Hi all,
Could anybody give me some pointers to estimation of jump-diffusion
and self-exciting processes(or more generally, counting processes with
stochastic intensity, such as doubly stochastic processes, Cox
processes, Hawkes processes) using the Bayesian approach, esp. using
MCMC and BUGS, or
Hi all,
I am working for reconstructing haplotype from individual's SNPs. But I have
met a problem that most of paper and software I found are focus on
reconstructing haplotype from population's SNPs, rather than individual's
SNPs. I wonder is there any R package can be used to solve such
*I did some search before, I saw in the Nabbles forum one question about it
but without replies*.
I have a program written in R. For regulatory purposes I need to make exe
program of it and distribute to some users (the reason they don't want that
I provide the raw R code and that users run it
Hello,
I am trying to convince our IT Manager that R is as safe as possible from IT
security point of view - could you point me to something on the web / some
reasons for why this is true? I do not think he has a specific concern but does
not know the software and would like to understand the
R-help,
I'm trying to remove some packages with the command
remove.packages but R 2.4.1 will come out with this:
remove.packages(pkgs=FLAssess, lib = C:\\Program
Files\\R\\R-2.4.1\\library\\FLAssess)
Error in .find.package(pkgs, lib) : there is no package called
'FLAssess'
Thanks in advance
Well, of course it isn't true -- no piece of software is 'as safe as
possible'. I think some IT managers would prefer not to run any OSes on
their machines -- now, that is pretty safe (especially if they are then
switched off to say energy).
You haven't told us your OS -- and that usually
Hello everybody,
I have a problem with accessing class attributes. I think it might be
due to namespace access restrictions or something similar, but I'm
unable to figure it out, maybe someone knows the trick how to do
it ...
I'm trying to extract some information from the summary object for
Hello everybody,
I have a problem with accessing class attributes. I think it might be
due to namespace access restrictions or something similar, but I'm
unable to figure it out, maybe someone knows the trick how to do
it ...
I'm trying to extract some information from the summary object for
Try this:
remove.packages(FLAssess, lib=.Library)
or
remove.packages(pkgs=FLAssess, lib = C:\\Program Files\\R\\R-2.4.1\\library)
On Wed, Apr 2, 2008 at 7:32 AM, Luis Ridao Cruz [EMAIL PROTECTED] wrote:
R-help,
I'm trying to remove some packages with the command
remove.packages but R
You may want to plot your smooth terms:
plot(can3.gam,residuals=TRUE,pch=1).
The 7 and 4 estimated degrees of freedom on the two middle terms can give
you a quite curvy smooth term, and you might overfit the data (as mentioned
before by somebody else). Also, you may want to look at the
You've tried:
tab - [EMAIL PROTECTED]
?
On Wed, Apr 2, 2008 at 7:59 AM, Benjamin Polak [EMAIL PROTECTED] wrote:
Hello everybody,
I have a problem with accessing class attributes. I think it might be
due to namespace access restrictions or something similar, but I'm
unable to figure it
Dear Vera,
If the smoker/non-smoker variable is exogenous (as seems to be implied by
your calling it a predictor) then you can simply create a 0/1 dummy
regressor for it and calculate covariances in the usual manner. The
coefficient for the variable would have the usual interpretation for a dummy
Hello Martin,
I can tell you from my experience that quite a few insurance companies in the
London Market use R.
If this is not enough, the following document might help you do find some good
arguments:
http://www.actuaries.org.uk/files/pdf/proceedings/giro2006/Maynard.pdf
Best regards,
Work's for me:
summary(lmer(Reaction ~ Days + (Days|Subject), sleepstudy))@AICtab
On Wed, Apr 2, 2008 at 9:36 AM, Benjamin Polak [EMAIL PROTECTED]
wrote:
Thanks, but it doesn't work, I get the error message:
'no slot of name AICtab for this object of class table'
On Wednesday, 2. April
Thanks for your help, Henrique!
It's the same problem as I stated in my original post. The code works
if it runs as a regular R script, but not if it runs within a custom
package. Somehow, if the code is in the package, it doesn't see the
attribute anymore. I don't understand why. I've played
On Wed, 2 Apr 2008, Henrique Dallazuanna wrote:
Work's for me:
summary(lmer(Reaction ~ Days + (Days|Subject), sleepstudy))@AICtab
I think the issue is that in his package he is not seeing the summary S4
generic from Matrix (which is the one lme4 sets methods on). The package
needs to
Ah, that was it! I added importFrom(Matrix, summary) to my NAMESPACE
file, and now it works.
Thanks
Ben
On Wednesday, 2. April 2008 14:59, Prof Brian Ripley wrote:
On Wed, 2 Apr 2008, Henrique Dallazuanna wrote:
Work's for me:
summary(lmer(Reaction ~ Days + (Days|Subject),
analysis of variance was signifigant
there are a couple of observations that are NA
I would like to do a means seperation
TukeyHSD or pairwise.t.test
how do I deal with the NAs
I will provide the data if necessary
--
Let's not spend our time and resources thinking about things that are
so
I have two .txt files with lists of generated data I want to plot them on the
same histogram. I'm aware of the histbackback function, but that is not really
what I am looking for, I just want them on the same histogram but so they are
still grouped separately (different colours, different norm
Our March-April 2008 course schedule is now available online! With R/S
Fundamentals and Programming Techniques courses at 7 cities including
New York City / April 28-29, 2008 ***
Please direct enquiries to Sue Turner: [EMAIL PROTECTED] Phone:
206 686 1578
Ask for Group Discount
hadley wickham [EMAIL PROTECTED] writes:
Please read this first:
http://www.perceptualedge.com/articles/visual_business_intelligence/dual-scaled_axes.pdf
It's a reasoned discussion of why it's a bad idea and proposes some
alternative methods.
I've read the article, and I'm not sure if I'm
Dear R users,
Many thanks for your answers.
I've made much progress since my last posting.
I have now the followuing problem. I've run the GAM model
mygam - gam(Y ~ factor(year)
+ m1.q02 + m1.q05y + m1.q05y2 + m1.q06 + m4b.q05 + m4b.q052 + m5a.q01
+ depratio + depratio2 + residence10y + urbrur +
Dear R Users,
I'm trying to find function that allow me to solve one nonlinear equation.
Functions that I found are good for optimization problems.
Any suggestions are welcome,
rob
__
R-help@r-project.org mailing list
?help.search(time)
?proc.time
?system.time
You can stick these in your code appropriately to keep track of elapsed
time. You could also count iterations, of course.
-- Bert Gunter
Genentech
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Lukas Rode
On Wednesday 02 April 2008 04:58:28 pm [EMAIL PROTECTED] wrote:
ro I'm trying to find function that allow me to solve one nonlinear
ro equation. Functions that I found are good for optimization problems.
You are not very specific. If you want what I guess you should have a look at
a CAS program
From: [EMAIL PROTECTED]
Date: 2008/04/02 Wed AM 09:58:28 CDT
To: r-help@r-project.org
Subject: [R] Nonlinear equation
hi: you need to give an example and details or
you won't get much response, if any.
Equation e.g. (A, B are known constants):
Lukas Rode a écrit :
Nowever, with regard to #2, I am lost. I would like to set a maximum time
limit (say, 1 minute) and if my procedure is still running then, I would
like to move on to the next model.
begin_time = as.difftime(format(Sys.time(), '%H:%M:%S'), units='secs');
for(...)
{
On Wed, 2 Apr 2008, francogrex wrote:
*I did some search before, I saw in the Nabbles forum one question about it
but without replies*.
I have a program written in R. For regulatory purposes I need to make exe
program of it and distribute to some users (the reason they don't want that
I
Also, note that depending on A and B there are likely to be multiple (or no)
solutions to your equation.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine
On 4/2/2008 11:24 AM, [EMAIL PROTECTED] wrote:
From: [EMAIL PROTECTED]
Date: 2008/04/02 Wed AM 09:58:28 CDT
To: r-help@r-project.org
Subject: [R] Nonlinear equation
hi: you need to give an example and details or
you won't get much response, if any.
Equation e.g. (A, B
Dear Bert and Mel,
thanks for your help, but I'm afraid this doesn't solve my problem.
As I wrote in my previous mail (cf quote below) in most cases I will not be
able to modify the code of the function that I want to run. This is why I
was asking for a wrapper solution similar to what tryCatch
On Wed, 2008-04-02 at 16:46 +0200, R RR wrote:
Dear R users,
Many thanks for your answers.
I've made much progress since my last posting.
I have now the followuing problem. I've run the GAM model
mygam - gam(Y ~ factor(year)
+ m1.q02 + m1.q05y + m1.q05y2 + m1.q06 + m4b.q05 + m4b.q052 +
Hi all,
I have count data (number of flowering individuals plus total number of
individuals) across 24 sites and 3 treatments (time since last burn).
Following recommendations in the R Book, I used a glm with the model y~
burn, with y being two columns (flowering, not flowering) and burn the time
On 4/2/2008 12:00 PM, Lukas Rode wrote:
Dear Bert and Mel,
thanks for your help, but I'm afraid this doesn't solve my problem.
As I wrote in my previous mail (cf quote below) in most cases I will not be
able to modify the code of the function that I want to run. This is why I
was asking
Paul,
Have you tried using BFGS without bounds?
sols - optim(rep(20,nvar), f, gr, method=BFGS, control=list(fnscale=-1))
This converges to a solution, although I don't know if the converged
solution is what you want.
Ravi.
You should look at AutoIt or Autohotkey for this.
Best,
Philippe Grosjean
Duncan Murdoch wrote:
On 4/2/2008 12:00 PM, Lukas Rode wrote:
Dear Bert and Mel,
thanks for your help, but I'm afraid this doesn't solve my problem.
As I wrote in my previous mail (cf quote below) in most cases I
ASR == Allen S Rout [EMAIL PROTECTED]
on Wed, 02 Apr 2008 10:39:31 -0400 writes:
ASR hadley wickham [EMAIL PROTECTED] writes:
Please read this first:
http://www.perceptualedge.com/articles/visual_business_intelligence/dual-scaled_axes.pdf
It's a reasoned discussion
On Wed, 2008-04-02 at 12:03 -0400, Wade Wall wrote:
Hi all,
I have count data (number of flowering individuals plus total number of
individuals) across 24 sites and 3 treatments (time since last burn).
Following recommendations in the R Book, I used a glm with the model y~
burn, with y
Dear list:
I have a data frame with student name, class he attended and marks for
subjects he attended.
Students took second exam if they performed badly in their first attempt. I
want to consider the test scores where they obtain highest median.
there are 6 classes. As a sample case, I will
On Wed, Apr 2, 2008 at 5:05 PM, [EMAIL PROTECTED] wrote:
hi: you need to give an example and details or
you won't get much response, if any.
Equation e.g. (A, B are known constants):
3log(gamma(x))-log(gamma(x)*gamma(2x))+(x-1)*A+B=0
uniroot() can solve that if you can
Hi R-friends:
I don't understand very well the parser.
if I do:
p=v=
q=5
eval(parse(text=paste(p,q,sep=)))
... then the value of v is 5, OK.
but I can't with strings, for example:
p=v=
q=hello friend
eval(parse(text=paste(p,q,sep=)))
.. error
and, I would need that v has the value
When I run R CMD check pkg the R-ex folder containing examples is created in
pkg.Rcheck/pkg, however, when I run R CMD build pkg or R CMD INSTALL --build
pkg, it is not created. Should the folder and its examples be created
manually? I am running R 2.6.2 on Windows XP.
Hi,
I have to read in data which looks like this:
SeriesA, 5, 5, 5, 5
SeriesB, 8, 5, 8, 8, 7, 10, 2, 7, 3
SeriesC, 5, 5, 8, 4, 7, 7, 4, 5
SeriesD, 5, 9, 5, 4, 2, 3, 10, 1
SeriesE, 7, 10, 9, 5, 8, 6, 10, 9, 5, 10, 4, 3, 2, 10, 8, 8, 10, 10, 10
SeriesF, 1, 2, 1, 5, 1, 7, 5, 7, 7, 3
There are
p=v=
q=5
eval(parse(text=paste(p,q,sep=)))
... then the value of v is 5, OK.
but I can't with strings, for example:
p=v=
q=hello friend
eval(parse(text=paste(p,q,sep=)))
.. error
Try:
eval(parse(text=paste(p,',q,',sep=)))
Regards,
Richie.
Mathematical Sciences Unit
HSL
Hi, I have tried search around this forum for the best way to access a
data.frame.. i got the feeling that no partial match is the way to make it
fast so I convert everything to factor.. but I'm still not 100% sure if
the following code will do it... is this the fastest way to do something
On Wed, 2 Apr 2008, Duncan Murdoch wrote:
On 4/2/2008 12:00 PM, Lukas Rode wrote:
Dear Bert and Mel,
thanks for your help, but I'm afraid this doesn't solve my problem.
As I wrote in my previous mail (cf quote below) in most cases I will not be
able to modify the code of the function that I
Mark Lyman mark.lyman at gmail.com writes:
When I run R CMD check pkg the R-ex folder containing examples is created in
pkg.Rcheck/pkg, however, when I run R CMD build pkg or R CMD INSTALL --build
pkg, it is not created. Should the folder and its examples be created
manually? I am
Hi,
If I understand:
x - SeriesA, 5, 5, 5, 5
SeriesB, 8, 5, 8, 8, 7, 10, 2, 7, 3
SeriesC, 5, 5, 8, 4, 7, 7, 4, 5
SeriesD, 5, 9, 5, 4, 2, 3, 10, 1
SeriesE, 7, 10, 9, 5, 8, 6, 10, 9, 5, 10, 4, 3, 2, 10, 8, 8, 10, 10, 10
SeriesF, 1, 2, 1, 5, 1, 7, 5, 7, 7, 3
dat - t(read.table(textConnection(x),
On Wed, 2 Apr 2008, Gavin Simpson wrote:
On Wed, 2008-04-02 at 12:03 -0400, Wade Wall wrote:
Hi all,
I have count data (number of flowering individuals plus total number of
individuals) across 24 sites and 3 treatments (time since last burn).
Following recommendations in the R Book, I
The freely available R package glmmADMB can do Adaptive
Gaussian Quadrature for this type of model,
since it is built using AD Model Builder's random effects
module which incorporates this feature.
There is now a beta version of the software for
people using R on the Mac intel platform.
The freely available R package glmmADMB can do Adaptive
Gaussian Quadrature for this type of model,
since it is built using AD Model Builder's random effects
module which incorporates this feature.
There is now a beta version of the software for
people using R on the Mac intel platform.
Hello, my name is Alfonso. I've applied the boot function to my data and
I've obtained a collection of new datasets to witch apply a function that
produce as a final measure the fish length in a concrete moment of its life. In
my function there is a factor, the cohort to witch the fish
Thanks, Ravi. The analytical solution, (x_1,x_2,...,x_10), should
satisfy this equality:
x_t / x_(t-1) = 0.3.
Unfortunately, the procedure that you suggest does not lead to a
solution that satisfies such an equality.
Paul
On Wed, Apr 2, 2008 at 5:12 PM, Ravi Varadhan [EMAIL PROTECTED] wrote:
Yes, that is very important. If you look at the ratios x[k]/x[k-1], they
are very close to 0.3 for the first few components, and then they start
slowly diverging (ratio becomes smaller than 0.3) from that.
So, optim is indeed finding a correct solution to the problem that you
actually posed.
Hey paul,
Chk out some of these points as mentioned somewhere earlier in R help too
1. Trying to exponentiate potentially negative numbers is also asking for
trouble
2. Use lgamma() or choose() or lchoose() rather than gamma() or
factorial()
3. Worry about
Charlotte Wright [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
I have two .txt files with lists of generated data I want to plot them on
the same histogram. I'm aware of the histbackback function, but that is not
really what I am looking for, I just want them on the same histogram
[EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
Dear R Users,
I'm trying to find function that allow me to solve one nonlinear equation.
Functions that I found are good for optimization problems.
Perhaps try nlm or optim functions.
Earl F. Glynn
Bioinformatics
Stowers Institute
z1 = read.zoo(chemmgL.csv, sep=,, header=T, format=%m/%d/%y)
I would like to the entire date field in the plot - 1/1/07 all that I
get now is 2007
I do not include data because it is to large of a data set for an email
--
Let's not spend our time and resources thinking about things that are
Hello -
I am having a very hard time deciding what it is you want here. Could
you be more specific? Given your 'data' data.frame, what do you want
the output to be?
yoo wrote:
Hi, I have tried search around this forum for the best way to access a
data.frame.. i got the feeling that no
[EMAIL PROTECTED] [EMAIL PROTECTED] [Mon, Mar 31, 2008 at 07:02:25AM CEST]:
As far as I know there is no function called 'APPLY'
There is one called 'apply', but why are you determined to use it here?
It is essentially concealed looping.
I always use apply instead of for when the steps can
There are examples of using axis or Axis with plot.zoo and xyplot.zoo
in ?plot.zoo
?xyplot.zoo
and
vignette(zoo-faq)
On Wed, Apr 2, 2008 at 2:55 PM, stephen sefick [EMAIL PROTECTED] wrote:
z1 = read.zoo(chemmgL.csv, sep=,, header=T, format=%m/%d/%y)
I would like to the entire date field in
Thanks for the recommendations, insights. I tried using glm.nb, but it
didn't seem to like my data. I received the message (subscript) logical
subscript too long. I am using the same dataframe as my previous glm. Do
you know if I need to put the data in a different format?
Thanks,
Wade
On
I'm using R-2.6.2 on Fedora Linux 9.
I've been experimenting with plotmath.
I wish it were easier to combine expressions in plotmath with values
from the R program itself. There are two parameters in the following
example, the mean mymean and standard deviation mystd. I am able
to use bquote
Dear R community,I wish to include a variable (e.g. slice of a below)
in another variable's name. My objective would be to get a variable-name
data_A and so on. How can I do this?
a-LETTERS[1:25]
a
[1] A B C D E F G H I J K L M N O P Q R
S T U V W X Y
paste(data_,a[1])-c(1,2,3)
Error in
?assign
b
On Apr 2, 2008, at 4:26 PM, Georg Ehret wrote:
Dear R community,I wish to include a variable (e.g. slice of a
below)
in another variable's name. My objective would be to get a variable-
name
data_A and so on. How can I do this?
a-LETTERS[1:25]
a
[1] A B C D E F G H I J K L M
You'll want to use paste within the function assign.
However, consider using a list object to store this data to avoid
clutter (both in your workspace and head) and make subsequent data
analysis function calls easier.
Best,
Erik Iverson
Georg Ehret wrote:
Dear R community,I wish to
On 4/2/2008 4:11 PM, Paul Johnson wrote:
I'm using R-2.6.2 on Fedora Linux 9.
I've been experimenting with plotmath.
I wish it were easier to combine expressions in plotmath with values
from the R program itself. There are two parameters in the following
example, the mean mymean and
R users,
Is it possible to do 'exact' permutation tests in R? If I run a perm.test or
permutation.test.discrete on a data set that has, for example, 720 possible
permutations, will that test permute ALL of those possible permutations, or
will it just permute 720 random permutations (thus
Hi all,
It is for sure that I could find more powerful packages to plot my data,
but this simple barplot() was doing well so far.
My problem now is that I would need to rotate bar labels.
Please, is this possible without going to use axis()?
I am trying to keep the workflow as simple as
Ricardo
The las argument will allow rotation of 90 degrees:
par(mfrow=c(2,2))
barplot(1:10, names=letters[1:10], las=0)
barplot(1:10, names=letters[1:10], las=1)
barplot(1:10, names=letters[1:10], las=2)
barplot(1:10, names=letters[1:10], las=3)
If you want to do other rotation angles then it
Thanks Peter,
Peter Alspach wrote:
Ricardo
The las argument will allow rotation of 90 degrees:
par(mfrow=c(2,2))
barplot(1:10, names=letters[1:10], las=0)
barplot(1:10, names=letters[1:10], las=1)
barplot(1:10, names=letters[1:10], las=2)
barplot(1:10, names=letters[1:10], las=3)
If
Wade Wall wade.wall at gmail.com writes:
Thanks for the recommendations, insights. I tried using glm.nb, but it
didn't seem to like my data. I received the message (subscript) logical
subscript too long. I am using the same dataframe as my previous glm. Do
you know if I need to put the
Wade Wall [EMAIL PROTECTED] wrote in
news:[EMAIL PROTECTED]:
Thanks for the recommendations, insights. I tried using glm.nb, but
it didn't seem to like my data. I received the message (subscript)
logical subscript too long. I am using the same dataframe as my
previous glm. Do you know if
Hi,
I am currently using R extensively to develop a statistical model and
currently learning its capabilities.
I am trying to develop a logistic regression model using glm and stepAIC
I constructed my formula as y ~ a + b + c + d
Now I wish to study the interaction between variables. So
Warning message:
In readChar(con, 5) : can only read in bytes in a non-UTF-8 MBCS locale
__
Chuntang YU
E-mail: [EMAIL PROTECTED]
__
[[alternative HTML version deleted]]
__
Thank you, everyone.
On Thu, Apr 3, 2008 at 10:22 AM, Chuntang YU [EMAIL PROTECTED] wrote:
Warning message:
In readChar(con, 5) : can only read in bytes in a non-UTF-8 MBCS locale
__
Chuntang YU
E-mail: [EMAIL PROTECTED]
Here's a question: I noticed that when I tried to create this simple
graph of rectangles and text, R appears to generate text that is
rasterized (this is seen both on the monitor and when the output is
directed to a pdf file). Any thoughts?
value.seq - c(4,as.character(seq(from=4,to=10)),11)
We haven't been told your OS or the graphics device or how you viewed PDF
output. But all text on screen devices is rasterized -- they are raster
devices. (That includes your pdf viewer.)
You are writing the label 9 times in the same place. I suspect what you
are seeing is a viewer artifact
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