mingan wrote:
Is there a way for me to get the source code ( C/C++ or FORTRAN) for a
specific R package ?
Well, it is *included* in the (source) package...
???
Uwe Ligges
thanks
__
R-help@stat.math.ethz.ch mailing list
Hello,
I'd like to create a model with a factor-type response variable. This is
an example:
mydata - data.frame(factor_var = as.factor(c(rep('one', 100), rep('two',
100), rep('three', 100))), real_var = c(rnorm(150), rnorm(150) + 5))
summary(mydata)
factor_var real_var
one
Hi,
I was wondering if anyone could give me advice regarding using the lmer
command in lme4 package to do logistic regression (mixed effects model).
I use the following command
lmer(ISH ~ArrayPathology2, random=~1|PatientID, data=HSDB4.noNA,
family=binomial)
where ISH is outcome(0 or 1),
Hi Margaret,
if you look at the help page of lmer() you'll see that there is no
'random' argument (as there is in lme() in the nlme package). The way
to specify random-effects structure in lmer() is through the 'formula'
argument. So in your case try this:
lmer(ISH ~ ArrayPathology2 +
At 16:52 3/05/2005 -0300, rene.raupp wrote:
Does anybory knows any work comparing R with other (charged) statistical
softwares (like Minitab, SPSS, SAS)?
I work in a brasilian government bureau and I intend to use R as our
preferable statistical software, but I have to show it's as good as the
Dear R users,
I did install R. 2.0.1, and try to load gap package.
However, below is the message shown when I did load it. Can anybody
please let me know my mistakes?
library()
library(gap)
Loading required package: MASS
Loading required package: genetics
Loading required package:
On 04-May-05 Maciej Bliziñski wrote:
Hello,
I'd like to create a model with a factor-type response variable.
This is an example:
mydata - data.frame(factor_var = as.factor(c(rep('one', 100),
rep('two', 100), rep('three', 100))), real_var = c(rnorm(150),
rnorm(150) + 5))
summary(mydata)
mingan wrote:
Is there a way for me to get the source code ( C/C++ or FORTRAN) for a
specific R package ?
The source to contributed packages is in CRAN
mirror/src/contrib/PACKAGES.html. You can find your CRAN mirror by
looking at the CRAN entry in options(repos). (You may need to call
Eduwin Pakpahan wrote:
Dear R users,
I did install R. 2.0.1, and try to load gap package.
However, below is the message shown when I did load it. Can anybody
please let me know my mistakes?
library()
library(gap)
Loading required package: MASS
Loading required package: genetics
Loading
On Wed, 4 May 2005, Maciej [iso-8859-2] BliziDski wrote:
I'd like to create a model with a factor-type response variable. This is
an example:
What you have done here is to fit a logistic regression. The
interpretation of that is covered in many good books: for example there
are plots of the
On Wed, 4 May 2005, Duncan Murdoch wrote:
mingan wrote:
Is there a way for me to get the source code ( C/C++ or FORTRAN) for a
specific R package ?
The source to contributed packages is in CRAN
mirror/src/contrib/PACKAGES.html. You can find your CRAN mirror by looking
at the CRAN entry in
Hai Lin wrote:
Hello R users,
I have R script files writen in my pc laptop. I encountered problems when I run those files in R in Mac OS X (10.3.5).
Are there any ways in R that can make .R files executable?
It should work, at once, given you have not used Windows specific
commands, hard
On Wed, 4 May 2005, Eduwin Pakpahan wrote:
Dear R users,
I did install R. 2.0.1, and try to load gap package.
Did you install the dependencies of that package and their
dependencies ...
library(help=gap)
...
Depends: MASS, genetics, R (= 2.0.0)
library(help=genetics)
Depends:
On 4 2005, at 11:35 , Uwe Ligges wrote:
Eduwin Pakpahan wrote:
Dear R users, I did install R. 2.0.1, and try to load gap package.
However, below is the message shown when I did load it. Can anybody
please let me know my mistakes?
library()
library(gap)
Loading required package: MASS Loading
I tried that but it didn't make any difference to the output.
David
On 04/05/05, Douglas Bates [EMAIL PROTECTED] wrote:
David Hugh-Jones wrote:
Is this a bug? Should I attach a test case?
Try setting verbose=TRUE in the call to gls first and see if that gives
you any insight into what is
On Wed, 04 May 2005 10:22:01 +0200
Cuvelier Etienne [EMAIL PROTECTED] wrote:
At 16:52 3/05/2005 -0300, rene.raupp wrote:
Does anybory knows any work comparing R with other (charged) statistical
softwares (like Minitab, SPSS, SAS)?
I work in a brasilian government bureau and I intend to use
On 4 2005, at 11:41 , Uwe Ligges wrote:
Hai Lin wrote:
Hello R users, I have R script files writen in my pc laptop. I
encountered problems when I run those files in R in Mac OS X
(10.3.5). Are there any ways in R that can make .R files executable?
It should work, at once, given you have not
On Wed, 4 May 2005, Constantinos Antoniou wrote:
On 4 ±Ê 2005, at 11:35 À¼, Uwe Ligges wrote:
Eduwin Pakpahan wrote:
Dear R users, I did install R. 2.0.1, and try to load gap package.
However, below is the message shown when I did load it. Can anybody
please let me know my mistakes?
Constantinos Antoniou wrote:
On 4 2005, at 11:35 , Uwe Ligges wrote:
Eduwin Pakpahan wrote:
Dear R users, I did install R. 2.0.1, and try to load gap package.
However, below is the message shown when I did load it. Can anybody
please let me know my mistakes?
library()
library(gap)
Loading
please see also my posting on R-sig-finance
https://stat.ethz.ch/pipermail/r-sig-finance/2005q2/000290.html
Best regards,
Stefan
---
Dr. Stefan Albrecht, CFA
Allianz Private Equity Partners GmbH
Giselastraße 4
D-80802 Munich, Germany
Thanks a lot for the answers (prof Ripley and Ted).
I'm trying to analyze a survey. Most of the variables are of factor
type, with values for example {no_at_all, a_little, mostly,
a_lot}.
I thought about mapping those answers to numbers, but I didn't know what
numbers should I assign them to:
Dear all,
I am trying to simulate the null distribution for the likelihood ratio
test statistic for testing 1 random effect versus no random effect. The
asymptotic null distribution should be a mixture of a chi-squared
distribution with 0 degrees of freedom and a chi-squared distribution
with
On 4 2005, at 12:06 , Prof Brian Ripley wrote:
On Wed, 4 May 2005, Constantinos Antoniou wrote:
On 4 2005, at 11:35 , Uwe Ligges wrote:
Eduwin Pakpahan wrote:
Dear R users, I did install R. 2.0.1, and try to load gap
package. However, below is the message shown when I did load it.
Can anybody
Dear R-users,
I'm experiencing a segmentation fault when using
hdf5load(file,load=FALSE). Library(hdf5) loads without problems but when
loading a file, R crashes. I compiled R under Unix (Solaris for Sun).
There is nothing wrong with the files, as I can run the same script at
another place where
First question, following the command model-spec.pgram(outcome, taper=0,
fast=F), does model$spec return spectrum densities? I found the outputs are
quite different from SPSS, although the frequencies are identical.
Second, is there any command available in R for Fisher's test? How to compute
I have timeseries data for some factors, and some missing values are there in
those factors, I want impute those missing values without disturbing the
distribution of that factor, and maintaining the correlation with other
factors. Pl. suggest me some imputation methods.
I tried some
Dear R experts,
My problem is as follows:
Suppose I have a data frame d comprising two variable a-c(1:10)
b-c(11:20).
I now want to select a subgroup according the values of b.
I know if I just want to select, say, b=17, I can use f-d[d$b==17] and R
will give me
f
a b
7 7 17
However, if
Sir, I wrote a mail in r-help, but it is not responding. If there is any change
in r-help address please forward me.
My problem is:
I have timeseries data for some factors, and some missing values are there in
those factors, I want impute those missing values without disturbing the
Hi,
anybody know a possibilities how i could avoid less nicely cut's in
function calls with sweave like:
randomForest(x = RELSHIP ~ ., data = R_RELSHIP[splitR_RELSHIP == 1,
], importance = T, n(*here is the cut in the pdf*)
tree = 1000, na.action = na.omit)
Until now i add expost
Dear all,
I am running Windows XP with several parallel installations of R (2.0.1;
2.1 and so on). How can I install JGR for the 2.0.1 version? I keep on
getting error messages when trying to install it.
Best wishes
Christoph
__
Maciej Blizi(Bñski [EMAIL PROTECTED] 5/4/2005 6:02:14 AM
I'm trying to analyze a survey. Most of the variables are of factor
type, with values for example {no_at_all, a_little, mostly,
a_lot}.
In that case, you probably want to look at ordinal logistic regression. This
is covered in
Hi,
I'm using anova.mlm sphericity tests/corrections, and I'm getting
different values than SAS. In order to be able to use these values for
publications, I'd need to know more about the SAS bug that is mentioned
in the Reference Manual.
- What exactly causes the different values?
- Is it just
On 05/04/05 11:13, Ramesh Kolluru wrote:
I have timeseries data for some factors, and some missing values are there in
those
factors, I want impute those missing values without disturbing the
distribution of
that factor, and maintaining the correlation with other factors. Pl. suggest
me
On Wed, 2005-05-04 at 11:14 +, Tu Yu-Kang wrote:
Dear R experts,
My problem is as follows:
Suppose I have a data frame d comprising two variable a-c(1:10)
b-c(11:20).
I now want to select a subgroup according the values of b.
I know if I just want to select, say, b=17, I can
try this:
d - data.frame(a=1:10, b=11:20)
e - c(13, 15, 17)
##
d. - subset(d, b %in% e)
d.
I hope it helps.
Best,
Dimitris
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel:
Please check the hdf5 package version numbers are the current one.
Does the file contain text strings? If so there has been a known problem
with hdf5 crashes and a recent update of hdf5 (which I do not know for
sure whether it fixes the problem or not). This manifested itself as
crashes on
Christoph Scherber wrote on 5/4/2005 4:44 AM:
Dear all,
I am running Windows XP with several parallel installations of R (2.0.1;
2.1 and so on). How can I install JGR for the 2.0.1 version? I keep on
getting error messages when trying to install it.
Best wishes
Christoph
Hi Christoph,
Which
Christoph Scherber wrote:
Dear all,
I am running Windows XP with several parallel installations of R (2.0.1;
2.1 and so on). How can I install JGR for the 2.0.1 version? I keep on
getting error messages when trying to install it.
I am sure Simon Urbanek et al. are happy to help you, but even
Tu Yu-Kang wrote:
Dear R experts,
My problem is as follows:
Suppose I have a data frame d comprising two variable a-c(1:10)
b-c(11:20).
I now want to select a subgroup according the values of b.
I know if I just want to select, say, b=17, I can use f-d[d$b==17] and
R will give
check this:
library(nlme)
B - 1000
N - 100
n - 5
x - rep(runif(N, -4, 4), each=n)
gr - rep(1:N, each=n)
T - numeric(B)
for(i in 1:B){
y - rnorm(N*n, 1 + 1.5*x)
L0 - lm(y~x)
L1 - lme(y~x, random=~1|gr, method=ML)
T[i] - anova(L1, L0)$L.Ratio[2]
}
hist(T, prob=TRUE,
In the help for rpart it says, This differs from the tree function
mainly in its handling of surrogate variables. And it says that an
rpart object is a superset of a tree object. Both cite Brieman et al.
1984. Both call external code which looks like martian poetry to me.
I've seen posts in the
I am running R 2.0.0, GOstats 1.1.1 and GO 1.7.0,
and when I use the function GOHyperG, I have the following error:
w1-as.list(hgu95av2LOCUSID)
w2-unique(unlist(w1))
set.seed(123)
myLL-sample(w2,100)
xx - GOHyperG(myLL)
Error in mget(x, env = GOTERM, ifnotfound = NA) :
recursive default
S-PLUS Essentials - Lee Perry 23-26th May 2005
This is the last chance to register for the course S-PLUS Essentials to be
held in Basingstoke on 23-26th May 2005. If you are unfamiliar with S-PLUS
or have been meaning to upgrade your S-PLUS skills, this is the course for
you.
Extract:
Hi
I would like to compare two differences of means.
I have the means of the log of one variable for two conditions for one product,
and for another product.
The differences look different between both products for the two conditions,
but a statistical test is required.
Thank you for any hint
Sabrina Carpentier wrote:
I am running R 2.0.0, GOstats 1.1.1 and GO 1.7.0,
The release versions of BioC require R-2.0.1. You might try upgrading
your R version and trying again, because I cannot replicate this error.
Note that if you upgrade to R-2.1.0 (the current version of R), you will
need
Let me redirect the topic a bit. I've been considering unbundling gregmisc.
The pro would be that people would find the component packages (i.e. gdata)
more easily. The con is that the packages have a number of
interdependencies, so you pretty much will need to get most of them anyway.
As the
test - data.frame(cbind(1:10,11:20))
names(test) - c(a, b)
test[test$b == 17,]
test[test$b %in% c(13, 15, 17),]
Tu Yu-Kang wrote:
Dear R experts,
My problem is as follows:
Suppose I have a data frame d comprising two variable a-c(1:10)
b-c(11:20).
I now want to select a subgroup
Hello,
I am new to R, and am having trouble getting the output I want from a
stratified bootstrap. I didn't recieve a reply the first time I posted
this question so I have tried to make it more clear. My data frame
(denboot) is set up as follows:
SITE cswa parea treat
1 BeanA3
Warnes, Gregory R wrote:
Let me redirect the topic a bit. I've been considering unbundling gregmisc.
The pro would be that people would find the component packages (i.e. gdata)
more easily. The con is that the packages have a number of
interdependencies, so you pretty much will need to get most
I have one comment, although it is a little off topic.
I have the gregmisc package installed (R-2.0.1 on Win2000). Whenever I use
the help.search function it comes back with the following warning:
Warning message:
no Rd contents for package 'gregmisc' in 'C:/local/R/rw210/library' in:
Dear R graphics gurus,
Another question about lattice graphics. This time I would like to plot
means and confidence intervals by group factor in a lattice graph. I can
not find any working lattice examples. Maybe a custom panel function is
the answer, but that is a bit beyond me for now.
The
It came up for me. However, that's just a speed comparison, which
said that R 1.9.0 was comparable with the best available, better than
most but not necessarily the best depending on the task.
I would think you might be more concerned with accuracy and ease of
use, and I
Warnes, Gregory R [EMAIL PROTECTED] writes:
Let me redirect the topic a bit. I've been considering unbundling
gregmisc. The pro would be that people would find the component
packages (i.e. gdata) more easily. The con is that the packages
have a number of interdependencies, so you pretty
Dear Peter,
This looks like a two-way ANOVA, with product as one factor and condition as
the other. The test that you describe is for the interaction between product
and condition.
I hope this helps,
John
John Fox
Department of Sociology
McMaster University
Sorry for disturbing you with another newbie question!
I have a data frame about coastal waters quality
parameters: for some parameters (e.g. NH3) I have only
1 observation for each sampling station and each
sampling date, while in other cases (chlorophyll) I
have 1 obs for each meter-depth for
how do I check the rank of a matrix ?
say
A= 1 0 0
0 1 0
then rank(A)=2
what is this function?
thanks
I did try help.search(rank), but all the returned help information
seem irrelevant to what I want.
I would like to know how people search for help information like this.
rpart does much more at C level, including pruning and cross-validation so
can be much faster.
It is also user-extensible.
tree was actually written to track down bugs in the then S implementation,
and so is much closer to the functionality in S. It is not where I would
have started from. It
[EMAIL PROTECTED] writes:
I have one comment, although it is a little off topic.
I have the gregmisc package installed (R-2.0.1 on Win2000). Whenever I use
the help.search function it comes back with the following warning:
Warning message:
no Rd contents for package 'gregmisc' in
You asked for a stratified bootstrap, not a stratified estimator. This is
explained in the reference (Davison Hinkley).
On Wed, 4 May 2005, Richard Chandler wrote:
Hello,
I am new to R, and am having trouble getting the output I want from a
stratified bootstrap. I didn't recieve a reply the
Hi Walmir,
Here is the long version of Frank Harrell's answer.
http://www.pitt.edu/~wpilib/statfaq/regrfaq.html
Paul
On Tue, 2005-05-03 at 08:21 -0500, Frank E Harrell Jr wrote:
walmir-rodrigues wrote:
Dear Fellows,
How can I do to proced a step wise regression in R, if it´s
see ?aggregate.
Sean
On May 4, 2005, at 11:43 AM, alessandro carletti wrote:
Sorry for disturbing you with another newbie question!
I have a data frame about coastal waters quality
parameters: for some parameters (e.g. NH3) I have only
1 observation for each sampling station and each
sampling
On Wed, 04 May 2005 13:40:18 +0200,
christian schulz (cs) wrote:
Hi,
anybody know a possibilities how i could avoid less nicely cut's in
function calls with sweave like:
randomForest(x = RELSHIP ~ ., data = R_RELSHIP[splitR_RELSHIP == 1,
], importance = T, n(*here is
mingan wrote:
how do I check the rank of a matrix ?
say
A= 1 0 0
0 1 0
then rank(A)=2
what is this function?
Well, calculating the rank is from the computational point of view a
very hard problem.
See ?qr
Uwe Ligges
thanks
I did try help.search(rank), but all the returned help
Have you considered something like the following:
matrix.rank - function(A, eps=sqrt(.Machine$double.eps)){
sv. - abs(svd(A)$d)
sum((sv./max(sv.))eps)
}
matrix.rank(A=diag(3))
#[1] 3
A - array(c(1,1,0,0), dim=c(2,2))
matrix.rank(A)
#[1] 1
mingan wrote:
how do I check the
mingan wrote on 5/4/2005 8:54 AM:
how do I check the rank of a matrix ?
say
A= 1 0 0
0 1 0
then rank(A)=2
what is this function?
thanks
I did try help.search(rank), but all the returned help information
seem irrelevant to what I want.
I would like to know how people search for
I have an R script that I run using
nohup R CMD BATCH r.in r.out
The code loops through data from the database and takes hours. The
problem is, in about an hour and a half after I start the script the
program stops and I get
/usr/lib/R/bin/BATCH: line 55: 14067 Done( echo
Announcing two upcoming Bioconductor short courses:
June 1-3 in Seattle, WA
Bioconductor Short Course
Details: http://www.bioconductor.org/signup
June 19-25 in Bressanone-Brixen
Computational and Statistical Aspects of Microarray Analysis
Details: http://www.economia.unimi.it/marray/2005/
Best
qr() returns an estimate of the rank. However the rank of a matrix isn't
really computable (or useful) in general in finite precision arithmetic. The
Hilbert matrix example (from help(svd)) is a good illustration:
hilbert - function(n) { i - 1:n; 1 / outer(i - 1, i, +) }
qr(hilbert(9))$rank
[1]
On Wed, 4 May 2005, Sean Davis wrote:
see ?aggregate.
Or maybe tapply, or its close relative, by:
by(df, list(df$station, df$date), function(x)
+ x$row[which.max(x$chlorophyll)])
: Ancona
: 21/06/01
[1] NA
: Castagneto
:
In this case, try a lower tolerance (1e-7 is the default):
qr(hilbert(9), tol = 1e-8)$rank
[1] 9
On 5/4/05, Huntsinger, Reid [EMAIL PROTECTED] wrote:
qr() returns an estimate of the rank. However the rank of a matrix isn't
really computable (or useful) in general in finite precision
I would like to add to this discussion a quote from the book
``Subset Selection in Regression'' by Alan J. Miller (Chapman and
Hall, London, 1990). On page 12 the author remarks that when using a
``black box'' variable selection technique
``Throwing in a few more variables produced by a
I'd like to model the relationship between m responses Y1, ..., Ym and a
single set of predictor variables X1, ..., Xr. Each response is assumed
to follow its own regression model, and the error terms in each model
can be correlated. My understanding is that although lm() handles
vector Y's on
This is the back trace.
Is my best shot recompiling R with debug flag to get better info from
teh debugger?
(gdb) r --no-save r.in r.out
Starting program: /usr/lib/R/bin/exec/R --no-save r.in r.out
(no debugging symbols found)
(no debugging symbols found)
(no debugging symbols found)
(no
Hi Cristian,
Christian Lederer [EMAIL PROTECTED] writes:
is the announced solution for the GO 1.7.0 installation already
publicly available?
I am running into the same trouble as described in below, using
2.0.1 under Ubuntu Hoary.
Sorry about that. No, the solution was not publicly
Hi!!
I was trying to analyze my data by doing a linear discriminants and I
encountered
problems with collinearity. So I am planning to do a PCA to extract
orthogonal
components and then analyze them using linear discriminants. I don't know
how to relate the orthogonal components back to my
On May 4, 2005, at 9:18 AM, Uwe Ligges wrote:
Christoph Scherber wrote:
Dear all,
I am running Windows XP with several parallel installations of R
(2.0.1; 2.1 and so on). How can I install JGR for the 2.0.1
version? I keep on getting error messages when trying to install it.
I am sure Simon
Gabor Grothendieck wrote:
In this case, try a lower tolerance (1e-7 is the default):
qr(hilbert(9), tol = 1e-8)$rank
[1] 9
But don't trust the results. For example, create a matrix with 4
identical copies of hilbert(9). This still has rank 9. It's hard to
find, though:
h9 - hilbert(9)
On Tue, May 03, 2005 at 02:31:28PM +1200, Paul Murrell wrote:
No function, but does this do what you want?
[snip]
Yes, that worked perfectly. Thanks for your help.
Steven Murdoch.
--
w: http://www.cl.cam.ac.uk/users/sjm217/
__
Dear R-users,
Insightful has a position open for a Senior Software Engineer in
computational finance. We are looking for someone with both solid software
engineering skills and experience in computational finance. It's a very
interesting position for the right person.
The job description is
You can search on this forum for different discussions on this topic. Also,
there are 2 somehow outdated publications comparing different software
including SAS, SPSS and S-Plus, which might be of some use for you. The
references are:
McCullough, B. D. (1998), Assessing the reliability of
Bela Bauer [EMAIL PROTECTED] writes:
Hi,
I'm using anova.mlm sphericity tests/corrections, and I'm getting
different values than SAS. In order to be able to use these values for
publications, I'd need to know more about the SAS bug that is
mentioned in the Reference Manual.
- What exactly
Hi there,
I am working on a project which needs the value of the interaction area under
two distributions( eatimated by kernel density estimators).
For example:
x-rnorm(100,0,1)
y-rnorm(100,0.2,1)
density(x) # This produces the summary of dependent variable and independent
variable.
How
For the example that Duncan just gave, using the matrix.rank function of
Spencer Graves (which uses singular value decomposition) I obtained the
following result:
exponent - -(7:16)
eps - 10^exponent
sapply(eps,mat=h9times4,function(x,mat)matrix.rank(mat,x))
[1] 6 7 7 8 8 9 9 9 9 9
This
Dear All
I would like to know whether it is possible with R to get the
mathematical expression of the density of a sum of two independent
continuous random variables.
Thanks in advance,
Paul
__
R-help@stat.math.ethz.ch mailing list
Hi,
A density object's x and y values can be accessed using $x and $y
(this is in ?density, under Value:)
obj - density(rnorm(100, 0, 1))
obj$x
obj$y
You may find it useful to force the from and to arguments to be
the same for the two calls to density(), if you want to work directly
from the x
One could also examine the eigenvalues themselves:
plot(log(abs(sort(-eigen(h9times4, T, T)$values
shows a graph with a definite gap between 9 and 10 suggesting
that 9 is the right number.
On 5/4/05, Ravi Varadhan [EMAIL PROTECTED] wrote:
For the example that Duncan just gave, using
Hello
I am a long-time SAS user, but am new to R. I specifically am looking for
information pertaining to generating graphics for web output. I would like
to create dynamic graphics (in the form of generalized reports) for my web
site that is written with php and mysql. Is 'R' capable of
http://pscl.stanford.edu/content.html has code
for poisson and negative binomial hurdle models,
as well as for zip models. Package zicounts on
CRAN may also be of interest.
HTH,
Simon.
I am interested in utilizing this so called double hurdle model
in my study. We can write the model in the
Bayesian Model Averaging (BMA) R Package available
Free software to carry out Bayesian Model Averaging (BMA)
in R is now available at
http://cran.us.r-project.org/src/contrib/Descriptions/BMA.html
BMA is a way of taking account of uncertainty about
the form of the model used by averaging across
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