2.6.1 to 2.6.2?
On Thursday 13 March 2008 06:05:15 pm Galkowski, Jan wrote: GJ (1) How do people manage an upgrade, from 2.6.1, say, to 2.6.2? 2.6.2 GJ will create its own subdirectory, obliging a copy of library contents to GJ the new spot. The documents are easier. You forgot to enlighten us about your system. From what you are telling I would guess its Windows (XP?). On my windows machine I install R in the very same directory of the old R. So you could create programs/R and there install your R but of course you must then alternate the suggested directory during the installation. GJ GJ (2) The problem with simply copying library contents is a fear of upward GJ incompatibilities. Am I worrying for naught here? Are packages upward GJ compatible but possibly not downwardly so? There is no problem within minor releases like 2.6.1 - 2.6.2 but on greater jumps update.packages offers the option checkbuilt which if set TRUE updates the packages to their next built. So if 2.7.0 is released and you install that are over your old you should enable this option. GJ (3) What about changing shortcuts, places for .Rprofile and the like? GJ Do people have scripts that do all these things at once? See above GJ GJ It would be nice to have a single control file where R binaries and GJ libraries and the like could be specified. That way, all that would GJ need to be done is edit one file with an uptick on a point release GJ number, say, and things would be fine. I don't think this is necessary. Cheers Stefan -- Microeconomics University of Erfurt __ 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] Using loop numbers in write.csv
See ?paste and ?assign, those will get what you want done.
At least in the second case, you might consider using a list, however.
You can then avoid the use of 'for' loops by using functions such as lapply.
Best,
Erik Iverson
Economics Guy wrote:
This is a question I have wanted to ask for a while but hesitated
because I was sut sure I would find the answer on my own, but as of
yet...no dice.
1) Is there a way to use the loop number in naming things in R.
Specifically I have a simulation that has two loops. I would like to
be able to write out the results to a csv file after each iteration.
something like:
for (i in 1:10){
exampleMatrix - matrix(runif(25, 0, 1),5, 5)
write.csv(exampleMatrix, file = resultsMatrix_i.csv)
}
Where I would get 10 csv files named resultsMatrix_1, resultsMatrix_2
... resultsMatrix_10.
2) On a similar note is there a way to use the loop number when naming things.
something like:
for (i in 1:10){
exampleMatrix_i - matrix(runif(25, 0, 1),5, 5)
}
Where I would then have 10 matrices in memory with the names
exampleMatrix_1, exampleMatrix_2 ... exampleMatrix_10.
Thanks,
EG
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Re: [R] Using loop numbers in write.csv
Thanks!
Double thanks to Phil, I used your guide to learn LaTeX many moons ago.
On Thu, Mar 13, 2008 at 1:26 PM, Greg Snow [EMAIL PROTECTED] wrote:
For filenames you can do something like:
file = paste(resultsMatrix_', i, sep='')
For naming objects in the workspace, there is a way, but you really
don't want to do that. It is better to store them in a list, for
example:
resultList - list()
for( i in 1:10){
resultList[[i]] - matrix(runif(25, 0, 1),5, 5)
}
If you want the elements of the list named you can do:
names( resultList ) - paste('resultMatrix_',1:10, sep='')
Now you have 10 matricies all grouped together in a list, you can access
a single matrix like resultList[[1]] or resultList$resultMatrix_1, or
you can do something to all of them using lapply or sapply. You are
much less likely to overwrite data by accident, you can save, copy,
load, delete, etc the whole set in 1 step rather than using a loop.
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Economics Guy
Sent: Thursday, March 13, 2008 11:07 AM
To: [EMAIL PROTECTED]
Subject: [R] Using loop numbers in write.csv
This is a question I have wanted to ask for a while but
hesitated because I was sut sure I would find the answer on
my own, but as of yet...no dice.
1) Is there a way to use the loop number in naming things in R.
Specifically I have a simulation that has two loops. I would
like to be able to write out the results to a csv file after
each iteration.
something like:
for (i in 1:10){
exampleMatrix - matrix(runif(25, 0, 1),5, 5)
write.csv(exampleMatrix, file = resultsMatrix_i.csv)
}
Where I would get 10 csv files named resultsMatrix_1,
resultsMatrix_2 ... resultsMatrix_10.
2) On a similar note is there a way to use the loop number
when naming things.
something like:
for (i in 1:10){
exampleMatrix_i - matrix(runif(25, 0, 1),5, 5)
}
Where I would then have 10 matrices in memory with the names
exampleMatrix_1, exampleMatrix_2 ... exampleMatrix_10.
Thanks,
EG
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Robi Ragan
Graduate Student
Department of Economics
Department of Political Science
The University of Georgia
robi.myweb.uga.edu
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using loop numbers in write.csv
For filenames you can do something like:
file = paste(resultsMatrix_', i, sep='')
For naming objects in the workspace, there is a way, but you really
don't want to do that. It is better to store them in a list, for
example:
resultList - list()
for( i in 1:10){
resultList[[i]] - matrix(runif(25, 0, 1),5, 5)
}
If you want the elements of the list named you can do:
names( resultList ) - paste('resultMatrix_',1:10, sep='')
Now you have 10 matricies all grouped together in a list, you can access
a single matrix like resultList[[1]] or resultList$resultMatrix_1, or
you can do something to all of them using lapply or sapply. You are
much less likely to overwrite data by accident, you can save, copy,
load, delete, etc the whole set in 1 step rather than using a loop.
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Economics Guy
Sent: Thursday, March 13, 2008 11:07 AM
To: [EMAIL PROTECTED]
Subject: [R] Using loop numbers in write.csv
This is a question I have wanted to ask for a while but
hesitated because I was sut sure I would find the answer on
my own, but as of yet...no dice.
1) Is there a way to use the loop number in naming things in R.
Specifically I have a simulation that has two loops. I would
like to be able to write out the results to a csv file after
each iteration.
something like:
for (i in 1:10){
exampleMatrix - matrix(runif(25, 0, 1),5, 5)
write.csv(exampleMatrix, file = resultsMatrix_i.csv)
}
Where I would get 10 csv files named resultsMatrix_1,
resultsMatrix_2 ... resultsMatrix_10.
2) On a similar note is there a way to use the loop number
when naming things.
something like:
for (i in 1:10){
exampleMatrix_i - matrix(runif(25, 0, 1),5, 5)
}
Where I would then have 10 matrices in memory with the names
exampleMatrix_1, exampleMatrix_2 ... exampleMatrix_10.
Thanks,
EG
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] label each bar by value
?text tmp - c(34,22,77) tmp.labels - c(cat, dog, sheep) tmp2 - barplot(tmp, ylim=c(0, max(tmp)+10)) text(1:3, tmp+2 , labels=tmp.labels) --- Aimin Yan [EMAIL PROTECTED] wrote: I want to label each bar on the top of bars when using barplot. anyone know how to do this? thanks __ 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] label each bar by value
There was a discussion on this a while back, see: http://tolstoy.newcastle.edu.au/R/e2/help/07/08/22858.html There is some good discussion there on why you may not want to do this (adding the numbers at the tops of bars tends to distort the visual comparison of heights, among other things). If you follow the thread for a while and think about what you really want to do, there are some examples of alternative ways to accomplish what you probably really want to do. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Aimin Yan Sent: Thursday, March 13, 2008 11:10 AM To: r-help@r-project.org Subject: [R] label each bar by value I want to label each bar on the top of bars when using barplot. anyone know how to do this? thanks __ 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] VGAM and persp function
Hi all, I loaded VGAM, which masks the persp function from graphics. How can I run the persp function after running VGAM? I tried reloading graphics but it did not work. Thank you. quan __ 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] [PS] Re: a more elegant way to get percentages? (now R books)
There has been a virtual population explosion of R books in recent years and we all have our favorites. You may wish to pick one oriented toward your specialty, but the absolute minimum lowest common denominator (by which I mean that it has the ground zero essential information that all users must share, not that it is minimal or incomplete) is the manual An Introduction to R, available by download from the Cran website. I don't mean to pick on you in particular, or on the authors of An introduction to R, but I really don't see how anyone in good conscience can recommend this to a new user of R. I think it does a great job of covering the basics, and is probably a good read after you've been using R for a year or so, but in goes into a lot of depth into things that you really don't need to know for doing practical, day-to-day data analysis. For example, you don't find out how to actually load data into R until page 30, while you get 3 page on the mode and length of objects at page 12. Do we really need to know that an empty (zero length) vector still has a mode? These comments are based on my experience teaching R to undergrad stat majors, and so may not apply to your audience. If you teach R in the same order as an introduction to R it takes you about 4 weeks before you can actually do anything useful with R, by which time the students are bored to tears. If you start with getting data into R and displaying the data with graphics, you can do useful things very quickly, providing interest and motivation, and then you can gradually introduce a more rigourous description of the components as needed. Hadley -- http://had.co.nz/ __ 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] cumsum list..
In this case you can simply do cumsum(a[x,]+a[y,]) Julian yoo wrote: Hi all, i have the following.. a - data.frame(data = seq(1,10)) i have indices: x - c(1, 5, 3, 9) y - c(2, 7, 4, 10) I want the cumsum of a[1:2], a[5:7], a[3:4]... is there an elegant way to do it without any loop? Thanks! __ 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] VGAM and persp function
Try graphics::persp( . . . Whin you run just persp, it runs the first copy it finds, with the graphics:: on the front in specifically runs the one from the graphics package. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Quan Li Sent: Thursday, March 13, 2008 11:50 AM To: r-help@r-project.org Subject: [R] VGAM and persp function Hi all, I loaded VGAM, which masks the persp function from graphics. How can I run the persp function after running VGAM? I tried reloading graphics but it did not work. Thank you. quan __ 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] smoothest way to upgrade R, say from 2.6.1 to 2.6.2?
I think Stefan has answered this so I will just add this about batchfiles. In the batchfiles distrirbution: http://batchfiles.googlecode.com is a file Rgui.bat. If you put that anywhere in your path and make your shortcut to that instead of to R itself then it will find the most recent version of R from the registry and start that so you don't have to update shortcuts each time you change R versions. There are also Rcmd.bat, sweave.bat and similar versions for the corresponding tasks. Using those you never have to set your path to R when installing or upgrading R on Windows. The most recent version of batchfiles is for Vista and the next to most recent is for XP as per home page. If you do want to move or copy your packages from one library to another movedir.bat and copydir.bat will do that. You can then use checkbuilt if its a major version change. There are also some other methods described in the Links on the home page. On Thu, Mar 13, 2008 at 1:23 PM, Stefan Grosse [EMAIL PROTECTED] wrote: On Thursday 13 March 2008 06:05:15 pm Galkowski, Jan wrote: GJ (1) How do people manage an upgrade, from 2.6.1, say, to 2.6.2? 2.6.2 GJ will create its own subdirectory, obliging a copy of library contents to GJ the new spot. The documents are easier. You forgot to enlighten us about your system. From what you are telling I would guess its Windows (XP?). On my windows machine I install R in the very same directory of the old R. So you could create programs/R and there install your R but of course you must then alternate the suggested directory during the installation. GJ GJ (2) The problem with simply copying library contents is a fear of upward GJ incompatibilities. Am I worrying for naught here? Are packages upward GJ compatible but possibly not downwardly so? There is no problem within minor releases like 2.6.1 - 2.6.2 but on greater jumps update.packages offers the option checkbuilt which if set TRUE updates the packages to their next built. So if 2.7.0 is released and you install that are over your old you should enable this option. GJ (3) What about changing shortcuts, places for .Rprofile and the like? GJ Do people have scripts that do all these things at once? See above GJ GJ It would be nice to have a single control file where R binaries and GJ libraries and the like could be specified. That way, all that would GJ need to be done is edit one file with an uptick on a point release GJ number, say, and things would be fine. I don't think this is necessary. Cheers Stefan -- Microeconomics University of Erfurt __ 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] Use of ellipses ... in argument list of optim(), integrate(), etc.
There is an entry in the NEWS file for 2.6.0: CHANGES IN R VERSION 2.6.0 SIGNIFICANT USER-VISIBLE CHANGES o integrate(), nlm(), nlminb(), optim(), optimize() and uniroot() now have '...' much earlier in their argument list. This reduces the chances of unintentional partial matching but means that the later arguments must be named in full. and there was a spate of instances of 'unintentional partial matching' at the time. I have have no idea what you mean by 'ellipses or .' -- this is literally '...', and ellipses (e.g. Unicode U+226) do not work. From http://en.wikipedia.org/wiki/Ellipsis Most programming languages other than Perl6 require the ellipsis to be written as a series of periods; a single (Unicode) ellipsis character cannot be used. Please use R-devel for questions about the design and development of R (see the posting guide). On Thu, 13 Mar 2008, Ravi Varadhan wrote: Hi, I have noticed that there is a change in the use of ellipses or . in R versions 2.6.1 and later. In versions 2.5.1 and earlier, the . were always at the end of the argument list, but in 2.6.1 they are placed after the main arguments and before method control arguments. This results in the user having to specify the exact (complete) names of the control arguments, i.e. partial matching is not allowed. An example with integrate() : integrate(function(x) exp(-x^2), lower=-Inf, upper=L, subdiv=1000) Error in f(x, ...) : unused argument(s) (subdiv = 1000) integrate(function(x) exp(-x^2), lower=-Inf, upper=L, subdivisions=1000) 1.633051 with absolute error 1.6e-06 Here is an example with optim(): res - optim(50, fw, meth=BFGS, control=list(maxit=2, temp=20, parscale=20)) Error in fn(par, ...) : unused argument(s) (meth = BFGS) FYI, I am using R version 2.6.1 on Windows XP. May I ask what the rationale behind this change is and also about the pros and cons of the two different ways of specifying (.)? Thank you very much. Best, Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: [EMAIL PROTECTED] Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html [[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. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] fast way to compare two matrices of combinations
On Thu, 13 Mar 2008, Mark W Kimpel wrote:
I have a list (length 750), each element containing a vector of unique
strings (unique gene ids), with length up to ~40 (median 15). I want to
compile a matrix of all possible triplets and their frequency within
gene elements. Using combn and a lot of looping, I am accomplishing this
but it is VERY slow.
I've tried to figure out a way to vectorize this, using match and
%in%, but can't get my mind around it.
Below is my code. sig.tf.pairs is the list. Suggestions?
First, be sure that your code does what you really intend for it to do.
Does this really do what you wanted?
if (length(intersect(triplets[,m], all.triplets[,k] == M))){
If so, then why does the first line below never produce an error?
count.vec - count.vec[,-redundant.vec]
is.null(dim(count.vec)) ## TRUE
You are basically tabulating. Use the functions that are built for that.
It looks like what you want is along these lines:
tab.combns - function(x) apply( combn( sort(x), M ),2,
function(x) paste(x,collapse=''))
tab.all - table( unlist( lapply(sig.tf.pairs,tab.combns) ) )
Chuck
Mark
M - 3 # 3 for triplets, etc.
##
# count all triplets
all.triplets - NULL
all.count.vec - NULL
for (i in 1:length(sig.tf.pairs)){
if (length(sig.tf.pairs[[i]] = M)){
triplets - combn(sig.tf.pairs[[i]], M, simplify = TRUE)
for (j in 1:ncol(triplets)){
o - order(triplets[,j])
triplets[,j] - triplets[o,j]
count.vec - rep(1, ncol(triplets))
}
if (is.null(all.count.vec)){
all.count.vec - count.vec
all.triplets - triplets
} else {
redundant.vec - NULL
for (k in 1:ncol(all.triplets)){
for (m in 1:ncol(triplets)){
if (length(intersect(triplets[,m], all.triplets[,k] == M))){
all.count.vec[k] - all.count.vec[k] + 1
redundant.vec - c(redundant.vec, m)
}
}
}
if(!is.null(redundant.vec)){
triplets - triplets[,-redundant.vec]
count.vec - count.vec[,-redundant.vec]
}
all.triplets - cbind(all.triplets, triplets)
all.count.vec - c(all.count.vec, count.vec)
}
}
}
###
--
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, Mobile VoiceMail
(317) 204-4202 Home (no voice mail please)
mwkimpelatgmaildotcom
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Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:[EMAIL PROTECTED] UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
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Re: [R] generalized linear mixed models with a beta distribution
Thanks for the tips and clarifications. I'm a newbie and don't always have the terminology down correctly. My understanding is that one should be able to use generalized linear mixed models to model response variables that take any of the exponential family of distributions. The beta distribution belongs to this family and can be modeled in PROC GLIMMIX in SAS. I was hoping to find something similar in R. Is modeling in nlme via a variance specification the best and/or only option available in R? For clarification, here's what I'm trying to model: I have a beta-distributed response variable (y). I have a fixed-effect explanatory variable (treatment), and I'd like to include a random term for individuals used in the experiment. The model in lmer would be: y ~ treatment + (1 | individual). As far as I can tell, the appropriate link function for the model would be the logit. Thanks again, Professor Ripley, for your comments and suggestions. Craig Prof Brian Ripley wrote: glmmPQL can fit the same GLM families as glm() can -- it does not list _any_ . Howver, the beta distribution does not give a GLM family and hence your subject line is strictly about a non-existent concept. I'm presuming that you want to model the logit of the mean of a beta by a random effects model -- it is unclear what you want to do with the other parameter. Note that the beta does fit into the framework of package gamlss, but I am not aware of an option for random effects in that framework. On Wed, 12 Mar 2008, Craig A Faulhaber wrote: Greetings, I am interested in using a generalized linear mixed model with data that best fits a beta distribution (i.e., the data is bounded between 0 and 1 but is not binomial). I noticed that the beta distribution is not listed as an option in the family objects for glmmPQL or lmer. I found a thread on this listserve from 2006 ([R] lmer and a response that is a proportion) that indicated that there was no package https://stat.ethz.ch/pipermail/r-help/2006-December/121567.html available for mixed effects models with a beta distribution at that time. This thread also indicated that package betareg did not allow inclusion of random effects. But it did suggest modelling this in nlme via a variance specification, and that remains a good suggestion. Does anyone know of a package or code for a generalized linear mixed model that allows a beta distribution? Transforming my data might allow me to use another family, but I would rather not transform the data if possible. Thanks for your help! Sincerely, Craig Faulhaber __ 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] Splitting a set of vectors in a list
I have a set of character vectors of uneven length that I have stored in a list. I can easily enough get any column of them using lapply but what I want is to be able to create a matrix of them. Other than some kind of brute force looping approach I have drawn a blank. Would somebody please suggest something? Thanks Example. mylist - list(aa=c(cat,peach ), bb=c(dog, apple, iron), cc = c(rabbit, orange, zinc, silk)) myfun - function(dff) dff[1] vect1 - unlist(lapply(mylist, myfun)) Looking for the perfect gift? Give the gift of Flickr! __ 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] smoothest way to upgrade R, say from 2.6.1 to 2.6.2?
If this _is_ Windows, the question is discussed in detail in the rw-FAQ. That document also discusses how to install packages into a site or personal library which can make upgrading easier. Another consideration not told to us was whether one wants to keep around a working copy of the older version. My dept does so (so students can use a consistent version when preparing their theses, for example), and that affects the choice of strategy. On Thu, 13 Mar 2008, Stefan Grosse wrote: On Thursday 13 March 2008 06:05:15 pm Galkowski, Jan wrote: GJ (1) How do people manage an upgrade, from 2.6.1, say, to 2.6.2? 2.6.2 GJ will create its own subdirectory, obliging a copy of library contents to GJ the new spot. The documents are easier. You forgot to enlighten us about your system. From what you are telling I would guess its Windows (XP?). On my windows machine I install R in the very same directory of the old R. So you could create programs/R and there install your R but of course you must then alternate the suggested directory during the installation. GJ GJ (2) The problem with simply copying library contents is a fear of upward GJ incompatibilities. Am I worrying for naught here? Are packages upward GJ compatible but possibly not downwardly so? There is no problem within minor releases like 2.6.1 - 2.6.2 but on greater jumps update.packages offers the option checkbuilt which if set TRUE updates the packages to their next built. So if 2.7.0 is released and you install that are over your old you should enable this option. GJ (3) What about changing shortcuts, places for .Rprofile and the like? GJ Do people have scripts that do all these things at once? See above GJ GJ It would be nice to have a single control file where R binaries and GJ libraries and the like could be specified. That way, all that would GJ need to be done is edit one file with an uptick on a point release GJ number, say, and things would be fine. I don't think this is necessary. Cheers Stefan -- Microeconomics University of Erfurt __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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] Plot contour over filled contour
Dear R-users, I haven't found a way in the searchable archive to overplot a contour (lines) over a surface. I have a (n,m) matrix that represents sea surface temperature that I have plotted using image.plot(), filled.contour() or image(). I would like to overplot this image with some contour lines of mixed layer depth values(same size matrix). How can I do this? Any help is appreciated, thank you, Emmanuel --- Dr. Emmanuel Devred Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, Nova Scotia, B2Y 4A2, Canada Ph: (1) 902 426-4681 Fax: (1) 902 426-9388 [EMAIL PROTECTED] http://myweb.dal.ca/edevred/ --- [[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] Use of ellipses ... in argument list of optim(), integrate(), etc.
Thanks to Tony Plate, Vince Goulet, and Prof. Brian Ripley (I apologize for not posting this to R-devel). It is nice to know that there can be no unintended side-effects of this new ellipsical convention, other than the inconvenience of having to provide complete names of arguments after the ellipsis. Best, Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: [EMAIL PROTECTED] Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html -Original Message- From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] Sent: Thursday, March 13, 2008 2:01 PM To: Ravi Varadhan Cc: r-help@r-project.org Subject: Re: [R] Use of ellipses ... in argument list of optim(), integrate(), etc. There is an entry in the NEWS file for 2.6.0: CHANGES IN R VERSION 2.6.0 SIGNIFICANT USER-VISIBLE CHANGES o integrate(), nlm(), nlminb(), optim(), optimize() and uniroot() now have '...' much earlier in their argument list. This reduces the chances of unintentional partial matching but means that the later arguments must be named in full. and there was a spate of instances of 'unintentional partial matching' at the time. I have have no idea what you mean by 'ellipses or .' -- this is literally '...', and ellipses (e.g. Unicode U+226) do not work. From http://en.wikipedia.org/wiki/Ellipsis Most programming languages other than Perl6 require the ellipsis to be written as a series of periods; a single (Unicode) ellipsis character cannot be used. Please use R-devel for questions about the design and development of R (see the posting guide). On Thu, 13 Mar 2008, Ravi Varadhan wrote: Hi, I have noticed that there is a change in the use of ellipses or . in R versions 2.6.1 and later. In versions 2.5.1 and earlier, the . were always at the end of the argument list, but in 2.6.1 they are placed after the main arguments and before method control arguments. This results in the user having to specify the exact (complete) names of the control arguments, i.e. partial matching is not allowed. An example with integrate() : integrate(function(x) exp(-x^2), lower=-Inf, upper=L, subdiv=1000) Error in f(x, ...) : unused argument(s) (subdiv = 1000) integrate(function(x) exp(-x^2), lower=-Inf, upper=L, subdivisions=1000) 1.633051 with absolute error 1.6e-06 Here is an example with optim(): res - optim(50, fw, meth=BFGS, control=list(maxit=2, temp=20, parscale=20)) Error in fn(par, ...) : unused argument(s) (meth = BFGS) FYI, I am using R version 2.6.1 on Windows XP. May I ask what the rationale behind this change is and also about the pros and cons of the two different ways of specifying (.)? Thank you very much. Best, Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: [EMAIL PROTECTED] Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html [[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. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Splitting a set of vectors in a list
What would you want your output matrix to look like given mylist? John Kane wrote: I have a set of character vectors of uneven length that I have stored in a list. I can easily enough get any column of them using lapply but what I want is to be able to create a matrix of them. Other than some kind of brute force looping approach I have drawn a blank. Would somebody please suggest something? Thanks Example. mylist - list(aa=c(cat,peach ), bb=c(dog, apple, iron), cc = c(rabbit, orange, zinc, silk)) myfun - function(dff) dff[1] vect1 - unlist(lapply(mylist, myfun)) Looking for the perfect gift? Give the gift of Flickr! __ 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] Splitting a set of vectors in a list
Ideally something like this: == t(cbind( c(cat , peach , NA, NA), bbb - c(dog , apple ,iron, NA), ccb - c(rabbit ,orange ,zinc , silk ))) == Thanks --- Erik Iverson [EMAIL PROTECTED] wrote: What would you want your output matrix to look like given mylist? John Kane wrote: I have a set of character vectors of uneven length that I have stored in a list. I can easily enough get any column of them using lapply but what I want is to be able to create a matrix of them. Other than some kind of brute force looping approach I have drawn a blank. Would somebody please suggest something? Thanks Example. mylist - list(aa=c(cat,peach ), bb=c(dog, apple, iron), cc = c(rabbit, orange, zinc, silk)) myfun - function(dff) dff[1] vect1 - unlist(lapply(mylist, myfun)) Looking for the perfect gift? Give the gift of Flickr! __ 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. [[elided trailing spam]] __ 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] Splitting a set of vectors in a list
If I understand correctly, try this: as.data.frame(lapply(mylist, `[`, 1:max(unlist(lapply(mylist, length) On 13/03/2008, John Kane [EMAIL PROTECTED] wrote: I have a set of character vectors of uneven length that I have stored in a list. I can easily enough get any column of them using lapply but what I want is to be able to create a matrix of them. Other than some kind of brute force looping approach I have drawn a blank. Would somebody please suggest something? Thanks Example. mylist - list(aa=c(cat,peach ), bb=c(dog, apple, iron), cc = c(rabbit, orange, zinc, silk)) myfun - function(dff) dff[1] vect1 - unlist(lapply(mylist, myfun)) Looking for the perfect gift? Give the gift of Flickr! __ 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 __ 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] default values
Thanks a lot.
You were right :-)
Professor Ripley can I use your SPLUS book for R too ?
2008/3/12, Prof Brian Ripley [EMAIL PROTECTED]:
On Wed, 12 Mar 2008, Dwayne Blind wrote:
Dear R users,
I wrote the following toy example to explain my problem :
a=0
f=function(x,y,z) {
if (a==0) x[1]+x[2]+y
if (a!=0) x[1]+x[2]+y+z
}
f(1:2,3)
I have not specified z and I get an error.
What was the error? It works for me (so I've no idea), and returns NULL,
the value of the last expression (invisibly). I think you intended
f - function(x, y, z) if (a==0) x[1]+x[2]+y else x[1]+x[2]+y+z
or
f - function(x, y, z) ifelse(a==0, x[1]+x[2]+y, x[1]+x[2]+y+z)
Although a=0, R seems to want to
know z because it's in the expression x[1]+x[2]+y+z.
So I tried to put a default value :
a=0
f=function(x,y,z=0) {
if (a==0) x[1]+x[2]+y
if (a!=0) x[1]+x[2]+y+z
}
f(1:2,3)
Why isn't it working ? Sometimes everything is fine even though a
parameter
is not specified.
Thanks a lot.
[[alternative HTML version deleted]]
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plot contour over filled contour
Devred, Emmanuel DevredE at mar.dfo-mpo.gc.ca writes: I haven't found a way in the searchable archive to overplot a contour (lines) over a surface. I have a (n,m) matrix that represents sea surface temperature that I have plotted using image.plot(), filled.contour() or image(). I would like to overplot this image with some contour lines of mixed layer depth values(same size matrix). How can I do this? When I search for contour (nothing else), the first item by Uwe Ligges is probably what you want: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/2211.html Dieter __ 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] smoothest way to upgrade R, say from 2.6.1 to 2.6.2?
Thanks to Stefan Grosse, Gabor Grothendieck, and Professor Ripley for all this guidance. I have collected the details, concatenating them below, for future reference. Sorry if attributions got muddled. It is WinXP Pro in the primary, and there's no need to keep around older versions. But there are (Debian) Linux users here interested in both the same question, and any caches of R-related shell goodies that might be out there, comparable to batchfiles, both for upgrades and other things, like maybe spawning multiple R processes and the like, or running headless Rs on several servers at once. I apologize for leaving that out, but I thought putting out a wild guess on this might draw comment and help. It did. Thanks much, again. -Original Message- From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] Sent: Thursday, March 13, 2008 2:12 PM To: Stefan Grosse Cc: r-help@r-project.org; Galkowski, Jan Subject: Re: [R] smoothest way to upgrade R, say from 2.6.1 to 2.6.2? If this _is_ Windows, the question is discussed in detail in the rw-FAQ. That document also discusses how to install packages into a site or personal library which can make upgrading easier. Another consideration not told to us was whether one wants to keep around a working copy of the older version. My dept does so (so students can use a consistent version when preparing their theses, for example), and that affects the choice of strategy. On Thu, 13 Mar 2008, Stefan Grosse wrote: On Thursday 13 March 2008 06:05:15 pm Galkowski, Jan wrote: GJ (1) How do people manage an upgrade, from 2.6.1, say, to 2.6.2? GJ 2.6.2 will create its own subdirectory, obliging a copy of library GJ contents to the new spot. The documents are easier. You forgot to enlighten us about your system. From what you are telling I would guess its Windows (XP?). On my windows machine I install R in the very same directory of the old R. So you could create programs/R and there install your R but of course you must then alternate the suggested directory during the installation. GJ GJ (2) The problem with simply copying library contents is a fear of GJ upward incompatibilities. Am I worrying for naught here? Are GJ packages upward compatible but possibly not downwardly so? There is no problem within minor releases like 2.6.1 - 2.6.2 but on greater jumps update.packages offers the option checkbuilt which if set TRUE updates the packages to their next built. So if 2.7.0 is released and you install that are over your old you should enable this option. GJ (3) What about changing shortcuts, places for .Rprofile and the like? GJ Do people have scripts that do all these things at once? See above GJ GJ It would be nice to have a single control file where R binaries GJ and libraries and the like could be specified. That way, all that GJ would need to be done is edit one file with an uptick on a point GJ release number, say, and things would be fine. [snip] GJ Where does this update.packages with the checkbuilt live? just type update.packages() in case of a major version change update.packages(checkbuilt=T) GJ Is all this described on the Wiki some place? Or in the docs? In the docs run ?update.packages or have a look at the admin guide http://cran.r-project.org/doc/manuals/R-admin.html [snip] I think Stefan has answered this so I will just add this about batchfiles. In the batchfiles distrirbution: http://batchfiles.googlecode.com is a file Rgui.bat. If you put that anywhere in your path and make your shortcut to that instead of to R itself then it will find the most recent version of R from the registry and start that so you don't have to update shortcuts each time you change R versions. There are also Rcmd.bat, sweave.bat and similar versions for the corresponding tasks. Using those you never have to set your path to R when installing or upgrading R on Windows. The most recent version of batchfiles is for Vista and the next to most recent is for XP as per home page. If you do want to move or copy your packages from one library to another movedir.bat and copydir.bat will do that. You can then use checkbuilt if its a major version change. There are also some other methods described in the Links on the home page. __ 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] Splitting a set of vectors in a list (Solved )
My thanks to Henrique Dallazuanna and Phil Spector.
Both solutions worked well.
Phil suggested that an alterative to my function would
be
vect1 = sapply(mylist,'[[',1)
and I see that Henrique used `[` in his solution.
Can you point me to some documentation that discusses
these usages. I have seen them before but I have never
actually figured out how to use them.?
Thanks.
Problem and solutions
mylist - list(aa=c(cat,peach ), bb=c(dog,
apple, iron),
cc = c(rabbit, orange, zinc, silk))
myfun - function(dff) dff[1]
vect1 - unlist(lapply(mylist, myfun))
# Desired output
t(cbind( c(cat , peach , NA, NA), bbb - c(dog
, apple ,iron, NA),
ccb - c(rabbit ,orange ,zinc , silk )))
# Phil Spector's approach
mlen = max(sapply(mylist,length))
eqlens = lapply(mylist,function(x)if(length(x) mlen)
c(x,rep('',mlen-length(x))) else x)
do.call(rbind,eqlens)
# Henrique Dallazuanna [EMAIL PROTECTED]
#I added the t()
t(as.data.frame(lapply(mylist, `[`,
1:max(unlist(lapply(mylist,
length))
[[elided trailing spam]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Splitting a set of vectors in a list (Solved )
On 13/03/2008, John Kane [EMAIL PROTECTED] wrote:
My thanks to Henrique Dallazuanna and Phil Spector.
Both solutions worked well.
Phil suggested that an alterative to my function would
be
vect1 = sapply(mylist,'[[',1)
and I see that Henrique used `[` in his solution.
Can you point me to some documentation that discusses
these usages. I have seen them before but I have never
actually figured out how to use them.?
See ?Extract
Thanks.
Problem and solutions
mylist - list(aa=c(cat,peach ), bb=c(dog,
apple, iron),
cc = c(rabbit, orange, zinc, silk))
myfun - function(dff) dff[1]
vect1 - unlist(lapply(mylist, myfun))
# Desired output
t(cbind( c(cat , peach , NA, NA), bbb - c(dog
, apple ,iron, NA),
ccb - c(rabbit ,orange ,zinc , silk )))
# Phil Spector's approach
mlen = max(sapply(mylist,length))
eqlens = lapply(mylist,function(x)if(length(x) mlen)
c(x,rep('',mlen-length(x))) else x)
do.call(rbind,eqlens)
# Henrique Dallazuanna [EMAIL PROTECTED]
#I added the t()
t(as.data.frame(lapply(mylist, `[`,
1:max(unlist(lapply(mylist,
length))
Looking for the perfect gift? Give the gift of Flickr!
http://www.flickr.com/gift/
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Splitting a set of vectors in a list (Solved )
or the suggestive :) ?[ b On Mar 13, 2008, at 2:58 PM, Henrique Dallazuanna wrote: On 13/03/2008, John Kane [EMAIL PROTECTED] wrote: Can you point me to some documentation that discusses these usages. I have seen them before but I have never actually figured out how to use them.? See ?Extract __ 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] default values
On Thu, 13 Mar 2008, Dwayne Blind wrote:
Thanks a lot.
You were right :-)
Professor Ripley can I use your SPLUS book for R too ?
'Modern Applied Statistics with S' and 'S Programming' both cover S and
its implementations in S-PLUS and R.
However, 'Modern Applied Statistics with S-PLUS' is now so last millenium
that it is an unreliable guide to recent versions of either.
2008/3/12, Prof Brian Ripley [EMAIL PROTECTED]:
On Wed, 12 Mar 2008, Dwayne Blind wrote:
Dear R users,
I wrote the following toy example to explain my problem :
a=0
f=function(x,y,z) {
if (a==0) x[1]+x[2]+y
if (a!=0) x[1]+x[2]+y+z
}
f(1:2,3)
I have not specified z and I get an error.
What was the error? It works for me (so I've no idea), and returns NULL,
the value of the last expression (invisibly). I think you intended
f - function(x, y, z) if (a==0) x[1]+x[2]+y else x[1]+x[2]+y+z
or
f - function(x, y, z) ifelse(a==0, x[1]+x[2]+y, x[1]+x[2]+y+z)
Although a=0, R seems to want to
know z because it's in the expression x[1]+x[2]+y+z.
So I tried to put a default value :
a=0
f=function(x,y,z=0) {
if (a==0) x[1]+x[2]+y
if (a!=0) x[1]+x[2]+y+z
}
f(1:2,3)
Why isn't it working ? Sometimes everything is fine even though a
parameter
is not specified.
Thanks a lot.
[[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.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Splitting a set of vectors in a list (Solved )
Ah ?Extract. Thanks
Unless I'm missing something there is nothing in the
Usage or Examples to suggest to a naive reader like me
that one can use an unbalanced [ or [[, that is
withoug a corresponding ] or ]].
I probably am just not understanding the details.
--- Henrique Dallazuanna [EMAIL PROTECTED] wrote:
On 13/03/2008, John Kane [EMAIL PROTECTED] wrote:
My thanks to Henrique Dallazuanna and Phil
Spector.
Both solutions worked well.
Phil suggested that an alterative to my function
would
be
vect1 = sapply(mylist,'[[',1)
and I see that Henrique used `[` in his solution.
Can you point me to some documentation that
discusses
these usages. I have seen them before but I have
never
actually figured out how to use them.?
See ?Extract
Thanks.
Problem and solutions
mylist - list(aa=c(cat,peach ), bb=c(dog,
apple, iron),
cc = c(rabbit, orange, zinc,
silk))
myfun - function(dff) dff[1]
vect1 - unlist(lapply(mylist, myfun))
# Desired output
t(cbind( c(cat , peach , NA, NA), bbb -
c(dog
, apple ,iron, NA),
ccb - c(rabbit ,orange ,zinc , silk )))
# Phil Spector's approach
mlen = max(sapply(mylist,length))
eqlens = lapply(mylist,function(x)if(length(x)
mlen)
c(x,rep('',mlen-length(x))) else x)
do.call(rbind,eqlens)
# Henrique Dallazuanna [EMAIL PROTECTED]
#I added the t()
t(as.data.frame(lapply(mylist, `[`,
1:max(unlist(lapply(mylist,
length))
Looking for the perfect gift? Give the gift
of Flickr!
http://www.flickr.com/gift/
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to cbind or rbind different lengths vectors/arrays without repeating the elements of the shorter vectors/arrays ?
I don't think you can. What is your desired output? You can always do c(1:2, 1:10) --- Ng Stanley [EMAIL PROTECTED] wrote: Hi, How to cbind or rbind different lengths vectors/arrays without repeating the elements of the shorter vectors/arrays ? cbind(1:2, 1:10) [,1] [,2] [1,]11 [2,]22 [3,]13 [4,]24 [5,]15 [6,]26 [7,]17 [8,]28 [9,]19 [10,]2 10 [[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. Looking for the perfect gift? Give the gift of Flickr! __ 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] Splitting a set of vectors in a list (Solved )
A example:
x - rnorm(5)
x[3]
`[`(x, 3)
`[[`(x, 3)
x[3:4]
`[`(x, 3:4)
`[[`(x, 3:4) # Error
On 13/03/2008, John Kane [EMAIL PROTECTED] wrote:
Ah ?Extract. Thanks
Unless I'm missing something there is nothing in the
Usage or Examples to suggest to a naive reader like me
that one can use an unbalanced [ or [[, that is
withoug a corresponding ] or ]].
I probably am just not understanding the details.
--- Henrique Dallazuanna [EMAIL PROTECTED] wrote:
On 13/03/2008, John Kane [EMAIL PROTECTED] wrote:
My thanks to Henrique Dallazuanna and Phil
Spector.
Both solutions worked well.
Phil suggested that an alterative to my function
would
be
vect1 = sapply(mylist,'[[',1)
and I see that Henrique used `[` in his solution.
Can you point me to some documentation that
discusses
these usages. I have seen them before but I have
never
actually figured out how to use them.?
See ?Extract
Thanks.
Problem and solutions
mylist - list(aa=c(cat,peach ), bb=c(dog,
apple, iron),
cc = c(rabbit, orange, zinc,
silk))
myfun - function(dff) dff[1]
vect1 - unlist(lapply(mylist, myfun))
# Desired output
t(cbind( c(cat , peach , NA, NA), bbb -
c(dog
, apple ,iron, NA),
ccb - c(rabbit ,orange ,zinc , silk )))
# Phil Spector's approach
mlen = max(sapply(mylist,length))
eqlens = lapply(mylist,function(x)if(length(x)
mlen)
c(x,rep('',mlen-length(x))) else x)
do.call(rbind,eqlens)
# Henrique Dallazuanna [EMAIL PROTECTED]
#I added the t()
t(as.data.frame(lapply(mylist, `[`,
1:max(unlist(lapply(mylist,
length))
Looking for the perfect gift? Give the gift
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--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
Yahoo! Canada Toolbar: Search from anywhere on the web, and bookmark your
favourite sites. Download it now at
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--
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Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Splitting a set of vectors in a list (Solved )
Blood ell ! Thanks very much, it does help give a
feel for what's happening. I'll have to do some
experimenting.
--- Henrique Dallazuanna [EMAIL PROTECTED] wrote:
A example:
x - rnorm(5)
x[3]
`[`(x, 3)
`[[`(x, 3)
x[3:4]
`[`(x, 3:4)
`[[`(x, 3:4) # Error
On 13/03/2008, John Kane [EMAIL PROTECTED] wrote:
Ah ?Extract. Thanks
Unless I'm missing something there is nothing in
the
Usage or Examples to suggest to a naive reader
like me
that one can use an unbalanced [ or [[, that is
withoug a corresponding ] or ]].
I probably am just not understanding the details.
--- Henrique Dallazuanna [EMAIL PROTECTED]
wrote:
On 13/03/2008, John Kane [EMAIL PROTECTED]
wrote:
My thanks to Henrique Dallazuanna and Phil
Spector.
Both solutions worked well.
Phil suggested that an alterative to my
function
would
be
vect1 = sapply(mylist,'[[',1)
and I see that Henrique used `[` in his
solution.
Can you point me to some documentation that
discusses
these usages. I have seen them before but I
have
never
actually figured out how to use them.?
See ?Extract
Thanks.
Problem and solutions
mylist - list(aa=c(cat,peach ),
bb=c(dog,
apple, iron),
cc = c(rabbit, orange, zinc,
silk))
myfun - function(dff) dff[1]
vect1 - unlist(lapply(mylist, myfun))
# Desired output
t(cbind( c(cat , peach , NA, NA), bbb
-
c(dog
, apple ,iron, NA),
ccb - c(rabbit ,orange ,zinc ,
silk )))
# Phil Spector's approach
mlen = max(sapply(mylist,length))
eqlens =
lapply(mylist,function(x)if(length(x)
mlen)
c(x,rep('',mlen-length(x))) else x)
do.call(rbind,eqlens)
# Henrique Dallazuanna
[EMAIL PROTECTED]
#I added the t()
t(as.data.frame(lapply(mylist, `[`,
1:max(unlist(lapply(mylist,
length))
Looking for the perfect gift? Give the
gift
of Flickr!
http://www.flickr.com/gift/
--
Henrique Dallazuanna
Curitiba-Paran�-Brasil
25� 25' 40 S 49� 16' 22 O
the web, and bookmark your favourite sites. Download
it now at
http://ca.toolbar.yahoo.com.
--
Henrique Dallazuanna
Curitiba-Paran�-Brasil
25� 25' 40 S 49� 16' 22 O
[[elided trailing spam]]
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[R] FW: Os resultados do seus comandos de email
Dear all, what is the best way to do this? end = c(2,6,4) I neeed: expand.grid(0:end[1],0:end[2],0:end[3]) Best regards JL _ Confira vídeos com notícias do NY Times, gols direto do Lance, videocas[[elided Hotmail spam]] __ 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] FW: Os resultados do seus comandos de email
Try: do.call(expand.grid, sapply(end, seq, from = 0)) On 13/03/2008, lamack lamack [EMAIL PROTECTED] wrote: Dear all, what is the best way to do this? end = c(2,6,4) I neeed: expand.grid(0:end[1],0:end[2],0:end[3]) Best regards JL _ Confira vídeos com notícias do NY Times, gols direto do Lance, videocas[[elided Hotmail spam]] __ 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 __ 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] How to manipulate data according to groups ?
?aggregate tt - matrix(c(rnorm(10), 1,1,2,2,1,3,3,3,3,2), ncol=2)) aggregate(t[,1], by=list(t[,2]), mean) should work --- Ng Stanley [EMAIL PROTECTED] wrote: Hi, I have a two columns data, the first column are values, and second column are the groups. For this example, there are 3 groups 1,2,3. How can I manipulate the values in the first column according to groups, say I would like to find mean, sum, and standard deviation for the different groups ? How do I plot data according to groups ? t - matrix(c(rnorm(10), 1,1,2,2,1,3,3,3,3,2), ncol=2) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] LIMMA: array spot summary options beyond duplicateCorrelation()
Hello Limma users A quick question, I hope: I have dual-channel spotted expression arrays in a simple loop design (no dye swaps), viz: 1 vs reference 2 vs 1 3 vs 2 reference vs 3 There are 4 replicate spots for each probe on each array. It seems as if getting meaningful spot summary results using duplicateCorrelation() is not possible in my case as the spots are not regularly spaced, and I don't *really* have enough arrays, no? So then what are my other options in Limma to summarise replicated spots? Thanks, Quin * * * * *Quin Wills* *DPhil candidate* * * *Department of Statistics* *University** of Oxford*** *1 South Parks Road* *Oxford*** *OX1 3TG United Kingdom* *01865 285 394* [[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] Warned about these three little maids...
Greetings all: Newcomer to R as I work on learning it to transfer my college classroom stats training to something more useful and accurate then that spreadsheet from Redmond which shall remain nameless. I'm running v2.6.2 on a Win XP Home system that I keep up to date with all the called for patches. Haven't added much to the basic install other than the bits and bobs needed to run the R Commander package and its plugins. I did, however, use the ctv library to add the Graphics view. When I reached the end of the install (a somewhat drawn out exercise as I haven't jumped into a high speed hookup yet) R warned me that gtkDevice, RGrace, and xgobi were not available. I use the Ontario, Canada mirror and they are indeed not listed among the install choices. A quick search on the names and I get the impression these three are not available for the Windows platform. Correct perception or no? Do I need them for a windows setup? Where would I find them if they are needed? Any help or advice much appreciated... -- Brian Lunergan Nepean, Ontario Canada --- __ 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] plotting zoo object
JAN FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC 1968NA 10.710.09.3 7.4 8.1 9.3 9.5 8.5 10.010.013.0 196913.09.9 7.0 5.9 NA 6.5 7.3 6.6 NA NA NA NA 197010.78.9 8.1 NA NA 7.1 7.7 NA 6.5 NA 8.3 NA 1971NA 11.6NA NA 7.8 NA NA 6.2 NA NA 8.4 NA x-read.zoo(textconnection, sep=,, format= %Y, header=TRUE) plot(x) #this plots all of the years by each month. I would like to plot one long time series from 1968 to 1971 #is there an easy way to do this? I can reformat the data in excel so that the index will be year then month, but this will take a while. the end goal is #to be able to apply some signal processing things like spectral density after fitting the seasonal trend etc. thanks Stephen -- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ 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] Warned about these three little maids...
You should consult the summary http://cran.r-project.org/bin/windows/contrib/checkSummaryWin.html to answer such questions. These are not part of the install of R -- you must have chosen to install some packages which depend on them. As to whether you need them -- that depends if you need the packages that depend on them. You are wrong about xgobi: it is on the CRAN extras site and a default repositories setup will find it. However, it is an interface to XGobi, and that is pretty much obsolete in favour of GGobi (and rggobi is its R interface). Package gtkDevice has been withdrawn. It should be possible to build package RGrace for Windows -- it only depends on packages RGtk2 and cairoDevice these days, and I've just done so. (Earlier versions were a different story.) However, it fails its checks as it incorrectly uses UTF8 (instead of UTF-8) for an encoding name. (So Cc:ing the maintainer.) On Thu, 13 Mar 2008, Brian Lunergan wrote: Greetings all: Newcomer to R as I work on learning it to transfer my college classroom stats training to something more useful and accurate then that spreadsheet from Redmond which shall remain nameless. I'm running v2.6.2 on a Win XP Home system that I keep up to date with all the called for patches. Haven't added much to the basic install other than the bits and bobs needed to run the R Commander package and its plugins. I did, however, use the ctv library to add the Graphics view. When I reached the end of the install (a somewhat drawn out exercise as I haven't jumped into a high speed hookup yet) R warned me that gtkDevice, RGrace, and xgobi were not available. I use the Ontario, Canada mirror and they are indeed not listed among the install choices. A quick search on the names and I get the impression these three are not available for the Windows platform. Correct perception or no? Do I need them for a windows setup? Where would I find them if they are needed? Any help or advice much appreciated... -- Brian Lunergan Nepean, Ontario Canada -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] manova with non-normal error distribution
This may be a silly question to ask, but, is it possible do do a MANOVA-style analysis with a generalized linear model? I have a data set that I'm working with that, for each variable (time in this case, as it's a repeated measures MANOVA) is fit much better using glm rather than a traditional linear model - even after transforming the data so that the resulting (I'm log transforming the data for lm, whereas under glm the data is most appropriate for a model with a poisson error and an exponential link). However, under glm, if I try and fit my matrix of response variable, I get the error Error: (subscript) logical subscript too long Is there a library or method of analysis that handles this type of problem? Much obliged! -Jarrett Jarrett Byrnes Population Biology Graduate Group, UC Davis Bodega Marine Lab 707-875-1969 http://www-eve.ucdavis.edu/stachowicz/byrnes.shtml [[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] zoo object: replace NAs from another zoo object
Hello, I have two zoo objects, new and old, indexed by chron objects. Their structure is like this: (05/25/06 00:00:00) NA NA NA (05/25/06 00:02:00) 948.20 24.198 0 (05/25/06 00:04:00) 948.26 20.640 0 (05/25/06 00:06:00) 948.37 19.653 0 (05/25/06 00:08:00) 948.48 19.135 0 (05/25/06 00:10:00) 948.54 22.510 0 (05/25/06 00:12:00) 948.55 27.175 0 (05/25/06 00:14:00) 948.46 30.075 0 (05/25/06 00:16:00) 948.59 28.815 0 (05/25/06 00:18:00) 948.96 27.938 0 old spans a larger range of dates than new. I would like to take all the values in new that are not NA and place them in old, matching the time indices. I have tried a number of variations on the themes of merge and replace, but can't get them to work, and the brute force for loop solution is unnacceptably slow. Could someone suggest a solution? Many thanks, Tim __ 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.
