[R] cluster analysis and null hypothesis testing
Hi, I am wondering if a Monte Carlo method (or equivalent) exist permitting to test the randomness of a cluster analysis (eg got by hclust(). I went through the package "fpc" (maybe too superficially) but dit not find such method. Thanks for any hint, Patrick Giraudoux __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
FW: [R] glmmPQL and random factors
I have just realised that I sent this to Per only. For those interested on the list: -Original Message- From: Gygax Lorenz FAT Sent: Tuesday, September 14, 2004 4:35 PM To: 'Per Toräng' Subject: RE: [R] glmmPQL and random factors Hi Per, > glmmPQL(Fruit.set~Treat1*Treat2+offset(log10(No.flowers)), > random=~1|Plot, family=poisson, data=...) > > Plot is supposed to be nested in (Treat1*Treat2). > Is this analysis suitable? As far as I understand the methods and with my experience using such analyses, I would say that the model is ok the way you specified it. glmmPQL (and the underlying lme) is so intelligent (a thousand thanks to the developpers!) as to recognise if the treatments are fixed per plot, i.e. only one level of the two treatments appears in each plot. The denominator degrees of freedom in the anova table are adjusted automatically. I.e. your denominator df should be the number of plots minus five, the number of dfs you need for the fixed effects (Treat1, Treat2, the interaction, the covariate and the one df you always loose from the total of observations). > Moreover, what is the meaning of typing > random=~1|Plot compared to random=~Treat1*Treat2|Plot? The first version means, that the intercept / overall mean can vary from plot to plot. I.e. each plot may have another mean due to the fact that it grows somewhere else in addition to the differing treatments. The second version tries to model a difference in reaction to treatment 1 and 2 for each of the plots (which does not make sense in your case as each plot is only subjected to one kind of treatment). In a crossed design, i.e. if you could have treated your plants individually and had all treatment combinations in each of the plots, the first version implies that all the plots react in the same consistent way to the treatments. I.e. that the general level of each plot may be different, but the differences due to treatment are the same in each plot, the reaction of the plots are shifted but have the same shape (this is the same as saying that you only consider main effects of treatment and plot). The second version allows to estimate the reactions for each plot, i.e. in addition to a general shift, the treatments may have (slightly) different effects in each plot. This is the same as saying that you consider interactions between your fixed and random effects. See also the terrific book by Pinheiro & Bates (Mixed Effects Modelling in S and S-Plus, Springer, 2000). Cheers, Lorenz - Lorenz Gygax Tel: +41 (0)52 368 33 84 / [EMAIL PROTECTED] Centre for proper housing of ruminants and pigs Swiss Federal Veterinary Office __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] getting started on Bayesian analysis
I've found Bayesian Methods: A Social and Behavioral Sciences Approach by Jeff Gill useful as an introduction. The examples are written in R and S with generalized scripts for doing a variety of problems. (Though I never got change-point analysis to successfully in R.) Best, Mark Hall Mark Hall Archaeological Research Facility UC Berkeley __ [EMAIL PROTECTED] 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] getting started on Bayesian analysis
I am an economist who decided it's high time that I learned some Bayesian statistics. I am following An Introduction to Modern Bayesian Econometrics by T. Lancaster. The book recommends using BUGS, but I wonder if there are any alternatives which are free software and fully integrated to R (which I have been using for more than two years for numerical computations.) I would like to learn what R packages (or other software) statisticians use for Bayesian analysis to R, if there are viable alternatives to BUGS, etc. A couple of references to relevant packages, books or online tutorials would help me a lot. Thanks Tamas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Spare some CPU cycles for testing lme?
On Sep 13, 2004, at 8:47 PM, Tamas K Papp wrote: It ran smoothly on my installation. version _ platform powerpc-apple-darwin6.8 arch powerpc os darwin6.8 system powerpc, darwin6.8 status major1 minor9.1 year 2004 month06 day 21 language R Typical lines from top (if it helps anything; around 45-50k iterations): 1225 R.bin 90.7% 2:55:12 162 1164 71.7M+ 13.7M 66.6M+ 228M+ 1225 R.bin 78.6% 3:18:27 162 1606 81.3M+ 13.7M 75.5M+ 234M+ I can confirm this. same installation __ [EMAIL PROTECTED] 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] pairs correlations colors
I have the following problem.
I want to use pairs function and get a matrix of scatterplots with the
correlations in the upper panel and the ordinary scatterplots in the
lower panel.
Moreover, I want to have points colored in five differet ways in the
lower panel, because I have five subgroups.
In order to do that I tried to combine examples on pairs function help.
I got a colored matrix using hints on iris dataset.
I got a black and white matrix with correlations using function
panel.cor, exactly as it is in the example.
Unfortunately, the line:
jpeg(filename="/home/valeria/Thesis/lung/fig/scatterplotcolnames.jpg")
pairs(aggiunta[,1:
6],labels=c("ALCAM","ITGB5","MSN","CSTB","DHCR24","TRIM29"), main =
"Scatterplots selected genes",pch=21,
bg = c("red", "green3", "blue",
"brown","orange")[aggiunta[,7]],upper.panel=panel.cor)
dev.off()
doesn't allow me to get the desidered matrix with colors and
correlations.
I also tried to create a function panel.col for the lower.panel:
## put colors on the lower panels
panel.col <- function(datiepheno)
{
usr <- par("usr"); on.exit(par(usr))
par(bg = c("red", "green3", "blue",
"brown","orange")[datiepheno[,7]],pch=21, usr = c(0, 1, 0, 1))
}
but it doesn't work as well.
Any idea?
I hope I'll be precise but not too much precise!
Thank you very much
Valeria
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[R] rolling n-step predictions for ARIMA models
Hello: I would like to generate rolling, multiperiod forecasts from an estimated ARIMA model, but the function predict.Arima seems only to generate forecasts from the last observation in the data set. To implement this, I was looking for an argument like 'newdata=' in predict.lm. I can write some code that does this for my particular problem, but might there exist a package/function that does this that I cannot find? Thanks, -Michael Michael J. Roberts Resource Economics Division Production, Management, and Technology USDA-ERS (202) 694-5557 (phone) (202) 694-5775 (fax) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] memory problem under windows
Did you read the *rest* of what the rw-FAQ says? Be aware though that Windows has (in most versions) a maximum amount of user virtual memory of 2Gb, and parts of this can be reserved by processes but not used. The version of the memory manager used from R 1.9.0 allocates large objects in their own memory areas and so is better able to make use of fragmented virtual memory than that used previously. R can be compiled to use a different memory manager which might be better at using large amounts of memory, but is substantially slower (making R several times slower on some tasks). So, it tells you about memory fragmentation, and it tells you about making R aware of large-memory versions of Windows and that an alternative memory manager can be used. If you actually tried those, the posting guide asks you to indicate it, so I presume you did not. Also, take seriously the idea of using a more capable operating system that is better able to manage 2Gb of RAM. On Tue, 14 Sep 2004, Christoph Lehmann wrote: > I have (still) some memory problems, when trying to allocate a huge array: > > WinXP pro, with 2G RAM > > I start R by calling: > > Rgui.exe --max-mem-size=2Gb (as pointed out in R for windows FAQ) > > R.Version(): i386-pc-mingw32, 9.1, 21.6.2004 > > ## and here the problem > x.dim <- 46 > y.dim <- 58 > slices <- 40 > volumes <- 1040 > a <- rep(0, x.dim * y.dim * slices * volumes) > dim(a) <- c(x.dim, y.dim, slices, volumes) > > gives me: "Error: cannot allocate vector of size 850425 Kb" > > even though > > memory.limit(size = NA) > yields2147483648 > > and > > memory.size() > gives 905838768 > > so why is that and what can I do against it? > > Many thanks for your kind help > > Cheers > > Christoph > > -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] memory problem under windows
Christoph Lehmann wrote: I have (still) some memory problems, when trying to allocate a huge array: WinXP pro, with 2G RAM I start R by calling: Rgui.exe --max-mem-size=2Gb (as pointed out in R for windows FAQ) Not sure that it actually says to use 2Gb there. You might try --max-mem-size=2000M, which seems to work better for me. HTH, Jim -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 __ [EMAIL PROTECTED] 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] memory problem under windows
I have (still) some memory problems, when trying to allocate a huge array: WinXP pro, with 2G RAM I start R by calling: Rgui.exe --max-mem-size=2Gb (as pointed out in R for windows FAQ) R.Version(): i386-pc-mingw32, 9.1, 21.6.2004 ## and here the problem x.dim <- 46 y.dim <- 58 slices <- 40 volumes <- 1040 a <- rep(0, x.dim * y.dim * slices * volumes) dim(a) <- c(x.dim, y.dim, slices, volumes) gives me: "Error: cannot allocate vector of size 850425 Kb" even though memory.limit(size = NA) yields 2147483648 and memory.size() gives 905838768 so why is that and what can I do against it? Many thanks for your kind help Cheers Christoph -- Christoph LehmannPhone: ++41 31 930 93 83 Department of Psychiatric NeurophysiologyMobile: ++41 76 570 28 00 University Hospital of Clinical Psychiatry Fax:++41 31 930 99 61 Waldau[EMAIL PROTECTED] CH-3000 Bern 60 http://www.puk.unibe.ch/cl/pn_ni_cv_cl_03.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] reshaping some data
Here is another variation. It uses LOCF which is last
observation carried forward -- a function which takes a
logical vector and for each element provides the index of
the last TRUE value. The version of LOCF here assumes
that the first element of the argument is TRUE which
happens to be the case here.
LOCF <- function(L) which(L)[cumsum(L}]
is.x <- substr(colnames(x),1,1) == "x"
x. <- unlist(x[,LOCF(is.x)[!is.x]])
names(x.) <- NULL
data.frame(x = x., y = unlist(x[,!is.x]), row.names = NULL)
I found Peter's solution particularly clever. Note that it
depends on the y colnames having the same first digit as the
corresponding x colnames; however they need not be in any
specific order, whereas the solution above and my previous
one below depend on the y names being immediately after the
x names but do not depend on the detailed content of the names.
In the present case both these assumptions appear to hold
but in different situations one or the other of these assumptions
might be preferable.
Gabor Grothendieck myway.com> writes:
:
: Try this:
:
: is.x <- substr(colnames(x),1,1) == "x" # TRUE if col name starts with x
: x. <- unlist(rep(x[,is.x], diff(which(c(is.x,TRUE)))-1)) # repeat x cols
: names(x.) <- NULL
: y. <- unlist(x[,!is.x])
: DF <- data.frame(x = x., y = y., row.names = NULL)
:
: Sundar Dorai-Raj PDF.COM> writes:
:
: :
: : Hi all,
: :I have a data.frame with the following colnames pattern:
: :
: : x1 y11 x2 y21 y22 y23 x3 y31 y32 ...
: :
: : I.e. I have an x followed by a few y's. What I would like to do is turn
: : this wide format into a tall format with two columns: "x", "y". The
: : structure is that xi needs to be associated with yij (e.g. x1 should
: : next to y11 and y12, x2 should be next to y21, y22, and y23, etc.).
: :
: : x y
: : x1 y11
: : x2 y21
: : x2 y22
: : x2 y23
: : x3 y31
: : x3 y32
: : ...
: :
: : I have looked at ?reshape but I didn't see how it could work with this
: : structure. I have a solution using nested for loops (see below), but
: : it's slow and not very efficient. I would like to find a vectorised
: : solution that would achieve the same thing.
: :
: : Now, for an example:
: :
: : x <- data.frame(x1 = 1: 5, y11 = 1: 5,
: : x2 = 6:10, y21 = 6:10, y22 = 11:15,
: : x3 = 11:15, y31 = 16:20,
: : x4 = 16:20, y41 = 21:25, y42 = 26:30, y43 = 31:35)
: : # which are the x columns
: : nmx <- grep("^x", names(x))
: : # which are the y columns
: : nmy <- grep("^y", names(x))
: : # grab y values
: : y <- unlist(x[nmy])
: : # reserve some space for the x's
: : z <- vector("numeric", length(y))
: : # a loop counter
: : k <- 0
: : n <- nrow(x)
: : seq.n <- seq(n)
: : # determine how many times to repeat the x's
: : repy <- diff(c(nmx, length(names(x)) + 1)) - 1
: : for(i in seq(along = nmx)) {
: :for(j in seq(repy[i])) {
: : # store the x values in the appropriate z indices
: : z[seq.n + k * n] <- x[, nmx[i]]
: : # move to next block in z
: : k <- k + 1
: :}
: : }
: : data.frame(x = z, y = y, row.names = NULL)
:
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Re: [R] A question please
Lawrence- Are you familiar with the computer software MARK (http://www.cnr.colostate.edu/~gwhite/mark/mark.htm)? It is a very complete package for analysis of capture-recapture data. I have written an interface to MARK in R but it isn't ready for distribution. I'm presently in the process of creating the R help files and turning it into an R package. No promises on when I'll be done though. Currently my R interface does not support all of the models nor capabilities in MARK. It is an evolving package. I developed it for my own use to be able to use the formula and design matrix capabilities in R to more easily develop models in MARK. I'm a little hesitant to send this message because I'm not looking to provide package support.You may also want to be aware of the package WISP for R written by Walter Zucchini and David Borchers as a companion to his book on abundance estimation. See http://www.ruwpa.st-and.ac.uk/estimating.abundance/WiSP/ I'd be interested in hearing of other responses that you receive. --jeff Lawrence Lessner wrote: Hi Does R have a proceedure/software for capture recapture? Thank you. Lawrence Lessner Please respond to [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] A question please
At "www.r-project.org" -> search -> "R site search", I just got 11 hits for "capture-recapture". Did you try this? They may not all be relevant, but I suspect that some of them might be. hope this helps. spencer graves Lawrence Lessner wrote: Hi Does R have a proceedure/software for capture recapture? Thank you. Lawrence Lessner Please respond to [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Spencer Graves, PhD, Senior Development Engineer O: (408)938-4420; mobile: (408)655-4567 __ [EMAIL PROTECTED] 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] A question please
Hi Does R have a proceedure/software for capture recapture? Thank you. Lawrence Lessner Please respond to [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Separation between tick marks and tick labels in lattice
On Tuesday 14 September 2004 11:44, Waichler, Scott R wrote: > I can't find a way to control the distance between tick marks and tick > labels > in lattice. In a stripplot I'm making these components are too close. > I don't > see anything like base graphics mgp in the scales list. There's none in the released version. There is a way in the r-devel version version, not via scales, but by the settings, e.g. something like trellis.par.set(axis.components = list(left = list(pad1 = 3))) Deepayan __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] reshaping some data
Try this:
is.x <- substr(colnames(x),1,1) == "x" # TRUE if col name starts with x
x. <- unlist(rep(x[,is.x], diff(which(c(is.x,TRUE)))-1)) # repeat x cols
names(x.) <- NULL
y. <- unlist(x[,!is.x])
DF <- data.frame(x = x., y = y., row.names = NULL)
Sundar Dorai-Raj PDF.COM> writes:
:
: Hi all,
:I have a data.frame with the following colnames pattern:
:
: x1 y11 x2 y21 y22 y23 x3 y31 y32 ...
:
: I.e. I have an x followed by a few y's. What I would like to do is turn
: this wide format into a tall format with two columns: "x", "y". The
: structure is that xi needs to be associated with yij (e.g. x1 should
: next to y11 and y12, x2 should be next to y21, y22, and y23, etc.).
:
: x y
: x1 y11
: x2 y21
: x2 y22
: x2 y23
: x3 y31
: x3 y32
: ...
:
: I have looked at ?reshape but I didn't see how it could work with this
: structure. I have a solution using nested for loops (see below), but
: it's slow and not very efficient. I would like to find a vectorised
: solution that would achieve the same thing.
:
: Now, for an example:
:
: x <- data.frame(x1 = 1: 5, y11 = 1: 5,
: x2 = 6:10, y21 = 6:10, y22 = 11:15,
: x3 = 11:15, y31 = 16:20,
: x4 = 16:20, y41 = 21:25, y42 = 26:30, y43 = 31:35)
: # which are the x columns
: nmx <- grep("^x", names(x))
: # which are the y columns
: nmy <- grep("^y", names(x))
: # grab y values
: y <- unlist(x[nmy])
: # reserve some space for the x's
: z <- vector("numeric", length(y))
: # a loop counter
: k <- 0
: n <- nrow(x)
: seq.n <- seq(n)
: # determine how many times to repeat the x's
: repy <- diff(c(nmx, length(names(x)) + 1)) - 1
: for(i in seq(along = nmx)) {
:for(j in seq(repy[i])) {
: # store the x values in the appropriate z indices
: z[seq.n + k * n] <- x[, nmx[i]]
: # move to next block in z
: k <- k + 1
:}
: }
: data.frame(x = z, y = y, row.names = NULL)
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Re: [R] reshaping some data
Bert,
Coming up with "nvec" was what I was missing. Modifying your solution
slightly, here's what I ended up with:
z <- x[, nmx]
nvec <- seq(length(nmx))
z <- unlist(z[, rep(nvec, repy)])
z2 <- data.frame(x = z, y = y, row.names = NULL)
Thanks again,
--sundar
Berton Gunter wrote:
Sundar:
As I understand it, you can easily create an index variable (a pointer,
actually) that will pick out the y columns in order:
z<-yourdataframe
y<-as.vector(z[,indexvar])
So if you could cbind() the x's, you'd be all set.
Again, assuming I understand correctly, the x column you want is:
x<-z[,-indexvar] ## still a frame/matrix
nvec<-seq(length=ncol(x))
x<-as.vector(x[,rep(nvec,times=nvec)])
HTH -- and even if I got it wrong, it was fun, so thanks.
-- Bert
-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
"The business of the statistician is to catalyze the scientific learning
process." - George E. P. Box
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Sundar
Dorai-Raj
Sent: Tuesday, September 14, 2004 9:16 AM
To: R-help
Subject: [R] reshaping some data
Hi all,
I have a data.frame with the following colnames pattern:
x1 y11 x2 y21 y22 y23 x3 y31 y32 ...
I.e. I have an x followed by a few y's. What I would like to
do is turn
this wide format into a tall format with two columns: "x", "y". The
structure is that xi needs to be associated with yij (e.g. x1 should
next to y11 and y12, x2 should be next to y21, y22, and y23, etc.).
x y
x1 y11
x2 y21
x2 y22
x2 y23
x3 y31
x3 y32
...
I have looked at ?reshape but I didn't see how it could work
with this
structure. I have a solution using nested for loops (see below), but
it's slow and not very efficient. I would like to find a vectorised
solution that would achieve the same thing.
Now, for an example:
x <- data.frame(x1 = 1: 5, y11 = 1: 5,
x2 = 6:10, y21 = 6:10, y22 = 11:15,
x3 = 11:15, y31 = 16:20,
x4 = 16:20, y41 = 21:25, y42 = 26:30, y43 = 31:35)
# which are the x columns
nmx <- grep("^x", names(x))
# which are the y columns
nmy <- grep("^y", names(x))
# grab y values
y <- unlist(x[nmy])
# reserve some space for the x's
z <- vector("numeric", length(y))
# a loop counter
k <- 0
n <- nrow(x)
seq.n <- seq(n)
# determine how many times to repeat the x's
repy <- diff(c(nmx, length(names(x)) + 1)) - 1
for(i in seq(along = nmx)) {
for(j in seq(repy[i])) {
# store the x values in the appropriate z indices
z[seq.n + k * n] <- x[, nmx[i]]
# move to next block in z
k <- k + 1
}
}
data.frame(x = z, y = y, row.names = NULL)
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Re: [R] reshaping some data
Try:
x <- data.frame(x1 = 1: 5, y11 = 1: 5,
x2 = 6:10, y21 = 6:10, y22 = 11:15,
x3 = 11:15, y31 = 16:20,
x4 = 16:20, y41 = 21:25, y42 = 26:30, y43 = 31:35)
df.names<-names(x)
ynames<-df.names[grep("y",df.names)]
xnames<-substring(sub("y","x",ynames),1,2)
cbind(unlist(x[,xnames]),unlist(x[,ynames]))
Peter
Sundar Dorai-Raj wrote:
Hi all,
I have a data.frame with the following colnames pattern:
x1 y11 x2 y21 y22 y23 x3 y31 y32 ...
I.e. I have an x followed by a few y's. What I would like to do is
turn this wide format into a tall format with two columns: "x", "y".
The structure is that xi needs to be associated with yij (e.g. x1
should next to y11 and y12, x2 should be next to y21, y22, and y23,
etc.).
x y
x1 y11
x2 y21
x2 y22
x2 y23
x3 y31
x3 y32
...
I have looked at ?reshape but I didn't see how it could work with this
structure. I have a solution using nested for loops (see below), but
it's slow and not very efficient. I would like to find a vectorised
solution that would achieve the same thing.
Now, for an example:
x <- data.frame(x1 = 1: 5, y11 = 1: 5,
x2 = 6:10, y21 = 6:10, y22 = 11:15,
x3 = 11:15, y31 = 16:20,
x4 = 16:20, y41 = 21:25, y42 = 26:30, y43 = 31:35)
# which are the x columns
nmx <- grep("^x", names(x))
# which are the y columns
nmy <- grep("^y", names(x))
# grab y values
y <- unlist(x[nmy])
# reserve some space for the x's
z <- vector("numeric", length(y))
# a loop counter
k <- 0
n <- nrow(x)
seq.n <- seq(n)
# determine how many times to repeat the x's
repy <- diff(c(nmx, length(names(x)) + 1)) - 1
for(i in seq(along = nmx)) {
for(j in seq(repy[i])) {
# store the x values in the appropriate z indices
z[seq.n + k * n] <- x[, nmx[i]]
# move to next block in z
k <- k + 1
}
}
data.frame(x = z, y = y, row.names = NULL)
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Re: [R] Signs of loadings from princomp on Windows
FWIW, I see the same behavior as Francisco on my Windows machine (also an installation of the windows binary without trying to install any special BLAS libraries): > library(MASS) > data(painters) > pca.painters <- princomp(painters[ ,1:4]) > loadings(pca.painters) Loadings: Comp.1 Comp.2 Comp.3 Comp.4 Composition 0.484 -0.376 0.784 -0.101 Drawing 0.424 0.187 -0.280 -0.841 Colour -0.381 -0.845 -0.211 -0.310 Expression 0.664 -0.330 -0.513 0.432 Comp.1 Comp.2 Comp.3 Comp.4 SS loadings 1.00 1.00 1.00 1.00 Proportion Var 0.25 0.25 0.25 0.25 Cumulative Var 0.25 0.50 0.75 1.00 > pca.painters <- princomp(painters[ ,1:4]) > loadings(pca.painters) Loadings: Comp.1 Comp.2 Comp.3 Comp.4 Composition -0.484 -0.376 0.784 -0.101 Drawing -0.424 0.187 -0.280 -0.841 Colour 0.381 -0.845 -0.211 -0.310 Expression -0.664 -0.330 -0.513 0.432 Comp.1 Comp.2 Comp.3 Comp.4 SS loadings 1.00 1.00 1.00 1.00 Proportion Var 0.25 0.25 0.25 0.25 Cumulative Var 0.25 0.50 0.75 1.00 > R.version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major1 minor9.1 year 2004 month06 day 21 language R > My machine is a dual-processor hp xw8000. I also get the same results with R 2.0.0 dev as in > R.version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status Under development (unstable) major2 minor0.0 year 2004 month09 day 13 language R > -- Tony Plate At Tuesday 10:25 AM 9/14/2004, Prof Brian Ripley wrote: On Tue, 14 Sep 2004, Francisco Chamu wrote: > I have run this on both Windows 2000 and XP. All I did was install > the binaries from CRAN so I think I am using the standard Rblas.dll. > > To reproduce what I see you must run the code at the beginning of the > R session. We did, as you said `start a clean session'. I think to reproduce what you see we have to be using your account on your computer. > After the second run, all subsequent runs give the same > result as the second set. > > Thanks, > Francisco > > > On Tue, 14 Sep 2004 08:29:25 +0200, Uwe Ligges > <[EMAIL PROTECTED]> wrote: > > Prof Brian Ripley wrote: > > > I get the second set each time, on Windows, using the build from CRAN. > > > Which BLAS are you using? > > > > > > Works also well for me with a self compiled R-1.9.1 (both with standard > > Rblas as well as with the Rblas.dll for Athlon CPU from CRAN). > > Is this a NT-based version of Windows (NT, 2k, XP)? > > > > Uwe > > > > > > > > > > > On Tue, 14 Sep 2004, Francisco Chamu wrote: > > > > > > > > >>I start a clean session of R 1.9.1 on Windows and I run the following code: > > >> > > >> > > >>>library(MASS) > > >>>data(painters) > > >>>pca.painters <- princomp(painters[ ,1:4]) > > >>>loadings(pca.painters) > > >> > > >>Loadings: > > >>Comp.1 Comp.2 Comp.3 Comp.4 > > >>Composition 0.484 -0.376 0.784 -0.101 > > >>Drawing 0.424 0.187 -0.280 -0.841 > > >>Colour -0.381 -0.845 -0.211 -0.310 > > >>Expression 0.664 -0.330 -0.513 0.432 > > >> > > >> Comp.1 Comp.2 Comp.3 Comp.4 > > >>SS loadings 1.00 1.00 1.00 1.00 > > >>Proportion Var 0.25 0.25 0.25 0.25 > > >>Cumulative Var 0.25 0.50 0.75 1.00 > > >> > > >>However, if I rerun the same analysis, the loadings of the first > > >>component have the opposite sign (see below), why is that? I have > > >>read the note > > >>in the princomp help that says > > >> > > >>"The signs of the columns of the loadings and scores are arbitrary, > > >> and so may differ between different programs for PCA, and even > > >> between different builds of R." > > >> > > >>However, I still would expect the same signs for two runs in the same session. > > >> > > >> > > >>>pca.painters <- princomp(painters[ ,1:4]) > > >>>loadings(pca.painters) > > >> > > >>Loadings: > > >>Comp.1 Comp.2 Comp.3 Comp.4 > > >>Composition -0.484 -0.376 0.784 -0.101 > > >>Drawing -0.424 0.187 -0.280 -0.841 > > >>Colour 0.381 -0.845 -0.211 -0.310 > > >>Expression -0.664 -0.330 -0.513 0.432 > > >> > > >> Comp.1 Comp.2 Comp.3 Comp.4 > > >>SS loadings 1.00 1.00 1.00 1.00 > > >>Proportion Var 0.25 0.25 0.25 0.25 > > >>Cumulative Var 0.25 0.50 0.75 1.00 > > >> > > >>>R.version > > >> > > >> _ > > >>platform i386-pc-mingw32 > > >>arch i386 > > >>os mingw32 > > >>system i386, mingw32 > > >>status > > >>major1 > > >>minor9.1 > > >>year 2004 > > >>month06 > > >>day 21 > > >>language R > > >> > > >>BTW, I have tried the same in R 1.9.1 on Debian and I can't reproduce > > >>what I see > > >>on Windows. In fact all the runs give the same as the second run on Windows. > > >> > > >>-Francisco > > >> > > >>__ > > >>[EMAIL PROTECTED] mailing list
RE: [R] Signs of loadings from princomp on Windows
Ditto here, although not from a fresh session. Also 1.9.1 binary from CRAN, on WinXPPro: > library(MASS) > data(painters) > pca.painters <- princomp(painters[ ,1:4]) > loadings(pca.painters) Loadings: Comp.1 Comp.2 Comp.3 Comp.4 Composition 0.484 -0.376 0.784 -0.101 Drawing 0.424 0.187 -0.280 -0.841 Colour -0.381 -0.845 -0.211 -0.310 Expression 0.664 -0.330 -0.513 0.432 Comp.1 Comp.2 Comp.3 Comp.4 SS loadings 1.00 1.00 1.00 1.00 Proportion Var 0.25 0.25 0.25 0.25 Cumulative Var 0.25 0.50 0.75 1.00 > pca.painters <- princomp(painters[ ,1:4]) > loadings(pca.painters) Loadings: Comp.1 Comp.2 Comp.3 Comp.4 Composition -0.484 -0.376 0.784 -0.101 Drawing -0.424 0.187 -0.280 -0.841 Colour 0.381 -0.845 -0.211 -0.310 Expression -0.664 -0.330 -0.513 0.432 Comp.1 Comp.2 Comp.3 Comp.4 SS loadings 1.00 1.00 1.00 1.00 Proportion Var 0.25 0.25 0.25 0.25 Cumulative Var 0.25 0.50 0.75 1.00 Andy > From: Sundar Dorai-Raj > > Hi all, > I was able to replicate Francisco's observation. I'm using R-1.9.1 > installed from binaries on Windows 2000 Pro. > > [Previously saved workspace restored] > > > library(MASS) > > data(painters) > > pca.painters <- princomp(painters[ ,1:4]) > > loadings(pca.painters) > > Loadings: > Comp.1 Comp.2 Comp.3 Comp.4 > Composition 0.484 -0.376 0.784 -0.101 > Drawing 0.424 0.187 -0.280 -0.841 > Colour -0.381 -0.845 -0.211 -0.310 > Expression 0.664 -0.330 -0.513 0.432 > > Comp.1 Comp.2 Comp.3 Comp.4 > SS loadings 1.00 1.00 1.00 1.00 > Proportion Var 0.25 0.25 0.25 0.25 > Cumulative Var 0.25 0.50 0.75 1.00 > > pca.painters <- princomp(painters[ ,1:4]) > > loadings(pca.painters) > > Loadings: > Comp.1 Comp.2 Comp.3 Comp.4 > Composition -0.484 -0.376 0.784 -0.101 > Drawing -0.424 0.187 -0.280 -0.841 > Colour 0.381 -0.845 -0.211 -0.310 > Expression -0.664 -0.330 -0.513 0.432 > > Comp.1 Comp.2 Comp.3 Comp.4 > SS loadings 1.00 1.00 1.00 1.00 > Proportion Var 0.25 0.25 0.25 0.25 > Cumulative Var 0.25 0.50 0.75 1.00 > > R.version > _ > platform i386-pc-mingw32 > arch i386 > os mingw32 > system i386, mingw32 > status > major1 > minor9.1 > year 2004 > month06 > day 21 > language R > > Francisco Chamu wrote: > > > I have run this on both Windows 2000 and XP. All I did was install > > the binaries from CRAN so I think I am using the standard Rblas.dll. > > > > To reproduce what I see you must run the code at the > beginning of the > > R session. After the second run, all subsequent runs give the same > > result as the second set. > > > > Thanks, > > Francisco > > > > > > On Tue, 14 Sep 2004 08:29:25 +0200, Uwe Ligges > > <[EMAIL PROTECTED]> wrote: > > > >>Prof Brian Ripley wrote: > >> > >>>I get the second set each time, on Windows, using the > build from CRAN. > >>>Which BLAS are you using? > >> > >> > >>Works also well for me with a self compiled R-1.9.1 (both > with standard > >>Rblas as well as with the Rblas.dll for Athlon CPU from CRAN). > >>Is this a NT-based version of Windows (NT, 2k, XP)? > >> > >>Uwe > >> > >> > >> > >> > >> > >>>On Tue, 14 Sep 2004, Francisco Chamu wrote: > >>> > >>> > >>> > I start a clean session of R 1.9.1 on Windows and I run > the following code: > > > > >library(MASS) > >data(painters) > >pca.painters <- princomp(painters[ ,1:4]) > >loadings(pca.painters) > > Loadings: > Comp.1 Comp.2 Comp.3 Comp.4 > Composition 0.484 -0.376 0.784 -0.101 > Drawing 0.424 0.187 -0.280 -0.841 > Colour -0.381 -0.845 -0.211 -0.310 > Expression 0.664 -0.330 -0.513 0.432 > > Comp.1 Comp.2 Comp.3 Comp.4 > SS loadings 1.00 1.00 1.00 1.00 > Proportion Var 0.25 0.25 0.25 0.25 > Cumulative Var 0.25 0.50 0.75 1.00 > > However, if I rerun the same analysis, the loadings of the first > component have the opposite sign (see below), why is that? I have > read the note > in the princomp help that says > > "The signs of the columns of the loadings and scores > are arbitrary, > and so may differ between different programs for PCA, and even > between different builds of R." > > However, I still would expect the same signs for two runs > in the same session. > > > > >pca.painters <- princomp(painters[ ,1:4]) > >loadings(pca.painters) > > Loadings: > Comp.1 Comp.2 Comp.3 Comp.4 > Composition -0.484 -0.376 0.784 -0.101 > Drawing -0.424 0.187 -0.280 -0.841 > Colour 0.381 -0.845 -0.211 -0.310 > Expression -0.664 -0.330 -0.513 0.432 > > Comp.1 Comp.2 Comp.3 Comp.4
[R] Separation between tick marks and tick labels in lattice
I can't find a way to control the distance between tick marks and tick labels in lattice. In a stripplot I'm making these components are too close. I don't see anything like base graphics mgp in the scales list. Thanks for your help, Scott Waichler Pacific Northwest National Laboratory Richland, Washington, USA [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] reshaping some data
Sundar:
As I understand it, you can easily create an index variable (a pointer,
actually) that will pick out the y columns in order:
z<-yourdataframe
y<-as.vector(z[,indexvar])
So if you could cbind() the x's, you'd be all set.
Again, assuming I understand correctly, the x column you want is:
x<-z[,-indexvar] ## still a frame/matrix
nvec<-seq(length=ncol(x))
x<-as.vector(x[,rep(nvec,times=nvec)])
HTH -- and even if I got it wrong, it was fun, so thanks.
-- Bert
-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
"The business of the statistician is to catalyze the scientific learning
process." - George E. P. Box
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Sundar
> Dorai-Raj
> Sent: Tuesday, September 14, 2004 9:16 AM
> To: R-help
> Subject: [R] reshaping some data
>
> Hi all,
>I have a data.frame with the following colnames pattern:
>
> x1 y11 x2 y21 y22 y23 x3 y31 y32 ...
>
> I.e. I have an x followed by a few y's. What I would like to
> do is turn
> this wide format into a tall format with two columns: "x", "y". The
> structure is that xi needs to be associated with yij (e.g. x1 should
> next to y11 and y12, x2 should be next to y21, y22, and y23, etc.).
>
> x y
> x1 y11
> x2 y21
> x2 y22
> x2 y23
> x3 y31
> x3 y32
> ...
>
> I have looked at ?reshape but I didn't see how it could work
> with this
> structure. I have a solution using nested for loops (see below), but
> it's slow and not very efficient. I would like to find a vectorised
> solution that would achieve the same thing.
>
> Now, for an example:
>
> x <- data.frame(x1 = 1: 5, y11 = 1: 5,
> x2 = 6:10, y21 = 6:10, y22 = 11:15,
> x3 = 11:15, y31 = 16:20,
> x4 = 16:20, y41 = 21:25, y42 = 26:30, y43 = 31:35)
> # which are the x columns
> nmx <- grep("^x", names(x))
> # which are the y columns
> nmy <- grep("^y", names(x))
> # grab y values
> y <- unlist(x[nmy])
> # reserve some space for the x's
> z <- vector("numeric", length(y))
> # a loop counter
> k <- 0
> n <- nrow(x)
> seq.n <- seq(n)
> # determine how many times to repeat the x's
> repy <- diff(c(nmx, length(names(x)) + 1)) - 1
> for(i in seq(along = nmx)) {
>for(j in seq(repy[i])) {
> # store the x values in the appropriate z indices
> z[seq.n + k * n] <- x[, nmx[i]]
> # move to next block in z
> k <- k + 1
>}
> }
> data.frame(x = z, y = y, row.names = NULL)
>
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> http://www.R-project.org/posting-guide.html
>
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Re: [R] Signs of loadings from princomp on Windows
Hi all, I was able to replicate Francisco's observation. I'm using R-1.9.1 installed from binaries on Windows 2000 Pro. [Previously saved workspace restored] > library(MASS) > data(painters) > pca.painters <- princomp(painters[ ,1:4]) > loadings(pca.painters) Loadings: Comp.1 Comp.2 Comp.3 Comp.4 Composition 0.484 -0.376 0.784 -0.101 Drawing 0.424 0.187 -0.280 -0.841 Colour -0.381 -0.845 -0.211 -0.310 Expression 0.664 -0.330 -0.513 0.432 Comp.1 Comp.2 Comp.3 Comp.4 SS loadings 1.00 1.00 1.00 1.00 Proportion Var 0.25 0.25 0.25 0.25 Cumulative Var 0.25 0.50 0.75 1.00 > pca.painters <- princomp(painters[ ,1:4]) > loadings(pca.painters) Loadings: Comp.1 Comp.2 Comp.3 Comp.4 Composition -0.484 -0.376 0.784 -0.101 Drawing -0.424 0.187 -0.280 -0.841 Colour 0.381 -0.845 -0.211 -0.310 Expression -0.664 -0.330 -0.513 0.432 Comp.1 Comp.2 Comp.3 Comp.4 SS loadings 1.00 1.00 1.00 1.00 Proportion Var 0.25 0.25 0.25 0.25 Cumulative Var 0.25 0.50 0.75 1.00 > R.version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major1 minor9.1 year 2004 month06 day 21 language R Francisco Chamu wrote: I have run this on both Windows 2000 and XP. All I did was install the binaries from CRAN so I think I am using the standard Rblas.dll. To reproduce what I see you must run the code at the beginning of the R session. After the second run, all subsequent runs give the same result as the second set. Thanks, Francisco On Tue, 14 Sep 2004 08:29:25 +0200, Uwe Ligges <[EMAIL PROTECTED]> wrote: Prof Brian Ripley wrote: I get the second set each time, on Windows, using the build from CRAN. Which BLAS are you using? Works also well for me with a self compiled R-1.9.1 (both with standard Rblas as well as with the Rblas.dll for Athlon CPU from CRAN). Is this a NT-based version of Windows (NT, 2k, XP)? Uwe On Tue, 14 Sep 2004, Francisco Chamu wrote: I start a clean session of R 1.9.1 on Windows and I run the following code: library(MASS) data(painters) pca.painters <- princomp(painters[ ,1:4]) loadings(pca.painters) Loadings: Comp.1 Comp.2 Comp.3 Comp.4 Composition 0.484 -0.376 0.784 -0.101 Drawing 0.424 0.187 -0.280 -0.841 Colour -0.381 -0.845 -0.211 -0.310 Expression 0.664 -0.330 -0.513 0.432 Comp.1 Comp.2 Comp.3 Comp.4 SS loadings 1.00 1.00 1.00 1.00 Proportion Var 0.25 0.25 0.25 0.25 Cumulative Var 0.25 0.50 0.75 1.00 However, if I rerun the same analysis, the loadings of the first component have the opposite sign (see below), why is that? I have read the note in the princomp help that says "The signs of the columns of the loadings and scores are arbitrary, and so may differ between different programs for PCA, and even between different builds of R." However, I still would expect the same signs for two runs in the same session. pca.painters <- princomp(painters[ ,1:4]) loadings(pca.painters) Loadings: Comp.1 Comp.2 Comp.3 Comp.4 Composition -0.484 -0.376 0.784 -0.101 Drawing -0.424 0.187 -0.280 -0.841 Colour 0.381 -0.845 -0.211 -0.310 Expression -0.664 -0.330 -0.513 0.432 Comp.1 Comp.2 Comp.3 Comp.4 SS loadings 1.00 1.00 1.00 1.00 Proportion Var 0.25 0.25 0.25 0.25 Cumulative Var 0.25 0.50 0.75 1.00 R.version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major1 minor9.1 year 2004 month06 day 21 language R BTW, I have tried the same in R 1.9.1 on Debian and I can't reproduce what I see on Windows. In fact all the runs give the same as the second run on Windows. -Francisco __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] repeated measures and covariance structures
Hello Chris, as far as I know from the Pinheiro and Bates book "Mixed-Effects Models in S and S-PLUS", the autoregressive parameter has to be specified only as initial value for the estimation. That is, the parameter will be estimated, but the result may depend on the prespecified value. You do not need to specify it. Then, 0 is used as initial value and this may work well (as in the example in Pinheiro and Bates, p. 241 f.). Christian PS: Have you been at a workshop on model selection near Munich in Nov. 2002? I suspect that I know who you are but I am not sure. On Tue, 14 Sep 2004, Chris Solomon wrote: > Hello- > > I'm trying to do some repeated measures ANOVAs. In the past, using SAS, > I have used the framework outlined in Littell et al.'s "SAS System for > Mixed Models", using the REPEATED statement in PROC MIXED to model > variation across time within an experimental unit. SAS allows you to > specify different within-unit covariance structures (e.g., compound > symmetric, AR(1), etc.) to determine the best model. > > I'm having trouble figuring out how to do a similar analysis in R. While > 'lme' will let you choose the class of correlation structure to use, it > seems to require that you specify this structure rather than using the > data to estimate the covariance matrix. For example, it seems that to > specify 'corAR1' as the correlation structure, you have to pick a value > for rho, the autoregressive parameter. > > So, my question: is there a way to tell 'lme' what sort of covariance > structure you'd like to model, and then let the function estimate the > covariances? Or, alternatively, is there a better way to go about this > sort of repeated measures analysis in R? I've exhausted my available R > resources and done a pretty good search of the help archives without > finding a clear answer. > > Thanks much! > Chris > > > > *** > Chris Solomon > Center for Limnology > Univ. of Wisconsin > Phone: (608) 263-2465 > > __ > [EMAIL PROTECTED] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > *** Christian Hennig Fachbereich Mathematik-SPST/ZMS, Universitaet Hamburg [EMAIL PROTECTED], http://www.math.uni-hamburg.de/home/hennig/ ### ich empfehle www.boag-online.de __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] repeated measures and covariance structures
On Tue, 14 Sep 2004, Chris Solomon wrote: > Hello- > > I'm trying to do some repeated measures ANOVAs. In the past, using SAS, > I have used the framework outlined in Littell et al.'s "SAS System for > Mixed Models", using the REPEATED statement in PROC MIXED to model > variation across time within an experimental unit. SAS allows you to > specify different within-unit covariance structures (e.g., compound > symmetric, AR(1), etc.) to determine the best model. > > I'm having trouble figuring out how to do a similar analysis in R. While > 'lme' will let you choose the class of correlation structure to use, it > seems to require that you specify this structure rather than using the > data to estimate the covariance matrix. For example, it seems that to > specify 'corAR1' as the correlation structure, you have to pick a value > for rho, the autoregressive parameter. Why does `it seems'? Your information is incorrect. > So, my question: is there a way to tell 'lme' what sort of covariance > structure you'd like to model, and then let the function estimate the > covariances? That is the default. Take a look at the examples in Venables & Ripley or Pinheiro & Bates (as recommended in the posting guide and the FAQ). > Or, alternatively, is there a better way to go about this > sort of repeated measures analysis in R? I've exhausted my available R > resources and done a pretty good search of the help archives without > finding a clear answer. Did you look at the references in the FAQ? > Chris Solomon > Center for Limnology > Univ. of Wisconsin You do know where the maintainer of the nlme package works, don't you? I am sure your University library has a copy or two of Pinheiro & Bates! -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Signs of loadings from princomp on Windows
On Tue, 14 Sep 2004, Francisco Chamu wrote: > I have run this on both Windows 2000 and XP. All I did was install > the binaries from CRAN so I think I am using the standard Rblas.dll. > > To reproduce what I see you must run the code at the beginning of the > R session. We did, as you said `start a clean session'. I think to reproduce what you see we have to be using your account on your computer. > After the second run, all subsequent runs give the same > result as the second set. > > Thanks, > Francisco > > > On Tue, 14 Sep 2004 08:29:25 +0200, Uwe Ligges > <[EMAIL PROTECTED]> wrote: > > Prof Brian Ripley wrote: > > > I get the second set each time, on Windows, using the build from CRAN. > > > Which BLAS are you using? > > > > > > Works also well for me with a self compiled R-1.9.1 (both with standard > > Rblas as well as with the Rblas.dll for Athlon CPU from CRAN). > > Is this a NT-based version of Windows (NT, 2k, XP)? > > > > Uwe > > > > > > > > > > > On Tue, 14 Sep 2004, Francisco Chamu wrote: > > > > > > > > >>I start a clean session of R 1.9.1 on Windows and I run the following code: > > >> > > >> > > >>>library(MASS) > > >>>data(painters) > > >>>pca.painters <- princomp(painters[ ,1:4]) > > >>>loadings(pca.painters) > > >> > > >>Loadings: > > >>Comp.1 Comp.2 Comp.3 Comp.4 > > >>Composition 0.484 -0.376 0.784 -0.101 > > >>Drawing 0.424 0.187 -0.280 -0.841 > > >>Colour -0.381 -0.845 -0.211 -0.310 > > >>Expression 0.664 -0.330 -0.513 0.432 > > >> > > >> Comp.1 Comp.2 Comp.3 Comp.4 > > >>SS loadings 1.00 1.00 1.00 1.00 > > >>Proportion Var 0.25 0.25 0.25 0.25 > > >>Cumulative Var 0.25 0.50 0.75 1.00 > > >> > > >>However, if I rerun the same analysis, the loadings of the first > > >>component have the opposite sign (see below), why is that? I have > > >>read the note > > >>in the princomp help that says > > >> > > >>"The signs of the columns of the loadings and scores are arbitrary, > > >> and so may differ between different programs for PCA, and even > > >> between different builds of R." > > >> > > >>However, I still would expect the same signs for two runs in the same session. > > >> > > >> > > >>>pca.painters <- princomp(painters[ ,1:4]) > > >>>loadings(pca.painters) > > >> > > >>Loadings: > > >>Comp.1 Comp.2 Comp.3 Comp.4 > > >>Composition -0.484 -0.376 0.784 -0.101 > > >>Drawing -0.424 0.187 -0.280 -0.841 > > >>Colour 0.381 -0.845 -0.211 -0.310 > > >>Expression -0.664 -0.330 -0.513 0.432 > > >> > > >> Comp.1 Comp.2 Comp.3 Comp.4 > > >>SS loadings 1.00 1.00 1.00 1.00 > > >>Proportion Var 0.25 0.25 0.25 0.25 > > >>Cumulative Var 0.25 0.50 0.75 1.00 > > >> > > >>>R.version > > >> > > >> _ > > >>platform i386-pc-mingw32 > > >>arch i386 > > >>os mingw32 > > >>system i386, mingw32 > > >>status > > >>major1 > > >>minor9.1 > > >>year 2004 > > >>month06 > > >>day 21 > > >>language R > > >> > > >>BTW, I have tried the same in R 1.9.1 on Debian and I can't reproduce > > >>what I see > > >>on Windows. In fact all the runs give the same as the second run on Windows. > > >> > > >>-Francisco > > >> > > >>__ > > >>[EMAIL PROTECTED] mailing list > > >>https://stat.ethz.ch/mailman/listinfo/r-help > > >>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > > >> > > >> > > > > > > > > > > > > -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] repeated measures and covariance structures
Yes. Try something akin to > fm1<- lme(y~time, data, random=~time|ID) > fm2<-update(fm1, correlation=corAR1(form~time|ID) You can then use anova(fm1,fm2) to compare. Harold -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Chris Solomon Sent: Tuesday, September 14, 2004 12:07 PM To: [EMAIL PROTECTED] Subject: [R] repeated measures and covariance structures Hello- I'm trying to do some repeated measures ANOVAs. In the past, using SAS, I have used the framework outlined in Littell et al.'s "SAS System for Mixed Models", using the REPEATED statement in PROC MIXED to model variation across time within an experimental unit. SAS allows you to specify different within-unit covariance structures (e.g., compound symmetric, AR(1), etc.) to determine the best model. I'm having trouble figuring out how to do a similar analysis in R. While 'lme' will let you choose the class of correlation structure to use, it seems to require that you specify this structure rather than using the data to estimate the covariance matrix. For example, it seems that to specify 'corAR1' as the correlation structure, you have to pick a value for rho, the autoregressive parameter. So, my question: is there a way to tell 'lme' what sort of covariance structure you'd like to model, and then let the function estimate the covariances? Or, alternatively, is there a better way to go about this sort of repeated measures analysis in R? I've exhausted my available R resources and done a pretty good search of the help archives without finding a clear answer. Thanks much! Chris *** Chris Solomon Center for Limnology Univ. of Wisconsin Phone: (608) 263-2465 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Signs of loadings from princomp on Windows
I have run this on both Windows 2000 and XP. All I did was install the binaries from CRAN so I think I am using the standard Rblas.dll. To reproduce what I see you must run the code at the beginning of the R session. After the second run, all subsequent runs give the same result as the second set. Thanks, Francisco On Tue, 14 Sep 2004 08:29:25 +0200, Uwe Ligges <[EMAIL PROTECTED]> wrote: > Prof Brian Ripley wrote: > > I get the second set each time, on Windows, using the build from CRAN. > > Which BLAS are you using? > > > Works also well for me with a self compiled R-1.9.1 (both with standard > Rblas as well as with the Rblas.dll for Athlon CPU from CRAN). > Is this a NT-based version of Windows (NT, 2k, XP)? > > Uwe > > > > > > On Tue, 14 Sep 2004, Francisco Chamu wrote: > > > > > >>I start a clean session of R 1.9.1 on Windows and I run the following code: > >> > >> > >>>library(MASS) > >>>data(painters) > >>>pca.painters <- princomp(painters[ ,1:4]) > >>>loadings(pca.painters) > >> > >>Loadings: > >>Comp.1 Comp.2 Comp.3 Comp.4 > >>Composition 0.484 -0.376 0.784 -0.101 > >>Drawing 0.424 0.187 -0.280 -0.841 > >>Colour -0.381 -0.845 -0.211 -0.310 > >>Expression 0.664 -0.330 -0.513 0.432 > >> > >> Comp.1 Comp.2 Comp.3 Comp.4 > >>SS loadings 1.00 1.00 1.00 1.00 > >>Proportion Var 0.25 0.25 0.25 0.25 > >>Cumulative Var 0.25 0.50 0.75 1.00 > >> > >>However, if I rerun the same analysis, the loadings of the first > >>component have the opposite sign (see below), why is that? I have > >>read the note > >>in the princomp help that says > >> > >>"The signs of the columns of the loadings and scores are arbitrary, > >> and so may differ between different programs for PCA, and even > >> between different builds of R." > >> > >>However, I still would expect the same signs for two runs in the same session. > >> > >> > >>>pca.painters <- princomp(painters[ ,1:4]) > >>>loadings(pca.painters) > >> > >>Loadings: > >>Comp.1 Comp.2 Comp.3 Comp.4 > >>Composition -0.484 -0.376 0.784 -0.101 > >>Drawing -0.424 0.187 -0.280 -0.841 > >>Colour 0.381 -0.845 -0.211 -0.310 > >>Expression -0.664 -0.330 -0.513 0.432 > >> > >> Comp.1 Comp.2 Comp.3 Comp.4 > >>SS loadings 1.00 1.00 1.00 1.00 > >>Proportion Var 0.25 0.25 0.25 0.25 > >>Cumulative Var 0.25 0.50 0.75 1.00 > >> > >>>R.version > >> > >> _ > >>platform i386-pc-mingw32 > >>arch i386 > >>os mingw32 > >>system i386, mingw32 > >>status > >>major1 > >>minor9.1 > >>year 2004 > >>month06 > >>day 21 > >>language R > >> > >>BTW, I have tried the same in R 1.9.1 on Debian and I can't reproduce > >>what I see > >>on Windows. In fact all the runs give the same as the second run on Windows. > >> > >>-Francisco > >> > >>__ > >>[EMAIL PROTECTED] mailing list > >>https://stat.ethz.ch/mailman/listinfo/r-help > >>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > >> > >> > > > > > > __ [EMAIL PROTECTED] 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] reshaping some data
Hi all,
I have a data.frame with the following colnames pattern:
x1 y11 x2 y21 y22 y23 x3 y31 y32 ...
I.e. I have an x followed by a few y's. What I would like to do is turn
this wide format into a tall format with two columns: "x", "y". The
structure is that xi needs to be associated with yij (e.g. x1 should
next to y11 and y12, x2 should be next to y21, y22, and y23, etc.).
x y
x1 y11
x2 y21
x2 y22
x2 y23
x3 y31
x3 y32
...
I have looked at ?reshape but I didn't see how it could work with this
structure. I have a solution using nested for loops (see below), but
it's slow and not very efficient. I would like to find a vectorised
solution that would achieve the same thing.
Now, for an example:
x <- data.frame(x1 = 1: 5, y11 = 1: 5,
x2 = 6:10, y21 = 6:10, y22 = 11:15,
x3 = 11:15, y31 = 16:20,
x4 = 16:20, y41 = 21:25, y42 = 26:30, y43 = 31:35)
# which are the x columns
nmx <- grep("^x", names(x))
# which are the y columns
nmy <- grep("^y", names(x))
# grab y values
y <- unlist(x[nmy])
# reserve some space for the x's
z <- vector("numeric", length(y))
# a loop counter
k <- 0
n <- nrow(x)
seq.n <- seq(n)
# determine how many times to repeat the x's
repy <- diff(c(nmx, length(names(x)) + 1)) - 1
for(i in seq(along = nmx)) {
for(j in seq(repy[i])) {
# store the x values in the appropriate z indices
z[seq.n + k * n] <- x[, nmx[i]]
# move to next block in z
k <- k + 1
}
}
data.frame(x = z, y = y, row.names = NULL)
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[R] repeated measures and covariance structures
Hello- I'm trying to do some repeated measures ANOVAs. In the past, using SAS, I have used the framework outlined in Littell et al.'s "SAS System for Mixed Models", using the REPEATED statement in PROC MIXED to model variation across time within an experimental unit. SAS allows you to specify different within-unit covariance structures (e.g., compound symmetric, AR(1), etc.) to determine the best model. I'm having trouble figuring out how to do a similar analysis in R. While 'lme' will let you choose the class of correlation structure to use, it seems to require that you specify this structure rather than using the data to estimate the covariance matrix. For example, it seems that to specify 'corAR1' as the correlation structure, you have to pick a value for rho, the autoregressive parameter. So, my question: is there a way to tell 'lme' what sort of covariance structure you'd like to model, and then let the function estimate the covariances? Or, alternatively, is there a better way to go about this sort of repeated measures analysis in R? I've exhausted my available R resources and done a pretty good search of the help archives without finding a clear answer. Thanks much! Chris *** Chris Solomon Center for Limnology Univ. of Wisconsin Phone: (608) 263-2465 __ [EMAIL PROTECTED] 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] date library and boxplots
Hello, I have been trying to use the date library (mdy.date) to create notched boxplots, but have not been successful. Can anybody help with the code for this command? Thank you, Stephanie __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Re: datalist
> "John" == John Zhang <[EMAIL PROTECTED]> > on Tue, 14 Sep 2004 10:11:15 -0400 (EDT) writes: John> Hi, John> The following is a cut/paste from http://developer.r-project.org/200update.txt: John> ... John> 3) When a package is installed, all the data sets are loaded to see John> what they produce. If this is undesirable (because they are John> enormous, or depend on other packages that need to be installed John> later, ...), add a `datalist' file to the data subdirectory as John> described in `Writing R Extensions'. John> ... John> I only saw a mentioning of 00Index in the description John> about the data subdirectory in Writing R John> Extensions/Package Subdirectories. Could someone point John> me to the right place or tell me what a 'datalist' John> file is supposed to be? You need "Writing R Extensions" from 'R-devel' aka "2.0.0 unstable". The manuals of the UN-released versions of R, are typically available from www.R-project.org, [Documentation] -> "Help pages" which points to http://stat.ethz.ch/R-manual/ But for the sake of it, here is the entry for 'datalist' (found very quickly in Emacs Info): If your data files are enormous you can speed up installation by providing a file `datalist' in the `data' subdirectory. This should have one line per topic that `data()' will find, in the format `foo' if `data(foo)' provides `foo', or `foo: bar bah' if `data(foo)' provides `bar' and `bah'. Regards, Martin __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Howto enlarge fonts size in R- Graphics?
Hello, Thomas Schönhoff wrote: Well, thanks, I'll have a look at your advices. regards Thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to show the symbol of Angstrom ?
Paul, Thank you very much! They all works!
Sean
On Tue, 14 Sep 2004, Paul Murrell wrote:
> Hi
>
>
> xiang li wrote:
> > Also, I am wondering if there is any source where the expressions of
> > many symbols are collected.
> > Thanks you very much!!!
>
>
> (Assuming you mean draw the angstrom symbol on a plot ...)
>
> There are several ways:
>
> (i) Specify the character code in octal. Assuming ISO Latin 1 encoding,
> something like ...
>plot(1, type="n")
>text(1, 1, "\305")
> ... or ...
>grid.newpage()
>grid.text("\305")
> ... should work. That should be ok on default setups for Windows and
> Unix. On the Mac it might have to be "\201" (untested) See, e.g.,
> http://czyborra.com/charsets/iso8859.html#ISO-8859-1 (Unix)
> http://www.microsoft.com/typography/unicode/1252.gif (Windows)
> http://kodeks.uni-bamberg.de/Computer/CodePages/MacStd.htm (Mac)
> for other standard "symbols".
>
> (ii) Use a mathematical expression. This won't look as good because the
> ring and the A are not a single coherent glyph, but it should work
> "everywhere" ...
>plot(1, type="n")
>text(1, 1, expression(ring(A)))
> ... or ...
>grid.newpage()
>grid.text(expression(ring(A)))
> ... demo(plotmath) shows the range of things you can do with this approach.
>
> (iii) Use a hershey font (again, should work on all platforms and
> encodings) ...
>plot(1, type="n")
>text(1, 1, "\\oA", vfont=c("sans serif", "plain"))
> ... or ...
>grid.newpage()
>grid.text("\\oA", gp=gpar(fontfamily="HersheySans"))
> ... demo(Hershey) shows the symbols available with this approach.
>
> Hope that helps.
>
> Paul
>
--
Li, Xiang (Sean) | [EMAIL PROTECTED]
Dept of Bioengineering, SEO, MC 063 | ph: (312) 355-2520
University of Illinois at Chicago | fax: (312) 996-5921
Chicago, IL 60607-7052, USA |
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Re: [R] erase columns
michele lux yahoo.it> writes: > Can somebody remember me which is the command to erase > columns from a data frame? To delete a single column assign NULL to it. That works because a data frame is a list and that works for lists. Here are three examples of deleting column 5, the Species column, from the iris data set: data(iris) iris[,5] <- NULL data(iris) iris$Species <- NULL data(iris) iris[,"Species"] <- NULL __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Getting the argument list within a function
"Roger D. Peng" <[EMAIL PROTECTED]> writes:
> Is there a way of getting the argument list of a function from within
> that function? For example, something like
>
> f <- function(x, y = 3) {
> fargs <- getFunctionArgList()
> print(fargs) ## Should be `alist(x, y = 3)'
> }
> f
function(x, y = 3) {
fargs <- formals(sys.function())
print(fargs) ## Should be equivalent to `alist(x=, y = 3)'
}
(Notice a couple of fine points...)
--
O__ Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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RE: [R] Getting the argument list within a function
Is formals() what you're looking for?
Andy
> From: Roger D. Peng
>
> Is there a way of getting the argument list of a function from within
> that function? For example, something like
>
> f <- function(x, y = 3) {
> fargs <- getFunctionArgList()
> print(fargs) ## Should be `alist(x, y = 3)'
> }
>
> Thanks,
>
> -roger
>
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> http://www.R-project.org/posting-guide.html
>
>
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Re: [R] Getting the argument list within a function
Ergh, yes, that's exactly it. I didn't realize you could use it in that way. Thanks, -roger Jeff Gentry wrote: Is there a way of getting the argument list of a function from within that function? For example, something like Would formals() work for you here? __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Getting the argument list within a function
> Is there a way of getting the argument list of a function from within > that function? For example, something like Would formals() work for you here? __ [EMAIL PROTECTED] 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] Getting the argument list within a function
Is there a way of getting the argument list of a function from within
that function? For example, something like
f <- function(x, y = 3) {
fargs <- getFunctionArgList()
print(fargs) ## Should be `alist(x, y = 3)'
}
Thanks,
-roger
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[R] Re: datalist
Hi, The following is a cut/paste from http://developer.r-project.org/200update.txt: ... 3) When a package is installed, all the data sets are loaded to see what they produce. If this is undesirable (because they are enormous, or depend on other packages that need to be installed later, ...), add a `datalist' file to the data subdirectory as described in `Writing R Extensions'. ... I only saw a mentioning of 00Index in the description about the data subdirectory in Writing R Extensions/Package Subdirectories. Could someone point me to the right place or tell me what a 'datalist' file is supposed to be? Thanks. JZ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] calculating memory usage
If you only have simple objects in your function, you might be able to
use a function like
totalMem <- function() {
sum(sapply(ls(all = TRUE), function(x) object.size(get(x / 2^20
}
which should give you a rough idea of the memory usage (in MB) in the
current environment.
-roger
Adaikalavan Ramasamy wrote:
I am comparing two different algorithms in terms of speed and memory
usage. I can calculate the processing time with proc.time() as follows
but am not sure how to calculate the memory usage.
ptm <- proc.time()
x <- rnorm(100)
proc.time() - ptm
I would like to be within R itself since I will test the algorithm
several hundred times and in batch mode. So manually looking up 'top'
may not be feasible. help.seach("memory") suggests memory.profile and gc
but I am not sure how to use these.
Sorry if this is a basic question. Thank you.
Regards, Adai
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Re: [R] calculating memory usage
On Tue, 14 Sep 2004, Adaikalavan Ramasamy wrote:
> Many thanks to Prof. Ripley. The problem is that memory.profile does not
> exist in *nix environment and there is probably a very good reason why.
memory.size?
>
> I was reading help(Memory) and in the Details section :
> You can find out the current memory consumption (the heap and cons
> cells used as numbers and megabytes) by typing 'gc()' at the R
> prompt.
>
> AFAICS, Ncells is the fixed memory used by the underlying R and Vcells
> is the variable part and depends on the calculations.
>
> Would I be able to say that the generating 10 million random numbers
> requires approximately 73.4 Mb (= 26.3 + 80.5 - 26.3 - 7.1) of memory ?
> I double checked this against memory.size() in Windows and they seem to
> agree. Thank you.
No, only that storing 10 million numbers requires 77.3 - 1.0Mb, and
> object.size(x)/1024^2
[1] 76.29397
> > gc()
> used (Mb) gc trigger (Mb)
> Ncells 456262 12.2 984024 26.3
> Vcells 122697 1.0 929195 7.1
> >
> > x <- rnorm(1000)
> > gc()
>used (Mb) gc trigger (Mb)
> Ncells 456274 12.2 984024 26.3
> Vcells 10123014 77.3 10538396 80.5
>
>
>
>
> On Mon, 2004-09-13 at 18:47, Prof Brian Ripley wrote:
> > On Mon, 13 Sep 2004, Adaikalavan Ramasamy wrote:
> >
> > > I am comparing two different algorithms in terms of speed and memory
> > > usage. I can calculate the processing time with proc.time() as follows
> > > but am not sure how to calculate the memory usage.
> > >
> > >ptm <- proc.time()
> > >x <- rnorm(100)
> > >proc.time() - ptm
> >
> > Hmm ... see ?system.time!
> >
> > > I would like to be within R itself since I will test the algorithm
> > > several hundred times and in batch mode. So manually looking up 'top'
> > > may not be feasible. help.seach("memory") suggests memory.profile and gc
> > > but I am not sure how to use these.
> >
> > I don't think you can. You can find out how much memory R is using NOW,
> > but not the peak memory usage during a calculation. Nor is that
> > particularly relevant, as it depends on what was gone on before, the word
> > length of the platform and the garbage collection settings.
> >
> > On Windows, starting in a clean session, calling gc() and memory.size(),
> > then calling your code and memory.size(max=TRUE) will give you a fair
> > idea, but `top' indicates some Unix-alike.
>
>
--
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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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Re: [R] calculating memory usage
Many thanks to Prof. Ripley. The problem is that memory.profile does not
exist in *nix environment and there is probably a very good reason why.
I was reading help(Memory) and in the Details section :
You can find out the current memory consumption (the heap and cons
cells used as numbers and megabytes) by typing 'gc()' at the R
prompt.
AFAICS, Ncells is the fixed memory used by the underlying R and Vcells
is the variable part and depends on the calculations.
Would I be able to say that the generating 10 million random numbers
requires approximately 73.4 Mb (= 26.3 + 80.5 - 26.3 - 7.1) of memory ?
I double checked this against memory.size() in Windows and they seem to
agree. Thank you.
> gc()
used (Mb) gc trigger (Mb)
Ncells 456262 12.2 984024 26.3
Vcells 122697 1.0 929195 7.1
>
> x <- rnorm(1000)
> gc()
used (Mb) gc trigger (Mb)
Ncells 456274 12.2 984024 26.3
Vcells 10123014 77.3 10538396 80.5
On Mon, 2004-09-13 at 18:47, Prof Brian Ripley wrote:
> On Mon, 13 Sep 2004, Adaikalavan Ramasamy wrote:
>
> > I am comparing two different algorithms in terms of speed and memory
> > usage. I can calculate the processing time with proc.time() as follows
> > but am not sure how to calculate the memory usage.
> >
> >ptm <- proc.time()
> >x <- rnorm(100)
> >proc.time() - ptm
>
> Hmm ... see ?system.time!
>
> > I would like to be within R itself since I will test the algorithm
> > several hundred times and in batch mode. So manually looking up 'top'
> > may not be feasible. help.seach("memory") suggests memory.profile and gc
> > but I am not sure how to use these.
>
> I don't think you can. You can find out how much memory R is using NOW,
> but not the peak memory usage during a calculation. Nor is that
> particularly relevant, as it depends on what was gone on before, the word
> length of the platform and the garbage collection settings.
>
> On Windows, starting in a clean session, calling gc() and memory.size(),
> then calling your code and memory.size(max=TRUE) will give you a fair
> idea, but `top' indicates some Unix-alike.
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Re: [R] Spare some CPU cycles for testing lme?
Prof Brian D Ripley wrote: As others have said, this needs tools not CPU cycles: gctorture or valgrind. Valgrind found (after a few seconds and on the first pass) ==23057== Invalid read of size 4 ==23057==at 0x3CF4E645: ssc_symbolic_permute (Mutils.c:373) ==23057==by 0x3CF5BF75: ssclme_create (ssclme.c:168) ==23057==by 0x80AF5E8: do_dotcall (/users/ripley/R/svn/R-devel/src/main/dotcode.c:640) ==23057==by 0x80CFA84: Rf_eval (/users/ripley/R/svn/R-devel/src/main/eval.c:399) ==23057== Address 0x3C7F3BD0 is 4 bytes before a block of size 524 alloc'd ==23057==at 0x3C01CB56: calloc (in /opt/local/lib/valgrind/vgpreload_memcheck.so) ==23057==by 0x80F9EBE: R_chk_calloc (/users/ripley/R/svn/R-devel/src/main/memory.c:2151) ==23057==by 0x3CF4E515: ssc_symbolic_permute (Mutils.c:352) ==23057==by 0x3CF5BF75: ssclme_create (ssclme.c:168) ==23057== ==23057== Use of uninitialised value of size 8 ==23057==at 0x80C0137: Rf_duplicate (/users/ripley/R/svn/R-devel/src/main/duplicate.c:160) ==23057==by 0x80BFA85: Rf_duplicate (/users/ripley/R/svn/R-devel/src/main/duplicate.c:101) ==23057==by 0x80BFEB3: Rf_duplicate (/users/ripley/R/svn/R-devel/src/main/duplicate.c:154) ==23057==by 0x816ED96: do_subset2_dflt (/users/ripley/R/svn/R-devel/src/main/subset.c:816) ==23057== ==23057== Conditional jump or move depends on uninitialised value(s) ==23057==at 0x3CF62229: ssclme_fitted (ssclme.c:1587) ==23057==by 0x80AF646: do_dotcall (/users/ripley/R/svn/R-devel/src/main/dotcode.c:646) ==23057==by 0x80CFA84: Rf_eval (/users/ripley/R/svn/R-devel/src/main/eval.c:399) ==23057==by 0x80D1D80: do_set (/users/ripley/R/svn/R-devel/src/main/eval.c:1280) which is pretty definitive evidence of a problem (possibly 2) in the code. I strongly recommend valgrind (http://valgrind.kde.org/) if you are using x86 Linux. It has found quite a few errors in R and in certain packages recently. The only thing to watch is that optimized BLASes will probably crash it. You're right. I had (at least) two thinko's in that code. The problems show up in the lme4 package but the errors in the C code are in the Matrix package. I will upload a repaired version of the Matrix package. __ [EMAIL PROTECTED] 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] overwriting a line in existing .csv file with new data
Dear R-users,
I have a data matrix with 20 rows and 10 columns which is stored in the hard drive as
.csv file called c:\DataFile.csv and a 10 elements vector called xVec.
I would like to be able to copy and paste the information contained in xVec into (say)
the 2nd row of DataFile.csv
Obviously, one way of doing this would be to read the matrix using read.csv() command,
implement the copy and paste manipulation and save the new matrix again using
write.table(). However, has anyone used an alternative method which does not require
use of the read.csv() command?
Regards
Marco Bianchi
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Re: [R] Howto enlarge fonts size in R- Graphics?
Prof Brian Ripley <[EMAIL PROTECTED]> writes: > The X11 device has an argument `pointsize' (which may well mean pixel size > in a particular implementation of X11, as my laptop for example has width, > height and pointsize all much smaller than specified): just increase it. > > The advice to look at ?par is incorrect if you want to scale everything, > as I think you do. > > If you want auto-launched windows to have a larger font, you need to write > a wrapper to X11 and set options(device=wrapper_name). Also, check out the dpi settings for your display (xdpyinfo). If this is set lower than the physical reality, then pointsizes are overestimated (so fonts are smaller than they should be). How to change it is left as an exercise BTW, it's 1.9.1, 1.91 is not in the plans (and wouldn't be for the next forty years or so). > On Tue, 14 Sep 2004, [ISO-8859-15] Thomas Schönhoff wrote: > > > I am fairly new to GNU R ! > > At the moment I am doing an intensive learning on the basics of GNU > > R-1.91, especially graphics like plots and alike, by reading the > > introductory docs! > > Well, except some occasional glitches (X11 output errors) everything > > seems to be fine, thanks to developers for this fine program! > > But there is a slight problem with the size of fonts in graphics, i.e. > > its very hard form me to read labels of variables in plots or other > > graphical representations! (yes, I am little short sighted) > > How may I mainpulate/enlarge the fonts size in graphics from within GNU R ? > > -- > 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 > > __ > [EMAIL PROTECTED] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R post-hoc and GUI
Il mar, 2004-09-14 alle 12:26, Prof Brian Ripley ha scritto: > BTW, I guess you are working on Windows, but have not told us what OS, > even. Please read the posting guide. sorry, i use DebianGNU/Linux and my collegues windows thanks paolo -- Paolo Ariano Neuroscience PhD Student @ UniTo Una non esclude l'altra ed entrambe non escludono i soldi - Paolo A. _ For your security, this mail has been scanned and protected by Inflex __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Spare some CPU cycles for testing lme?
As others have said, this needs tools not CPU cycles: gctorture or valgrind.
Valgrind found (after a few seconds and on the first pass)
==23057== Invalid read of size 4
==23057==at 0x3CF4E645: ssc_symbolic_permute (Mutils.c:373)
==23057==by 0x3CF5BF75: ssclme_create (ssclme.c:168)
==23057==by 0x80AF5E8: do_dotcall
(/users/ripley/R/svn/R-devel/src/main/dotcode.c:640)
==23057==by 0x80CFA84: Rf_eval
(/users/ripley/R/svn/R-devel/src/main/eval.c:399)
==23057== Address 0x3C7F3BD0 is 4 bytes before a block of size 524 alloc'd
==23057==at 0x3C01CB56: calloc (in
/opt/local/lib/valgrind/vgpreload_memcheck.so)
==23057==by 0x80F9EBE: R_chk_calloc
(/users/ripley/R/svn/R-devel/src/main/memory.c:2151)
==23057==by 0x3CF4E515: ssc_symbolic_permute (Mutils.c:352)
==23057==by 0x3CF5BF75: ssclme_create (ssclme.c:168)
==23057==
==23057== Use of uninitialised value of size 8
==23057==at 0x80C0137: Rf_duplicate
(/users/ripley/R/svn/R-devel/src/main/duplicate.c:160)
==23057==by 0x80BFA85: Rf_duplicate
(/users/ripley/R/svn/R-devel/src/main/duplicate.c:101)
==23057==by 0x80BFEB3: Rf_duplicate
(/users/ripley/R/svn/R-devel/src/main/duplicate.c:154)
==23057==by 0x816ED96: do_subset2_dflt
(/users/ripley/R/svn/R-devel/src/main/subset.c:816)
==23057==
==23057== Conditional jump or move depends on uninitialised value(s)
==23057==at 0x3CF62229: ssclme_fitted (ssclme.c:1587)
==23057==by 0x80AF646: do_dotcall
(/users/ripley/R/svn/R-devel/src/main/dotcode.c:646)
==23057==by 0x80CFA84: Rf_eval
(/users/ripley/R/svn/R-devel/src/main/eval.c:399)
==23057==by 0x80D1D80: do_set
(/users/ripley/R/svn/R-devel/src/main/eval.c:1280)
which is pretty definitive evidence of a problem (possibly 2) in the code.
I strongly recommend valgrind (http://valgrind.kde.org/) if you are using
x86 Linux. It has found quite a few errors in R and in certain packages
recently. The only thing to watch is that optimized BLASes will probably
crash it.
On Mon, 13 Sep 2004, Frank Samuelson wrote:
> If anyone has a few extra CPU cycles to spare,
> I'd appreciate it if you could verify a problem that I
> have encountered. Run the code
> below and tell me if it crashes your R before
> completion.
>
> library(lme4)
> data(bdf)
> dump<-sapply( 1:5, function(i) {
> fm <- lme(langPOST ~ IQ.ver.cen + avg.IQ.ver.cen, data = bdf,
>random = ~ IQ.ver.cen | schoolNR);
> cat(" ",i,"\r")
> 0
> })
>
> The above code simply reruns the example from the
> lme help page a large number of times and returns a bunch
> of 0's, so you'll need to have the lme4 and Matrix
> packages installed. It might take a while to complete,
> but you can always nice it and let it run.
>
> I'm attempting to bootstrap lme() from the lme4 package,
> but it causes a
> segfault after a couple hundred iterations. This happens on
> my Linux x86 RedHat 7.3, 8.0, 9.0, FC1 systems w/ 1.9.1
> and devel 2.0.0 (not all possible combinations actually
> tested.)
> I've communicated w/ Douglas Bates about this and he
> doesn't appear to have the problem.
--
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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Re: [R] Excel TDIST and TINV
Brian Ripley wrote:
> We are hardly likely to know what those are in Excel. Possibly pt
> and qt, but see help.search("Student t distribution") for where to
> look for what R provides.
>
> I also do not know what Chauvenet's criterion has to do with
> Student's t, and
>
> http://www.me.umn.edu/education/courses/me8337/chauvenet.txt
>
> states that the latter would be incorrect.
See also
http://www.stat.uiowa.edu/~jcryer/JSMTalk2001.pdf
for insight into the ``wisdom'' of using Excel in the first place.
cheers,
Rolf Turner
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Re: [R] Howto enlarge fonts size in R- Graphics?
The X11 device has an argument `pointsize' (which may well mean pixel size in a particular implementation of X11, as my laptop for example has width, height and pointsize all much smaller than specified): just increase it. The advice to look at ?par is incorrect if you want to scale everything, as I think you do. If you want auto-launched windows to have a larger font, you need to write a wrapper to X11 and set options(device=wrapper_name). On Tue, 14 Sep 2004, [ISO-8859-15] Thomas Schönhoff wrote: > I am fairly new to GNU R ! > At the moment I am doing an intensive learning on the basics of GNU > R-1.91, especially graphics like plots and alike, by reading the > introductory docs! > Well, except some occasional glitches (X11 output errors) everything > seems to be fine, thanks to developers for this fine program! > But there is a slight problem with the size of fonts in graphics, i.e. > its very hard form me to read labels of variables in plots or other > graphical representations! (yes, I am little short sighted) > How may I mainpulate/enlarge the fonts size in graphics from within GNU R ? -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Howto enlarge fonts size in R- Graphics?
Thomas Schönhoff wrote: Hi, I am fairly new to GNU R ! At the moment I am doing an intensive learning on the basics of GNU R-1.91, especially graphics like plots and alike, by reading the introductory docs! Well, except some occasional glitches (X11 output errors) everything seems to be fine, thanks to developers for this fine program! But there is a slight problem with the size of fonts in graphics, i.e. its very hard form me to read labels of variables in plots or other graphical representations! (yes, I am little short sighted) How may I mainpulate/enlarge the fonts size in graphics from within GNU R ? See ?plot, ?plot.default and ?par, in particular look out for all arguments containing the letters "cex" Uwe Ligges BTW: It is called R-1.9.1 Thanks for your time Thomas System: GNU/Linux (Debian Sid) GNU R: 1.91 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Howto enlarge fonts size in R- Graphics?
Hi Thomas! Try ?par at the R prompt, there you will get all the necessary information to change the appearance of graphics. Daniel -- Daniel Hoppe Department of Marketing University of Vienna Bruenner Strasse 72 1210 Vienna Austria > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Thomas > Schönhoff > Sent: Tuesday, September 14, 2004 10:47 AM > To: R User-Liste > Subject: [R] Howto enlarge fonts size in R- Graphics? > > > Hi, > > I am fairly new to GNU R ! > At the moment I am doing an intensive learning on the basics of GNU > R-1.91, especially graphics like plots and alike, by reading the > introductory docs! > Well, except some occasional glitches (X11 output errors) everything > seems to be fine, thanks to developers for this fine program! > But there is a slight problem with the size of fonts in > graphics, i.e. > its very hard form me to read labels of variables in plots or other > graphical representations! (yes, I am little short sighted) > How may I mainpulate/enlarge the fonts size in graphics from > within GNU R ? > > Thanks for your time > > Thomas > > > > System: GNU/Linux (Debian Sid) > GNU R: 1.91 > > __ > [EMAIL PROTECTED] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read > the posting guide! http://www.R-project.org/posting-guide.html > __ [EMAIL PROTECTED] 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] Howto enlarge fonts size in R- Graphics?
Hi, I am fairly new to GNU R ! At the moment I am doing an intensive learning on the basics of GNU R-1.91, especially graphics like plots and alike, by reading the introductory docs! Well, except some occasional glitches (X11 output errors) everything seems to be fine, thanks to developers for this fine program! But there is a slight problem with the size of fonts in graphics, i.e. its very hard form me to read labels of variables in plots or other graphical representations! (yes, I am little short sighted) How may I mainpulate/enlarge the fonts size in graphics from within GNU R ? Thanks for your time Thomas System: GNU/Linux (Debian Sid) GNU R: 1.91 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Spare some CPU cycles for testing lme?
Hello,
Frank Samuelson schrieb:
If anyone has a few extra CPU cycles to spare,
I'd appreciate it if you could verify a problem that I
have encountered. Run the code
below and tell me if it crashes your R before
completion.
library(lme4)
data(bdf)
dump<-sapply( 1:5, function(i) {
fm <- lme(langPOST ~ IQ.ver.cen + avg.IQ.ver.cen, data = bdf,
random = ~ IQ.ver.cen | schoolNR);
cat(" ",i,"\r")
0
})
I also tested your code by using R-1.91 under Debian Sid. After hundreds
of iterations it ended up with the already noticed "segmentation fault"
HTH
Thomas
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Re: [R] R post-hoc and GUI
More importantly -- if you are looking for something "not beta", you
need to be very careful. "beta" quality is in the eyes of the
claimer, and it isn't uniform.
In fact, while you could wrap up a usable GUI for your specific needs,
it might be less of a waste of time to write simple functions and
spend the time with training.
Why, I can imagine that the arguments about GUIs would waste more time
than would be spent creating a cheatsheet and the functions/scripts to
simplify everything.
Of course, your situation might differ.
best,
-tony
Christian Schulz <[EMAIL PROTECTED]> writes:
> Perhaps the package Rcmdr is a compromise for the
> people don't like command-line software.
>
> christian
>
>
> Am Dienstag, 14. September 2004 12:02 schrieb Paolo Ariano:
>> Hi *
>> i've done my anova anlysis but now i need post-hoc test, are these
>> included in R ?
>>
>> I've a Big problem, working with people that don't like to use
>> command-line software (but prefer something like openoffice) does
>> someone is trying to do a usable GUI for R ? i'm reading something on R
>> commander SciView and others but all seem to be beta. I'd like to make
>> possible to make anova and post-hoc more simple to my collegues ;)
>>
>> thanks
>> paolo
>
> __
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>
--
Anthony Rossini Research Associate Professor
[EMAIL PROTECTED]http://www.analytics.washington.edu/
Biomedical and Health Informatics University of Washington
Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
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Re: [R] R post-hoc and GUI
On Tue, 14 Sep 2004, Paolo Ariano wrote: > i've done my anova anlysis but now i need post-hoc test, are these > included in R ? Yes, in function TukeyHSD and in package multcomp for example. There are worked examples in the MASS scripts. > I've a Big problem, working with people that don't like to use > command-line software (but prefer something like openoffice) does > someone is trying to do a usable GUI for R ? i'm reading something on R > commander SciView and others but all seem to be beta. I'd like to make > possible to make anova and post-hoc more simple to my collegues ;) That's your choice, but have you looked at package Rcmdr? You cna extend its menus if you want to. BTW, I guess you are working on Windows, but have not told us what OS, even. Please read the posting guide. -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R post-hoc and GUI
Perhaps the package Rcmdr is a compromise for the people don't like command-line software. christian Am Dienstag, 14. September 2004 12:02 schrieb Paolo Ariano: > Hi * > i've done my anova anlysis but now i need post-hoc test, are these > included in R ? > > I've a Big problem, working with people that don't like to use > command-line software (but prefer something like openoffice) does > someone is trying to do a usable GUI for R ? i'm reading something on R > commander SciView and others but all seem to be beta. I'd like to make > possible to make anova and post-hoc more simple to my collegues ;) > > thanks > paolo __ [EMAIL PROTECTED] 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] R-2.0.0 CMD check . and datasets
Hello everyone I'm having a little difficulty with R-2.0.0 CMD check. My field is Bayesian calibration of computer models. The problem is that I have a large collection of toy datasets, that in R-1.9.1 were specified with lines like this: x.toy <- 1:6 y.toy <- computer.model(x.toy) z.toy <- reality(x.toy) in file ./data/toys.R ; functions computer.model() and reality() are defined in ./R/calibrator.R. [In this application, the (toy) functions computer.model() and reality() are the objects of inference, as per the standard Bayesian approach. The functions are nonrandom in that they are deterministic but random in the Bayesian sense. Thus y.toy and z.toy are observations of (random) functions]. In the Real World, one would have access to x.toy, y.toy, and z.toy but not (of course) computer.model() or reality(). These functions should never be seen or referred to because they are Unknown. So, in many of the code examples, I use things like "some.function(y.toy, z.toy)" . . . and I need y.toy and z.toy to be consistent between different functions. I think R-2.0.0 sources ./data/toys.R *before* the files in ./R/ ; and this throws an error in R2 CMD check, because the functions are not found. What is best practice to generate this kind of toy dataset? -- Robin Hankin Uncertainty Analyst Southampton Oceanography Centre SO14 3ZH tel +44(0)23-8059-7743 [EMAIL PROTECTED] (edit in obvious way; spam precaution) __ [EMAIL PROTECTED] 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] R post-hoc and GUI
Hi * i've done my anova anlysis but now i need post-hoc test, are these included in R ? I've a Big problem, working with people that don't like to use command-line software (but prefer something like openoffice) does someone is trying to do a usable GUI for R ? i'm reading something on R commander SciView and others but all seem to be beta. I'd like to make possible to make anova and post-hoc more simple to my collegues ;) thanks paolo -- Paolo Ariano Neuroscience PhD Student @ UniTo Una non esclude l'altra ed entrambe non escludono i soldi - Paolo A. _ For your security, this mail has been scanned and protected by Inflex __ [EMAIL PROTECTED] 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] glmmPQL and random factors
Hello! I have tested the effect of two treatments on fruit set, i.e. fruits per plant. The treatments had two levels each giving four different treatment combinations. Forty separated plots were subjected to one of the treatment combinations so each combination was replicated ten times. I intend to analyze my data using the glmmPQL procedure in the following way. glmmPQL(Fruit.set~Treat1*Treat2+offset(log10(No.flowers)), random=~1|Plot, family=poisson, data= ) Plot is supposed to be nested in (Treat1*Treat2). Is this analysis suitable? Moreover, what is the meaning of typing random=~1|Plot compared to random=~Treat1*Treat2|Plot? Cheers Per Toräng [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] erase columns
?subset /E *** REPLY SEPARATOR *** On 9/14/2004 at 10:44 AM michele lux wrote: >>>Can somebody remember me which is the command to erase >>>columns from a data frame? >>>Thanks Michele >>> >>> >>> >>>___ >>> >>>http://it.seriea.fantasysports.yahoo.com/ >>> >>>__ >>>[EMAIL PROTECTED] mailing list >>>https://stat.ethz.ch/mailman/listinfo/r-help >>>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Witold Eryk Wolski @ MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin'v' tel: 0049-30-83875219/ \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] maximization subject to constaint
On Mon, 13 Sep 2004, Shuangge Ma wrote:
constrOptim() will do this, but it isn't a particularly efficient
algorithm when the number of constraints is large.
-thomas
Hello:
I have been trying to program the following maximization problem and would
definitely welcome some help.
the target function: sum_{i} f(alpha, beta'X_{i}),
where alpha and beta are unknown d-dim parameter,
f is a known function an X_{i} are i.i.d. r.v.
I need to maximize the above sum, under the constaint that:
beta'X_{i}+alpha<=1, for i=1,...,n.
For one dimension, it is kind of trivial. What should I do with high
dimensional alpha and beta? Thanks for your time,
Shuangge Ma, Ph.D.
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Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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RE: [R] erase columns
Hi,
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of michele lux
Sent: Dienstag, 14. September 2004 10:44
To: [EMAIL PROTECTED]
Subject: [R] erase columns
Can somebody remember me which is the command to erase
columns from a data frame?
Thanks Michele
I hope the following code-piece helps what you are looking for:
mydf <- as.data.frame(matrix(runif(100),ncol=5))
### if you want to erase the third column, do:
mydf <- mydf[,-3]
mydf2 <- as.data.frame(matrix(runif(100),ncol=20))
### if you want to erase the first, third and twentieth column, do:
mydf2 <- mydf2[,-c(1,5,20)]
Ciao,
Roland
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[R] erase columns
Can somebody remember me which is the command to erase columns from a data frame? Thanks Michele ___ http://it.seriea.fantasysports.yahoo.com/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Can I find the datetime an object was last assigned to/saved?
rhotrading.com> writes: > I'm using v 1.9.1 under Windoz XP. > > Can I do the equivalent of "ls -l" on my R objects? R's "ls()" lists > only the names. Check out this thread where it was previously discussed: http://tolstoy.newcastle.edu.au/R/help/04/05/0207.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Can I find the datetime an object was last assigned to/saved?
Prof Brian Ripley wrote: On Tue, 14 Sep 2004, Uwe Ligges wrote: [EMAIL PROTECTED] wrote: I'm using v 1.9.1 under Windoz XP. Can I do the equivalent of "ls -l" on my R objects? R's "ls()" lists only the names. For example ll() in package gregmisc. But that does not give datetimes, since they are not recorded. Ups, sorry. Forgot the subject line while reading the body ... Uwe It also needs a warning on object sizes, which had it credited its use of object.size you would have been able to find. Would the maintainer please 1) Give credit where credit is due and add a \seealso, and 2) Include an appropriate warning. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Can I find the datetime an object was last assigned to/saved?
On Tue, 14 Sep 2004, Uwe Ligges wrote: > [EMAIL PROTECTED] wrote: > > > I'm using v 1.9.1 under Windoz XP. > > > > Can I do the equivalent of "ls -l" on my R objects? R's "ls()" lists > > only the names. > > For example ll() in package gregmisc. But that does not give datetimes, since they are not recorded. It also needs a warning on object sizes, which had it credited its use of object.size you would have been able to find. Would the maintainer please 1) Give credit where credit is due and add a \seealso, and 2) Include an appropriate warning. -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] memory allocation error message
On 14 Sep 2004, Peter Dalgaard wrote: > "Prodromos Zanis" <[EMAIL PROTECTED]> writes: > > > Dear all > > > > I use the library(netCDF) to read in NCEP data. The file I want to > > read has size 113 Mb. When i try to read it I get the following > > message: > > > > Error: cannot allocate vector of size 221080 Kb > > In addition: Warning message: > > Reached total allocation of 255Mb: see help(memory.size) > > > > I get a similar message when I try to read a file with 256 Mb in a > > PC with 2 GigaByte RAM. > > > > Is there something that I can do to handle this problem of reading > > big netCDF files with R-project. > > Did you read help(memory.size)? and follow instructions therein? Also, netCDF has been withdrawn from CRAN, and you might want to use ncdf or RNetCDF instead. (Windows ports of both are available now: see the ReadMe on the CRAN windows contrib area.) If the message really was similar you are using R < 1.6.0 and need to upgrade. -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Can I find the datetime an object was last assigned to/saved?
[EMAIL PROTECTED] wrote: I'm using v 1.9.1 under Windoz XP. Can I do the equivalent of "ls -l" on my R objects? R's "ls()" lists only the names. For example ll() in package gregmisc. Uwe Ligges Thanks! David L. Reiner Rho Trading 440 S. LaSalle St -- Suite 620 Chicago IL 60605 312-362-4963 (voice) 312-362-4941 (fax) [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] memory allocation error message
Prodromos Zanis wrote: Dear all I use the library(netCDF) to read in NCEP data. The file I want to read has size 113 Mb. When i try to read it I get the following message: Error: cannot allocate vector of size 221080 Kb In addition: Warning message: Reached total allocation of 255Mb: see help(memory.size) So this is an R version < 1.9.0 ! 1. Please upgrade. 2. Please read ?Memory and learn how to increase the maximum amount of memory consumed by R under Windows. Uwe Ligges I get a similar message when I try to read a file with 256 Mb in a PC with 2 GigaByte RAM. Is there something that I can do to handle this problem of reading big netCDF files with R-project. I look forward for your help. Prodromos Zanis Dr. Prodromos Zanis Research Centre for Atmospheric Physics and Climatology Academy of Athens 3rd September 131, Athens 11251, Greece Tel. +30 210 8832048 Fax: +30 210 8832048 e-mail: [EMAIL PROTECTED] Web address: http://users.auth.gr/~zanis/ * [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
