Hi Dieter,
Yes, I´ve tried both options. The anova(lme(...)) gives me good results
for the fixed effects part, but what I´m specifically interested in is
what to do with the random effects.
I have tried glmmPQL (generalized linear mixed-effects models), which
did in fact greatly help account
does it solve to a part your problem, if you use read.table() instead of
scan, since it imports data directly to a data.frame?
let me know, if it helps
Nawaaz Ahmed wrote:
I'm trying to read in datasets with roughly 150,000 rows and 600
features. I wrote a function using scan() to read it in (I
If you have heteroscedasticity problems, the nlme package has many
varFunctions (e.g., varPower, varIdent, etc.) that could assist you in
fitting it. The usage of GLMMs is mainly for discrete and count data
that you cannot fit with lme.
Testing between competing lme models should be done via
I would like to display output to a tcltk window from e.g. a call to
summary().
I tried to get something else than oneliners into a text window of the
kind found at:
http://bioinf.wehi.edu.au/~wettenhall/RTclTkExamples/TextWindows.html
But without success.
Henrik
I currently build two different versions of each Windows binary: the
rw.exe full installation program (with the next release looking to
be around 25 Megabytes), and a series of 8 diskette-sized files named
miniR*.
The miniR files only include a minimal installation of R, and are
rarely
Dear helpers,
thank you very much for your advice.
After starting a new R-session this morning, I was also unable to replicate the
problem, although the old session showed still the same problem.
One suggestion was that I maybe redefined some functions, but this was not the
case. I only loaded
Henrik Andersson [EMAIL PROTECTED] writes:
I would like to display output to a tcltk window from e.g. a call to
summary().
I tried to get something else than oneliners into a text window of the
kind found at:
http://bioinf.wehi.edu.au/~wettenhall/RTclTkExamples/TextWindows.html
I need to install a selected set of packages on a number of machines (in a
computer lab). Some of these machines are not connected to internet. Is it
possible to download all the packages and make a kind of repository on a CD,
and then install.packages from the CD?
Vikas
I am trying to understand how the SOM algorithm works
using library(class) SOM function.
I have a 1000*10 matrix and I want to be able to
summarize the different types of 10-element vectors.
In my real world case it is likely that most of the
1000 values are of one kind the rest of other (this is
Dear R users,
I have tried to write a function which gives the step-wise integral for
an exponential function (moving from -3 to 3 in steps of 0.1, where the
output for every step shall be the integral under the curve of y against x.
However, something seems to be wrong with this function; can
Dear Peter and Henrik,
What the Rcmdr does may be overkill for Henrik's application, since it also
intercepts error and warning messages, and tries to take the behaviour of
the R console. The relevant functions are in the file Commander.R in the
source package; the principal one is:
doItAndPrint
Vikas Rawal wrote:
I need to install a selected set of packages on a number of machines (in a computer lab). Some of these machines are not connected to internet. Is it possible to download all the packages and make a kind of repository on a CD, and then install.packages from the CD?
Yes, just
Christoph Scherber wrote:
Dear R users,
I have tried to write a function which gives the step-wise integral for
an exponential function (moving from -3 to 3 in steps of 0.1, where the
output for every step shall be the integral under the curve of y against x.
However, something seems to be
The syntax you have you used is not correct. integrate() needs as
first argument a function! see ?integrate for more info.
a possible solution could be:
x - seq(-3, 3, 0.1)
y - exp(x)
##
integral - function(z, a, b, step.){
cc - numeric(n - (b-a)/step.)
f - function(x) exp(x)
for(i
I can usually read in large tables by very careful usage of
read.table() without having to resort to scan(). In particular, using
the `colClasses', `nrows', and `comment.char' arguments correctly can
greatly reduce memory usage (and increase speed) when reading in data.
Converting from a list
Duncan == Duncan Murdoch [EMAIL PROTECTED]
on Fri, 04 Feb 2005 09:50:22 + writes:
Duncan I currently build two different versions of each
Duncan Windows binary: the rw.exe full installation
Duncan program (with the next release looking to be around
Duncan 25
In case others are looking for a simple way to read in .jpeg files as
ordinary matrices, here is my solution. I am only interested in greyscale
images, so you will have to alter the following if you want colour.
Most .jpegs are colour, so first step is to open the file with ImageMagick
display
On Thu, 3 Feb 2005 16:34:17 -0800, you wrote:
|=[:o) You will have a degree in statistics, be fluent in R and the Microsoft
|=[:o) Office suite (especially Excel, Word and PowerPoint). SQL query skills
are
|=[:o) very helpful as is real-world business and marketing experience.
|=[:o)
Hello
I would like to use the source(command) and write the output into a file.
I am using
outputfile=file(output.txt, open=wt)
sink(outputfile, type=output)
source(input.R, echo=TRUE)
Unfortunately the result has prompted commands. How can I avoid the
prompted commands data(iris), ...?
Thanks
Hi All,
I am trying to generate a function from a linear model. I think there
should be build-in function that perform this action but I've had no
luck finding it.
For example, I have a model created using lm().
model - lm(sat.d~1+sat.n+I(sat.n^2))
What I would like to have is a
Hello,
I would like to use Bayesian Networks with R.
I have already installed the package called deal which has succefully unpacked
(package 'deal' successfully unpacked and MD5 sums checked)
.
But when I try to write - network (df)
I have that kind of error message (be low)!
rats -
For some reason, using the qcc package, I'm unable to use the plotmath
notation in the title. Can anyone see what I'm doing wrong?
library(qcc)
a - rnorm(100)
qcc(a,type=xbar.one,title=expression(bar(X)),ylab=expression(CFU/ft^3)
)
This seems to not let the expression be evaluated, so I tried:
I don't think there's an automatic way to do this but you might try
something like:
model - lm(sat.d~1+sat.n+I(sat.n^2))
f - function(x) { predict(model, data.frame(sat.n = x)) }
-roger
Tony Han Bao wrote:
Hi All,
I am trying to generate a function from a linear model. I think there
should be
for(i in 1:dims[1]) x[i,]-rev(x[i,]) #flip the image vertically
Courtesy of Rolf Turner, here is a much better way to flip vertically:
x - x[,ncol(x):1]
Bill
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
NDIKUMAGENGE Alice wrote:
Hello,
I would like to use Bayesian Networks with R.
I have already installed the package called deal which has succefully unpacked (package 'deal' successfully unpacked and MD5 sums checked)
.
But when I try to write - network (df)
I have that kind of error message
I guess you are using R on Windows, and install the binary version of the
package. (Please tell us, as the Posting Guide asks, rather than leave us
guessing.)
Did you load the package with `library(deal)' before using the functions?
Andy
From: NDIKUMAGENGE Alice
Hello,
I would like
predict() can do that for you without giving you the explicit form of the
prediction function. I believe Prof. Harrell has facilities in his
Design/Hmisc packages for producing functions from fitted models.
Andy
From: Tony Han Bao
Hi All,
I am trying to generate a function from a linear
On Fri, 4 Feb 2005 14:46:03 +0100, Martin Maechler
[EMAIL PROTECTED] wrote :
Duncan == Duncan Murdoch [EMAIL PROTECTED]
on Fri, 04 Feb 2005 09:50:22 + writes:
Duncan The miniR files only include a minimal installation
Duncan of R, and are rarely tested. Rather than building
Shawn Way wrote:
For some reason, using the qcc package, I'm unable to use the plotmath
notation in the title. Can anyone see what I'm doing wrong?
library(qcc)
a - rnorm(100)
qcc(a,type=xbar.one,title=expression(bar(X)),ylab=expression(CFU/ft^3)
)
This seems to not let the expression be
Urs Wagner wrote:
Hello
I would like to use the source(command) and write the output into a file.
I am using
outputfile=file(output.txt, open=wt)
sink(outputfile, type=output)
source(input.R, echo=TRUE)
Unfortunately the result has prompted commands. How can I avoid the
prompted commands
Very nice! I can't wait to buy the book.
I have some plots I am working on that are surprisingly difficult to do :
http://www.oplnk.net/~ajackson/weather/Temperature_2000.png
and others in that directory for an example.
The challenge was coloring in the polygons which were, in some cases, defined
Hi,
I'm wondering why
48 %/% 2 gives 24
but
4.8 %/% 0.2 gives 23...
I'm not trying to round up here, but to find out how many times
something fits into something else, and the answer should have been the
same for both examples, no?
On a different topic, I like the behavior of NAs better in R
Hello,
I develop some R package on Linux machine with C subroutines.
The programs in C are well compiled on Linux machine and so I have some .so
files.
Now, I want to do the same work on windows, so I install R (the last version)
on windows, with Active Perl and djgpp, which is, as I know, the
Dear all,
does anybody know if there is a way to implement the following idea:
if for example I have a C/C++ structure of form:
struct {
int size;
char * data;
} SData;
in C code I could create some implementation that would create this
structure by pointer and fill in the data, so I would
Depire Alexandre wrote:
Hello,
I develop some R package on Linux machine with C subroutines.
The programs in C are well compiled on Linux machine and so I have some .so
files.
Now, I want to do the same work on windows, so I install R (the last version)
on windows, with Active Perl and djgpp,
Denis Chabot wrote:
Hi,
I'm wondering why
48 %/% 2 gives 24
but
4.8 %/% 0.2 gives 23...
I'm not trying to round up here, but to find out how many times
something fits into something else, and the answer should have been the
same for both examples, no?
No. Not from the perspective of a digital
It's the difference between integers and reals: 48 and 24 are
integers; 4.8 and 0.2 are floating point numbers. Consider:
(4.8+.Machine$double.eps) %/% (0.2-.Machine$double.eps)
[1] 24
(4.8-.Machine$double.eps) %/% (0.2+.Machine$double.eps)
[1] 23
Does this help? spencer graves
Denis Chabot [EMAIL PROTECTED] writes:
Hi,
I'm wondering why
48 %/% 2 gives 24
but
4.8 %/% 0.2 gives 23...
I'm not trying to round up here, but to find out how many times
something fits into something else, and the answer should have been
the same for both examples, no?
Well, you
I think you should have a look at external pointers (type EXTPTRSXP). They
are used in the R source . See, for example, memory.c. Also see the
developer page notes on weak references, finalizers, etc, which you'll need
to be familiar with.
This is really an R-devel question!
Reid Huntsinger
It's convention in mathematics that the empty sum is 0. You can think of
this as a generalization of 0*x = 0.
Reid Huntsinger
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Denis Chabot
Sent: Friday, February 04, 2005 11:01 AM
To:
Hi,
I am doing some research on feature selection for classfication
problem using genetic algorithm in a wrapper approach. I am wondering
if there is some package which is already built for this purpose. I
was advised before about dprep package but I don't think it used GA
there (if I am wrong,
On Fri, 4 Feb 2005, Uwe Ligges wrote:
Depire Alexandre wrote:
Hello,
I develop some R package on Linux machine with C subroutines.
The programs in C are well compiled on Linux machine and so I have some
.so files.
Now, I want to do the same work on windows, so I install R (the last
version) on
On windows, I install the last version of MinGW, I change path environment
variable,
but when on command windows, I try to compute R CMD SHLIB inv.c I have the
following error:
'make' is unknown.
I have mingw32-make.exe, but R don't use it, ?? I think it is'nt normal, but
I don't know how
Is it easier to compute .dll on linux, via cross-compiler ?
Le vendredi 4 Février 2005 18:37, Prof Brian Ripley a écrit :
On Fri, 4 Feb 2005, Uwe Ligges wrote:
Depire Alexandre wrote:
Hello,
I develop some R package on Linux machine with C subroutines.
The programs in C are well compiled
From: Depire Alexandre
On windows, I install the last version of MinGW, I change
path environment
variable,
but when on command windows, I try to compute R CMD SHLIB
inv.c I have the
following error:
'make' is unknown.
I have mingw32-make.exe, but R don't use it, ?? I think it
On Fri, 4 Feb 2005, Uwe Ligges wrote:
Urs Wagner wrote:
Hello
I would like to use the source(command) and write the output into a file.
I am using
outputfile=file(output.txt, open=wt)
sink(outputfile, type=output)
source(input.R, echo=TRUE)
Unfortunately the result has prompted commands. How can
To my knowledge, two packages have an implementation of an evolutionary, or
genentic, algorithm. Gafit is a curve fitting package and rgenoud for
function minimisation (combined with, iirc, a derivative-based Quasi-Newton
approach for unconstrained problems). One thing, in the S-Plus robust
Depire Alexandre wrote:
Is it easier to compute .dll on linux, via cross-compiler ?
The Windows way described in README.packages is not hard, you just have
to follow the advices. Once your system has been set up, it's the same
as native compiling on Linux.
Uwe Ligges
Le vendredi 4 Février 2005
Depire Alexandre wrote:
On windows, I install the last version of MinGW, I change path environment
variable,
but when on command windows, I try to compute R CMD SHLIB inv.c I have the
following error:
'make' is unknown.
I have mingw32-make.exe, but R don't use it, ?? I think it is'nt normal,
Dear List:
I am having some difficulty constructing a matrix that must take a
specific form. The matrix must be have a lower block of non-zero values
and the rest must all be zero. For example, if I am building an n X n
matrix, then the first n/2 rows need to be zero and the first n/2
columns
Is this what you want?
mat - matrix(0, 4, 4)
mat[col(mat) 2 row(mat) 2] - 100
mat
[,1] [,2] [,3] [,4]
[1,]0000
[2,]0000
[3,]00 100 100
[4,]00 100 100
Andy
From: Doran, Harold
Dear List:
I am having some difficulty
Hi.
I have a problem that I can't seem to find an optimal way of solving other
than by doing things manually. I'm trying to subset a data frame by the
number of observations that occurred at a given row but want to take into
account the number of observations of preceding rows. Here's an example.
Does the following do what you want:
vl.mat - matrix(0,4,4)
i34 - 3:4
vl.mat[i34,i34] - 100
vl.mat
[,1] [,2] [,3] [,4]
[1,]0000
[2,]0000
[3,]00 100 100
[4,]00 100 100
spencer graves
Doran, Harold wrote:
Dear List:
I am having
Unless I'm missing something, all you need to do is create the
large matrix and then replace the submatrix via subscripting
the rows and columns:
ans - matrix(0, n, n)
sub.seq - floor(n/2 + 1):n
ans[sub.seq, sub.seq] - submatrix
Patrick Burns
Burns Statistics
[EMAIL PROTECTED]
+44 (0)20 8525 0696
i'd like to use the C interface to R in a program i'm writing. as a
starting point, i'm trying to create a very simple C program that uses
R. i've read the R documentation on this, but i'm having trouble
figuring out where SEXP is defined and how to use it.
i noticed someone else on this list
Is there an R function that I can use to calculate the p-value from the
Z statistics computed for the relationship between chance and observed
proportions in predictions. More sprcifically I am refering to proportional
chance criteria (Cpro). Details are in Huberty's book on Applied
discriminant
Denis Chabot chabotd at globetrotter.net writes:
: The sum of a vector having at least one NA but also valid data gives NA
: if we do not specify na.rm=T. But with na.rm=T, we are telling sum to
: give the sum of valid data, ignoring NAs that do not tell us anything
: about the value of a
See if this helps:
http://www.ci.tuwien.ac.at/Conferences/useR-2004/Keynotes/Dalgaard.pdf
Andy
From: [EMAIL PROTECTED]
i'd like to use the C interface to R in a program i'm writing. as a
starting point, i'm trying to create a very simple C program that uses
R. i've read the R
array chip wrote:
Hi,
when I generated a survfit() object, I can get number
of patients at risk at various time points by using
summary():
fit-survfit(Surv(time,status)~class,data=mtdata)
summary(fit)
class=1
time n.risk n.event survival std.err lower 95% CI
upper 95% CI
Have you looked at the times argument to the summary method?
--Matt
Matt Austin
Statistician
Amgen
One Amgen Center Drive
M/S 24-2-C
Thousand Oaks CA 93021
(805) 447 - 7431
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of array chip
Sent: Friday,
Dear R helpers,
MyPkg passes R CMD check on Linux machines.
However, when I 'R CMD check myPkg' on Windows,
the libs subdirectory is not being created.
If I install the package and then create the libs
subdirectory manually and copy the dll files to it,
the package seems to work fine
(but
dear R wizards: is it possible to specify different arrow head styles?
E.g., a solid arrow head? Or a bent arrow head? Or a longer or
shorter arrow head? (perhaps through an add in?) I guess I could
write this myself, but since arrows is built-in, I was hoping it had
some flexibility
On Fri, Feb 04, 2005 at 09:09:37PM +0100, Roger Bivand wrote:
Well, it is documented in the Writing R Extensions manual:
http://cran.r-project.org/doc/manuals/R-exts.html#System-and-foreign-language-interfaces
thanks. reading through that a second time made all the difference.
i still
Hello,
it seems that the main results of survival analysis with package survival
are shown only as side effects of the print method.
If I compute e.g. a Kaplan-Meier estimate by
km.survdur-survfit(s.survdur)
then I can simply print the results by
km.survdur
Call: survfit(formula =
Thank you. That is useful. But is it possible to download all the packages in
one go, or would one have download each one by one?
Vikas
-Original Message-
From: Uwe Ligges [EMAIL PROTECTED]
To: Vikas Rawal [EMAIL PROTECTED]
Date: Fri, 04 Feb 2005 13:55:42 +0100
Subject: Re: [R]
A half-way decent ftp client would allow you to get all files in a
directory, so that ought to be quite easy.
Andy
From: Vikas Rawal
Thank you. That is useful. But is it possible to download all
the packages in one go, or would one have download each one by one?
Vikas
-Original
Doran, Harold HDoran at air.org writes:
:
: Dear List:
:
: I am having some difficulty constructing a matrix that must take a
: specific form. The matrix must be have a lower block of non-zero values
: and the rest must all be zero. For example, if I am building an n X n
: matrix, then the
Soukup, Matt SoukupM at cder.fda.gov writes:
:
: Hi.
:
: I have a problem that I can't seem to find an optimal way of solving other
: than by doing things manually. I'm trying to subset a data frame by the
: number of observations that occurred at a given row but want to take into
: account the
Gabor Grothendieck ggrothendieck at myway.com writes:
:
: Soukup, Matt SoukupM at cder.fda.gov writes:
:
: :
: : Hi.
: :
: : I have a problem that I can't seem to find an optimal way of solving other
: : than by doing things manually. I'm trying to subset a data frame by the
: : number of
Hi,
When I am using ldahist function I would like to
specify different colors for each of the groups in the
data I am using. Is it possible? If not does anybody
know of another function to plot multiple histograms
on one plot for different groups.
Thanks
=
Thanks
Fairouz Makhlouf
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