Hi
On 3 Nov 2005 at 16:03, CG Pettersson wrote:
Date sent: Thu, 03 Nov 2005 16:03:05 +0100
From: CG Pettersson <[EMAIL PROTECTED]>
To: r-help@stat.math.ethz.ch
Subject:[R] Problems with abline adding regression line to a
graph
>
On 3 Nov 2005, [EMAIL PROTECTED] wrote:
> I am looking for a way to search a file for position of some
> expression, from within R. My current code:
>
> sha1Pos = gregexpr("", readChar(filename,
> file.info(filename)$size))[[1]]
>
> Works fine for small files, but text files I will be working with
Hello all,
I'm attempting to plot the functions from a generalized linear model
while iterating over multiple levels of a factor in the model. In
other words, I have a data set
Block, Treatment.Level, Response.Level
So, the glm and code to plot should be
logit.reg<-glm(formula = Respo
RSiteSearch("FIGARCH") revealed that Diethelm Wuertz prepared an R
interface to Ox Garch. However, "Ox and all its components are
copyright of Jurgen A. Doornik. The Console (command line) versions may
be used freely for academic research and teaching purposes only.
Commercial users
You could try using the COM interface rather than the ODBC
interface. Try code such as this:
library(RDCOMClient)
xls <- COMCreate("Excel.Application")
xls[["Workbooks"]]$Open("MySpreadsheet.xls")
sheet <- xls[["ActiveSheet"]]
mydata <- sheet[["UsedRange"]][["value"]]
xls$Quit()
# convert mydata
On 11/3/05, Andy Bunn <[EMAIL PROTECTED]> wrote:
> > How can I modify the example below to put a dot at the mean of each
> violin
> > plot? I assume I use panel.points but that's as far as I can go.
> >
> > bwplot(voice.part ~ height, singer,
> > panel = function(..., box.ratio) {
I just wanted to make one clarification about my statement: "After some
time, my collegues at the Food and Drug Adminstration have finally
acknowledged R as a powerful statistical computing environment." I did not
intend for this to read that R has been acknowledged as being 21 CFR Part
11 complia
If I understand you correctly, you cannot do this with a data.frame, which
must be rectangular with equal numbers of entries (columns) in each row. See
?.data.frame and read "An Introduction to R" for these basics. You could
make the 3rd column for exhaustive = NA (or maybe an empty string, "") I
Hello!
First time posting here:
Here is my code:
x <- c(1:22)
finaloutput=cidrm=NULL
finaldiversityoutput=diversitym=NULL
diversityinfo=read.table("Diversity_info.txt", header=T, sep="\t",
row.names=NULL)
attach(diversityinfo)
diversitynr=nrow(diversityinfo)
diversitytemp <- matrix(0,nrow=diver
Hello,
I was wondering if there is a way to use R with the Sun Grid Engine,
as opposed to using Rmpi. Our sge has a lammpi parrallel environment
as well. Does anyone have a script to submit a batch R job using the
SGE scheduler? Or can point me to a good tutorial?
Thanks
_
> How can I modify the example below to put a dot at the mean of each violin
> plot? I assume I use panel.points but that's as far as I can go.
>
> bwplot(voice.part ~ height, singer,
> panel = function(..., box.ratio) {
> panel.violin(..., col = "transparent",
>
Dieter Menne <[EMAIL PROTECTED]> writes:
> Andreas Cordes stud.uni-goettingen.de> writes:
>
> >
> > Hi,
> > I would like to fit a model for a factorial design that allows for
> > unequal variances in all groups. If I am not mistaken, this can be done
> > in lm by specifying weights.
>
> > A
"Kevin Wright" <[EMAIL PROTECTED]> wrote in message
news:[EMAIL PROTECTED]
> >From my experience (somewhat of a guess):
> Excel uses the first 16 rows of data to determine if a column is numeric
or
> character. The data type which is most common in the first 16 rows will
then
> be used for the who
Dear Rs:
BY having the following code:
candidates<-expand.grid(e=c("nearest-neighbor","exaustive"),
d=c(70,75,80,85,90,92,94,96,98,99),
n=c(20,25,30,35,40))
results in :
e d n
1 nearest-neighbor 70 20
2 exaustive 70 20
3 nearest-neighbor 75 20
4 exaustive 75 20
90 exaustive 90
Hi
Sara Mouro wrote:
> Dear all,
>
> How can I explian and solve the error message:
> "margins too large"
Do you mean "figure margins too large"? If so, it means that there is
not enough room for your plot; try making the graphics window (or page
size) bigger. Depending on how "stan
The problem is in src/nmath/pnbeta.c, which has an iteration limit of
100, not enough for these problems. Increasing the iteration limit to
1000 seems to work.
-thomas
On Mon, 24 Oct 2005, Ken Kelley wrote:
> Hello all.
>
> It seems that the pf() function when used with noncentral p
On 11/3/05, Alpert, William <[EMAIL PROTECTED]> wrote:
> I swear I've scoured the help files and several texts before posting
> what feels like a dumb newbie question.
>
> How can I draw two kernel density plots in the same frame ? I have
> similar variables in two separate data frames, and I would
Hello all,
I'm a relatively new user of R, having mostly used it only for plotting so
far. I'm also not very familiar with regression methods, hence forgive my
greenness on the topic.
What I want to do in R is multivariate nonparametric regression, with a slight
hitch. From my experimental data
Andreas Cordes stud.uni-goettingen.de> writes:
>
> Hi,
> I would like to fit a model for a factorial design that allows for
> unequal variances in all groups. If I am not mistaken, this can be done
> in lm by specifying weights.
> A function intended to specify weights for unequal variance st
Hi,
anyone knows about any functions in R can get multidimensional integration
not over a multidimensional rectangle (not adapt).
For example, I tried the following function f(x,n)=x^n/n!
phi.fun<-function(x,n)
{ if (n==1) {
x
}else{
integrate(phi.fun, lower=0, up
Is there a way to specify a Z matrix using the lmer function, where the
model is written as y = X*Beta + Z*u + e?
I am trying to reproduce smoothing methods illustrated in the paper
"Smoothing with Mixed Model Software" my Long Ngo and M.P. Wand.
published in the /Journal of Statistical Softwar
Hi Spencer: Just realized I may have misunderstood your comments about
branching--you may have been thinking about a restart. Sorry if I
misrepresented them.
See below:
On 11/3/05 11:03 AM, "Spencer Graves" <[EMAIL PROTECTED]> wrote:
> Hi, Andy and Peter:
>
> That's interesting. I still li
Hi,
I would like to fit a model for a factorial design that allows for
unequal variances in all groups. If I am not mistaken, this can be done
in lm by specifying weights.
A function intended to specify weights for unequal variance structures
is provided in the nlme library with the varIdent fun
Hi Spencer & Andy: Thanks for your thoughtful input! I did at one point
look at the optim() function & run debug on it (wasn't aware of
browser--that's helpful!). My impression is that optim() simply calls a C
function that handles the maximization. So if I want to break out of my
likelihood fu
Dear R users;
Ive got two questions concerning nlme library 3.1-65 (running on R 2.2.0 /
Win XP Pro). The first one is related to augPred function. Ive been working
with a nonlinear mixed model with no problems so far. However, when the
parameters of the model are specified in terms of some ot
If you meant QR vs. inverting X'X for linear regression, the motivation for
using QR is not speed, but numerical stability. There's no univerally good
least squares algorithm that would be uniformly better than anything else
for any kind of data.
Andy
> From: Jari Oksanen
>
>
> On 3 Nov 2005,
Thanks for all the response. I think plotting a cdf or taking transformation
could make the plot look better.
But my further question is how to set the breaks to make the histogram
concentrate in the interval of (0.01,0.2). I can even ignore the other parts of
the values.
Thanks!
Leaf
=
To plot two Kernel densities you can use matplot:
x1<-density(rnorm(100))
x2<-density(rnorm(100))
matplot(cbind(x1$y,x2$y), type="l")
Or if both distributions are really very similar and you don't have to
adjust the axes you can simply use
plot(x1)
lines(x2, col="red")
Finally if you want to
How can I modify the example below to put a dot at the mean of each violin
plot? I assume I use panel.points but that's as far as I can go.
bwplot(voice.part ~ height, singer,
panel = function(..., box.ratio) {
panel.violin(..., col = "transparent",
Here's a function that you can customize to fit your needs. lst is a named list.
multicomp <- function(lst)
{
clr <- c("darkgreen","red","blue","brown","magenta")
alldens <- lapply(lst,function(x) {density(x,from=min(x),to=max(x))})
allx <- sapply(alldens,function(d) {d$x})
ally <- sapply(alldens,
I swear I've scoured the help files and several texts before posting
what feels like a dumb newbie question.
How can I draw two kernel density plots in the same frame ? I have
similar variables in two separate data frames, and I would like to show
their two histograms/densities in a single pict
On 11/3/2005 11:12 AM, SANDRINE COELHO wrote:
> Hello,
>
> I am running R on XP Windows machine, and frequently I have enable to start
> R. I
> have this message: "Fatal Error: cannot find unused tempdir name". I don't
> know
> why.
This has come up before. When R starts up, it tries to create
> Just wondering if anyone knows of any text mining projects in
> R...I googled
> a bit but didn't get anything...
RSiteSearch("text mining") turns up 85 hits...
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLE
Peter Dalgaard <[EMAIL PROTECTED]> writes:
> Alvarez Pedro <[EMAIL PROTECTED]> writes:
>
> > On page 22 of the R-introduction guide it's written:
> >
> > the quadratic form x^{'} A^{-1} x which is used in
> > multivariate computations, should be computed by
> > something like x%*%solve(A,x), rat
On 3 Nov 2005, at 17:25, Robin Hankin wrote:
> Hi Alvarez
>
>
> If you define
>
> quad.form.inv <- function (M, x)
> {
> drop(crossprod(x, solve(M, x)))
> }
>
> then you will avoid an expensive call to %*% as well.
>
Is %*% really expensive in all platforms? I had a function that used QR
d
Hi all,
Just wondering if anyone knows of any text mining projects in R...I googled
a bit but didn't get anything...
TIA,
ken
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http:
On 11/3/2005 10:46 AM, Peter Dalgaard wrote:
> Duncan Murdoch <[EMAIL PROTECTED]> writes:
>
>> On 11/3/2005 9:11 AM, Soukup, Mat wrote:
>> > Hi.
>> >
>> > After some time, my collegues at the Food and Drug Adminstration have
>> > finally acknowledged R as a powerful statistical computing environm
Anyone interested in voting for R to be included in the annual
Pricelessware list (Windows freeware list voted on by the readers
of the alt.comp.freeware newsgroup, see www.pricelesswarehome.org)
can reply to this message:
http://groups.google.com/group/alt.comp.freeware/msg/d9e52e406d9e2ceb
simp
Hello,
I am running R on XP Windows machine, and frequently I have enable to start R. I
have this message: "Fatal Error: cannot find unused tempdir name". I don't know
why.
Thanks, in advance, for your help
Sandrine Coelho
__
R-help@stat.math.ethz.ch
Hi, Andy and Peter:
That's interesting. I still like the idea of making my own local
copy, because I can more easily add comments and test ideas while
working through the code. I haven't used "debug", but I think I should
try it, because some things occur when running a function tha
Hi,
I'm fitting poisson regression models to counts of birds in
1x1 km squares using several environmental variables as predictors.
I do this in a stepwise way, using the stepAIC function. However the
resulting models appear to be overparametrized, since too much
variables were included.
Hi All,
I am trying to apply MDS for 4 groups in my data. The
groups are:
groups = list( Day1C=c(9), Day1T=c(7,8,10),
Day2C=c(1,2,3,6,11,13,14,15), Day2T=c(4,5,12,16,17,18)
)
When I do the MDS plot the group1 member appears twice
instead of one time in the plot. I don't know why this
is happen
Duncan Murdoch <[EMAIL PROTECTED]> writes:
> On 11/3/2005 9:11 AM, Soukup, Mat wrote:
> > Hi.
> >
> > After some time, my collegues at the Food and Drug Adminstration have
> > finally acknowledged R as a powerful statistical computing environment.
> > However, in order to comply with the Office o
On 03-Nov-05 Kilian Hagemann wrote:
> Hi there,
>
> I'm new to R but I thought this is the most likely place I
> could get advice or hints w.r.t the following problem:
>
> I have a series of measurements xi with associated uncertainties dxi.
> I would like to construct the probability density his
>From my experience (somewhat of a guess):
1.
Excel uses the first 16 rows of data to determine if a column is numeric or
character. The data type which is most common in the first 16 rows will then
be used for the whole column. If you sort the data so that at least the
first 9 rows have characte
Hi Alvarez
If you define
quad.form.inv <- function (M, x)
{
drop(crossprod(x, solve(M, x)))
}
then you will avoid an expensive call to %*% as well.
HTH
Robin
On 3 Nov 2005, at 13:01, Alvarez Pedro wrote:
> On page 22 of the R-introduction guide it's written:
>
> the quadratic form x
I just downloaded the file from that location, and took a quick look. At
least the only thing that R CMD check under 2.2.0 only complained about the
file report.Rd. The problem seems to be
\keyword { print }
instead of
\keyword{print}
If no one else is aware of any other problems with t
Would this be ok (on Windows, use grep on UNIX):
# line numbers of all lines conitaining R in the R README file
setwd(R.home())
as.numeric(sub(":.*", "", system("findstr /n R README", intern = TRUE)))
On 11/3/05, Tuszynski, Jaroslaw W. <[EMAIL PROTECTED]> wrote:
> Hi,
>
> I am looking for a way
Hi,
I am looking for a way to search a file for position of some expression,
from within R. My current code:
sha1Pos = gregexpr("", readChar(filename,
file.info(filename)$size))[[1]]
Works fine for small files, but text files I will be working with might get
up to Gb range, so I was trying to a
Apologies for coming to this so late...
Variance is rarely known in real life data. You should really consult the
book `Local Regression and Likelihood' by Prof. Loader for the details on
simultaneous confidence bands. `Locfit' is the support software for that
book.
Andy
> From: Michael Gälger
Has anyone done anything on a Python client for Rserve?
Simon Urbanek (Rserve dev) tells me he heard of some people working on
it a couple of years ago but nothing came of it. If anyone has done
anything, or might find it interesting, please get in touch with me.
I know there's also the RSPytho
Hello all,
R2.1.1, W2k
I try to make a plot of a simple regression model in this way:
> with(njfA_bcd, {
+ plot(TC_OS.G31,Prot,cex = 2, col = "red", xlab= "TC/OS at GS32",
+ ylab="Grain crude protein (CP)")
+ })
This part works well and produces the datapoints as red circles.
When I try to add
On 11/3/2005 9:11 AM, Soukup, Mat wrote:
> Hi.
>
> After some time, my collegues at the Food and Drug Adminstration have
> finally acknowledged R as a powerful statistical computing environment.
> However, in order to comply with the Office of Information and Technology
> standards there are a cou
Alvarez Pedro <[EMAIL PROTECTED]> writes:
> On page 22 of the R-introduction guide it's written:
>
> the quadratic form x^{'} A^{-1} x which is used in
> multivariate computations, should be computed by
> something like x%*%solve(A,x), rather than computing
> the inverse of A.
>
> Why isn't it g
Dear alltogether,
I tried pan() to impute NAs for longitudinal data.
The terminology in the following output follows the pan manpage. No data
are attached to this script as this may be too huge.
y = 15 responses
pred = at first just intercept was tried (later on covariates should follow)
subj =
Hi.
After some time, my collegues at the Food and Drug Adminstration have
finally acknowledged R as a powerful statistical computing environment.
However, in order to comply with the Office of Information and Technology
standards there are a couple of questions about whether R could interfere
with
On Thu, 2005-11-03 at 08:33 -0500, Liaw, Andy wrote:
> The `Value' section of ?merge does say that `... in all cases the result has
> no special row names', so you're left to handle that on your own. One
> possibility is to use
>
> result <- merge(mat1, mat2, all=TRUE, sort=FALSE)
>
> so that
Hi,
what about padding both datasets with dummy missing records ... and then
play with cbind and rbind
... like e.g.
> species5<-c(NA,NA,NA,NA)
> modmat2<-cbind(mat2,species1,species5)
and then similarly with mat1 ...
e.g.
species2<-c(NA,NA,NA,NA,NA)
> modmad1<-cbind(mat1,species2,species
And that was the only combination I didn't try, duhh.
As you say, it works. Excellent! TX! They'll be a
number of pleased usres too.
--- Duncan Murdoch <[EMAIL PROTECTED]> wrote:
> Mikkel Grum wrote:
> > I've tried your proposal in a number of ways, and
> > there must be something I'm not underst
On Thu, 3 Nov 2005, Alvarez Pedro wrote:
> On page 22 of the R-introduction guide it's written:
>
> the quadratic form x^{'} A^{-1} x which is used in
> multivariate computations, should be computed by
> something like x%*%solve(A,x), rather than computing
> the inverse of A.
>
> Why isn't it good
The `Value' section of ?merge does say that `... in all cases the result has
no special row names', so you're left to handle that on your own. One
possibility is to use
result <- merge(mat1, mat2, all=TRUE, sort=FALSE)
so that the sorting is not done, then you can just do
rownames(result) <
you could use something like:
mat1$id1 <- 1:nrow(mat1)
mat2$id2 <- 1:nrow(mat2)
out <- merge(mat1, mat2, all = TRUE)
out[order(out$id1, out$id2), ]
I hope it helps.
Best,
Dimitris
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
On Thu, 3 Nov 2005, Gavin Simpson wrote:
> Dear List,
>
> I often have to merge two or more data frames containing unique row
> names but with some columns (names) common to the two data frames and
> some columns not common. This toy example will explain the kind of setup
> I am talking about:
>
Alvarez Pedro wrote:
> On page 22 of the R-introduction guide it's written:
>
> the quadratic form x^{'} A^{-1} x which is used in
> multivariate computations, should be computed by
> something like x%*%solve(A,x), rather than computing
> the inverse of A.
>
> Why isn't it good to compute t(x) %
Hi there,
I'm new to R but I thought this is the most likely place I could get advice or
hints w.r.t the following problem:
I have a series of measurements xi with associated uncertainties dxi. I would
like to construct the probability density histogram of this data where each
density estimate
Pedro:
Solving the equation in this fashion can be computationally slow and
unstable. There is R an article in R News that answers this question
directly and is a pretty easy read with good examples. Check it out at
the following link:
http://cran.r-project.org/doc/Rnews/Rnews_2004-1.pdf
-
Alternatively, just type debug(optim) before using it, then step through it
by hitting enter repeatedly...
When you're done, do undebug(optim).
Andy
> From: Spencer Graves
>
> Have you looked at the code for "optim"? If you
> execute "optim", it
> will list the code. You can copy th
Dear List,
I often have to merge two or more data frames containing unique row
names but with some columns (names) common to the two data frames and
some columns not common. This toy example will explain the kind of setup
I am talking about:
mat1 <- as.data.frame(matrix(rnorm(20), nrow = 5))
mat2
On page 22 of the R-introduction guide it's written:
the quadratic form x^{'} A^{-1} x which is used in
multivariate computations, should be computed by
something like x%*%solve(A,x), rather than computing
the inverse of A.
Why isn't it good to compute t(x) %*% solve(A) %*% x?
Thanks a lot for h
Context: Pentium 4 with FreeBSD 5.4 and R 2.2.0
I'm trying to install
the package ROracle under R.
To start with I installed the oracle8-
client from the ports and referred to it via the variable $HOME_ORACLE
as /usr/local/oracle8-client. Then I started R. After issuing install.
packages("ROracl
>
>
>get.hist.quote(instrument="INR/USD", provider="oanda", start="2005-10-20")
>
>
>trying URL
>'http://www.oanda.com/convert/fxhistory?lang=en&date1=10%2F20%2F2005&date=11%2F01%2F2005&date_fmt=us&exch=INR&exch2=&expr=USD&expr2=&margin_fixed=0&&SUBMIT=Get+Table&format=ASCII&redirected=1'
>Conte
Please read the `R Data Import/Export Manual' and the help page for
write.table.
Is this really rw1061, that is R 1.6.1? If so you need to upgrade, as
write.table is _very_ much more efficient in recent versions.
On Thu, 3 Nov 2005 [EMAIL PROTECTED] wrote:
>
> I have to work with really huge
Hi
As I now exclusively use copy paste method to transfer data from
Excel to R I tried it and I got correctly a factor column when there
were some non numeric data in Excel.
Ctrl-C in Excel
mydf<-read.delim("clipboard") in R
Are you sure that a respective column in Excel has values 275a and
Mikkel Grum wrote:
> I've tried your proposal in a number of ways, and
> there must be something I'm not understanding. If I
> run your script (using source() in RGui, or ctrl-R
> from the R Editor, I get:
It requires a command line console, i.e. it will only work in Rterm, not
Rgui. I was assum
I have to work with really huge matrices (about 1000*1000 or more). And I want
to save those matrices in some file on my computer.
I tried to do so by using the command
write.tabe(SMatrix,file="C:/Programme/rw1061/SMatrix.txt",sep="
",quote=FALSE,row.names=FALSE,col.names=FALSE)
SMatrix is the
I've tried your proposal in a number of ways, and
there must be something I'm not understanding. If I
run your script (using source() in RGui, or ctrl-R
from the R Editor, I get:
> conout <- file('CONOUT$','w')
Error in file("CONOUT$", "w") : unable to open
connection
In addition: Warning message:
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