[R] How to find out the trend during a time period?
Hi all: I have a dataset which contains two variables: Y and time y-c(228,189,232,198,252,315) time-2003:2008 How can I find out the trend(increase/decrease) of y along the time period? If I use: lm(y~time) The lm command treats time as natural number,but not date. So maybe lm isn't appropriate. Then,which function could be used? Thanks a lot for your help. My best [[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] times
Hi! I have an input table with a column Dates in the format month/day/year (eg. 5/11/1999 and a column Times in the format hours/minutes (eg. 15:20). In R I need to convert them into chron objects to extract colums only containing months, days, minutes, .. For the dates it is no problem if I write: dmy.lwc-chron(dates=lwc.file[,1],format=(dates=m/d/y)) But it does not work the same way for the times if I write: hm.lwc-chron(times=lwc.file[,2],format=(times=h:m)) Error-Message: Error in convert.times(times., fmt) : format h:m may be incorrect In addition: Warning message: In is.na(out$s) : is.na() applied to non-(list or vector) of type 'NULL' Why should the format h:m not be correct? -- View this message in context: http://r.789695.n4.nabble.com/times-tp3016621p3016621.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Creating truly global variable within function within namespace
I am trying to create a function with a package with a NAMESPACE that
will save() some variables, distribute an Rdata file to another
computer, where it will be load()ed. The problem is that this load()
tries to load the namespace of the package on the original computer
that created the .Rdata file, but this package need not be loaded on
the new computer.
This example function is in a package in a namespace :
create.global.function - function(x, FUN, ...) {
environment(FUN) - .GlobalEnv
assign(.GLOBAL.FUN, function(x) { FUN(x, ...) }, env=.GlobalEnv)
environment(.GLOBAL.FUN) - .GlobalEnv
save(list = ls(envir = .GlobalEnv, all.names = TRUE),
file = /tmp/.Rdata,
envir = .GlobalEnv)
}
And then if I quit my session and then try to load(/tmp/.Rdata)
without loading the package, it will try to loadNamespace from the
.Rdata file and then fail.
Is it possible to fully strip the namespace out of the .GLOBAL.FUN
before I save() it such that it can be loaded into other R instances
without trying to load the namespace?
Thanks for any pointers ..
- Murray
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Re: [R] add diagonal line
On Wed, 2010-10-27 at 13:17 -0200, Marcelo Lima wrote: Hi, I would like to add a line on the diagonal of a covariance matrix, is there a quick way to do it besides abline? Thanks! What's wrong with abline()? It does exactly what you want. By the way, reproducible example such as requested by David would something like: cmat - matrix(rnorm(100), ncol = 10) diag(cmat) - 1 contour(1:10, 1:10, cmat) abline(11, -1, col = red, lwd = 2) box() I.e. some code with example data that shows us what you are trying to do. It is not always possible to grep the meaning from a textual description sufficiently well to be able to move from there to code. This is discussed in the posting guide. HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ 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 find out the trend during a time period?
On 28.10.2010 06:50, Lao Meng wrote: Hi all: I have a dataset which contains two variables: Y and time y-c(228,189,232,198,252,315) time-2003:2008 How can I find out the trend(increase/decrease) of y along the time period? If I use: lm(y~time) The lm command treats time as natural number,but not date. What is date? WHere is the reproducible example? Uwe Ligges So maybe lm isn't appropriate. Then,which function could be used? Thanks a lot for your help. My best [[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] overloading the generic primitive functions + and [
How can I add a new method to the generic function [ or + I want to create a S3 and S4 class that will use the [ and + method in a different way. How can I overload the generic primitive [ or + so the method dispatch will work correctly for my class? I saw an example of this in the ggplot2 package where different objects are joined using the + primitive. Still, I could not figure out how to do that. Can someone give a small code example to show how that works? TIA Mark Mark Heckmann Dipl. Wirt.-Ing. cand. Psych. Vorstraße 93 B01 28359 Bremen Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com [[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] Tukeys after(g)lmer
Hello, I have a model I made with a binomially distributed response, 2 vectors and two factors with 5 and 12 levels respectively, and a random effect (intercept). What I am interested in is doing a post-hoc test to tell which levels of the factors differ from each other. crfk-lmer((Ro~1+mhr+tra+h+m+(1|PubName)), family=binomial,data=t1) Ro is binomial mhr is a vector tra is a vector h is a factor m is a factor PubName is a factor(obviously) I have found this; https://stat.ethz.ch/pipermail/r-help/attachments/20081223/f3dd4d21/attachment.pl These work: glht(mod1, linfct=mcp(category=Tukey) glht(mod1, linfct=mcp(comp=Tukey) And figured out as much as that the problem is my binomial response. Now I am trying to weigh my alternatives, and find the best way to present the data. As far as I have read, it seems post-hoc tests are not implemented (yet?), maybe due to that they are murky at best in theese circumstances at least according to what I could read of the net. An alternative would be to re fit the model with other contrasts (shifting the base in the pre specified contrasts would do the trick, or specifying not orthogonal tukey contrasts going from high to low estimates) The third alternative would be to just fit some other orthogonal contrasts structure, but that would not make all the comparisons I am interested in. A third option is to do a stepwise deletion and combine the closest levels and test the models in a likelihood ratio test (models fit with ML since the fixed effects change) and see which could be combined. Are there better alternatives? /Henrik __ 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] overloading the generic primitive functions + and [
On Thu, Oct 28, 2010 at 9:31 AM, Mark Heckmann mark.heckm...@gmx.de wrote:
How can I add a new method to the generic function [ or +
I want to create a S3 and S4 class that will use the [ and + method in a
different way.
How can I overload the generic primitive [ or + so the method dispatch
will work correctly for my class?
I saw an example of this in the ggplot2 package where different objects are
joined using the + primitive.
Still, I could not figure out how to do that.
Can someone give a small code example to show how that works?
With S3 method stuff, to override + its as easy as writing Ops.{class}:
a=hello
b=world
a+b
Error in a + b : non-numeric argument to binary operator
class(a)=ss
class(b)=ss
Ops.ss=function(e1,e2){paste(e1,e2)}
a+b
[1] hello world
better make sure I haven't broken anything:
c=1
d=2
c+d
[1] 3 *phew*
The Ops function should really have a handler for all possible
operators (*, /, - etc) or fail with an error - see Ops.Date for
example.
With S4 classes... umm.. signatures... setMethod... setGeneric...
errr. something... representations... setClass this that... yeah.
Something like that.
Barry
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[R] updating a local package
Hi folks I have inherited a package which was created before release 2.10 and I need to have it working in release 2.12 There is a folder containing the Man, Data and R subfolders, and the description file, and there is also the corresponding zip file. I can install the package from the zip file, but when I try to load it I get the message :- Error: package was built before R 2.10.0: please re-install it If I try to rebuild the zip file using C:\Program Files\R\R-2.12.0\bin\R.exe CMD build my.library.folder I get pages and pages of warnings and error messages, many of which seem to refer to the Man folder. Having never built a formal package before, I'm a bit stuck for what to do next ... Presumably the expected structure of the folders has changed but the documentation on packages looks scary - can anyone suggest the best way forward - even if its only RTFM ! thanks Bob Kinley [[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] replace text at certain positions in a file
Hello, I am working with R version 2.10.1 under windows. In a text file, I need to replace all characters at certain column positions with blanks. For example, say the file contains two lines and looks like this: ab34cd78e fg3 hi78j I'd like to replace everything at positions 3-4 and 7-8 with blanks, so the output should be: ab cd e fg hi j [I'm not sure if this is really an R question(?), solutions outside of R - maybe via shell() or so - are welcome!] Thanks, Heinrich. __ 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] updating a local package
Essential infrastructure work has been done in the meantime, both ion the documentation system and on the location of binaries. That means you really need to reinstall the package and hence you need to start with a source package. Details for installing from source are given in the manual R Installation and Administartion. Uwe Ligges On 28.10.2010 11:23, Robert Kinley wrote: Hi folks I have inherited a package which was created before release 2.10 and I need to have it working in release 2.12 There is a folder containing the Man, Data and R subfolders, and the description file, and there is also the corresponding zip file. I can install the package from the zip file, but when I try to load it I get the message :- Error: package was built before R 2.10.0: please re-install it If I try to rebuild the zip file using C:\Program Files\R\R-2.12.0\bin\R.exe CMD build my.library.folder I get pages and pages of warnings and error messages, many of which seem to refer to the Man folder. Having never built a formal package before, I'm a bit stuck for what to do next ... Presumably the expected structure of the folders has changed but the documentation on packages looks scary - can anyone suggest the best way forward - even if its only RTFM ! thanks Bob Kinley [[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] replace text at certain positions in a file
I'd just import the positions I like using read.fwf() or otherwise you can replace strings at certain positions, see ?substr Uwe Ligges On 28.10.2010 11:26, RINNER Heinrich wrote: Hello, I am working with R version 2.10.1 under windows. In a text file, I need to replace all characters at certain column positions with blanks. For example, say the file contains two lines and looks like this: ab34cd78e fg3 hi78j I'd like to replace everything at positions 3-4 and 7-8 with blanks, so the output should be: ab cd e fg hi j [I'm not sure if this is really an R question(?), solutions outside of R - maybe via shell() or so - are welcome!] Thanks, Heinrich. __ 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] Changing origin of line in radial plot
On 10/28/2010 07:14 AM, Gonzalo Garcia-Perate wrote:
I am creating radial plots to visualise popularity of a series of
topics, I was wondering if someone has come across a radial plot in
which the lines originate from the edge of the plot instead of the
centre, does anyone know how can this be achieved in R? Are there any
good reasons not to do it?
Hi Gonzalo,
This is an interesting suggestion. I suppose it could be done with an
invert routine that swapped the center coordinates for those of the
outer ring of the annular grid for each radial line. I think I have seen
something like this to illustrate some sort of genetic information.
Yep, down about line 139 in my code you could define xposmax and yposmax
if the new argument invert was TRUE, then
if(invert) {
xposmax-cos(radial.pos[i,])*maxlength
yposmax-sin(radial.pos[i,])*maxlength
}
if(match(r,rptype,0)) {
if(invert)
segments(xposmax,yposmax,xpos,ypos,
col=linecol,lty=ltype,lwd=lwidth,...)
else
segments(0,0,xpos,ypos,col=linecol,
lty=ltype,lwd=lwidth,...)
Untested, but it might do what you want.
Jim
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[R] 0.3 is not 0.3, bug in seq() function?
Dear List, I've been running a numerical simulation and I found this odd error in my code where the which command could not identify which rows of a column of data.frame were corresponding to the value 0.3. There are 7 unique values in this column (0.01,0.05,0.1,0.2,0.3,0.4,0.5), and this does not work only for 0.3. So I looked at the column and manually tried to use the which() command, and the results were all FALSE despite I could see those number. So I recreated my sequence of number and tested: seq(0.1,0.5,0.1)[3]==0.3 which gave me FALSE!!! All the other numbers (0.1,0.2,0.4,0.5) give me TRUE, but 0.3 was not working. So I did: seq(0.1,0.5,0.1)[3]-0.3 which gave me 5.551115e-17. If you run a similar sequence like: seq(0.2,0.6,0.1)[2]==0.3 this will still give me FALSE. No, for my own purpose, I fixed the problem in this way: zerothree=seq(0.1,0.5,0.1)[3] which(data[,1]==zerothree) but I guess this bug is a bit of problem...Apologies if it is the wrong place to post this bug, and apologies also if this was a known issue. My version of R is : platform x86_64-pc-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 10.1 year 2009 month 12 day14 svn rev50720 language R version.string R version 2.10.1 (2009-12-14) Many Thanks, Enrico __ 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] updating a local package
your advice to useR CMD INSTALL source.library did the trick and I now understand packages a little better. many thanks Bob Kinley Uwe Ligges lig...@statistik.tu-dortmund.de 28/10/2010 10:30 To Robert Kinley kinley_rob...@lilly.com cc r-help@r-project.org Subject Re: [R] updating a local package Essential infrastructure work has been done in the meantime, both ion the documentation system and on the location of binaries. That means you really need to reinstall the package and hence you need to start with a source package. Details for installing from source are given in the manual R Installation and Administartion. Uwe Ligges On 28.10.2010 11:23, Robert Kinley wrote: Hi folks I have inherited a package which was created before release 2.10 and I need to have it working in release 2.12 There is a folder containing the Man, Data and R subfolders, and the description file, and there is also the corresponding zip file. I can install the package from the zip file, but when I try to load it I get the message :- Error: package was built before R 2.10.0: please re-install it If I try to rebuild the zip file using C:\Program Files\R\R-2.12.0\bin\R.exe CMD build my.library.folder I get pages and pages of warnings and error messages, many of which seem to refer to the Man folder. Having never built a formal package before, I'm a bit stuck for what to do next ... Presumably the expected structure of the folders has changed but the documentation on packages looks scary - can anyone suggest the best way forward - even if its only RTFM ! thanks Bob Kinley [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] times
I couldn't figure that out, but you can work around it by adding the seconds chron(dates=lwc.file[,1],times=paste(lwc.file[,2],':00',sep='')) Tom 2010/10/28 thoeb t.hoebin...@gmail.com: Hi! I have an input table with a column Dates in the format month/day/year (eg. 5/11/1999 and a column Times in the format hours/minutes (eg. 15:20). In R I need to convert them into chron objects to extract colums only containing months, days, minutes, .. For the dates it is no problem if I write: dmy.lwc-chron(dates=lwc.file[,1],format=(dates=m/d/y)) But it does not work the same way for the times if I write: hm.lwc-chron(times=lwc.file[,2],format=(times=h:m)) Error-Message: Error in convert.times(times., fmt) : format h:m may be incorrect In addition: Warning message: In is.na(out$s) : is.na() applied to non-(list or vector) of type 'NULL' Why should the format h:m not be correct? -- View this message in context: http://r.789695.n4.nabble.com/times-tp3016621p3016621.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] 0.3 is not 0.3, bug in seq() function?
Enrico, The same happens with other numbers/sequences. seq(0.1,0.9,0.1)[7]==0.7 [1] FALSE seq(0.1,1.3,0.1)[12]==1.2 [1] FALSE Rounding seems to fix it, round(seq(0.1,0.5,0.1),1)[3]==0.3 round(seq(0.1,0.9,0.1),1)[7]==0.7 round(seq(0.1,1.3,0.1),1)[12]==1.2 They all return TRUE. Dr. Rubén Roa-Ureta AZTI - Tecnalia / Marine Research Unit Txatxarramendi Ugartea z/g 48395 Sukarrieta (Bizkaia) SPAIN -Mensaje original- De: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] En nombre de Enrico R. Crema Enviado el: jueves, 28 de octubre de 2010 12:24 Para: r-help@r-project.org Asunto: [R] 0.3 is not 0.3, bug in seq() function? Dear List, I've been running a numerical simulation and I found this odd error in my code where the which command could not identify which rows of a column of data.frame were corresponding to the value 0.3. There are 7 unique values in this column (0.01,0.05,0.1,0.2,0.3,0.4,0.5), and this does not work only for 0.3. So I looked at the column and manually tried to use the which() command, and the results were all FALSE despite I could see those number. So I recreated my sequence of number and tested: seq(0.1,0.5,0.1)[3]==0.3 which gave me FALSE!!! All the other numbers (0.1,0.2,0.4,0.5) give me TRUE, but 0.3 was not working. So I did: seq(0.1,0.5,0.1)[3]-0.3 which gave me 5.551115e-17. If you run a similar sequence like: seq(0.2,0.6,0.1)[2]==0.3 this will still give me FALSE. No, for my own purpose, I fixed the problem in this way: zerothree=seq(0.1,0.5,0.1)[3] which(data[,1]==zerothree) but I guess this bug is a bit of problem...Apologies if it is the wrong place to post this bug, and apologies also if this was a known issue. My version of R is : platform x86_64-pc-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 10.1 year 2009 month 12 day14 svn rev50720 language R version.string R version 2.10.1 (2009-12-14) Many Thanks, Enrico __ 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] 0.3 is not 0.3, bug in seq() function?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 28/10/10 12:23, Enrico R. Crema wrote: Dear List, I've been running a numerical simulation and I found this odd error in my code where the which command could not identify which rows of a column of data.frame were corresponding to the value 0.3. There are 7 unique values in this column (0.01,0.05,0.1,0.2,0.3,0.4,0.5), and this does not work only for 0.3. So I looked at the column and manually tried to use the which() command, and the results were all FALSE despite I could see those number. So I recreated my sequence of number and tested: seq(0.1,0.5,0.1)[3]==0.3 which gave me FALSE!!! All the other numbers (0.1,0.2,0.4,0.5) give me TRUE, but 0.3 was not working. So I did: seq(0.1,0.5,0.1)[3]-0.3 which gave me 5.551115e-17. If you run a similar sequence like: seq(0.2,0.6,0.1)[2]==0.3 this will still give me FALSE. No, for my own purpose, I fixed the problem in this way: zerothree=seq(0.1,0.5,0.1)[3] which(data[,1]==zerothree) but I guess this bug is a bit of problem...Apologies if it is the wrong place to post this bug, and apologies also if this was a known issue. My version of R is : platform x86_64-pc-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 10.1 year 2009 month 12 day14 svn rev50720 language R version.string R version 2.10.1 (2009-12-14) This is not a bug, but based on the internal representation of numbers in the binary format. Numbers like 0.3 can not be represented as exactly 0.3, wherefore errors accumulate in a sequence. I can't provide you a link for more details, but the topic comes up every now and then in this mailing list. Cheers, Rainer Many Thanks, Enrico __ 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. - -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Tel:+33 - (0)9 53 10 27 44 Cell: +27 - (0)8 39 47 90 42 Fax (SA): +27 - (0)8 65 16 27 82 Fax (D) : +49 - (0)3 21 21 25 22 44 Fax (FR): +33 - (0)9 58 10 27 44 email: rai...@krugs.de Skype: RMkrug -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkzJVOEACgkQoYgNqgF2egpVXACeNO9GyRh9XKLg1g4EhcFs4Qa5 WXgAmgOdNB/xgmRS4UsMaEtunxS6NB/u =azme -END PGP SIGNATURE- __ 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] updating a local package
On 28.10.2010 12:26, Robert Kinley wrote: your advice to useR CMD INSTALL source.library It's a *package*, not a library. Uwe did the trick and I now understand packages a little better. many thanks Bob Kinley Uwe Liggeslig...@statistik.tu-dortmund.de 28/10/2010 10:30 To Robert Kinleykinley_rob...@lilly.com cc r-help@r-project.org Subject Re: [R] updating a local package Essential infrastructure work has been done in the meantime, both ion the documentation system and on the location of binaries. That means you really need to reinstall the package and hence you need to start with a source package. Details for installing from source are given in the manual R Installation and Administartion. Uwe Ligges On 28.10.2010 11:23, Robert Kinley wrote: Hi folks I have inherited a package which was created before release 2.10 and I need to have it working in release 2.12 There is a folder containing the Man, Data and R subfolders, and the description file, and there is also the corresponding zip file. I can install the package from the zip file, but when I try to load it I get the message :- Error: package was built before R 2.10.0: please re-install it If I try to rebuild the zip file using C:\Program Files\R\R-2.12.0\bin\R.exe CMD build my.library.folder I get pages and pages of warnings and error messages, many of which seem to refer to the Man folder. Having never built a formal package before, I'm a bit stuck for what to do next ... Presumably the expected structure of the folders has changed but the documentation on packages looks scary - can anyone suggest the best way forward - even if its only RTFM ! thanks Bob Kinley [[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] 0.3 is not 0.3, bug in seq() function?
Well...thanks to everybody for suggestions and reading...I guess I have to study more! Enrico On 28 Oct 2010, at 11:48, Rainer M Krug wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 28/10/10 12:23, Enrico R. Crema wrote: Dear List, I've been running a numerical simulation and I found this odd error in my code where the which command could not identify which rows of a column of data.frame were corresponding to the value 0.3. There are 7 unique values in this column (0.01,0.05,0.1,0.2,0.3,0.4,0.5), and this does not work only for 0.3. So I looked at the column and manually tried to use the which() command, and the results were all FALSE despite I could see those number. So I recreated my sequence of number and tested: seq(0.1,0.5,0.1)[3]==0.3 which gave me FALSE!!! All the other numbers (0.1,0.2,0.4,0.5) give me TRUE, but 0.3 was not working. So I did: seq(0.1,0.5,0.1)[3]-0.3 which gave me 5.551115e-17. If you run a similar sequence like: seq(0.2,0.6,0.1)[2]==0.3 this will still give me FALSE. No, for my own purpose, I fixed the problem in this way: zerothree=seq(0.1,0.5,0.1)[3] which(data[,1]==zerothree) but I guess this bug is a bit of problem...Apologies if it is the wrong place to post this bug, and apologies also if this was a known issue. My version of R is : platform x86_64-pc-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 10.1 year 2009 month 12 day14 svn rev50720 language R version.string R version 2.10.1 (2009-12-14) This is not a bug, but based on the internal representation of numbers in the binary format. Numbers like 0.3 can not be represented as exactly 0.3, wherefore errors accumulate in a sequence. I can't provide you a link for more details, but the topic comes up every now and then in this mailing list. Cheers, Rainer Many Thanks, Enrico __ 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. - -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Tel:+33 - (0)9 53 10 27 44 Cell: +27 - (0)8 39 47 90 42 Fax (SA): +27 - (0)8 65 16 27 82 Fax (D) : +49 - (0)3 21 21 25 22 44 Fax (FR): +33 - (0)9 58 10 27 44 email: rai...@krugs.de Skype: RMkrug -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkzJVOEACgkQoYgNqgF2egpVXACeNO9GyRh9XKLg1g4EhcFs4Qa5 WXgAmgOdNB/xgmRS4UsMaEtunxS6NB/u =azme -END PGP SIGNATURE- __ 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] updating a local package
I stand corrected :0) Robert Kinley Uwe Ligges lig...@statistik.tu-dortmund.de 28/10/2010 11:54 To Robert Kinley kinley_rob...@lilly.com cc r-help@r-project.org Subject Re: [R] updating a local package On 28.10.2010 12:26, Robert Kinley wrote: your advice to useR CMD INSTALL source.library It's a *package*, not a library. Uwe did the trick and I now understand packages a little better. many thanks Bob Kinley Uwe Liggeslig...@statistik.tu-dortmund.de 28/10/2010 10:30 To Robert Kinleykinley_rob...@lilly.com cc r-help@r-project.org Subject Re: [R] updating a local package Essential infrastructure work has been done in the meantime, both ion the documentation system and on the location of binaries. That means you really need to reinstall the package and hence you need to start with a source package. Details for installing from source are given in the manual R Installation and Administartion. Uwe Ligges On 28.10.2010 11:23, Robert Kinley wrote: Hi folks I have inherited a package which was created before release 2.10 and I need to have it working in release 2.12 There is a folder containing the Man, Data and R subfolders, and the description file, and there is also the corresponding zip file. I can install the package from the zip file, but when I try to load it I get the message :- Error: package was built before R 2.10.0: please re-install it If I try to rebuild the zip file using C:\Program Files\R\R-2.12.0\bin\R.exe CMD build my.library.folder I get pages and pages of warnings and error messages, many of which seem to refer to the Man folder. Having never built a formal package before, I'm a bit stuck for what to do next ... Presumably the expected structure of the folders has changed but the documentation on packages looks scary - can anyone suggest the best way forward - even if its only RTFM ! thanks Bob Kinley [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] overloading the generic primitive functions + and [
Dear Barry, this is really interesting. However I could not understand
this line:
Ops.ss=function(e1,e2){paste(e1,e2)}
Where you have told R to behave + function differently when it faces
ss class?
What should be the ideal approach if I what to use * function?
Thanks,
On Thu, Oct 28, 2010 at 2:47 PM, Barry Rowlingson
b.rowling...@lancaster.ac.uk wrote:
On Thu, Oct 28, 2010 at 9:31 AM, Mark Heckmann mark.heckm...@gmx.de wrote:
How can I add a new method to the generic function [ or +
I want to create a S3 and S4 class that will use the [ and + method in a
different way.
How can I overload the generic primitive [ or + so the method dispatch
will work correctly for my class?
I saw an example of this in the ggplot2 package where different objects are
joined using the + primitive.
Still, I could not figure out how to do that.
Can someone give a small code example to show how that works?
With S3 method stuff, to override + its as easy as writing Ops.{class}:
a=hello
b=world
a+b
Error in a + b : non-numeric argument to binary operator
class(a)=ss
class(b)=ss
Ops.ss=function(e1,e2){paste(e1,e2)}
a+b
[1] hello world
better make sure I haven't broken anything:
c=1
d=2
c+d
[1] 3 *phew*
The Ops function should really have a handler for all possible
operators (*, /, - etc) or fail with an error - see Ops.Date for
example.
With S4 classes... umm.. signatures... setMethod... setGeneric...
errr. something... representations... setClass this that... yeah.
Something like that.
Barry
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Re: [R] Changing origin of line in radial plot
Jim, thanks for your reply, it works! but the results are not what I
expected. What the code does now is completely reverse the central
chart area, so what was coloured before now is white, see here
http://www.flickr.com/photos/gonzillaaa/
What I was hoping for, was having the same length lines (very short
ones and very long ones) but stemming from the edge of the plot. Any
suggestions?
Thank you,
On 28 October 2010 10:42, Jim Lemon j...@bitwrit.com.au wrote:
On 10/28/2010 07:14 AM, Gonzalo Garcia-Perate wrote:
I am creating radial plots to visualise popularity of a series of
topics, I was wondering if someone has come across a radial plot in
which the lines originate from the edge of the plot instead of the
centre, does anyone know how can this be achieved in R? Are there any
good reasons not to do it?
Hi Gonzalo,
This is an interesting suggestion. I suppose it could be done with an
invert routine that swapped the center coordinates for those of the outer
ring of the annular grid for each radial line. I think I have seen something
like this to illustrate some sort of genetic information.
Yep, down about line 139 in my code you could define xposmax and yposmax if
the new argument invert was TRUE, then
if(invert) {
xposmax-cos(radial.pos[i,])*maxlength
yposmax-sin(radial.pos[i,])*maxlength
}
if(match(r,rptype,0)) {
if(invert)
segments(xposmax,yposmax,xpos,ypos,
col=linecol,lty=ltype,lwd=lwidth,...)
else
segments(0,0,xpos,ypos,col=linecol,
lty=ltype,lwd=lwidth,...)
Untested, but it might do what you want.
Jim
--
Gonzalo Garcia-Perate
PhD candidate, Bartlett School of Architecture, Building,
Environmental Design Planning.
University College London. Gower Street, London WC1E 6BT
g.garcia-per...@ucl.ac.uk
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Re: [R] replace text at certain positions in a file
On Thu, Oct 28, 2010 at 5:26 AM, RINNER Heinrich heinrich.rin...@tirol.gv.at wrote: Hello, I am working with R version 2.10.1 under windows. In a text file, I need to replace all characters at certain column positions with blanks. For example, say the file contains two lines and looks like this: ab34cd78e fg3 hi78j I'd like to replace everything at positions 3-4 and 7-8 with blanks, so the output should be: ab cd e fg hi j [I'm not sure if this is really an R question(?), solutions outside of R - maybe via shell() or so - are welcome!] Try this: s - c(ab34cd78e, fg3 hi78j) sub(^(..)..(..).., \\1 \\2 , s) [1] ab cd e fg hi j -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.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] times
On Thu, Oct 28, 2010 at 1:06 AM, thoeb t.hoebin...@gmail.com wrote: Hi! I have an input table with a column Dates in the format month/day/year (eg. 5/11/1999 and a column Times in the format hours/minutes (eg. 15:20). In R I need to convert them into chron objects to extract colums only containing months, days, minutes, .. For the dates it is no problem if I write: dmy.lwc-chron(dates=lwc.file[,1],format=(dates=m/d/y)) But it does not work the same way for the times if I write: hm.lwc-chron(times=lwc.file[,2],format=(times=h:m)) Error-Message: Error in convert.times(times., fmt) : format h:m may be incorrect In addition: Warning message: In is.na(out$s) : is.na() applied to non-(list or vector) of type 'NULL' Why should the format h:m not be correct? This has been discussed before. See: http://r.789695.n4.nabble.com/zoo-read-intraday-data-tp3010256p3010312.html -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Install Error
Hi, I'm running into the error below when doing R CMD INSTALL MyPackage.tar.gz. This didn't use to be this way and I am at a loss as to where this might be coming from. Any pointers where to look? Joh ** building package indices ... Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 8 elements ERROR: installing package indices failed __ 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 find out the trend during a time period?
2010/10/28 Uwe Ligges lig...@statistik.tu-dortmund.de: On 28.10.2010 06:50, Lao Meng wrote: Hi all: I have a dataset which contains two variables: Y and time y-c(228,189,232,198,252,315) time-2003:2008 How can I find out the trend(increase/decrease) of y along the time period? If I use: lm(y~time) The lm command treats time as natural number,but not date. What is date? WHere is the reproducible example? The code the poster displayed is reproducible -- the problem is more that its not entirely clear what is desired. If the worry is that there can be different numbers of days in different years due to leap years then one could use the number of days between January 1st of each year and January 1st of the first year like this (where y and time are from the original post): d - as.Date(paste(time, 1, 1, sep = -)) d - as.numeric(d - d[1]) d [1]0 365 731 1096 1461 1826 lm(y ~ d) Call: lm(formula = y ~ d) Coefficients: (Intercept)d 193.52454 0.04615 -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Clustering
I am looking to use R in order to determine the number of extreme events for a high frequency (20 minutes) dataset of wave heights that spans 25 years (657,432) data points. I require the number, spacing and duration of the extreme events as an output. I have briefly used the clusters function in evd package. Can anyone suggest a more appropriate package to use for such a large dataset? Thanks, Doug -- View this message in context: http://r.789695.n4.nabble.com/Clustering-tp3017056p3017056.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] Install Error
On 28/10/2010 7:54 AM, Johannes Graumann wrote: Hi, I'm running into the error below when doing R CMD INSTALL MyPackage.tar.gz. This didn't use to be this way and I am at a loss as to where this might be coming from. Any pointers where to look? Joh ** building package indices ... Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 8 elements ERROR: installing package indices failed You may get more informative error information if you do the install from within R. Supposing you've used setwd() to go to the directory where your package lives, try install.packages(MyPackage.tar.gz, repos=NULL, type=source) If that fails, then traceback() will tell you where the failure happened. 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.
Re: [R] 0.3 is not 0.3, bug in seq() function?
Enrico R. Crema enryu_cr...@yahoo.it 28/10/2010 12:08:55
Well...thanks to everybody for suggestions and reading...I guess I
have to study more!
...
On 28/10/10 12:23, Enrico R. Crema wrote:
I can't provide you a link for more details,
The canonical link is R FAQ 7.31 in the 'Frequently Asked Questions'
issued as part of the R HTML Help system.
Steve E
***
This email and any attachments are confidential. Any use...{{dropped:8}}
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Re: [R] 0.3 is not 0.3, bug in seq() function?
Hi, It is a know issue, reported in the FAQ 7.31. Ivan Le 10/28/2010 13:08, Enrico R. Crema a écrit : Well...thanks to everybody for suggestions and reading...I guess I have to study more! Enrico On 28 Oct 2010, at 11:48, Rainer M Krug wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 28/10/10 12:23, Enrico R. Crema wrote: Dear List, I've been running a numerical simulation and I found this odd error in my code where the which command could not identify which rows of a column of data.frame were corresponding to the value 0.3. There are 7 unique values in this column (0.01,0.05,0.1,0.2,0.3,0.4,0.5), and this does not work only for 0.3. So I looked at the column and manually tried to use the which() command, and the results were all FALSE despite I could see those number. So I recreated my sequence of number and tested: seq(0.1,0.5,0.1)[3]==0.3 which gave me FALSE!!! All the other numbers (0.1,0.2,0.4,0.5) give me TRUE, but 0.3 was not working. So I did: seq(0.1,0.5,0.1)[3]-0.3 which gave me 5.551115e-17. If you run a similar sequence like: seq(0.2,0.6,0.1)[2]==0.3 this will still give me FALSE. No, for my own purpose, I fixed the problem in this way: zerothree=seq(0.1,0.5,0.1)[3] which(data[,1]==zerothree) but I guess this bug is a bit of problem...Apologies if it is the wrong place to post this bug, and apologies also if this was a known issue. My version of R is : platform x86_64-pc-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 10.1 year 2009 month 12 day14 svn rev50720 language R version.string R version 2.10.1 (2009-12-14) This is not a bug, but based on the internal representation of numbers in the binary format. Numbers like 0.3 can not be represented as exactly 0.3, wherefore errors accumulate in a sequence. I can't provide you a link for more details, but the topic comes up every now and then in this mailing list. Cheers, Rainer Many Thanks, Enrico __ 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. - -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Tel:+33 - (0)9 53 10 27 44 Cell: +27 - (0)8 39 47 90 42 Fax (SA): +27 - (0)8 65 16 27 82 Fax (D) : +49 - (0)3 21 21 25 22 44 Fax (FR): +33 - (0)9 58 10 27 44 email: rai...@krugs.de Skype: RMkrug -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkzJVOEACgkQoYgNqgF2egpVXACeNO9GyRh9XKLg1g4EhcFs4Qa5 WXgAmgOdNB/xgmRS4UsMaEtunxS6NB/u =azme -END PGP SIGNATURE- __ 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. -- Ivan CALANDRA PhD Student University of Hamburg Biozentrum Grindel und Zoologisches Museum Abt. Säugetiere Martin-Luther-King-Platz 3 D-20146 Hamburg, GERMANY +49(0)40 42838 6231 ivan.calan...@uni-hamburg.de ** http://www.for771.uni-bonn.de http://webapp5.rrz.uni-hamburg.de/mammals/eng/mitarbeiter.php __ 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] Install Error
Duncan Murdoch wrote: On 28/10/2010 7:54 AM, Johannes Graumann wrote: Hi, I'm running into the error below when doing R CMD INSTALL MyPackage.tar.gz. This didn't use to be this way and I am at a loss as to where this might be coming from. Any pointers where to look? Joh ** building package indices ... Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 8 elements ERROR: installing package indices failed You may get more informative error information if you do the install from within R. Supposing you've used setwd() to go to the directory where your package lives, try install.packages(MyPackage.tar.gz, repos=NULL, type=source) If that fails, then traceback() will tell you where the failure happened. Duncan Murdoch Thanks for the pointer, but there doesn't seem to be more information ... install.packages(MyPackage.tar.gz, repos=NULL, type=source) Installing package(s) into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) * installing *source* package ‘MyPackage’ ... ** R ** data ** demo ** exec ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 8 elements ERROR: installing package indices failed * removing ‘/usr/local/lib/R/site-library/MyPackage’ * restoring previous ‘/usr/local/lib/R/site-library/MyPackage’ Warning message: In install.packages(MyPackage.tar.gz, repos = NULL, type = source) : installation of package 'MyPackage.tar.gz' had non-zero exit status traceback() No traceback available __ 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] scatterplot3d; scaling point symbols to depth of graph
Hi I'm trying to scale the point symbols on a 3d plot so that the ones at the front are larger than the ones at the back. I'm trying to give the image some perspective. Given this code... library(scatterplot3d) data=array(c(0,5,9), c(3,3)) scatterplot3d(data, pch=19, cex.symbols=10-data[,2], color=c(red,blue,black)); data [,1] [,2] [,3] [1,]000 [2,]555 [3,]999 which gives a vector for cex.symbols as 10-data[,2] [1] 10 5 1 I would expect the largest point to be the red one at the origin but the image I get has the black symbol at co-ords 9,9,9 as the largest and red at 0,0,0 the smallest. Then if I do... data=array(c(0,9,5), c(3,3)) data [,1] [,2] [,3] [1,]000 [2,]999 [3,]555 scatterplot3d(data, pch=19, cex.symbols=10-data[,2], color=c(red,blue,black)); 10-data[,2] [1] 10 1 5 I'd expect the position and size of the points to be the same but the colour of blue and black to be exchanged. But the size of the points also changes such that the red point at 0,0,0 is the medium size and the black at 5,5,5 is the smallest. So is it possible to get the points described by each row in data to be scaled by the values in data[,2]? Many thanks John sessionInfo() R version 2.11.1 (2010-05-31) i386-redhat-linux-gnu locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8LC_COLLATE=en_US.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] scatterplot3d_0.3-30 loaded via a namespace (and not attached): [1] tools_2.11.1 [[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] Calculate percent occurrence of different values
Hello, I am relatively new to R. I am trying to do the following and cannot figure out a relatively fast, clean method of doing it in R. Here is a simple sample of what my data set looks like: ID TryNum Dir 1 1 1 1 1 1 2 4 1 1 3 2 1 2 1 4 1 2 2 3 2 1 1 3 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 4 2 3 2 1 2 3 1 3 3 1 1 1 3 1 2 4 3 1 3 1 3 1 4 3 3 2 1 4 3 2 2 3 I would like to calculate the percent occurrence of each possible value of Dir (in this case, there are four: 1, 2, 3 and 4) for each ID and Num. E.g., so the output would be a table with each row as a different value of ID (in this case, 1, 2 and 3), and there would be a separate column for each instance of Dir for each instance of Num (in this case, for each of the 4 values of Num, there would be 4 columns for Dir). In this case, the first entry of this table would be .5, since for ID 1, when Num=1, Dir=1 in one out of two cases. Any help would be greatly appreciated! Thank you. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R and Matlab
Dear Group, I am looking for ways to use R and Matlab. Doing the data transformations in R and using the data in Matlab to analyze with some pre-defined scripts. Any good ways to transfer the data into matlab in its most recent version? I tried using R.matlab but the writeMat output is not readable by Matlab. I just need to output a data.frame and read it as is into matlab where I can do any needed transformations on the variables. Thanks, S __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Regular time series with irregular start and end dates
Dear Gabor, Many thanks for your suggestions, I could not get seq(as.Date(2005-09-13), as.Date(2006-10-15), by = 16) to work with ts so have chosen to use the zooreg solution you suggested. In the end, all I want to do is graph the values with the correct time scale on the x-axis. Later we may think about time series analyses. Once again, many thanks. Wesley Gabor Grothendieck ggrothendi...@gmail.com 27/10/2010 16:38 On Wed, Oct 27, 2010 at 10:01 AM, Wesley Roberts wrobe...@csir.co.za wrote: Dear R users, I have a quick question regarding creating an index for a zoo object. I am using R 2.12 on winxp. I have read through the R archives searching for information on dates and time series analysis and nothing seems to cover my question. I am extracting data from a time series of remote sensing data. The frequency of the data is 16 days which means I cant use ts (ts likes months single days etc) and have thus been trying to replicate the following dates using ISOdatetime. 09/13/2005 09/29/2005 10/15/2005 10/31/2005 11/16/2005 12/02/2005 12/18/2005 So far, the only method I have found to be successful is the following a-ISOdatetime(2005, 9, c(13,29), 0, 0, 0) b-ISOdatetime(2005, 10, c(15,31), 0, 0, 0) c-ISOdatetime(2005, 11, c(16), 0, 0, 0) d-ISOdatetime(2005, 12, c(2,18), 0, 0, 0) e-c(a,b,c,d) sort(e) [1] 2005-09-13 SAST 2005-09-29 SAST 2005-10-15 SAST 2005-10-31 SAST [5] 2005-11-16 SAST 2005-12-02 SAST 2005-12-18 SAST This is obviously highly convoluted and is not an appropriate solution. I would appreciate some advice as to how I would go about creating an index that starts at date 2005-09-13 and creates the next date 16 days ahead till the finishing date 2006-10-15. Also, given the nature of my time series would I be able to use ts instead of zoo? Try this: seq(as.Date(2005-09-13), as.Date(2006-10-15), by = 16) or if the reason you want this is that you have 25 values and want to make a zoo/zooreg series from them starting at the indicate Date then just do this (were we use 1:25 for the values of the series for purposes of example): zooreg(1:25, as.Date(2005-09-13), deltat = 16) -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com -- This message is subject to the CSIR's copyright terms and conditions, e-mail legal notice, and implemented Open Document Format (ODF) standard. The full disclaimer details can be found at http://www.csir.co.za/disclaimer.html. This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. MailScanner thanks Transtec Computers for their support. __ 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] Calculate percent occurrence of different values
Try this: prop.table(xtabs(~ paste(ID, Num) + Dir, x), 1) On Thu, Oct 28, 2010 at 7:06 AM, Vanessa J vanja...@hotmail.com wrote: Hello, I am relatively new to R. I am trying to do the following and cannot figure out a relatively fast, clean method of doing it in R. Here is a simple sample of what my data set looks like: ID TryNum Dir 1 1 1 1 1 1 2 4 1 1 3 2 1 2 1 4 1 2 2 3 2 1 1 3 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 4 2 3 2 1 2 3 1 3 3 1 1 1 3 1 2 4 3 1 3 1 3 1 4 3 3 2 1 4 3 2 2 3 I would like to calculate the percent occurrence of each possible value of Dir (in this case, there are four: 1, 2, 3 and 4) for each ID and Num. E.g., so the output would be a table with each row as a different value of ID (in this case, 1, 2 and 3), and there would be a separate column for each instance of Dir for each instance of Num (in this case, for each of the 4 values of Num, there would be 4 columns for Dir). In this case, the first entry of this table would be .5, since for ID 1, when Num=1, Dir=1 in one out of two cases. Any help would be greatly appreciated! Thank you. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Please help me about Monte Carlo Permutation
Dear R experts, I am sorry for my inability. I have the following dataset: Qtot Itot 1 73 684 2 64 451 3 71 378 4 65 284 5 47 179 6 31 117 7 19 69 Now I need to perform Monte Carlo Pertutation test underlaying the following condition. Condition In order to choose randomly (5000 times) for the Qtot in the interval 0 to the maximum possible value of Qtot for each observed value of the independent variable (Itot), Monte Carlo tests needed to be perform to test the null hypothesis. The maximum observed value is either the calculated size of the regional pool (Interpolated value), or the measured size of the actual pool. Each time correlation coefficient (r) between independent and dependent variable has to be calculated in order to achieve the empirical distribution of r for the null hypothesis conditions. Now please help me how to do? I have also intalled combinat library in R. But could not perform by myself. I will be highly grateful. Thanks. -- Chitra Bahadur Baniya (PhD) Lecturer Central Department of Botany Tribhuvan University Kirtipur Kathmandu, Nepal -- View this message in context: http://r.789695.n4.nabble.com/Please-help-me-about-Monte-Carlo-Permutation-tp3017131p3017131.html Sent from the R help mailing list archive at Nabble.com. [[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] R and Matlab
I am looking for ways to use R and Matlab. Doing the data transformations in R and using the data in Matlab to analyze with some pre-defined scripts. Any good ways to transfer the data into matlab in its most recent version? I tried using R.matlab but the writeMat output is not readable by Matlab. It used to work, but I didn't need it for quite a while (a year or so ago, and with Matlab either 2007 or 2008a). I just tried, and neither does it work for me. You should notify the maintainer of R.matlab and include an example (code and data, e.g. with dput). I noticed that library (R.matlab) does not load the Rcompression package, but also after library (Rcompression), the resulting file was not read by Matlab. I tried loading a saved data.frame in Matlab 2008b on an Win XP computer: it doesn't find any variables inside the .mat file (and whos -file ...) doesn't show a variable. The other way round with a stupid little vector it worked. An R session (with only the 2nd try, after library (Rcompression)) is attached below. I just need to output a data.frame and read it as is into matlab where I can do any needed transformations on the variables. If you need to transfer the data right NOW, there's always csv. Claudia library (hyperSpec) Loading required package: lattice Package hyperSpec, version 0.95 To get started, try vignette (introduction, package = hyperSpec) package?hyperSpec vignette (package = hyperSpec) If you use this package please cite it appropriately. citation(hyperSpec) will give you the correct reference. The project is hosted on http://r-forge.r-project.org/projects/hyperspec/ sessionInfo () R version 2.12.0 (2010-10-15) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C LC_TIME=en_US.utf8 [4] LC_COLLATE=en_US.utf8 LC_MONETARY=C LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=CLC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hyperSpec_0.95lattice_0.19-13 R.matlab_1.3.3R.oo_1.7.4 R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] grid_2.12.0 library (Rcompression) x = flu[[]] writeMat (flu.mat, flu) Error in dim(x) - length(x) : invalid first argument writeMat (flu.mat, x) sessionInfo () R version 2.12.0 (2010-10-15) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C LC_TIME=en_US.utf8 [4] LC_COLLATE=en_US.utf8 LC_MONETARY=C LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=CLC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Rcompression_0.8-0 hyperSpec_0.95 lattice_0.19-13R.matlab_1.3.3 R.oo_1.7.4 [6] R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] grid_2.12.0 -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 0 40 5 58-37 68 email: cbelei...@units.it __ 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] RGTK2 - Entry Point not found
I have a problem loading RGtk2 Platform: Windows XP R 2.11.1 In the popup window I get: The procedure entry point cairo_clip_extends could not be located in the dynamic link library libcairo-2.dll and in the R command: Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R/R-211~1.1/library/RGtk2/libs/RGtk2.dll': LoadLibrary failure: The specified procedure could not be found. Eryk __ 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] [SOLVED] Re: Install Error
Johannes Graumann wrote: Hi, I'm running into the error below when doing R CMD INSTALL MyPackage.tar.gz. This didn't use to be this way and I am at a loss as to where this might be coming from. Any pointers where to look? Joh ** building package indices ... Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 8 elements ERROR: installing package indices failed I was working on new functionality and had a no-zipped data file in the data directory ... chance finding in google put me on that track ... Works again. Joh __ 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] RGTK2 - Entry Point not found
I have a problem loading RGtk2 Platform: Windows XP R 2.11.1 In the popup window I get: The procedure entry point cairo_clip_extends could not be located in the dynamic link library libcairo-2.dll and in the R command: Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R/R-211~1.1/library/RGtk2/libs/RGtk2.dll': LoadLibrary failure: The specified procedure could not be found. Eryk __ 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] [SOLVED] Re: Install Error
Johannes Graumann wrote: Johannes Graumann wrote: Hi, I'm running into the error below when doing R CMD INSTALL MyPackage.tar.gz. This didn't use to be this way and I am at a loss as to where this might be coming from. Any pointers where to look? Joh ** building package indices ... Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 8 elements ERROR: installing package indices failed I was working on new functionality and had a no-zipped data file in the data directory ... chance finding in google put me on that track ... Works again. Joh Wishlist item here https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14426 Joh __ 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] overloading the generic primitive functions + and [
On 10/28/2010 02:17 AM, Barry Rowlingson wrote:
On Thu, Oct 28, 2010 at 9:31 AM, Mark Heckmann mark.heckm...@gmx.de wrote:
How can I add a new method to the generic function [ or +
I want to create a S3 and S4 class that will use the [ and + method in a
different way.
How can I overload the generic primitive [ or + so the method dispatch
will work correctly for my class?
I saw an example of this in the ggplot2 package where different objects are
joined using the + primitive.
Still, I could not figure out how to do that.
Can someone give a small code example to show how that works?
With S3 method stuff, to override + its as easy as writing Ops.{class}:
a=hello
b=world
a+b
Error in a + b : non-numeric argument to binary operator
class(a)=ss
class(b)=ss
Ops.ss=function(e1,e2){paste(e1,e2)}
a+b
[1] hello world
better make sure I haven't broken anything:
c=1
d=2
c+d
[1] 3 *phew*
The Ops function should really have a handler for all possible
operators (*, /, - etc) or fail with an error - see Ops.Date for
example.
With S4 classes... umm.. signatures... setMethod... setGeneric...
errr. something... representations... setClass this that... yeah.
Something like that.
The more-or-less literal translation of your S3 to S4 is
setClass(SS, character)
setMethod(Ops, c(SS, SS), function(e1, e2) paste(e1, e2))
Not so hard, eh? Though then like your S3 implementation this makes all
'Ops' (see ?Ops) the same for SS objects. For + alone
setMethod(+, c(SS, SS), function(e1, e2) paste(e1, e2))
One might typically use a group generic like Ops (or Arith for a narrow
set of operations in S4) when wanting to delegate to a slot of a class,
e.g.,
setClass(Person, representation(age=numeric))
setMethod(Arith, c(Person, Person), function(e1, e2) {
callGeneric(e...@age, e...@age)
})
Phred = new(Person, age=32)
Phrank = new(Person, age=37)
Phred - Phrank
[1] -5
Phred * Phrank
[1] 1184
Martin
Barry
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--
Computational Biology
Fred Hutchinson Cancer Research Center
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Re: [R] RGTK2 - Entry Point not found
The stable version of RGtk2 requires GTK version 2.8.0 or higher (and its dependencies). -- Mi³ego dnia [[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] R and Matlab
Is there a particular reason you can't use csv? write.csv() in R It seems that you can read csv in Matlab with this http://www.mathworks.com/help/techdoc/ref/importdata.html Tom 2010/10/28 Claudia Beleites cbelei...@units.it: I am looking for ways to use R and Matlab. Doing the data transformations in R and using the data in Matlab to analyze with some pre-defined scripts. Any good ways to transfer the data into matlab in its most recent version? I tried using R.matlab but the writeMat output is not readable by Matlab. It used to work, but I didn't need it for quite a while (a year or so ago, and with Matlab either 2007 or 2008a). I just tried, and neither does it work for me. You should notify the maintainer of R.matlab and include an example (code and data, e.g. with dput). I noticed that library (R.matlab) does not load the Rcompression package, but also after library (Rcompression), the resulting file was not read by Matlab. I tried loading a saved data.frame in Matlab 2008b on an Win XP computer: it doesn't find any variables inside the .mat file (and whos -file ...) doesn't show a variable. The other way round with a stupid little vector it worked. An R session (with only the 2nd try, after library (Rcompression)) is attached below. I just need to output a data.frame and read it as is into matlab where I can do any needed transformations on the variables. If you need to transfer the data right NOW, there's always csv. Claudia library (hyperSpec) Loading required package: lattice Package hyperSpec, version 0.95 To get started, try vignette (introduction, package = hyperSpec) package?hyperSpec vignette (package = hyperSpec) If you use this package please cite it appropriately. citation(hyperSpec) will give you the correct reference. The project is hosted on http://r-forge.r-project.org/projects/hyperspec/ sessionInfo () R version 2.12.0 (2010-10-15) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C LC_TIME=en_US.utf8 [4] LC_COLLATE=en_US.utf8 LC_MONETARY=C LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hyperSpec_0.95 lattice_0.19-13 R.matlab_1.3.3 R.oo_1.7.4 R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] grid_2.12.0 library (Rcompression) x = flu[[]] writeMat (flu.mat, flu) Error in dim(x) - length(x) : invalid first argument writeMat (flu.mat, x) sessionInfo () R version 2.12.0 (2010-10-15) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C LC_TIME=en_US.utf8 [4] LC_COLLATE=en_US.utf8 LC_MONETARY=C LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Rcompression_0.8-0 hyperSpec_0.95 lattice_0.19-13 R.matlab_1.3.3 R.oo_1.7.4 [6] R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] grid_2.12.0 -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 0 40 5 58-37 68 email: cbelei...@units.it __ 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] overloading the generic primitive functions + and [
On Thu, Oct 28, 2010 at 2:12 PM, Martin Morgan mtmor...@fhcrc.org wrote: Not so hard, eh? Though then like your S3 implementation this makes all 'Ops' (see ?Ops) Except you have to re-run the set* things every R session: setClass(SS, character) setMethod(Ops, c(SS, SS), function(e1, e2) paste(e1, e2)) a=new(SS,hello) b=new(SS,world) a+b [1] hello world q() Save workspace image? [y/n/c]: y ...start R again... [Previously saved workspace restored] a=new(SS,hello) b=new(SS,world) a+b Error in a + b : non-numeric argument to binary operator It seems the SS class is preserved but the method definition isn't. Otherwise new(SS,hello) fails. That's one of the things that confuses me about S4 - its use of invisible global things. ls(all.names=TRUE) shows me the bits: ls(all.names=TRUE) [1] a .__C__SS .requireCachedGenerics It seems that .__C__SS is the class definition, and the .requireCachedGenerics seems to imply I've done something with 'Ops': .requireCachedGenerics [[1]] [1] Ops but doesn't actually store and restore my definition. A bug? I dunno. Version 2.10.1 if anyone cares. I don't. I'll just go back to my S3 method which is just as simple and works when I restore the .RData I saved things to. Each to their own! Barry __ 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] overloading the generic primitive functions + and [
On Thu, Oct 28, 2010 at 12:14 PM, Christofer Bogaso
bogaso.christo...@gmail.com wrote:
Dear Barry, this is really interesting. However I could not understand
this line:
Ops.ss=function(e1,e2){paste(e1,e2)}
Where you have told R to behave + function differently when it faces
ss class?
What should be the ideal approach if I what to use * function?
You can get the character string of the operator from '.Generic', for example:
Ops.ss=function(e1,e2){
if(.Generic==+){
return(paste(e1,e2))
}
if(.Generic==*){
return(rep(e1,e2))
}
stop(No definition for ,.Generic)
}
Giving:
a*5
[1] hello hello hello hello hello
a+world
[1] hello world
a/2
Error in Ops.ss(a, 2) : No definition for /
Note how S3 methods are dispatched only by reference to the first
argument (on the left of the operator). I think S4 beats this by
having signatures that can dispatch depending on both arguments.
Barry
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Re: [R] RGTK2 - Entry Point not found
Failed to load RGtk2 dynamic library, attempting to install it. trying URL 'http://downloads.sourceforge.net/gladewin32/gtk-2.12.9-win32-2.exe' Content type 'application/x-msdownload' length 7378984 bytes (7.0 Mb) I run the complete setup of GTK . Hence, I assume Version 2.12.9 is installed on my box. My path variable starts with: %GTK_BASEPATH%\bin; Any other ideas? 2010/10/28 Łukasz Ręcławowicz lukasz.reclawow...@gmail.com: The stable version of RGtk2 requires GTK version 2.8.0 or higher (and its dependencies). -- Miłego dnia -- Witold Eryk Wolski Heidmark str 5 D-28329 Bremen tel.: 04215261837 __ 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] Key combination that removes all R objects
Dear readers, There is a combination of keys that I have (on several occasions now) typed by accident into R (2.10.0) which removes all the objects in the environment, and clears the console, as though I had typed rm(list=ls()). Unfortunately I don't know what the combination of keys are, so I am struggling to find out more about this behaviour on my own and I was hoping that someone has come across it before. Does anyone i) know what combination of keys this is (so that I am more cautious around them in future) or better yet, ii) know how to disable this shortcut? Thanks for your time, Claire Issued by UBS AG or affiliates to professional investors for information only and its accuracy/completeness is not guaranteed. All opinions may change without notice and may differ to opinions/recommendations expressed by other business areas of UBS. UBS may maintain long/short positions and trade in instruments referred to. Unless stated otherwise, this is not a personal recommendation, offer or solicitation to buy/sell and any prices/quotations are indicative only. UBS may provide investment banking and other services to, and/or its employees may be directors of, companies referred to. To the extent permitted by law, UBS does not accept any liability arising from the use of this communication. \251 UBS 2010. All rights reserved. Intended for recipient only and not for further distribution without the consent of UBS. UBS Limited is a company registered in England Wales under company number 2035362, whose registered office is at 1 Finsbury Avenue, London, EC2M 2PP, United Kingdom. UBS AG (London Branch) is registered as a branch of a foreign company under number BR004507, whose registered office is at 1 Finsbury Avenue, London, EC2M 2PP, United Kingdom. UBS Clearing and Execution Services Limited is a company registered in England Wales under company number 03123037, whose registered office is at 1 Finsbury Avenue, London, EC2M 2PP, United Kingdom. UBS reserves the right to retain all messages. Messages are protected and accessed only in legally justified cases. __ 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] bugs when using R-2.12.0 Please HELP!
Hi, R-help group, I kinda meeting a question when using R-2.12.0(Previous version is 2.10.0): When I typed library(Biobase), everything is alright! But when I type library(genefilter), it doesn't work! And echo this: Error in library.dynam(lib, package, package.lib) : DLL 'RSQLite' not found: maybe not installed for this architecture? Error: package/namespace load failed for 'genefilter' Please someone tell me what's wrong with this? 3ks a lot! Tony [[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] bugs when using R-2.12.0 Please HELP!
On Oct 28, 2010, at 10:01 AM, Hao Wu wrote: Hi, R-help group, I kinda meeting a question when using R-2.12.0(Previous version is 2.10.0): When I typed library(Biobase), everything is alright! But when I type library(genefilter), it doesn't work! And echo this: Error in library.dynam(lib, package, package.lib) : DLL 'RSQLite' not found: maybe not installed for this architecture? Error: package/namespace load failed for 'genefilter' Please someone tell me what's wrong with this? I guess the obvious question i: Have you have (re-?) installed RSQLiite? Couple of other points: You should post the results of sessionInfo(). It will automatically cure many of the remaining information deficiencies in your question. Labeling user error or failure to read informative error messages as bugs is annoying to many of the authors and maintainers of R (a group of which I am not a member). A word which has less implication of software deficiencies would be problems. This is really about BioConductor and it has its own mailing list. -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Heatmap construction problems
I am very new to R and don't have any computer program experience whatsoever. I am trying to generate a heatmap of the following data: Phylum,AI,AJT,BY,GA,Grt,Sm Acidobacteria,0.5,0.7,2.7,0.1,2.6,1.0 Actinobacteria,33.7,65.1,9.7,2.0,3.9,2.1 Bacteroidetes,9.7,5.6,0.7,13.2,41.1,21.6 CCM11b,0.0,0.0,0.0,0.0,0.0,0.1 Chlamydiae,0.1,0.1,0.0,0.0,1.0,0.2 Chlorobi,0.0,0.0,0.0,0.0,0.7,1.0 Chloroflexi,0.1,0.2,0.6,0.2,0.8,0.6 Cyanobacteria,18.7,0.0,1.0,1.5,0.9,0.3 Ellusimicrobiales,0.0,0.0,0.0,0.0,0.0,0.0 Firmicutes,1.0,7.6,8.3,31.9,2.1,6.9 Gemmatimonadetes,5.0,0.3,0.3,0.0,0.1,0.0 GN02,0.0,0.0,0.0,0.0,0.0,0.5 Nitrospirae,0.0,0.2,1.1,0.0,0.0,0.0 NKB19,0.0,0.0,0.9,0.0,0.0,0.0 OP8,0.0,0.1,0.0,0.0,0.0,0.0 OP10,0.6,0.2,0.5,0.0,0.6,0.6 Planctomycetes,0.9,0.5,6.5,2.2,2.0,2.3 Alphaproteobacteria,7.8,10.7,21.8,12.2,5.3,26.8 Betaproteobacteria,9.9,2.8,8.9,21.7,8.3,21.9 Deltaproteobacteria,0.5,0.2,1.8,2.0,1.2,7.1 Epsilonproteobacteria,0.0,0.0,0.0,0.1,0.0,0.2 Gammaproteobacteria,4.0,2.5,8.0,9.4,24.7,5.4 SC4,0.0,0.0,0.0,0.0,0.7,0.0 SM2F11,0.0,0.0,0.0,0.0,0.2,0.0 SPAM,0.0,0.1,0.0,0.0,0.1,0.1 Synergistes,0.0,0.0,0.0,0.1,0.0,0.0 Deinococcus-Thermus,0.0,0.0,0.0,0.0,0.0,0.0 TM6,0.1,0.0,0.0,0.0,0.1,0.0 TM7,0.0,0.1,0.4,0.0,0.4,0.1 Verrucomicrobia,3.8,2.1,23.2,2.9,1.3,0.5 WPS-2,0.0,0.0,0.1,0.0,0.0,0.0 WS3,0.0,0.0,0.0,0.0,0.0,0.1 Uncl Bacteria,3.7,1.2,3.7,0.4,1.9,0.8 I am a microbiologist. What I want to do is construct a heatmap showing the relative abundance of each phylum. The far left column of my table contains all of the phylum names I observed in a set of 6 water samples and each of the columns to the right contains the relative abundance (%) of each phylum in each water sample. I have tried constructing a heatmap using the ggplot guidelines listed at the following site: http://learnr.wordpress.com/2010/01/26/ggplot2-quick-heatmap-plotting/ I can generate a heatmap using this method, but would like to alter the scale. I would like it so that I can have a little more complex gradient ranging from 0% to the highest relative abundance that I observe in the above table (65.1%). The default scale I get using the link above is just a relative intensity scale ranging from 1 to 5 (where white represent low percentages and steelblue represented high percentages). This is alright but for phyla that are present at relative abundance of less than 5% all appear to be white (or non-existant). Is there anyway to fix this? Any help would be greatly appreciated. Thanks, Chris __ 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] adding environment variables
Hi All, I am developing a package that requires information about the location of a set of files that will be used often in the calculations. In my current version, I define the location in the main file that calls all the subfunctions. This works fine when you are installing from source, but will not work so well if I want people to be able to install binary versions of the package. Therefore, I think the best way to encode the information would be through the use of an environment variable, that could then be read by Sys.getenv(VARIABLE) when the function is called. In the help, I found a few different ways to set environment variables, but the easiest way (from my reading anyways) seemed to be by creating the file Renviron.site in the R_HOME/etc directory and adding the variable there. I am interested in opinions from the list, or other suggestions on how to do this. For those who are interested, the package does a lot of parsing of KEGG KGML files, and to speed up calculations I offer advice that they should download a copy of the KGML directory for their organism to their local machine, and I want the package to know where those files are at runtime. Thanks in advance, -Robert Robert M. Flight, Ph.D. University of Louisville Bioinformatics Laboratory University of Louisville Louisville, KY PH 502-852-0467 EM robert.fli...@louisville.edu EM rfligh...@gmail.com Williams and Holland's Law: If enough data is collected, anything may be proven by statistical methods. __ 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] Please help me about Monte Carlo Permutation
This is one way. I read your two columns of data into two variables, x and y. Then: test - replicate(5000, cor(x, sample(y))) hist(test) Kjetil On Thu, Oct 28, 2010 at 9:49 AM, Chitra cbban...@gmail.com wrote: Dear R experts, I am sorry for my inability. I have the following dataset: Qtot Itot 1 73 684 2 64 451 3 71 378 4 65 284 5 47 179 6 31 117 7 19 69 Now I need to perform Monte Carlo Pertutation test underlaying the following condition. Condition In order to choose randomly (5000 times) for the Qtot in the interval 0 to the maximum possible value of Qtot for each observed value of the independent variable (Itot), Monte Carlo tests needed to be perform to test the null hypothesis. The maximum observed value is either the calculated size of the regional pool (Interpolated value), or the measured size of the actual pool. Each time correlation coefficient (r) between independent and dependent variable has to be calculated in order to achieve the empirical distribution of r for the null hypothesis conditions. Now please help me how to do? I have also intalled combinat library in R. But could not perform by myself. I will be highly grateful. Thanks. -- Chitra Bahadur Baniya (PhD) Lecturer Central Department of Botany Tribhuvan University Kirtipur Kathmandu, Nepal -- View this message in context: http://r.789695.n4.nabble.com/Please-help-me-about-Monte-Carlo-Permutation-tp3017131p3017131.html Sent from the R help mailing list archive at Nabble.com. [[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] coxph linear.predictors
To close the issue: S.ave - survfit(fit) # this is average survival S.1 - (S.ave$surv)^exp(fit$linear.predictors[1]) # get subject 1 S.1 [1] 0.848450223861993 0.696973203043377 0.530604282995790 0.391136296063732 0.228370373409774 0.132991279576665 0.071742127376216 [8] 0.030988671457923 0.012340713882587 0.004553665545169 0.000865566322530 0.000135746409544 survfit(fit,new=ovarian[1,])$surv # subject 1 from survfit [1] 0.848450223861993 0.696973203043377 0.530604282995791 0.391136296063732 0.228370373409774 0.132991279576665 0.071742127376216 [8] 0.030988671457923 0.012340713882587 0.004553665545169 0.000865566322530 0.000135746409544 A single call to survfit will suffice for thousands of subjects, avoiding the iterative loop calculations inside survfit. Stephen Bond -Original Message- From: David Winsemius [mailto:dwinsem...@comcast.net] Sent: Wednesday, October 27, 2010 1:15 PM To: Bond, Stephen Cc: r-help@r-project.org Subject: Re: [R] coxph linear.predictors On Oct 27, 2010, at 12:12 PM, Bond, Stephen wrote: I would like to be able to construct hazard rates (or unconditional death prob) Hazards are not probabilities (since probabilities are constrained to the range [0,1] and hazards are unbounded upward.) for many subjects from a given survfit. This will involve adjusting the ( n.event/n.risk) with (coxph object )$linear.predictors I must be having another silly day as I cannot reproduce the linear predictor: fit - coxph(Surv(futime, fustat) ~ age, data = ovarian) fit$linear.predictors[1] [1] 2.612756 That's the linear predictor (the beta*X) and that particular number only applies to the first case. coef(fit)*model.matrix(fit)[1,1] age 11.69021 I don't know what that might be and you are not telling us what you think it is. The above is based on the help listing for coxph.object coefficients: the coefficients of the linear predictor, which multiply the columns of the model matrix. If the model is over-determined there will be missing values in the vector corresponding to the redundant columns in the model matrix. Also, please comment whether n.event/n.risk The Nelson-Aalen estimator of the cumulative hazard as a function of intervals prior to t is sum( n-event(t)/ n.risk(t)) gives the baseline hazard exp(alpha) ? No. The baseline hazard, as you are calling this, would be an estimate for persons with all covariates = 0, so in this case is for women of age=0. (Not a particularly interpretable result in many situations. The baseline hazard following treated ovarian cancer for neonates is not medically sensible.) What is the purpose of this request? Is someone telling you you need to provide estimates for instantaneous hazards? -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R and Matlab
On 10/28/2010 03:16 PM, Thomas Levine wrote: Is there a particular reason you can't use csv? (Not sure whether I'm meant - as I also suggested csv to Santosh) But: - It used to work, so there may be code existing that is broken now (e.g. I do have such code, but at least for the moment it doesn't matter). Thus the information may very well be of interest for the maintainer. - csv is fine for a matrix (or a vector) or a data.frame. How about arrays, lists, more than one variable? I think the default file format changed to v7.3 (though I'm not sure whether that is just for large variables). Unfortunately -v switch of load (that used e.g. to allow reading of V4 files) is gone, and I can't see anything to specify the .mat file format version. The curious thing is that readMat does accept the file produced by Matlab 2008b. If it is a matter of writeMat writing an old file format, I'd have expected that rather load should still be able to read the writeMat generated file than readMat being able to read Matlab's .mat file. my 2 ct Claudia write.csv() in R It seems that you can read csv in Matlab with this http://www.mathworks.com/help/techdoc/ref/importdata.html Tom 2010/10/28 Claudia Beleitescbelei...@units.it: I am looking for ways to use R and Matlab. Doing the data transformations in R and using the data in Matlab to analyze with some pre-defined scripts. Any good ways to transfer the data into matlab in its most recent version? I tried using R.matlab but the writeMat output is not readable by Matlab. It used to work, but I didn't need it for quite a while (a year or so ago, and with Matlab either 2007 or 2008a). I just tried, and neither does it work for me. You should notify the maintainer of R.matlab and include an example (code and data, e.g. with dput). I noticed that library (R.matlab) does not load the Rcompression package, but also after library (Rcompression), the resulting file was not read by Matlab. I tried loading a saved data.frame in Matlab 2008b on an Win XP computer: it doesn't find any variables inside the .mat file (and whos -file ...) doesn't show a variable. The other way round with a stupid little vector it worked. An R session (with only the 2nd try, after library (Rcompression)) is attached below. I just need to output a data.frame and read it as is into matlab where I can do any needed transformations on the variables. If you need to transfer the data right NOW, there's always csv. Claudia library (hyperSpec) Loading required package: lattice Package hyperSpec, version 0.95 To get started, try vignette (introduction, package = hyperSpec) package?hyperSpec vignette (package = hyperSpec) If you use this package please cite it appropriately. citation(hyperSpec) will give you the correct reference. The project is hosted on http://r-forge.r-project.org/projects/hyperspec/ sessionInfo () R version 2.12.0 (2010-10-15) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C LC_TIME=en_US.utf8 [4] LC_COLLATE=en_US.utf8 LC_MONETARY=C LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=CLC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hyperSpec_0.95lattice_0.19-13 R.matlab_1.3.3R.oo_1.7.4 R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] grid_2.12.0 library (Rcompression) x = flu[[]] writeMat (flu.mat, flu) Error in dim(x)- length(x) : invalid first argument writeMat (flu.mat, x) sessionInfo () R version 2.12.0 (2010-10-15) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C LC_TIME=en_US.utf8 [4] LC_COLLATE=en_US.utf8 LC_MONETARY=C LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=CLC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Rcompression_0.8-0 hyperSpec_0.95 lattice_0.19-13R.matlab_1.3.3 R.oo_1.7.4 [6] R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] grid_2.12.0 -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127 Trieste phone: +39 0 40 5 58-37 68 email: cbelei...@units.it __ 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. -- Claudia Beleites Dipartimento dei Materiali e delle Risorse Naturali Università degli Studi di Trieste Via Alfonso Valerio 6/a I-34127
Re: [R] Key combination that removes all R objects
I am not aware of the existance of a shortcut that would do what you describe. On Windows, one could hit Ctrl-M, followed by R, but then one gets a prompt, asking for confirmation to remove all objects, but this can't be what you are referring to. Are you perhaps using Tinn-R and (accidentally) hitting F12 (which does in fact exactly what you describe)? Best, -- Wolfgang Viechtbauer Department of Methodology and Statistics School for Public Health and Primary Care Maastricht University, P.O. Box 616 6200 MD Maastricht, The Netherlands Tel: +31 (43) 388-2277 Fax: +31 (43) 361-8388 Web: http://www.wvbauer.com Original Message From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of claire-c.jo...@ubs.com Sent: Thursday, October 28, 2010 16:10 To: r-help@r-project.org Subject: [R] Key combination that removes all R objects Dear readers, There is a combination of keys that I have (on several occasions now) typed by accident into R (2.10.0) which removes all the objects in the environment, and clears the console, as though I had typed rm(list=ls()). Unfortunately I don't know what the combination of keys are, so I am struggling to find out more about this behaviour on my own and I was hoping that someone has come across it before. Does anyone i) know what combination of keys this is (so that I am more cautious around them in future) or better yet, ii) know how to disable this shortcut? Thanks for your time, Claire __ 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] Merging nested lists
On Wed, 27 Oct 2010, Charles C. Berry wrote:
On Wed, 27 Oct 2010, Alex P. wrote:
Hello All,
I have multiple list of lists in the form of
Mylist1[[N]][[K]]$Name_i,
with N=1..6, K=1..3, and i=1..7. Each Name_i is a matrix. I have 30 of
these objects Mylist1, Mylist2, ...
I would like to merge these lists by each Name_i using rbind, but I
couldn't figure out how to do it. What I want at the end is a single list
of lists, again in the form of Mylist[[N]][[K]]$Name_i. Manually doing it
is not feasible given the large number of Mylist objects.
Turn them into a single array of mode 'list', then do the rbind'ing, and save
the result as an array (or see ?relist for imposing the nested structure of
the orignal lists)
Something like:
I see a few hiccups below.
Maybe Alex P. should include a minimal, self-contained example that
RespondeRs could try out...
objs - paste('MyList',1:30,sep='')
big.list - lapply( objs, get )
for (i in 1:4) big.list - unlist(big.list,recursive=FALSE)
for (i in 1:3) ...
dim( big.list ) - c(30, 6, 3, 7 )
dim( big.list ) - rev( c(30, 6, 3, 7 ) )
res - apply( big.list, 2:4, rbind )
dim(res) - c( 30, 3, 7 )
res - apply( big.list, 1:3, function(x) list( do.call( rbind, x ) ))
Chuck
HTH,
Chuck
Thanks in advance,
Alex
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Charles C. Berry(858) 534-2098
Dept of Family/Preventive
Medicine
E mailto:cbe...@tajo.ucsd.edu UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:cbe...@tajo.ucsd.edu UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
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[R] Rsolnp examples
I'm interested in the Rsolnp package. For their primary function solnp, one example is given, and there is a reference to unit tests. Anyone know where these can be found? Also, Rsolnp is used in a few other packages (e.g., depmixS4), but I cannot seem to find source illustrating its call sequence, and the precise definition of the functions passed. Can anyone help? Thanks, - 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] runtime on ising model
Mike, I'm not sure what you mean about removing foo but I think the method
is sound in diagnosing a program issue and the results speak for themselves.
I did invert my if statement at the suggestion of a CS professor (who also
suggested recoding in C, but I'm in an applied math program and haven't had
the time to take programming courses, which i know would be helpful)
Anyway, with the statement as:
if( !(k %in% c(10^4,10^5,10^6,10^7)) ){
#do nothing
} else {
q - q+1
Out[[q]] - M
}
run times were back to around 20 minutes. So as best I can tell something
happens in the if statement causing the computer to work ahead, as the
professor suggests. I'm no expert on R (and have no desire to try looking at
the R source code (it would only confuse me)) but if anyone can offer
guidance on how the if statement works (Does R try to work ahead? Under what
conditions does it try to work ahead so I can try to exploit this
behavior) I would greatly appreciate it.
If it would require too much knowledge of the computer system to understand
I doubt I would be able to make use of it, but maybe someone else could
benefit.
On Tue, Oct 26, 2010 at 3:24 PM, Mike Marchywka marchy...@hotmail.comwrote:
Date: Tue, 26 Oct 2010 12:53:14 -0400
From: mike...@gmail.com
To: j...@bitwrit.com.au
CC: r-help@r-project.org
Subject: Re: [R] runtime on ising model
I have an update on where the issue is coming from.
I commented out the code for pos[k+1] - M[i,j] and the if statement
for
time = 10^4, 10^5, 10^6, 10^7 and the storage and everything ran
fast(er).
Next I added back in the pos statements and still runtimes were good
(around 20 minutes).
So I'm left with something is causing problems in:
I haven't looked at this since some passing interest in magnetics
decades ago, something about 8-tracks and cassettes, but you have
to be careful with conclusions like I removed foo and problem
went away therefore problem was foo. Performance issues are often
caused by memory, not CPU limitations. Removing anything with a big
memory footprint could speed things up. IO can be a real bottleneck.
If you are talking about things on minute timescales, look at task
manager and see if you are even CPU limited. Look for page faults
or IO etc. If you really need performance and have a task which
is relatively simple, don't ignore c++ as a way to generate data
points and then import these into R for analysis.
In short, just because you are focusing on math it doesn't mean
the computer is limited by that.
## Store state at time 10^4, 10^5, 10^6, 10^7
if( k %in% c(10^4,10^5,10^6,10^7) ){
q - q+1
Out[[q]] - M
}
Would there be any reason R is executing the statements inside the if
before getting to the logical check?
Maybe R is written to hope for the best outcome (TRUE) and will just
throw
out its work if the logic comes up FALSE?
I guess I can always break the for loop up into four parts and store the
state at the end of each, but thats an unsatisfying solution to me.
Jim, I like the suggestion of just pulling one big sample, but since I
can
get the runtimes under 30 minutes just by removing the storage piece I
doubt
I would see any noticeable changes by pulling large sample vectors.
Thanks,
Michael
On Tue, Oct 26, 2010 at 6:22 AM, Jim Lemon wrote:
On 10/26/2010 04:50 PM, Michael D wrote:
So I'm in a stochastic simulations class and I having issues with the
amount
of time it takes to run the Ising model.
I usually don't like to attach the code I'm running, since it will
probably
make me look like a fool, but I figure its the best way I can find any
bits
I can speed up run time.
As for the goals of the exercise:
I need the state of the system at time=1, 10k, 100k, 1mill, and 10mill
and the percentage of vertices with positive spin at all t
Just to be clear, i'm not expecting anyone to tell me how to program
this
model, cause I know what I have works for this exercise, but it takes
far
too long to run and I'd like to speed it up by replacing slow
operations
wherever possible.
Hi Michael,
One bottleneck is probably the sampling. If it doesn't grab too much
memory, setting up a vector of the samples (maybe a million at a time
if 10
million is too big - might be able to rewrite your sample vector when
you
store the state) and using k (and an offset if you don't have one big
vector) to index it will give you some speed.
Jim
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
Re: [R] RGTK2 - Entry Point not found
W dniu 28 pa¼dziernika 2010 16:09 u¿ytkownik W Eryk Wolski wewol...@gmail.com napisa³: Any other ideas? Restart R and then try load library :) -- Mi³ego dnia [[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] runtime on ising model
On Oct 28, 2010, at 11:52 AM, Michael D wrote:
Mike, I'm not sure what you mean about removing foo but I think the
method
is sound in diagnosing a program issue and the results speak for
themselves.
I did invert my if statement at the suggestion of a CS professor
(who also
suggested recoding in C, but I'm in an applied math program and
haven't had
the time to take programming courses, which i know would be helpful)
Anyway, with the statement as:
if( !(k %in% c(10^4,10^5,10^6,10^7)) ){
#do nothing
} else {
q - q+1
Out[[q]] - M
}
run times were back to around 20 minutes.
Have you tried replacing all of those 10^x operations with their
integer equivalents, c(1L, 10L, 100L)? Each time through
the loop you are unnecessarily calling the ^ function 4 times. You
could also omit the last one. 10^7, during testing since M at the
last iteration (k=10^7) would be the final value and you could just
assign the state of M at the end. So we have eliminated 4*10^7
unnecessary ^ calls and 10^7 unnecessary comparisons. (The CS
professor is perhaps used to having the C compiler do all thinking of
this sort for him.)
--
David
So as best I can tell something
happens in the if statement causing the computer to work ahead, as the
professor suggests. I'm no expert on R (and have no desire to try
looking at
the R source code (it would only confuse me)) but if anyone can offer
guidance on how the if statement works (Does R try to work ahead?
Under what
conditions does it try to work ahead so I can try to exploit this
behavior) I would greatly appreciate it.
If it would require too much knowledge of the computer system to
understand
I doubt I would be able to make use of it, but maybe someone else
could
benefit.
On Tue, Oct 26, 2010 at 3:24 PM, Mike Marchywka
marchy...@hotmail.comwrote:
Date: Tue, 26 Oct 2010 12:53:14 -0400
From: mike...@gmail.com
To: j...@bitwrit.com.au
CC: r-help@r-project.org
Subject: Re: [R] runtime on ising model
I have an update on where the issue is coming from.
I commented out the code for pos[k+1] - M[i,j] and the if
statement
for
time = 10^4, 10^5, 10^6, 10^7 and the storage and everything ran
fast(er).
Next I added back in the pos statements and still runtimes were
good
(around 20 minutes).
So I'm left with something is causing problems in:
I haven't looked at this since some passing interest in magnetics
decades ago, something about 8-tracks and cassettes, but you have
to be careful with conclusions like I removed foo and problem
went away therefore problem was foo. Performance issues are often
caused by memory, not CPU limitations. Removing anything with a big
memory footprint could speed things up. IO can be a real bottleneck.
If you are talking about things on minute timescales, look at task
manager and see if you are even CPU limited. Look for page faults
or IO etc. If you really need performance and have a task which
is relatively simple, don't ignore c++ as a way to generate data
points and then import these into R for analysis.
In short, just because you are focusing on math it doesn't mean
the computer is limited by that.
## Store state at time 10^4, 10^5, 10^6, 10^7
if( k %in% c(10^4,10^5,10^6,10^7) ){
q - q+1
Out[[q]] - M
}
Would there be any reason R is executing the statements inside the
if
before getting to the logical check?
Maybe R is written to hope for the best outcome (TRUE) and will just
throw
out its work if the logic comes up FALSE?
I guess I can always break the for loop up into four parts and
store the
state at the end of each, but thats an unsatisfying solution to me.
Jim, I like the suggestion of just pulling one big sample, but
since I
can
get the runtimes under 30 minutes just by removing the storage
piece I
doubt
I would see any noticeable changes by pulling large sample vectors.
Thanks,
Michael
On Tue, Oct 26, 2010 at 6:22 AM, Jim Lemon wrote:
On 10/26/2010 04:50 PM, Michael D wrote:
So I'm in a stochastic simulations class and I having issues
with the
amount
of time it takes to run the Ising model.
I usually don't like to attach the code I'm running, since it will
probably
make me look like a fool, but I figure its the best way I can
find any
bits
I can speed up run time.
As for the goals of the exercise:
I need the state of the system at time=1, 10k, 100k, 1mill, and
10mill
and the percentage of vertices with positive spin at all t
Just to be clear, i'm not expecting anyone to tell me how to
program
this
model, cause I know what I have works for this exercise, but it
takes
far
too long to run and I'd like to speed it up by replacing slow
operations
wherever possible.
Hi Michael,
One bottleneck is probably the sampling. If it doesn't grab too
much
memory, setting up a vector of the samples (maybe a million at a
time
if 10
million is too big - might be able to rewrite your sample vector
when
you
[R] Returning highs and lows in R
I'm having trouble returning a rolling n period highest value for a data set. For each day I want to calculate the highest value over the last 3 days. I am using the following packages: zoo, xts, quantmod and TTR. Thanks, Jason GLD.Close 2010-10-01128.91 2010-10-04128.46 2010-10-05130.99 2010-10-06131.81 2010-10-07130.37 2010-10-08131.66 2010-10-11132.29 2010-10-12131.96 2010-10-13134.07 2010-10-14134.75 2010-10-15133.68 2010-10-18134.28 2010-10-19130.11 2010-10-20131.32 2010-10-21129.47 2010-10-22129.73 2010-10-25130.85 2010-10-26130.88 2010-10-27129.52 [[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] removing margin space between columns in lattice plots
On Sat, Oct 23, 2010 at 9:25 AM, Stephen T. obsessiv...@hotmail.com wrote: Hi list, From the xyplot() documentation I'm guessing this may not be possible, but is there a way to specify a scale definition something between relation=free and relation=same such that the scales are fixed across rows and column margins are removed for a M x N conditioning plot (sort of like ggplot2 plots)? I find that the margin spacing in between each panel is taking up a lot of space and looking for a solution (and perhaps I'm doing something wrong but ggplot2 is extremely slow on my machine [Mac 10.5 running R 2.12] so I am unable to use it effectively...). Check out ?combineLimits from the latticeExtra package. -Deepayan __ 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] Returning highs and lows in R
Hi Jason, Please consider the following example: require(zoo) z2 - zoo(rnorm(6)) z2 1 2 3 4 5 6 -0.53305704 -1.09374867 1.55171109 -0.05830751 -0.25987647 -0.02009973 rollapply(z2, 3, max, by = 1) 2 3 4 5 1.55171109 1.55171109 1.55171109 -0.02009973 See ?rollapply for more information. HTH, Jorge On Thu, Oct 28, 2010 at 12:27 PM, Jason Kwok wrote: I'm having trouble returning a rolling n period highest value for a data set. For each day I want to calculate the highest value over the last 3 days. I am using the following packages: zoo, xts, quantmod and TTR. Thanks, Jason GLD.Close 2010-10-01128.91 2010-10-04128.46 2010-10-05130.99 2010-10-06131.81 2010-10-07130.37 2010-10-08131.66 2010-10-11132.29 2010-10-12131.96 2010-10-13134.07 2010-10-14134.75 2010-10-15133.68 2010-10-18134.28 2010-10-19130.11 2010-10-20131.32 2010-10-21129.47 2010-10-22129.73 2010-10-25130.85 2010-10-26130.88 2010-10-27129.52 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Please help me about Monte Carlo Permutation
Dear Kjetil, Thanks a lot for your help. I could not get histogram when I ask by R. It simply gave me blank plot between frequency and test. I want to plot sample (y) verses xl. Can you please tell me are both variables were permuted or only x? Thanking your help, Chitra -- View this message in context: http://r.789695.n4.nabble.com/Please-help-me-about-Monte-Carlo-Permutation-tp3017131p3017634.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] Returning highs and lows in R
On 2010-10-28 09:27, Jason Kwok wrote: I'm having trouble returning a rolling n period highest value for a data set. For each day I want to calculate the highest value over the last 3 days. I am using the following packages: zoo, xts, quantmod and TTR. Isn't that exactly what rollmax() does? -Peter Ehlers Thanks, Jason GLD.Close 2010-10-01128.91 2010-10-04128.46 2010-10-05130.99 2010-10-06131.81 2010-10-07130.37 2010-10-08131.66 2010-10-11132.29 2010-10-12131.96 2010-10-13134.07 2010-10-14134.75 2010-10-15133.68 2010-10-18134.28 2010-10-19130.11 2010-10-20131.32 2010-10-21129.47 2010-10-22129.73 2010-10-25130.85 2010-10-26130.88 2010-10-27129.52 [[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] adding copies of rows toa data frame based upon start and end dates
Hello All and thanks in advance for any advice. I have a data frame with rows corresponding radio-collared animals (see sample data below). There is a start date (DATESTART), and end date (DATEEND), and the number of days on air (DAYSONAIR). What I would like to do is add a column called DATE to so that each row ID has a row for every day that the radio collar was on the air while copying all other data. For example ID 1001 would expand into 48 rows beginning with 4/17/91 and ending with 6/4/91. all other values would remain the same for each new rowUnfortunately I have not gotten anywhere with my attempts Thank you!! IDGRIDFOODWB1WB2SADRUGFREQDATESTART DATECOLLARDATEENDDAYSONAIR 100110319999FAI14824/17/91 4/17/916/4/9148.00 100210659671MAC14084/17/91 4/17/916/25/9169.00 100310325662FAI07694/17/91 4/17/916/4/93779.00 100410322655FAC15614/18/91 4/18/915/27/9139.00 93100510654899MAI12884/18/91 4/18/915/27/9139.00 94100610301651MAC15934/18/91 4/18/917/11/9184.00 95100710349669FAI15214/18/91 4/18/9111/2/91198.00 [[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] Returning highs and lows in R
Jason: Please read AND FOLLOW the posting guide on how to ask clear questions. Here, you need to more carefully define what you mean by the last 3 days. Do you mean:(a) the last 3 values in the series (including or excluding the present one?) or the last 3 calendar days -- e.g. for 10-05, only 10-05 and 10-04, since 10-01 is not within the last 3 calendar days.Also, do you have missing values, and, if so, how do you want to handle them. If you mean the former, for small amounts of data without any missings(say 100 million numeric values or less) and small n (like n=3), it's easy and should be pretty fast just to produce lagged columns and use pmax rowwise. If you mean the latter and have missing values, it may be considerably more difficult. However, offering anything more seems pointless until you have adequately specified what you want. Reproducible data and code for a start. Cheers, Bert On Thu, Oct 28, 2010 at 9:27 AM, Jason Kwok jayk...@gmail.com wrote: I'm having trouble returning a rolling n period highest value for a data set. For each day I want to calculate the highest value over the last 3 days. I am using the following packages: zoo, xts, quantmod and TTR. Thanks, Jason GLD.Close 2010-10-01 128.91 2010-10-04 128.46 2010-10-05 130.99 2010-10-06 131.81 2010-10-07 130.37 2010-10-08 131.66 2010-10-11 132.29 2010-10-12 131.96 2010-10-13 134.07 2010-10-14 134.75 2010-10-15 133.68 2010-10-18 134.28 2010-10-19 130.11 2010-10-20 131.32 2010-10-21 129.47 2010-10-22 129.73 2010-10-25 130.85 2010-10-26 130.88 2010-10-27 129.52 [[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. -- Bert Gunter Genentech Nonclinical Biostatistics __ 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] overloading the generic primitive functions + and [
Note how S3 methods are dispatched only by reference to the first argument (on the left of the operator). I think S4 beats this by having signatures that can dispatch depending on both arguments. That's somewhat of a simplification for primitive binary operators. R actually looks up the method for both input classes, and returns a error if they are different. Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University 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.
[R] ggplot2: facet_grid with only one level does not display the graph with the facet_grid level in title
Hi All, Here is the code that I'll be referring to: p - ggplot(wastran.data, aes(PER_KEY, EVENTS)) (p - p + facet_grid( pool.short ~ .) + stat_summary(aes(y=EVENTS), fun.y = sum, geom=line) + opts(axis.text.x = theme_text(angle = 90, hjust=1), title=Events (15min.) vs. Time: Facet pool, strip.text.y = theme_text()) ) Now, depending on preceding parameters, the 'pool.short' factor variable in 'wastran.data' can have one distinct factor level or it can have more than one. When 'pool.short' has more than one factor level, the graph performs as I expect, with multiple rows of graphs with the value of the 'pool.short' variable displayed on the right-hand side of the graph. When 'pool.short' has only one factor level, the value is NOT displayed on the right-hand side. However, I'd still like it displayed, even though it has only one value. Can someone tell me how to tweak this code to make it still display when it has only 1 factor level? If this code is unclear, I will be happy to take some time and generate an artificial but reproducible self-contained example. I left in the stat_summary layer in this code in case it is interfering with the desired output (but I suspect is is superfluous, but I am not confident enough to say that with absolute certainty). Thanks, Matt [[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] lattice key subtitle
On Tue, Oct 26, 2010 at 2:49 AM, Alexandru Dumitrescu alexandru.dumitre...@gmail.com wrote: Hello everybody, Is there a way to add a subtitle to a lattice key? None specifically for that purpose, but latticeExtra does have a mergedTrellisLegendGrob() function that may help: mylegend - mergedTrellisLegendGrob(list(fun = draw.key, args = list(key = simpleKey(month.name[1:3], title = Months))), list(fun = grid::textGrob, args = list(subtitle)), vertical = TRUE) xyplot(1 ~ 1, legend = list(top = list(fun = mylegend))) mergedTrellisLegendGrob() was written as a helper function for c.trellis(), but the plan is to eventually make it a bit more general tool for combining legends. -Deepayan It is important form me that the subtitle must be linked to the key because those graphs are produced on a daily temporal scale, and the numbers of rectangles from the key may be different from day to day. Thank you, Alexandru Dumitrescu [[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] RGTK2 - Entry Point not found
2010/10/28 W Eryk Wolski wewol...@gmail.com Failed to load RGtk2 dynamic library, attempting to install it. trying URL ' http://downloads.sourceforge.net/gladewin32/gtk-2.12.9-win32-2.exe' Content type 'application/x-msdownload' length 7378984 bytes (7.0 Mb) I run the complete setup of GTK . Hence, I assume Version 2.12.9 is installed on my box. My path variable starts with: %GTK_BASEPATH%\bin; Any other ideas? It may be that you have some other cairo DLL in your PATH that is somehow conflicting with the one installed with GTK+... 2010/10/28 £ukasz Rêc³awowicz lukasz.reclawow...@gmail.com: The stable version of RGtk2 requires GTK version 2.8.0 or higher (and its dependencies). -- Mi³ego dnia -- Witold Eryk Wolski Heidmark str 5 D-28329 Bremen tel.: 04215261837 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] runtime on ising model
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of David Winsemius
Sent: Thursday, October 28, 2010 9:20 AM
To: Michael D
Cc: r-help@r-project.org
Subject: Re: [R] runtime on ising model
On Oct 28, 2010, at 11:52 AM, Michael D wrote:
Mike, I'm not sure what you mean about removing foo but I
think the
method
is sound in diagnosing a program issue and the results speak for
themselves.
I did invert my if statement at the suggestion of a CS professor
(who also
suggested recoding in C, but I'm in an applied math program and
haven't had
the time to take programming courses, which i know would be helpful)
Anyway, with the statement as:
if( !(k %in% c(10^4,10^5,10^6,10^7)) ){
#do nothing
} else {
q - q+1
Out[[q]] - M
}
run times were back to around 20 minutes.
Did that one change really make a difference?
R does not evaluate anything in the if or else
clauses of an if statement before evaluating
the condition.
Have you tried replacing all of those 10^x operations with their
integer equivalents, c(1L, 10L, 100L)? Each time through
the loop you are unnecessarily calling the ^ function 4 times. You
could also omit the last one. 10^7, during testing since M at the
last iteration (k=10^7) would be the final value and you could just
assign the state of M at the end. So we have eliminated 4*10^7
unnecessary ^ calls and 10^7 unnecessary comparisons. (The CS
professor is perhaps used to having the C compiler do all
thinking of
this sort for him.)
%in% is a relatively expensive function. Use == if you
can. E.g., compare the following 2 ways of stashing
something at times 1e4, 1e5, and 1e6:
system.time({z - integer()
for(k in seq_len(1e6))
if(k %in% set) z[length(z)+1]-k
print(z)})
[1] 1 10 100
user system elapsed
46.790 0.023 46.844
system.time({z - integer()
nextCheckPoint - 10^4
for(k in seq_len(1e6))
if( k == nextCheckPoint ) {
nextCheckPoint - nextCheckPoint * 10
z[length(z)+1]-k
}
print(z)})
[1] 1 10 100
user system elapsed
4.529 0.013 4.545
With such a large number of iterations it pays to
remove unneeded function calls in arithmetic expressions.
R does not optimize them out - it is up to you to
do that. E.g.,
system.time(for(i in seq_len(1e6)) sign(pi)*(-1))
user system elapsed
6.802 0.014 6.818
system.time(for(i in seq_len(1e6)) -sign(pi))
user system elapsed
3.896 0.011 3.911
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
--
David
So as best I can tell something
happens in the if statement causing the computer to work
ahead, as the
professor suggests. I'm no expert on R (and have no desire to try
looking at
the R source code (it would only confuse me)) but if anyone
can offer
guidance on how the if statement works (Does R try to work ahead?
Under what
conditions does it try to work ahead so I can try to exploit this
behavior) I would greatly appreciate it.
If it would require too much knowledge of the computer system to
understand
I doubt I would be able to make use of it, but maybe someone else
could
benefit.
On Tue, Oct 26, 2010 at 3:24 PM, Mike Marchywka
marchy...@hotmail.comwrote:
Date: Tue, 26 Oct 2010 12:53:14 -0400
From: mike...@gmail.com
To: j...@bitwrit.com.au
CC: r-help@r-project.org
Subject: Re: [R] runtime on ising model
I have an update on where the issue is coming from.
I commented out the code for pos[k+1] - M[i,j] and the if
statement
for
time = 10^4, 10^5, 10^6, 10^7 and the storage and everything ran
fast(er).
Next I added back in the pos statements and still
runtimes were
good
(around 20 minutes).
So I'm left with something is causing problems in:
I haven't looked at this since some passing interest in magnetics
decades ago, something about 8-tracks and cassettes, but you have
to be careful with conclusions like I removed foo and problem
went away therefore problem was foo. Performance issues are often
caused by memory, not CPU limitations. Removing anything with a big
memory footprint could speed things up. IO can be a real
bottleneck.
If you are talking about things on minute timescales, look at task
manager and see if you are even CPU limited. Look for page faults
or IO etc. If you really need performance and have a task which
is relatively simple, don't ignore c++ as a way to generate data
points and then import these into R for analysis.
In short, just because you are focusing on math it doesn't mean
the computer is limited by that.
## Store state at time 10^4,
[R] R shp(ESRI) point patterns and marks
I have a point dataset (ESRI shp file) each point has an associated weight (grams) These are the weights of animal bones recovered from an archaeological excavation I am trying to import the shp file and then do a density plot of the weight data, so: #Import shp file library(spatstat) library(maptools) library(sp) S - readShapePoints(flint.shp) SP - as(S, SpatialPoints) P - as(SP, ppp) So that brings in the shp file but I want to assign the marks(m) so I can do something like: plot(density(P, 10)) But based on the weights (grams (not spatial weighting)) Can anyone help? Thanks Gary -- View this message in context: http://r.789695.n4.nabble.com/R-shp-ESRI-point-patterns-and-marks-tp3017683p3017683.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] Control of axis limits in multiple panel lattice plots
On Wed, Oct 27, 2010 at 6:45 AM, Peter Davenport pwdavenp...@gmail.com wrote: I've found the solution to this in an old post of Deepayan's: lattice.options(axis.padding = list(numeric=0)) Or xyplot(a~b|c,data=test.df, scales = list(axs = i)) -Deepayan Best, Peter On 27 October 2010 09:28, Peter Davenport pwdavenp...@gmail.com wrote: Unwanted space (padding?) is introduced at the extremes of the x and y axes of my lattice plots. I've tried defining the scales using xlim, scale and num.limits in x.scale.components, but haven't succeded in getting overriding the introduction of extra space. Here's the problem: test.df-data.frame(a=runif(100,0,1),b=c(runif(50,0,1),runif(50,0,2)),c=c(rep(c(A,B),c(50,50 1) Space appears when I plot multiple panels: xyplot(a~b|c,data=test.df) 2) I can get rid of the space by explicitly defining scales (shown for x axis)... xyplot(a~b|c,data=test.df ,scale=list(x=list(limits=c(0,2),at=seq(0,2,0.5))) ) 3) ...but not when relation=free: xyplot(a~b|c,data=test.df ,scale=list(x=list(relation=free,limits=list(c(0,1),c(0,2)),at=seq(0,2,0.5))) ) Peter Davenport __ 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] svm online course in R
Hi, Dear Community, Several days ago, I received one email about the online svm course in R, I try to find it. Can someone forward the information to me. Thanks! -- Sincerely, Changbin -- [[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] GBM and Extracting the Model
Hi all, I have found a couple posts on this topic but could not (yet) find an answer. Is there a way to extract the model (trees and weights) from the GBM package in order to program the prediction in a non R environment (SQL database)? The constraint of not using R is based on production requirements of the institution. Any help or pointers would be appreciated - GBM is providing fantastic results but need a way to put it into a production environment. 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] Returning highs and lows in R
Thanks for the help. I'm looking to calculate rolling max and means for the last 3 observations in my data including AND not including the current observation. I'm not sure how to offset the observations used. For the 3 period max, I would like to return the max value over the last 3 observations not including today. When I use the rollapply function to take the max, it will look look back 1 observation, take the current observation and look forward 1 observation. I would like to return look back observations 1-3 and return the max. merge(xx,rollapply(xx,3,max)) GLD.Close GLD.Close.1 2010-04-01110.26 NA 2010-04-05110.89 111.03 2010-04-06111.03 112.49 2010-04-07112.49 112.65 2010-04-08112.65 113.64 2010-04-09113.64 113.64 2010-04-12113.01 113.64 2010-04-13112.69 113.03 2010-04-14113.03 113.65 2010-04-15113.65 113.65 2010-04-16111.24 113.65 2010-04-19111.15 111.46 2010-04-20111.46 112.31 2010-04-21112.31 112.31 2010-04-22111.84 113.19 2010-04-23113.19 113.19 2010-04-26112.75 114.63 2010-04-27114.63 114.63 2010-04-28114.31 114.63 2010-04-29114.28 115.36 2010-04-30115.36 NA On Thu, Oct 28, 2010 at 12:45 PM, Bert Gunter gunter.ber...@gene.comwrote: Jason: Please read AND FOLLOW the posting guide on how to ask clear questions. Here, you need to more carefully define what you mean by the last 3 days. Do you mean:(a) the last 3 values in the series (including or excluding the present one?) or the last 3 calendar days -- e.g. for 10-05, only 10-05 and 10-04, since 10-01 is not within the last 3 calendar days.Also, do you have missing values, and, if so, how do you want to handle them. If you mean the former, for small amounts of data without any missings(say 100 million numeric values or less) and small n (like n=3), it's easy and should be pretty fast just to produce lagged columns and use pmax rowwise. If you mean the latter and have missing values, it may be considerably more difficult. However, offering anything more seems pointless until you have adequately specified what you want. Reproducible data and code for a start. Cheers, Bert On Thu, Oct 28, 2010 at 9:27 AM, Jason Kwok jayk...@gmail.com wrote: I'm having trouble returning a rolling n period highest value for a data set. For each day I want to calculate the highest value over the last 3 days. I am using the following packages: zoo, xts, quantmod and TTR. Thanks, Jason GLD.Close 2010-10-01128.91 2010-10-04128.46 2010-10-05130.99 2010-10-06131.81 2010-10-07130.37 2010-10-08131.66 2010-10-11132.29 2010-10-12131.96 2010-10-13134.07 2010-10-14134.75 2010-10-15133.68 2010-10-18134.28 2010-10-19130.11 2010-10-20131.32 2010-10-21129.47 2010-10-22129.73 2010-10-25130.85 2010-10-26130.88 2010-10-27129.52 [[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. -- Bert Gunter Genentech Nonclinical Biostatistics [[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] adding environment variables
Take a look in ?Sys.setenv On Thu, Oct 28, 2010 at 12:21 PM, Robert M. Flight rfligh...@gmail.comwrote: Hi All, I am developing a package that requires information about the location of a set of files that will be used often in the calculations. In my current version, I define the location in the main file that calls all the subfunctions. This works fine when you are installing from source, but will not work so well if I want people to be able to install binary versions of the package. Therefore, I think the best way to encode the information would be through the use of an environment variable, that could then be read by Sys.getenv(VARIABLE) when the function is called. In the help, I found a few different ways to set environment variables, but the easiest way (from my reading anyways) seemed to be by creating the file Renviron.site in the R_HOME/etc directory and adding the variable there. I am interested in opinions from the list, or other suggestions on how to do this. For those who are interested, the package does a lot of parsing of KEGG KGML files, and to speed up calculations I offer advice that they should download a copy of the KGML directory for their organism to their local machine, and I want the package to know where those files are at runtime. Thanks in advance, -Robert Robert M. Flight, Ph.D. University of Louisville Bioinformatics Laboratory University of Louisville Louisville, KY PH 502-852-0467 EM robert.fli...@louisville.edu EM rfligh...@gmail.com Williams and Holland's Law: If enough data is collected, anything may be proven by statistical methods. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] runtime on ising model
On Oct 28, 2010, at 12:20 PM, David Winsemius wrote:
On Oct 28, 2010, at 11:52 AM, Michael D wrote:
Mike, I'm not sure what you mean about removing foo but I think the
method
is sound in diagnosing a program issue and the results speak for
themselves.
I did invert my if statement at the suggestion of a CS professor
(who also
suggested recoding in C, but I'm in an applied math program and
haven't had
the time to take programming courses, which i know would be helpful)
Anyway, with the statement as:
if( !(k %in% c(10^4,10^5,10^6,10^7)) ){
#do nothing
} else {
q - q+1
Out[[q]] - M
}
run times were back to around 20 minutes.
Have you tried replacing all of those 10^x operations with their
integer equivalents, c(1L, 10L, 100L)? Each time through
the loop you are unnecessarily calling the ^ function 4 times. You
could also omit the last one. 10^7, during testing since M at the
last iteration (k=10^7) would be the final value and you could just
assign the state of M at the end. So we have eliminated 4*10^7
unnecessary ^ calls and 10^7 unnecessary comparisons. (The CS
professor is perhaps used to having the C compiler do all thinking
of this sort for him.)
Bill Dunlap's suggestion to use == instead of %in% cut the time to
1/3 of what it had been even after the pre-calculation of the integer
values( which only improved the looping times by 30%). The combination
of the two with:
if (k ==1L|k==10L|k==100L ) { ... }
... resulted in an improvement by a factor or 12.006/2.523 or 475% for
the interim checking and printing operation using Bill's test suite.
--
David
So as best I can tell something
happens in the if statement causing the computer to work ahead, as
the
professor suggests. I'm no expert on R (and have no desire to try
looking at
the R source code (it would only confuse me)) but if anyone can offer
guidance on how the if statement works (Does R try to work ahead?
Under what
conditions does it try to work ahead so I can try to exploit this
behavior) I would greatly appreciate it.
If it would require too much knowledge of the computer system to
understand
I doubt I would be able to make use of it, but maybe someone else
could
benefit.
On Tue, Oct 26, 2010 at 3:24 PM, Mike Marchywka marchy...@hotmail.com
wrote:
Date: Tue, 26 Oct 2010 12:53:14 -0400
From: mike...@gmail.com
To: j...@bitwrit.com.au
CC: r-help@r-project.org
Subject: Re: [R] runtime on ising model
I have an update on where the issue is coming from.
I commented out the code for pos[k+1] - M[i,j] and the if
statement
for
time = 10^4, 10^5, 10^6, 10^7 and the storage and everything ran
fast(er).
Next I added back in the pos statements and still runtimes were
good
(around 20 minutes).
So I'm left with something is causing problems in:
I haven't looked at this since some passing interest in magnetics
decades ago, something about 8-tracks and cassettes, but you have
to be careful with conclusions like I removed foo and problem
went away therefore problem was foo. Performance issues are often
caused by memory, not CPU limitations. Removing anything with a big
memory footprint could speed things up. IO can be a real bottleneck.
If you are talking about things on minute timescales, look at task
manager and see if you are even CPU limited. Look for page faults
or IO etc. If you really need performance and have a task which
is relatively simple, don't ignore c++ as a way to generate data
points and then import these into R for analysis.
In short, just because you are focusing on math it doesn't mean
the computer is limited by that.
## Store state at time 10^4, 10^5, 10^6, 10^7
if( k %in% c(10^4,10^5,10^6,10^7) ){
q - q+1
Out[[q]] - M
}
Would there be any reason R is executing the statements inside
the if
before getting to the logical check?
Maybe R is written to hope for the best outcome (TRUE) and will
just
throw
out its work if the logic comes up FALSE?
I guess I can always break the for loop up into four parts and
store the
state at the end of each, but thats an unsatisfying solution to me.
Jim, I like the suggestion of just pulling one big sample, but
since I
can
get the runtimes under 30 minutes just by removing the storage
piece I
doubt
I would see any noticeable changes by pulling large sample vectors.
Thanks,
Michael
On Tue, Oct 26, 2010 at 6:22 AM, Jim Lemon wrote:
On 10/26/2010 04:50 PM, Michael D wrote:
So I'm in a stochastic simulations class and I having issues
with the
amount
of time it takes to run the Ising model.
I usually don't like to attach the code I'm running, since it
will
probably
make me look like a fool, but I figure its the best way I can
find any
bits
I can speed up run time.
As for the goals of the exercise:
I need the state of the system at time=1, 10k, 100k, 1mill, and
10mill
and the percentage of vertices with positive spin at all
Re: [R] wait for graph to finish plotting
pdf(file = ~/Dropbox/phd/results/graphs/TEST%03d.pdf)
for (dataset in
c(breastCancer,pima,heartDisease,crx,ionosphere,votes))
{
p - eval(parse(text=paste(dataset,Probs,sep=)))
m - melt(t(p))
title - titles[[dataset]]
filename=paste(~/Dropbox/phd/results/graphs/,dataset,Probs_barcharts.eps,sep=)
barchart(value~X1|X2,data=m,origin=0,layout=c(1,10),scales=list(alternating=1,tck=c(0.6,0)),ylab=Difference
from test
probabilities,xlab=Interval,col=c(rep(black,8),red,white,blue),main=title,ylim=c(-1,1))
}
dev.off()
Tal Galili tal.gal...@gmail.com writes:
Could you please paste the exact code you are using? (the one with the pdf and
dev.off, outside the loop )
Contact
Details:---
Contact me: tal.gal...@gmail.com | 972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com (English)
--
On Sat, Oct 23, 2010 at 4:53 PM, n...@aleblanc.cotse.net wrote:
David Winsemius dwinsem...@comcast.net writes:
On Oct 22, 2010, at 12:50 PM, n...@aleblanc.cotse.net wrote:
Tal Galili tal.gal...@gmail.com writes:
I suspect that using dev.copy2eps Is not going to help you here.
Please try again using:
pdf(...) # Check: ?pdf
for(i in something)
{
plot(things)
}
dev.off()
But give pdf() the file path.
Make sure you can make it work with simple plots. then check it on
your
situation, and let us know if it works :)
(I had it work with very heavy plots - so I trust it will work for
you)
(p.s: please keep cc'ing the r-help list so others will know the
stage of your
problem, in case others would like to add more help :) )
Cheers,
Tal
The problem is that the filename changes with each iteration of the
loop, so I need to
save the graph inside the loop.
I tried this:
for(...)
{
...
pdf(...)
barplot(...)
}
but I just got a load of empty graphs.
Because you failed to follow Ted directions to use dev.off()
pdf() just opens the file for writing, dev.off() executes the writing
and closes properly.
--
David.
I just tried with dev.off() but still the same problem.
I tried with pdf() and dev.off() inside the loop, and with them outside
(pdf before the loop,
and dev.off after). Same results each time: an empty pdf file.
I am using R version 2.11.1 if this makes any difference.
--
aleblanc
Hi Tal,
--
aleblanc
__
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] Returning highs and lows in R
I figured out how to offset my observations by 1 period by using the rollapply(xx,3,max,align=right), which would calculate the mean for (current observation, obs - 1 and obs -2 ). How would I further offset by 1 more period? Thanks, Jason On Thu, Oct 28, 2010 at 1:29 PM, Jason Kwok jayk...@gmail.com wrote: Thanks for the help. I'm looking to calculate rolling max and means for the last 3 observations in my data including AND not including the current observation. I'm not sure how to offset the observations used. For the 3 period max, I would like to return the max value over the last 3 observations not including today. When I use the rollapply function to take the max, it will look look back 1 observation, take the current observation and look forward 1 observation. I would like to return look back observations 1-3 and return the max. merge(xx,rollapply(xx,3,max)) GLD.Close GLD.Close.1 2010-04-01110.26 NA 2010-04-05110.89 111.03 2010-04-06111.03 112.49 2010-04-07112.49 112.65 2010-04-08112.65 113.64 2010-04-09113.64 113.64 2010-04-12113.01 113.64 2010-04-13112.69 113.03 2010-04-14113.03 113.65 2010-04-15113.65 113.65 2010-04-16111.24 113.65 2010-04-19111.15 111.46 2010-04-20111.46 112.31 2010-04-21112.31 112.31 2010-04-22111.84 113.19 2010-04-23113.19 113.19 2010-04-26112.75 114.63 2010-04-27114.63 114.63 2010-04-28114.31 114.63 2010-04-29114.28 115.36 2010-04-30115.36 NA On Thu, Oct 28, 2010 at 12:45 PM, Bert Gunter gunter.ber...@gene.comwrote: Jason: Please read AND FOLLOW the posting guide on how to ask clear questions. Here, you need to more carefully define what you mean by the last 3 days. Do you mean:(a) the last 3 values in the series (including or excluding the present one?) or the last 3 calendar days -- e.g. for 10-05, only 10-05 and 10-04, since 10-01 is not within the last 3 calendar days.Also, do you have missing values, and, if so, how do you want to handle them. If you mean the former, for small amounts of data without any missings(say 100 million numeric values or less) and small n (like n=3), it's easy and should be pretty fast just to produce lagged columns and use pmax rowwise. If you mean the latter and have missing values, it may be considerably more difficult. However, offering anything more seems pointless until you have adequately specified what you want. Reproducible data and code for a start. Cheers, Bert On Thu, Oct 28, 2010 at 9:27 AM, Jason Kwok jayk...@gmail.com wrote: I'm having trouble returning a rolling n period highest value for a data set. For each day I want to calculate the highest value over the last 3 days. I am using the following packages: zoo, xts, quantmod and TTR. Thanks, Jason GLD.Close 2010-10-01128.91 2010-10-04128.46 2010-10-05130.99 2010-10-06131.81 2010-10-07130.37 2010-10-08131.66 2010-10-11132.29 2010-10-12131.96 2010-10-13134.07 2010-10-14134.75 2010-10-15133.68 2010-10-18134.28 2010-10-19130.11 2010-10-20131.32 2010-10-21129.47 2010-10-22129.73 2010-10-25130.85 2010-10-26130.88 2010-10-27129.52 [[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. -- Bert Gunter Genentech Nonclinical Biostatistics [[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] Please help me about Monte Carlo Permutation
I'm not sure is this correct, but maybe you are looking for something like
this:
test-function(){
permuted.Qtot-permn(data$Qtot)
n-length(permuted.Qtot)
correlation-rep(NA,n)
for(i in 1:n){
correlation[i]-cor(data$Itot,permuted.Qtot[[i]])}
p-sum(correlation=cor(data$Qtot,data$Itot))/n
print(paste(P-value:, round(p,5)),quote=F)
}
test()
--
Mi³ego dnia
[[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 enable Arial font for postcript/pdf figure on Windows?
Hi, I need to generate some figure using the Arial font as a requirement for PLoS. Following their guidelines, I have converted the windows font files arial.tff files to .afm using tff2afm (exec file from MikTeX), but when I try to generate a postcript file, the postcript device does not recognize the .afm files. The code I use to test the new font is the following: postscript(file=try.ps, horizontal=F, onefile=F, width=4, height=4, family=c(C:/MyDoc/arial.afm, C:/MyDoc/arialbd.afm, C:/MyDoc/ariali.afm, C:/MyDoc/arialbi.afm), pointsize=12) hist(rnorm(100)) dev.off() And I get the warnings: In postscript(file = try.ps, horizontal = F, onefile = F, ... : unknown AFM entity encountered Is there another way to convert .tff files into .afm on Windows, or any other way to use Arial in pdf/postcript on Windows? Thank you very much, Agnes [[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] wait for graph to finish plotting
On Oct 28, 2010, at 1:27 PM, n...@aleblanc.cotse.net wrote:
pdf(file = ~/Dropbox/phd/results/graphs/TEST%03d.pdf)
for (dataset in
c(breastCancer,pima,heartDisease,crx,ionosphere,votes))
{
p - eval(parse(text=paste(dataset,Probs,sep=)))
m - melt(t(p))
title - titles[[dataset]]
filename=paste(~/Dropbox/phd/results/
graphs/,dataset,Probs_barcharts.eps,sep=)
barchart(value~X1|
X2
,data
=
m
,origin
=
0
,layout
=c(1,10),scales=list(alternating=1,tck=c(0.6,0)),ylab=Difference
from test probabilities,xlab=Interval,col=c(rep(black,
8),red,white,blue),main=title,ylim=c(-1,1))
}
dev.off()
Now you have changed plotting functions from plot and barplot over to
barchart (a Lattice function) and were not aware of FAQ 7.22:
http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-do-lattice_002ftrellis-graphics-not-work_003f
--
David.
Tal Galili tal.gal...@gmail.com writes:
Could you please paste the exact code you are using? (the one with
the pdf and
dev.off, outside the loop )
Contact
On Sat, Oct 23, 2010 at 4:53 PM, n...@aleblanc.cotse.net wrote:
David Winsemius dwinsem...@comcast.net writes:
On Oct 22, 2010, at 12:50 PM, n...@aleblanc.cotse.net wrote:
Tal Galili tal.gal...@gmail.com writes:
I suspect that using dev.copy2eps Is not going to help you here.
Please try again using:
pdf(...) # Check: ?pdf
for(i in something)
{
plot(things)
}
dev.off()
But give pdf() the file path.
Make sure you can make it work with simple plots. then check it
on
your
situation, and let us know if it works :)
(I had it work with very heavy plots - so I trust it will work for
you)
(p.s: please keep cc'ing the r-help list so others will know the
stage of your
problem, in case others would like to add more help :) )
Cheers,
Tal
The problem is that the filename changes with each iteration of the
loop, so I need to
save the graph inside the loop.
I tried this:
for(...)
{
...
pdf(...)
barplot(...)
}
but I just got a load of empty graphs.
Because you failed to follow Ted directions to use dev.off()
pdf() just opens the file for writing, dev.off() executes the
writing
and closes properly.
--
David.
I just tried with dev.off() but still the same problem.
I tried with pdf() and dev.off() inside the loop, and with them
outside
(pdf before the loop,
and dev.off after). Same results each time: an empty pdf file.
I am using R version 2.11.1 if this makes any difference.
--
aleblanc
Hi Tal,
--
aleblanc
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Generate random percentages and placing vectors
Thanks for the help! However, for the code in #2, it seems to just randomly split up the vectors. I would still like to keep the integrity of each vector. For example: if v1 = (1,2,3) v2 = (4,5,6) output = (0,0,0,1,2,3,0,0,0,0,4,5,6,0,0,0,0,0,0,0,0,0,0,0,0) - which has a specified length of 25 With v1 and v2 inserted in at random locations. On Wed, Oct 27, 2010 at 10:25 AM, Jonathan P Daily jda...@usgs.gov wrote: 1) rands - runif(5) rands - rands/sum(rands)*100 2) # assume vectors are v1, v2, etc. v_all - c(v1, v2, ...) v_len - length(v_all) output - rep(0,25) output[sample(1:25, v_len)] - v_all -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly From: Aaron Lee aaron.zl@gmail.com To: r-help@r-project.org Date: 10/27/2010 11:06 AM Subject: [R] Generate random percentages and placing vectors Sent by: r-help-boun...@r-project.org -- Hello everyone, I have two questions: 1.) I would like to generate random percentages that add up to 100. For example, if I need 5 percentages, I would obtain something like: 20, 30, 40, 5, 5. Is there some way to do this in R? 2.) I would like to insert vectors of specified length into a larger vector of specified length randomly, and fill the gaps with zeroes. For example, if I have 3 vectors of length 3, 2, and 2 with values and I would like to randomly place them into a vector of length 25 made of 0's. Thank you in advance! -Aaron [[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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Returning highs and lows in R
I was able to get what I wanted using the lag function to offset an addition period. lag(rollapply(xx,3,max),-2) or lag(rollapply(xx,3,max,align=right),-1) Thanks. Jason On Thu, Oct 28, 2010 at 1:49 PM, Jason Kwok jayk...@gmail.com wrote: I figured out how to offset my observations by 1 period by using the rollapply(xx,3,max,align=right), which would calculate the mean for (current observation, obs - 1 and obs -2 ). How would I further offset by 1 more period? Thanks, Jason On Thu, Oct 28, 2010 at 1:29 PM, Jason Kwok jayk...@gmail.com wrote: Thanks for the help. I'm looking to calculate rolling max and means for the last 3 observations in my data including AND not including the current observation. I'm not sure how to offset the observations used. For the 3 period max, I would like to return the max value over the last 3 observations not including today. When I use the rollapply function to take the max, it will look look back 1 observation, take the current observation and look forward 1 observation. I would like to return look back observations 1-3 and return the max. merge(xx,rollapply(xx,3,max)) GLD.Close GLD.Close.1 2010-04-01110.26 NA 2010-04-05110.89 111.03 2010-04-06111.03 112.49 2010-04-07112.49 112.65 2010-04-08112.65 113.64 2010-04-09113.64 113.64 2010-04-12113.01 113.64 2010-04-13112.69 113.03 2010-04-14113.03 113.65 2010-04-15113.65 113.65 2010-04-16111.24 113.65 2010-04-19111.15 111.46 2010-04-20111.46 112.31 2010-04-21112.31 112.31 2010-04-22111.84 113.19 2010-04-23113.19 113.19 2010-04-26112.75 114.63 2010-04-27114.63 114.63 2010-04-28114.31 114.63 2010-04-29114.28 115.36 2010-04-30115.36 NA On Thu, Oct 28, 2010 at 12:45 PM, Bert Gunter gunter.ber...@gene.comwrote: Jason: Please read AND FOLLOW the posting guide on how to ask clear questions. Here, you need to more carefully define what you mean by the last 3 days. Do you mean:(a) the last 3 values in the series (including or excluding the present one?) or the last 3 calendar days -- e.g. for 10-05, only 10-05 and 10-04, since 10-01 is not within the last 3 calendar days.Also, do you have missing values, and, if so, how do you want to handle them. If you mean the former, for small amounts of data without any missings(say 100 million numeric values or less) and small n (like n=3), it's easy and should be pretty fast just to produce lagged columns and use pmax rowwise. If you mean the latter and have missing values, it may be considerably more difficult. However, offering anything more seems pointless until you have adequately specified what you want. Reproducible data and code for a start. Cheers, Bert On Thu, Oct 28, 2010 at 9:27 AM, Jason Kwok jayk...@gmail.com wrote: I'm having trouble returning a rolling n period highest value for a data set. For each day I want to calculate the highest value over the last 3 days. I am using the following packages: zoo, xts, quantmod and TTR. Thanks, Jason GLD.Close 2010-10-01128.91 2010-10-04128.46 2010-10-05130.99 2010-10-06131.81 2010-10-07130.37 2010-10-08131.66 2010-10-11132.29 2010-10-12131.96 2010-10-13134.07 2010-10-14134.75 2010-10-15133.68 2010-10-18134.28 2010-10-19130.11 2010-10-20131.32 2010-10-21129.47 2010-10-22129.73 2010-10-25130.85 2010-10-26130.88 2010-10-27129.52 [[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. -- Bert Gunter Genentech Nonclinical Biostatistics [[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] RWeka, java.lang.NullPointerException
Dear all, I have trained a J48 classifier in RWeka but when I try to predict on new data I get the following exceptions: fit - J48(...) yNew - predict(fit, x, type=probability); Error in .jcall(RWekaInterfaces, [D, distributionForInstances, .jcast(classifier, : java.lang.NullPointerException What could be the cause of this ? I am using R version 2.10.0 on a Linux server. Thanks, Markus [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] help with help()
Hi all Just this morning I upgraded to R 2.12.0 (for Mac OS X 10.6.4). All went well until I needed to run a help() or help.search() in my session, which I'm running within Emacs (ESS 5.3.7). Say I need help with the command 'density'. When I type help(density) or ?density the ESS help buffer opens, it is titled *help[R](density)* but it contains only a couple of lines saying, e.g., Error in help(density, htmlhelp = FALSE) : unused argument(s) (htmlhelp = FALSE) This is a problem only running R within emacs. The command help() works fine if I run R at the command line in a terminal window or if I use the stand-alone R application. Thank you in advance Claudia -- Claudia Tebaldi Research Scientist, Climate Central http://www.climatecentral.org [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help with help()
On Oct 28, 2010, at 1:20 PM, claudia tebaldi wrote: Hi all Just this morning I upgraded to R 2.12.0 (for Mac OS X 10.6.4). All went well until I needed to run a help() or help.search() in my session, which I'm running within Emacs (ESS 5.3.7). Say I need help with the command 'density'. When I type help(density) or ?density the ESS help buffer opens, it is titled *help[R](density)* but it contains only a couple of lines saying, e.g., Error in help(density, htmlhelp = FALSE) : unused argument(s) (htmlhelp = FALSE) This is a problem only running R within emacs. The command help() works fine if I run R at the command line in a terminal window or if I use the stand-alone R application. Thank you in advance Claudia Put the following in your ~/.emacs file: (setq inferior-ess-r-help-command help(\%s\, help_type=\html\)\n) You might also want to update to ESS 5.11: http://ess.r-project.org/index.php?Section=download or consider using Vincent Goulet's pre-packaged Emacs 23/ESS install: http://vgoulet.act.ulaval.ca/en/ressources/emacs/mac HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] runtime on ising model
Date: Thu, 28 Oct 2010 09:58:40 -0700
From: wdun...@tibco.com
To: dwinsem...@comcast.net; mike...@gmail.com
CC: r-help@r-project.org
Subject: Re: [R] runtime on ising model
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of David Winsemius
Sent: Thursday, October 28, 2010 9:20 AM
To: Michael D
Cc: r-help@r-project.org
Subject: Re: [R] runtime on ising model
On Oct 28, 2010, at 11:52 AM, Michael D wrote:
Mike, I'm not sure what you mean about removing foo but I
think the
method
is sound in diagnosing a program issue and the results speak for
themselves.
Agreed on first part but not second- empirical debugging rarely
produces compelling results in isolation. As a collection
of symptons fine but not conclusive- if you learn c++ you will
find out about all kinds of things like memory corruption that
never make sense :) Here, the big concern is issues with memory
as you never determined to be CPU limited although based on
others comments you likely are in any case.
I did invert my if statement at the suggestion of a CS professor
(who also
suggested recoding in C, but I'm in an applied math program and
haven't had
the time to take programming courses, which i know would be helpful)
Anyway, with the statement as:
if( !(k %in% c(10^4,10^5,10^6,10^7)) ){
#do nothing
} else {
q - q+1
Out[[q]] - M
}
run times were back to around 20 minutes.
Did that one change really make a difference?
R does not evaluate anything in the if or else
clauses of an if statement before evaluating
the condition.
What is at issue here? That is, the OP claimed inverting polarity
sped things up, suggesting that the branch mattered. AFAIK he
never actually proved which branch was taken. This could
imply many things or nothing: one branch may be slow, or cause
a page fault, or the test may fail fast but succed slowly( testing
huge array for equality for example) .
Have you tried replacing all of those 10^x operations with their
integer equivalents, c(1L, 10L, 100L)? Each time through
the loop you are unnecessarily calling the ^ function 4 times. You
could also omit the last one. 10^7, during testing since M at the
last iteration (k=10^7) would be the final value and you could just
assign the state of M at the end. So we have eliminated 4*10^7
unnecessary ^ calls and 10^7 unnecessary comparisons. (The CS
professor is perhaps used to having the C compiler do all
thinking of
this sort for him.)
%in% is a relatively expensive function. Use == if you
can. E.g., compare the following 2 ways of stashing
something at times 1e4, 1e5, and 1e6:
system.time({z - integer()
for(k in seq_len(1e6))
if(k %in% set) z[length(z)+1]-k
print(z)})
[1] 1 10 100
user system elapsed
46.790 0.023 46.844
system.time({z - integer()
nextCheckPoint - 10^4
for(k in seq_len(1e6))
if( k == nextCheckPoint ) {
nextCheckPoint - nextCheckPoint * 10
z[length(z)+1]-k
}
print(z)})
[1] 1 10 100
user system elapsed
4.529 0.013 4.545
With such a large number of iterations it pays to
remove unneeded function calls in arithmetic expressions.
R does not optimize them out - it is up to you to
do that. E.g.,
system.time(for(i in seq_len(1e6)) sign(pi)*(-1))
user system elapsed
6.802 0.014 6.818
system.time(for(i in seq_len(1e6)) -sign(pi))
user system elapsed
3.896 0.011 3.911
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
--
David
So as best I can tell something
happens in the if statement causing the computer to work
ahead, as the
professor suggests. I'm no expert on R (and have no desire to try
looking at
the R source code (it would only confuse me)) but if anyone
can offer
guidance on how the if statement works (Does R try to work ahead?
Under what
conditions does it try to work ahead so I can try to exploit this
behavior) I would greatly appreciate it.
If it would require too much knowledge of the computer system to
understand
I doubt I would be able to make use of it, but maybe someone else
could
benefit.
On Tue, Oct 26, 2010 at 3:24 PM, Mike Marchywka
wrote:
Date: Tue, 26 Oct 2010 12:53:14 -0400
From: mike...@gmail.com
To: j...@bitwrit.com.au
CC: r-help@r-project.org
Subject: Re: [R] runtime on ising model
I have an update on where the issue is coming from.
I commented out the code for pos[k+1] - M[i,j] and the if
statement
for
time = 10^4, 10^5, 10^6, 10^7 and the storage and everything ran
fast(er).
Next I added back in the pos statements and still
runtimes were
good
(around 20 minutes).
So I'm left with something is causing problems in:
I haven't looked at this since some passing interest in
Re: [R] help with help()
On Oct 28, 2010, at 1:32 PM, Marc Schwartz wrote: On Oct 28, 2010, at 1:20 PM, claudia tebaldi wrote: Hi all Just this morning I upgraded to R 2.12.0 (for Mac OS X 10.6.4). All went well until I needed to run a help() or help.search() in my session, which I'm running within Emacs (ESS 5.3.7). Say I need help with the command 'density'. When I type help(density) or ?density the ESS help buffer opens, it is titled *help[R](density)* but it contains only a couple of lines saying, e.g., Error in help(density, htmlhelp = FALSE) : unused argument(s) (htmlhelp = FALSE) This is a problem only running R within emacs. The command help() works fine if I run R at the command line in a terminal window or if I use the stand-alone R application. Thank you in advance Claudia Put the following in your ~/.emacs file: (setq inferior-ess-r-help-command help(\%s\, help_type=\html\)\n) You might also want to update to ESS 5.11: http://ess.r-project.org/index.php?Section=download or consider using Vincent Goulet's pre-packaged Emacs 23/ESS install: http://vgoulet.act.ulaval.ca/en/ressources/emacs/mac One quick additional note. The above .emacs inclusion requires ESS 5.5 or greater. So you will definitely need to update. 5.3.7 is over two years old. Marc __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help with help()
Hi, Is it possible to upgrade your version of Emacs and ESS (ESS is up to 5.11)? The official website for ESS is: http://ess.r-project.org/ Vincent Goulet also maintains a nice distribution of the latest Emacs bundled with AUCTeX and ESS for Mac at: http://vgoulet.act.ulaval.ca/en/ressources/emacs/mac It is very easy to install :) I am not sure that there is an htmlhelp argument anymore. Cheers, Josh On Thu, Oct 28, 2010 at 11:20 AM, claudia tebaldi claudia.teba...@gmail.com wrote: Hi all Just this morning I upgraded to R 2.12.0 (for Mac OS X 10.6.4). All went well until I needed to run a help() or help.search() in my session, which I'm running within Emacs (ESS 5.3.7). Say I need help with the command 'density'. When I type help(density) or ?density the ESS help buffer opens, it is titled *help[R](density)* but it contains only a couple of lines saying, e.g., Error in help(density, htmlhelp = FALSE) : unused argument(s) (htmlhelp = FALSE) This is a problem only running R within emacs. The command help() works fine if I run R at the command line in a terminal window or if I use the stand-alone R application. Thank you in advance Claudia -- Claudia Tebaldi Research Scientist, Climate Central http://www.climatecentral.org [[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. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help with help()
claudia tebaldi wrote: Hi all Just this morning I upgraded to R 2.12.0 (for Mac OS X 10.6.4). All went well until I needed to run a help() or help.search() in my session, which I'm running within Emacs (ESS 5.3.7). That's very old version of ESS, I have no problems with 2.12.0 with ESS 5.11 on Emacs 23.2 at home. Also, there is an ESS-help mailing list for ESS questions, usually very responsive and all the developers read it. Say I need help with the command 'density'. When I type help(density) or ?density the ESS help buffer opens, it is titled *help[R](density)* but it contains only a couple of lines saying, e.g., Error in help(density, htmlhelp = FALSE) : unused argument(s) (htmlhelp = FALSE) This is a problem only running R within emacs. The command help() works fine if I run R at the command line in a terminal window or if I use the stand-alone R application. Thank you in advance Claudia __ 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] Clustering
I have worked with seismic data measured at 100hz, and had no trouble locating events in long records (several times the size of your dataset). 20 minutes is high frequency? what kind of waves are these? what is the wavelength? some details would help. albyn On Thu, Oct 28, 2010 at 05:00:10AM -0700, dpender wrote: I am looking to use R in order to determine the number of extreme events for a high frequency (20 minutes) dataset of wave heights that spans 25 years (657,432) data points. I require the number, spacing and duration of the extreme events as an output. I have briefly used the clusters function in evd package. Can anyone suggest a more appropriate package to use for such a large dataset? Thanks, Doug -- View this message in context: http://r.789695.n4.nabble.com/Clustering-tp3017056p3017056.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. -- Albyn Jones Reed College jo...@reed.edu __ 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] scatterplot3d; scaling point symbols to depth of graph
It's a bug (since I did not expect people to change the size of the symbols vectorized). Will provide a fix tomorrow. Uwe On 28.10.2010 11:28, John Coulthard wrote: Hi I'm trying to scale the point symbols on a 3d plot so that the ones at the front are larger than the ones at the back. I'm trying to give the image some perspective. Given this code... library(scatterplot3d) data=array(c(0,5,9), c(3,3)) scatterplot3d(data, pch=19, cex.symbols=10-data[,2], color=c(red,blue,black)); data [,1] [,2] [,3] [1,]000 [2,]555 [3,]999 which gives a vector for cex.symbols as 10-data[,2] [1] 10 5 1 I would expect the largest point to be the red one at the origin but the image I get has the black symbol at co-ords 9,9,9 as the largest and red at 0,0,0 the smallest. Then if I do... data=array(c(0,9,5), c(3,3)) data [,1] [,2] [,3] [1,]000 [2,]999 [3,]555 scatterplot3d(data, pch=19, cex.symbols=10-data[,2], color=c(red,blue,black)); 10-data[,2] [1] 10 1 5 I'd expect the position and size of the points to be the same but the colour of blue and black to be exchanged. But the size of the points also changes such that the red point at 0,0,0 is the medium size and the black at 5,5,5 is the smallest. So is it possible to get the points described by each row in data to be scaled by the values in data[,2]? Many thanks John sessionInfo() R version 2.11.1 (2010-05-31) i386-redhat-linux-gnu locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8LC_COLLATE=en_US.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] scatterplot3d_0.3-30 loaded via a namespace (and not attached): [1] tools_2.11.1 [[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] Generate random percentages and placing vectors
Try this: out - rep(0, 25) out[embed(seq(out), 3)[sample(1:(length(out) - 2), 2),]] - rev(rbind(v1, v2)) On Thu, Oct 28, 2010 at 3:59 PM, Aaron Lee aaron.zl@gmail.com wrote: Thanks for the help! However, for the code in #2, it seems to just randomly split up the vectors. I would still like to keep the integrity of each vector. For example: if v1 = (1,2,3) v2 = (4,5,6) output = (0,0,0,1,2,3,0,0,0,0,4,5,6,0,0,0,0,0,0,0,0,0,0,0,0) - which has a specified length of 25 With v1 and v2 inserted in at random locations. On Wed, Oct 27, 2010 at 10:25 AM, Jonathan P Daily jda...@usgs.gov wrote: 1) rands - runif(5) rands - rands/sum(rands)*100 2) # assume vectors are v1, v2, etc. v_all - c(v1, v2, ...) v_len - length(v_all) output - rep(0,25) output[sample(1:25, v_len)] - v_all -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly From: Aaron Lee aaron.zl@gmail.com To: r-help@r-project.org Date: 10/27/2010 11:06 AM Subject: [R] Generate random percentages and placing vectors Sent by: r-help-boun...@r-project.org -- Hello everyone, I have two questions: 1.) I would like to generate random percentages that add up to 100. For example, if I need 5 percentages, I would obtain something like: 20, 30, 40, 5, 5. Is there some way to do this in R? 2.) I would like to insert vectors of specified length into a larger vector of specified length randomly, and fill the gaps with zeroes. For example, if I have 3 vectors of length 3, 2, and 2 with values and I would like to randomly place them into a vector of length 25 made of 0's. Thank you in advance! -Aaron [[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 http://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How do I install (download) a package with my own package?
I want to create my own package in which some of my functions depend on functions already existing in another package that is not part of the default library (i.e. when you install R for the first time, you need to download that package to access the functions.) Is there a way to bundle this existing package with the package I will create so that one doesn't have to install my package and then the package in which some of my functions depend on? Thanks! Ian [[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.
