[R] Matrix multiplication (with multidimensional array)
Hi All, I am wondering if there is an efficient way to do the following matrix multiplication, a[1,,] 1, 2 3, 4 a[2,,] 4, 3 2, 1 b[1,,]5,6 7,8 b[2,,]8,7 6,5 I need the result c, with c[1,,] = a[1,,] %*% b[1,,] c[2,,] = a[2,,] %*% b[2,,] Thanks in advance for any help. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problem with dgamma ?
Hi All, Here 's what I got using dgamma function : > nu<-.2 > nu*log(nu)-log(gamma(nu))+(nu-1)*log(1)-nu*(1) [1] -2.045951 > dgamma(1,nu,nu,1) [1] 0.0801333 > dgamma(1,nu,nu,0) [1] NaN Warning message: NaNs produced in: dgamma(x, shape, scale, log) Could anyone tell me what is wrong here ? I am using R-2.4.1 on windows XP. Thanks a lot. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problem with saving R plot in Emacs
Hi, I am having problem with saving figures when I use R in Emacs (ESS). Whenever I try to save a plot, the Emacs freezes and I have to close it. I am using Win XP , R binaries, Emacs for windows. Somebody got the same problem ? Can I get some suggestions ? thanks a lot tong __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Compiling C codes in Windows
Thank you all for the help . It seems I only need to change the back slash to forward slash to get things work . As to using Cygwin as the shell, I couldn't find an instruction dedicated to Cygwin, should I just follow the " Installing R under Unix-alikes " ? Is there an easier way, like making use of the installed binaries. I will post future questions to R-devel. Thanks again. tong - Original Message - From: Duncan Murdoch <[EMAIL PROTECTED]> Date: Monday, April 2, 2007 9:21 am Subject: Re: [R] Compiling C codes in Windows To: Martin Morgan <[EMAIL PROTECTED]> Cc: Tong Wang <[EMAIL PROTECTED]>, R help > On 4/2/2007 4:53 AM, Martin Morgan wrote: > > Tong Wang <[EMAIL PROTECTED]> writes: > > > >> Hi All, > > [...] > >> After I followed all the instructions in " Building R for > Windows" > > [...] > >> Anyway, I assumed that I need to run this command in Cygwin > > > > No, do this from a DOS shell. > > Cygwin is fine as a shell (it's what I use), but the rest of your > advice > is correct: > > > The usual problems are either missing > > components from the installation steps outlined in Building R for > > Windows, or an incorrect PATH variable so that windows or cygwin > > versions of programs are used rather than MinGW / Rtools. > > Duncan Murdoch > > > > > Also, this question belongs on the R-devel list, where those doing > > development work are more likely to see and respond to your > > questions. > > > > Hope that helps, > > > > Martin Morgan > >> > >> $ make all recommended > >> make: ./Rpwd.exe: Command not found > >> make[1]: ./Rpwd.exe: Command not found > >> make --no-print-directory -C front-ends Rpwd > >> make -C ../../include -f Makefile.win version > >> make Rpwd.exe > >> gcc -O3 -Wall -pedantic -I../../include -c rpwd.c -o rpwd.o > >> rpwd.c:22:20: direct.h: No such file or directory > >> rpwd.c: In function `main': > >> rpwd.c:42: warning: implicit declaration of function `chdir' > >> rpwd.c:45: warning: implicit declaration of function `getcwd' > >> make[3]: *** [rpwd.o] Error 1 > >> make[2]: *** [Rpwd] Error 2 > >> make[1]: *** [front-ends/Rpwd.exe] Error 2 > >> make: *** [all] Error 2 > >> > >> > >> Can I get some help with my quesitons , and some suggestions > concerning the best way to solve the whole problem ? > >> > >> THanks a lot for your help.. > >> > >> tong > >> > >> __ > >> R-help@stat.math.ethz.ch mailing list > >> https://stat.ethz.ch/mailman/listinfo/r-help > >> PLEASE do read the posting guide http://www.R- > project.org/posting-guide.html > >> and provide commented, minimal, self-contained, reproducible code. > > > > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Compiling C codes in Windows
Hi All, I have been struggling to figure out how to compile c codes for R use. I am using Win XP + Cygwin + R binaries. After I followed all the instructions in " Building R for Windows" from Murdoch's website, I tried to Run something like : R CMD SHLIB C:\R\test.c , but still didn't get any output. My first question is, does this mean I already did something wrong ? Anyway, I assumed that I need to run this command in Cygwin, so I started to reinstall R in Cygwin by compiling the source (I assume it is not possible to call the precompiled binaries from Cygwin). But I ran into the following problem when I ran "make all recommended" in src/gnuwin32/ $ make all recommended make: ./Rpwd.exe: Command not found make[1]: ./Rpwd.exe: Command not found make --no-print-directory -C front-ends Rpwd make -C ../../include -f Makefile.win version make Rpwd.exe gcc -O3 -Wall -pedantic -I../../include -c rpwd.c -o rpwd.o rpwd.c:22:20: direct.h: No such file or directory rpwd.c: In function `main': rpwd.c:42: warning: implicit declaration of function `chdir' rpwd.c:45: warning: implicit declaration of function `getcwd' make[3]: *** [rpwd.o] Error 1 make[2]: *** [Rpwd] Error 2 make[1]: *** [front-ends/Rpwd.exe] Error 2 make: *** [all] Error 2 Can I get some help with my quesitons , and some suggestions concerning the best way to solve the whole problem ? THanks a lot for your help.. tong __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problem with Cygwin
Hi All ,
I am trying to compile some c codes with R CMD SHLIB on Cygwin. But I got
the following error
WARNING: ignoring environment value of R_HOME
ERROR: R_HOME ('/home/Owner/r/R-2.0.1') not found
I have set the environment variable R_HOME pointing to the current R
installation, but the R command
still looks in the old directory, Could someone help me out here ?
Thanks a lot .
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Re: [R] Keep R packages in the R installation
Hi, Yes, I am using Windows XP. Thanks a lot for your help. tong - Original Message - From: Robert Duval <[EMAIL PROTECTED]> Date: Sunday, April 1, 2007 5:29 pm Subject: Re: [R] Keep R packages in the R installation To: Tong Wang <[EMAIL PROTECTED]> Cc: R help > You don't say which OS you're using. But I infer from your other > posting that is MS Windows. > > In which case you can follow the instructions in the FAQ's for Windows > > http://cran.r-project.org/bin/windows/base/rw-FAQ.html#What_0027s- > the-best-way-to-upgrade_003f > > ... and also read the mailing list posting guide > > best > robert > > On 4/1/07, Tong Wang <[EMAIL PROTECTED]> wrote: > > Hi, > > I just got a quick question here, when I install a new > version of R , is there an easy to keep the installed R packages ? > > > > > > Thanks a lot for any help. > > > > tong > > > > __ > > R-help@stat.math.ethz.ch mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html> and provide commented, minimal, self-contained, > reproducible code. > > > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Compile C codes for R use.
Hi, all I was learning to compile C code for use in R, but I got stuck on the first step. I am using the R in windows ( 2.4.1 binary) , I opened the command prompt (Run) in windows and issued : R CMD SHLIB C:\cygwin\home\Owner\R\test.c but no object file was created , could someone tell me what is wrong ? And is there a more convenient way to isssue the the above command, it is really troublesome to have to open the windows command prompt all the time. Thanks a lot for your help\ tong __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Keep R packages in the R installation
Hi, I just got a quick question here, when I install a new version of R , is there an easy to keep the installed R packages ? Thanks a lot for any help. tong __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Really need help here
Hi there,
I had a serious problem here . Consider the following Bayesian
model(discretized variance gamma):
#Likelihood
J[i]<-lambda*G[i]+sigma*sqrt(G[i])*rnorm(0,1)
G[i]<-rgamma(1/nu,1/nu)
#Prior:
nu<-rinvgamma(m,M)
# Parameters
lambda=-.04 ; sigam=.38; nu=6.48; m=10,M=10 ; T=5000 (length of data)
An author claimed that he got posterior distribution of nu with standard
deviation .0965
But I could only get posterior sd=.84 with the same setting. I have been
working on my code for quite a while
, but still don't see what is wrong with it. I would really appreciate it if
any body could fit this model and let me
know if you can get it and how ? I attached my R code with data generating and
posterior simulating functions,
I used the slice sampler to do it , you could use your own version of slice
sampler or other generic samplers.
Again , I would really appreciate any help that could save me from the pain.
vg <- function(T=5000,nu=6.48,n.iter=1000,beta=-.04,sig=.38,m=10,M=10){
#--- Data Generating -#
G <- rgamma(T,1/nu,1/nu)
J <- rnorm(T,beta*G,sig*sqrt(G))
#--- Gibbs Sampler ---#
nu.stor <- rep(NA,n.iter)
for(i in 1:n.iter){
G <- MCslice1D(dgamma(x,1/nu,1/nu,log=TRUE)+dnorm(J, beta*x,
sig*sqrt(x),log=TRUE),w=20,m=10,x0=G)
nu <-
MCslice1D(log(dinvgamma(x,m,M))-T*log(x)*1/x-T*log(gamma(1/x))+(1/x-1)*sum(log(G))-sum(G)/x,
w=3,m=12, x0=nu)
nu.stor[i] <- nu
}
return(list(nu=nu.stor))
}
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[R] problem with rinvgamma ?
Hi, By rinvgamma(1,1.33,2.33) , am I supposed to get a var=3 ? Tried it many times , not even close. Why is this? thanks a lot . best __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] slice sampler
Hi there,
I wrote a slice sampler (one dimension) , After testing it, I found it
working well on some standard distributions, but problematic with others. I
have thought about it but really can't figure out how to improve it, so I
attached the code here
and hope that someone here is willing to try it out and give me some feedback.
I would really appreciate it.
I basicly followed neal 03 to write the code. The code might looks a
little strange as I allowed sampling a vector of parameters , that is , it
could update multiple targets with different parameter but same form of
distribution. A example
of usage is as follows:
output[i] <- slice1d(dnorm(x,1,1,log=TRUE),
x0=output[i-1],w=2,m=6,trunc=c(-Inf,Inf),prec=1e-4)
things to notice here are: expression has to be on LOG scale, w is the
expanding wideth, m is the # of expanding trials,
prec is the precision, this is used to control against those distributions with
huge kurtosis (with very sharp peak), so that the sampler wouldn't spend a lot
of time approaching the right value.
One example that it doesn't work well on isdgamma(x,.1,.1,log=TRUE)
Thanks a lot in advance.
best,
CODE:
slice1d <- function (expr,x0=NULL,w,m,trunc=c(-Inf,Inf),prec=.0001){
sexpr <- substitute(expr)
if (!(is.call(sexpr) && match("x", all.vars(sexpr), nomatch = 0)))
stop("'expr' must be a function or an expression containing 'x'")
expr <- sexpr
y.log <- eval(expr, envir=list(x=x0),enclos = if(is.null(list(...)$env))
parent.frame() else list(...)$env)-rexp(1)
k <- length(y.log)
if(k!=length(x0))
stop("The dimension of y.log and x0 have to agree")
U <- runif(k)
L <- x0-w*U
R <- L+w
U <- runif(k)
J <- floor(m*U)
K <- m-1-J
temp <- (L0)&(y.logtrunc[2])
R <- as.vector(R)
R[temp] <- trunc[2]
vec.cond <- rep(!temp,k)
while(sum(vec.cond)!=0)
{vec.cond <- ((K>0)&(y.logtrunc[2])
R[temp] <- trunc[2]
K[temp] <- 0
K[vec.cond] <- K[vec.cond]-1}
vec.cond <- rep(FALSE,k)
x1 <- rep(NA,k)
count <- 0
repeat{
U <- runif((k-sum(vec.cond)))
x1[!vec.cond] <- L[!vec.cond]+U*(R[!vec.cond]-L[!vec.cond])
vec.cond <- ((y.logx0] <- x1[x1>x0]
count <- count+1
if (count>=1) stop("dead loop")
}
}
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[R] Question on computing mv-norm density
Hi, I am trying to figure out how to evaluate the density function of multivariate normal efficiently for a large data set, the data set should look like this (take d=2 for example): datamean sigma 2.131, 3.000 1.000,1.000 1 0 0 1 1.231,5.1412.000,2.000 .5 -.1 . . -.1 .4 . that is , I need SUM_i (log(dmvnorm(d[i], mu[i], sigma[i])). tried to rewrite the dmvnorm function from mvtnorm package, but could not find a satisfactory method to avoid using loops. ( using those "apply" functions seem to be slower than loops) . May I get some suggestion on this ? Thanks a lot in advance. best __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] A question about dput
Hi, I am trying to output a R data set for use in WinBugs, I used dput(list(x=rnorm(100),N=100),file="bug.dat") But I can't get the intended format:list(x=c(...),N=100), instead, I got something like this (copied the first two lines): []737472756374757265286C6973742878 structure(list(x [0010]203D2063282D302E3336333136313033 =c(-0.36316103 Did I do something wrong here ? Thanks a lot for any help tong __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Question about the xgobi package
Hi,
When I tried an example of the xgobi function, I got the following error.
Could someone explain to me
what is wrong ? Thanks a lot.
xgobi(crabs,colors=c("SkyBlue","SlateBlue","Orange","Red")[rep(1:4,each=50)])
c:/PROGRA~1/R/R-23~1.1/library/xgobi/scripts/xgobi.bat -vtitle 'crabs' -std mmx
C:/DOCUME~1/ADMINI~1/LOCALS~1/Temp/Rtmp1FVirb/xgobi-crabs2c3b6032
The system cannot find the path specified.
tong
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[R] Questions about paste and assign
Hi,
I would like to assign a value to a member b of the list a in position
3, by calling:
assign( target, 2.34, 3)
My question is what the "target" should be. I tried target <- paste("a", $,
"b") and something else,
but haven't got the right answer yet.
BTW, if I attached a list named "mylist" in position 3, to refer to this
environment, besides 3, what's the
right name ?
Thanks a lot for any help
tong
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[R] What command does the "cin >> " in R ?
Hi all, Sorry about the simple question, but I have searched the web with " prompt , input " etc. and never got the answer . thanks a lot tong __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A question about R environment
Hi, Thanks a lot for your response, but it is strange that when I do attach() , I got the follow error: Error in attach(e) : attach only works for lists and data frames Any suggestions on this? tong - Original Message - From: Henrik Bengtsson <[EMAIL PROTECTED]> Date: Monday, January 8, 2007 10:40 pm Subject: Re: [R] A question about R environment To: Gabor Grothendieck <[EMAIL PROTECTED]> Cc: Tong Wang <[EMAIL PROTECTED]>, R help > sourceTo() in R.utils will allow you to source() a file into an > environment. > /Henrik > > On 1/9/07, Gabor Grothendieck <[EMAIL PROTECTED]> wrote: > > Try this: > > > > > e <- new.env() > > > e$f <- function(x)x > > > attach(e) > > > search() > > [1] ".GlobalEnv""e" "package:stats" > > [4] "package:graphics" "package:grDevices" "package:utils" > > [7] "package:datasets" "package:methods" "Autoloads" > > [10] "package:base" > > > f > > function(x)x > > > > On 1/8/07, Tong Wang <[EMAIL PROTECTED]> wrote: > > > Hi all, > > > > > > I created environment "mytoolbox" by : mytoolbox <- > new.env(parent=baseenv())> > Is there anyway I put it in the search > path ? > > > > > > If you need some background : > > > In a project, I often write some small functions, and load > them into my workspace directly, so when I list the objects > > > with ls(), it looks pretty messy. So I am wondering if it is > possible to creat an environment, and put these tools into > > > this environment. For example, I have functionsfun1(), > fun2() ..and creat an environment mytoolbox which > > > contains all these functions. And it should be somewhere in > the search path: ".GlobalEnv""mytoolbox" > "package:methods" > > > > > > __ > > > R-help@stat.math.ethz.ch mailing list > > > https://stat.ethz.ch/mailman/listinfo/r-help > > > PLEASE do read the posting guide http://www.R- > project.org/posting-guide.html > > > and provide commented, minimal, self-contained, reproducible code. > > > > > > > __ > > R-help@stat.math.ethz.ch mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html> and provide commented, minimal, self-contained, > reproducible code. > > > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A question about R environment
Francois (sorry can't type the right letter) , thanks a million for the
detailed response, you have really cool functions there !
Philippe : I will definitely follow your advice later, but I got some time
pressure from the current project, so have to go with the easy sol. now ,
thanks a lot.
Happy new year every one!
cheers
tong
- Original Message -
From: Philippe Grosjean <[EMAIL PROTECTED]>
Date: Monday, January 8, 2007 10:09 pm
Subject: Re: [R] A question about R environment
To: François Pinard <[EMAIL PROTECTED]>, Tong Wang <[EMAIL PROTECTED]>, R help
> Please, don't reinvent the wheel: putting functions in a dedicated
> environment is one of the things done by R packages (together with
> a
> good documentation of the function, and making them easily
> installable
> on any R implementation). So, this is probably the time for you to
> read
> the "Writing R extensions" manual, and to start implementing your
> own R
> package!
> Best,
>
> Philippe Grosjean
>
> François Pinard wrote:
> > [Tong Wang]
> >
> >> I created environment "mytoolbox" by : mytoolbox <-
> >> new.env(parent=baseenv()). Is there anyway I put it in the
> search
> >> path? In a project, I often write some small functions, and
> load them
> >> into my workspace directly, so when I list the objects with
> ls(), it
> >> looks pretty messy. So I am wondering if it is possible to
> creat an
> >> environment, and put these tools into this environment. For
> example,
> >> I have functions fun1(), fun2() ... and creat an environment
> mytoolbox
> >> which contains all these functions. And it should be somewhere
> in the
> >> search path: ".GlobalEnv" "mytoolbox" "package:methods".
> >
> > Here is a trick, shown as a fairly simplified copy of my
> ~/.Rprofile.
> > It allows for a few simple functions always available, yet
> without
> > having to create a package, and leaving ls() and any later .RData
> file
> > unencumbered.
> >
> > The idea is to use local() to prevent any unwanted clutter to
> leak out
> > (my real ~/.Rprofile holds more than shown below and use
> temporary
> > variables), to initialise a list meant to hold a bunch of
> functions or
> > other R things, and to save that list on the search path.
> >
> > This example also demonstrate a few useful functions for when I
> read the
> > R mailing list. I often need to transfer part of emails containing
> > code excerpts within the window where R executes, while removing
> > quotation marks, white lines and other noise. I merely highlight-
> select
> > part of the message with the mouse, and then, within R, do things
> like:>
> >xs() source the highlighted region
> >xd() read in a data.frame
> >xm() read in a matrix
> >xe() evaluate and print an expression
> >xv() read a list of values as a vector
> >
> > The list above in decreasing order of usefulness (for me).
> Except for
> > xs(), which has no automatic printout, you may either let the
> others
> > print what they got, or assign their value to some variable.
> Arguments
> > are also possible, for example like this:
> >
> >xd(T) read in a data.frame when the first line holds column
> names>
> >
> >
> > if (interactive()) {
> > local({
> >
> > fp.etc <- list()
> >
> > fp.etc$xsel.vector <- function (...) {
> > connexion <- textConnection(xselection())
> > on.exit(close(connexion))
> > scan(connexion, ...)
> > }
> > fp.etc$xsel.dataframe <- function (...) {
> > connexion <- textConnection(xselection())
> > on.exit(close(connexion))
> > read.table(connexion, ...)
> > }
> > fp.etc$xsel.matrix <- function (...) {
> > connexion <- textConnection(xselection())
> > on.exit(close(connexion))
> > data.matrix(read.table(connexion, ...))
> > }
> > fp.etc$xsel.eval <- function (...) {
> > connexion <- textConnection(xselection())
> > on.exit(close(connexion))
> > eval(parse(connexion, ...))
> > }
> > fp.etc$xsel.source <- function (...) {
> > connexion <- textConnection(xselection())
> > on.exit(close(con
[R] A question about R environment
Hi all, I created environment "mytoolbox" by : mytoolbox <- new.env(parent=baseenv()) Is there anyway I put it in the search path ? If you need some background : In a project, I often write some small functions, and load them into my workspace directly, so when I list the objects with ls(), it looks pretty messy. So I am wondering if it is possible to creat an environment, and put these tools into this environment. For example, I have functionsfun1(), fun2() .. and creat an environment mytoolbox which contains all these functions. And it should be somewhere in the search path: ".GlobalEnv""mytoolbox""package:methods" __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] need help with debug package
I think I have figured out part of the answer, when I entered a debugger, the
calling environment (parent frame)
refers to the debugger program, instead of the mainfun( ). But is there
anyway to solve this problem ?
thanks
- Original Message -
From: Tong Wang <[EMAIL PROTECTED]>
Date: Wednesday, January 3, 2007 9:30 pm
Subject: need help with debug package
To: R help
> Hi all,
> I met a problem while using the debug package, I have the
> following program:
>
> mainfun<- function(){
> beta<-1
> result<-subfun(beta+x)
> }
>
> subfun<-function(expr){
> y <- eval(expr, envir=list(x=c(1,2)),enclos =
> parent.frame()) return(y)
> }
>
> I have no problem using this program without calling the debug
> package. but once
> I mtrace(subfun), the debugger can't find all the beta after
> entering subfun , and give
> the message : "Error in beta : non-numeric argument to binary
> operator"
> Is there anyway to get around ?
>
> thanks a lot
> happy new year
>
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[R] need help with debug package
Hi all,
I met a problem while using the debug package, I have the following
program:
mainfun<- function(){
beta<-1
result<-subfun(beta+x)
}
subfun<-function(expr){
y <- eval(expr, envir=list(x=c(1,2)),enclos = parent.frame())
return(y)
}
I have no problem using this program without calling the debug package. but
once
I mtrace(subfun), the debugger can't find all the beta after entering subfun ,
and give
the message : "Error in beta : non-numeric argument to binary operator"
Is there anyway to get around ?
thanks a lot
happy new year
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[R] A question about debug package
Hi all, I am using the debug package, and I would like some commands executed automatically as I quit by qqq( ), I tried the on.exit( ) , but it doesn't work in this case. Any suggestions on this? thanks a lot . tong __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] A quesiton on data manipulation
Hi, I have a data set (data frame) describing some features of the students in a high school in the following format: Stu IDYear feature 1 feature 2 . 1001 1990 1001 1991 1001 1992 1002 1990 1002 1991 1002 1992 Some features of a few of these students are missing, I would like to ignore those students in my analysis, but I really can' t figure out a neat way to do this in R. I need to remove all the info. of a student (indicated by ID no.) if there are NA's in his/her features. Could someone give me a quick tutorial on this ? I would really appreciate. best __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Question about managing searching path
Hi all,
I'm having sometrouble with managing the seach path, in a function , I
need to attach some data set at the begining
and detach them at the end, say, myfunction<- function() { attach(mylist);
.detach(mylist) } ,
the problem is, since I am still debugging this code, sometimes it got error
and ended before reaching the end, thus
the data is left in the searching path.
What 's the right way to make mylist detached no matter what ?
Thanks a lot.
best
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[R] How to make the debuger stop at the warnings
Hi, I am using the debug package, is there any way I can tell the debuger to stop when a warning message come out ? Thanks a lot. best __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to repeat vectors ?
Hi, Thanks you guys for all the help. I learned a lot from it. It looks using apply() is not an efficient way, since all it does is looping through each row(or col) , which would be slow for large matrix, right ? cheers - Original Message - From: Gabor Grothendieck <[EMAIL PROTECTED]> Date: Saturday, September 30, 2006 4:54 am Subject: Re: [R] How to repeat vectors ? To: Tong Wang <[EMAIL PROTECTED]> Cc: r-help@stat.math.ethz.ch > Here are 4 approaches in order from most compact > to least. #1 only works for numeric matrices, # 2 is > a shorter versio of your solution using rep.vec and # 3 > is from Alex's post and is likely what I would > use in practice. > > m <- matrix(1:4, 2) # test matrix > > # 1 - m must be numeric for this one to work > kronecker(m, rep(1,2)) > > # 2 > apply(m, 2, rep, each = 2) # 2 > > # 3 - from Alex's post > m[rep(1:nrow(m), each = 2),] > > # 4 > matrix(rbind(c(m), c(m)), nc = ncol(m)) > > On 9/30/06, Tong Wang <[EMAIL PROTECTED]> wrote: > > I just figured out a way to do this: > > rep.vec <- function(X,n) > return(t(array(rep(X,n),c(length(X),n> > > Then,apply(MyMatrix, 2, rep.vec,2) > > > > Is there a better way ? Is there an internal function to repeat > a vector or matrix ? > > > > Thanks a lot. > > > > > > - Original Message - > > From: Tong Wang <[EMAIL PROTECTED]> > > Date: Friday, September 29, 2006 11:23 pm > > Subject: How to repeat vectors ? > > To: r-help@stat.math.ethz.ch > > > > > Hi, > > >If I have a matrix , say a11 a12 > > > a21 a22 > > >Is there a routine to get: a11 a12 > > > a11 a12 > > > a21 a22 > > > a21 a22 > > > > > > Thanks a lot for any help. > > > > > > best > > > > > > > __ > > R-help@stat.math.ethz.ch mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html> and provide commented, minimal, self-contained, > reproducible code. > > > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Can I avoid loops here ?
Thanks Gabor, I will be more specific next time.
best
- Original Message -
From: Gabor Grothendieck <[EMAIL PROTECTED]>
Date: Saturday, September 30, 2006 10:38 pm
Subject: Re: [R] Can I avoid loops here ?
To: Tong Wang <[EMAIL PROTECTED]>
Cc: R help
> Try:
>
> mapply("%*%", mylist1, mylist2, SIMPLIFY = FALSE)
>
> Please provide self-contained examples as requested on
> the last line of every message to r-help. That means the
> data for X1, X2, Y1, Y2 should be included so one can
> run the code you post.
>
> On 10/1/06, Tong Wang <[EMAIL PROTECTED]> wrote:
> > Hi,
> > I have two lists of matrices, and I would like to get a
> list of term by term product, say,
> > mylist1<- list( X1,X2); mylist2<-list(Y1,Y2)
> >
> > Need: mylist3<-list(X1%*%Y1,X2%*%Y2)
> >
> > Is there a way that allows me to do this without loops ?
> >
> > Thanks a lot.
> >
> > best
> >
> > __
> > R-help@stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html> and provide commented, minimal, self-contained,
> reproducible code.
> >
>
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Can I avoid loops here ?
Hi, I have two lists of matrices, and I would like to get a list of term by term product, say, mylist1<- list( X1,X2); mylist2<-list(Y1,Y2) Need: mylist3<-list(X1%*%Y1,X2%*%Y2) Is there a way that allows me to do this without loops ? Thanks a lot. best __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to repeat vectors ?
I just figured out a way to do this: rep.vec <- function(X,n)return(t(array(rep(X,n),c(length(X),n Then,apply(MyMatrix, 2, rep.vec,2) Is there a better way ? Is there an internal function to repeat a vector or matrix ? Thanks a lot. - Original Message - From: Tong Wang <[EMAIL PROTECTED]> Date: Friday, September 29, 2006 11:23 pm Subject: How to repeat vectors ? To: r-help@stat.math.ethz.ch > Hi, >If I have a matrix , say a11 a12 > a21 a22 >Is there a routine to get: a11 a12 > a11 a12 > a21 a22 > a21 a22 > > Thanks a lot for any help. > > best > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to repeat vectors ?
Hi, If I have a matrix , say a11 a12 a21 a22 Is there a routine to get: a11 a12 a11 a12 a21 a22 a21 a22 Thanks a lot for any help. best __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] strange warning message
Hi Duncan: Thank you for your help last time, since I do not use NULL to indicate empty enviroment, I think I'm fine. And yes, I did upgrade my R version recently, but how comes I still get this warning for new files created and saved after that update ? Is there anyway to get rid of this message ? Thanks a lot . best - Original Message - From: Duncan Murdoch <[EMAIL PROTECTED]> Date: Saturday, September 23, 2006 5:59 pm Subject: Re: [R] strange warning message To: Tong Wang <[EMAIL PROTECTED]> Cc: r-help@stat.math.ethz.ch > On 9/23/2006 7:15 PM, Tong Wang wrote: > > Hi Everyone, > > I recently start to get this warning message, while loading > files in to R. Could someone tell me what does it mean ? > > I am using R 2.3.0 with Emacs on WinXP. > > > > use of NULL environment is deprecated > > The files were saved in an earlier version of R, which used NULL to > indicate the base environment. R is telling you that NULL is not a > legal environment. It should be automatically converted to baseenv(). > > In a number of cases, people used NULL to indicate an empty > environment > (even though there was no such thing when NULL was used); if that's > true > for your code, then you'll need to fix it. emptyenv() now gives > you an > empty environment if that's what you really want. > > Duncan Murdoch > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to pass expression as an argument
Hi,
I am writing a function and need to pass a function expression as an
argument, for instance,
myfun <- function( express) {
x<- c(1,2,3)
y<-express
}
if I call the above function by myfun( x*2 ), I get 2 as the result,
instead of 2,4,6 , could someone help me to
fix this problem ?
Furthermore, is that possible to operate this expression on different
variables? for example, in myfun(), I
might want to get u*2, z*2, etc. without having to say x<-u, x<-z to match
the expression.
Thanks a lot for your help.
best
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and provide commented, minimal, self-contained, reproducible code.
[R] strange warning message
Hi Everyone, I recently start to get this warning message, while loading files in to R. Could someone tell me what does it mean ? I am using R 2.3.0 with Emacs on WinXP. use of NULL environment is deprecated Thanks a lot for any help best __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to generating diagnal blocks ?
Hi, I am trying to creat a matrix with diagnal blocks, say, I have a matrix X of any dimension (nxm) ,and would like to have: X X X . otherwise space filled with 0's. Is there a handy way to do this ? Thanks a lot in advance. best __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Need help with dataset formation problem
Hi, I have a data set , say, X : [1][2] mean 0 .8 sd1 3 I need to use it in do.call() , so when I refer to the first col of X, I need it to be a list with members mean, sd. thus I constructed X as a list of list : X[[1]]<- list(mean=0, sd=1), X[[2]]<-.. But this dataset is useless in other cases, for example, I can't pull out all the means as a vector. Can I get some suggestions on what's the best way to handle it? (except preparing two copies of this data with different formats) Thanks a lot in advance. best __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Question about do.call()
Hi, I'm writing a function f() which includes probability density function computation, I would like to make this generic, that is , I will specify the density when I call f(), here's what I wrote: do.call(den, args=list(d, arg)) the question is , say, if I let den=dnorm, I have to replace arg with mean=??, sd=??, etc. but I tried arg=c(mean=..,sd=..) and arg="mean=..,sd=..", neither of these worked. What is the right way to do this ? Thanks a lot tong __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] What is the matrix version of min()
Hi, THANK YOU ALL for the prompt reply. cheers. - Original Message - From: Robin Hankin <[EMAIL PROTECTED]> Date: Wednesday, September 6, 2006 1:42 am Subject: Re: [R] What is the matrix version of min() To: Tong Wang <[EMAIL PROTECTED]> Cc: R help > Tong > > you need to use apply(). The second argument specifies whether > you want to work with rows or columns. The point of this is that > min() and max() operate on vectors and give a single value, > and you want to "apply" this function to all rows or all columns: > > > a <- matrix(rnorm(30),5,6) > > apply(a,2,max) > [1] 2.6413241 0.9842076 1.7989560 0.6999855 2.0542201 0.1162821 > > apply(a,1,max) > [1] 1.1771370 0.9811693 2.6413241 0.9842076 2.0542201 > > > > HTH > > rksh > > > On 6 Sep 2006, at 09:37, Tong Wang wrote: > > > Hi, > > Is there a function which operates on a matrix and return a > > vector of min/max of each rol/col ? > > say, X= 2, 1 > > 3, 4 > > min.col(X)=c(2,1) > > > > thanks a lot. > > > > tong > > > > __ > > R-help@stat.math.ethz.ch mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/posting- > > > guide.html > > and provide commented, minimal, self-contained, reproducible code. > > -- > Robin Hankin > Uncertainty Analyst > National Oceanography Centre, Southampton > European Way, Southampton SO14 3ZH, UK > tel 023-8059-7743 > > > > > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] What is the matrix version of min()
Hi, Is there a function which operates on a matrix and return a vector of min/max of each rol/col ? say, X= 2, 1 3, 4 min.col(X)=c(2,1) thanks a lot. tong __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A question about gc()
Yes, I am using R in windows, sorry for not being specific.
You are right, I have stored too much stuff, and I need to trash some data in
the process.
Problem solved for me, Thank you very much.
tong
- Original Message -
From: Prof Brian Ripley <[EMAIL PROTECTED]>
Date: Tuesday, September 5, 2006 3:42 am
Subject: Re: [R] A question about gc()
To: Tong Wang <[EMAIL PROTECTED]>
Cc: R help
> On Tue, 5 Sep 2006, Tong Wang wrote:
>
> > Hi everyone,
>
> > I am doing some intensive computation: 5 regressions of
> the
> > form Y~X with each y of size (1,1000) , even if I break invoke
> gc() for
> > a few time in the loop, it still breaks down at some point with
> the
> > error message:
>
> gc() does not reclaim memory for you beyond what R has already done.
>
> > Error in .signalSimpleWarning("Reached total allocation of
> 1024Mb: see help(memory.size)", :
> > recursive default argument reference
>
> > After getting this, even if I call gc() and resume the
> computation, it
> > won't move at all. May I get some suggestions what should I do to
> get
> > around this problem ?
>
> Consult the rw-FAQ (since you seem to be using Windows without
> telling us)
> and the help page the message mentions.
>
> It looks as if you are trying to store too many objects. If you
> have lots
> of RAM you can increase that limit (see the previous para), but you
> are
> getting uncomfortably close to the address space limit of your OS.
>
> Perhaps you can only save the part of the fit you need, or save()
> the
> objects to separate files and rm() them, and postprocess them in a
> later
> session?
>
> --
> Brian D. Ripley, [EMAIL PROTECTED]
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UKFax: +44 1865 272595
>
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Quick question about lm()
Thanks a lot for your help. tong - Original Message - From: Christos Hatzis <[EMAIL PROTECTED]> Date: Monday, September 4, 2006 10:54 pm Subject: RE: [R] Quick question about lm() To: 'Tong Wang' <[EMAIL PROTECTED]>, r-help@stat.math.ethz.ch > Say, > > my.lm <- lm(y ~ x, data=my.data) > > Then if you try: > > names(summary(my.lm)) > > you will see the components of the summary.lm object. The > coefficients and > t-statistics can be extracted by > > summary(my.lm)$coefficients > > and similarly for the r-squared and other statistics provided in > the summary > report. > > -Christos > > > -----Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Tong Wang > Sent: Tuesday, September 05, 2006 1:35 AM > To: r-help@stat.math.ethz.ch > Subject: [R] Quick question about lm() > > Hi, > Feel awkward to ask , but really couldn't find a answer > anywhere, How > could I extract the R^2 and t-stat. from the > result of lm()? > Thanks a lot. > > best > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.htmland provide commented, minimal, self-contained, > reproducible code. > > > > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] A question about gc()
Hi everyone,
I am doing some intensive computation: 5 regressions of the form Y~X
with each y of size (1,1000) ,
even if I break invoke gc() for a few time in the loop, it still breaks down at
some point with the error message:
Error in .signalSimpleWarning("Reached total allocation of 1024Mb: see
help(memory.size)", :
recursive default argument reference
After getting this, even if I call gc() and resume the computation, it won't
move at all.
May I get some suggestions what should I do to get around this problem ?
Thanks a lot.
tong
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Quick question about lm()
Hi, Feel awkward to ask , but really couldn't find a answer anywhere, How could I extract the R^2 and t-stat. from the result of lm()? Thanks a lot. best __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] identify high dimension data point
Hi there, I am having some trouble with the Identify() function, it looks that the identify() function only works on the plot of 2-dimension data set. In high-dimension case , if I use pairs() + identify() in hope to observe all the components of the data point I selected, I get error message. Is there anyway to get around this ? Plus, I also need it to actually compare all the components of the picked data point with "mydataset" to choose the closest one. Thanks million in advance. best tong __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How to change the label in plot.ts ?
Hi you guys: I have been wondering if there is any way to change the labeling in plot.ts( ), for example , if I plot two sequences, i always got y labels as "series1", "series2", I tried to use ylab=c((expression(mu_1)),(expression(mu_2))), but it doesn't work. thanks in advance for any help best. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How to import data as numeric array?
Did some search but couldn't find useful result. I am trying to read a n*m dimension data with read.table, what i need is a numeric array, is there any efficient way to allow me get this array directly instead of a list? I tried to use as.array() to change the mode, but seems it doesn't work and i got this error message: "Error in "dimnames<-.data.frame"(`*tmp*`, value = list(function (M) : invalid dimnames given for data frame " what's wrong with the dimension names , should i delete them? how can i do that? Thanks a lot for any help. tong wang __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How to search an element in matrix ?
Hi you guys, I know this might be too simple a question to post, but i searched a lot still couldn't find it. Just want to find an element in matrix and return its index , i think there should be some matrix version of "match" which only works for vector to me. thanks in advance for your help. best, tong __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
