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On Sun, Jun 26, 2011 at 2:17 AM, elisheva corn elishevac...@gmail.com wrote:
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HTH,
Jorge
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Another option is
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Best,
Ista
On Sun, Jun 26, 2011 at 2:25 AM, Jorge Ivan Velez
jorgeivanve...@gmail.com wrote:
Check R-help Subscribers at https://stat.ethz.ch/mailman/listinfo/r-help
HTH,
Jorge
On Sun, Jun 26, 2011 at 2:17 AM, elisheva corn
Dear List,
Can anyone please explain the difference between cluster() and
frailty() in a coxph? I am a bit puzzled about it. Would appreciate
any useful reference or direction.
cheers,
Ehsan
marginal.model - coxph(Surv(time, status) ~ rx + cluster(litter), rats)
frailty.model -
Hey,
I just read another post about calling R from C. Someone on
stackoverflow (DWin makes me suspect its David W.?) referenced this:
http://www.math.univ-montp2.fr/~pudlo/R_files/call_R.pdf
Which made me think: Why is a loop in R bad, but in C not?
And where exactly does looping cost the
Dear Community,
my program below runs quite slow and I'm not sure whether the http-requests are
to blame for this. Also, when running it gradually increases the memory usage
enormously. After the program finishes, the memory is not freed. Can someone
point out a problem in the code? Sorry my
For the same reason the Cray XMP was fast at numerical computations... a loop
written in a low level language can be optimized to work faster than one
written in a higher level language. The XMP optimized loops into hardware, but
R just optimizes them in C code, exposed to the R programmer as
Hi Ehsan,
My understanding (hopefully someone will jump in if this is wrong) is
that cluster() identifies a variable that is an indicator for
correlated observations (rats in a litter, children in a classroom,
etc.). The relative risk from treatment (rx) is for a random sample
of rats.
Probably the easiest way to think
about it is that most of the extra
time is the overhead of calling a
function. So counting the number
of calls to R functions is going to
tell you how much overhead there is.
(Remember that functions call other
functions.)
On 26/06/2011 08:21, Jeff Newmiller
I use the following function which does not uses loops and seems to be
pretty fast:
dmvnorm - function (x, mu, Sigma, df, log = FALSE) {
if (!is.matrix(x))
x - rbind(x)
p - nrow(Sigma)
ed - eigen(Sigma, symmetric = TRUE)
ev - ed$values
if (!all(ev = -1e-06 *
Hi R users,
I want to know whether there is a fast method to compute the nonzeroes for
each column of dgCMatrix.
For summation or average I can use colSums or colMeans. To count the
non-zeroes I write a function
colCounts - function(Mat) {
M1 - apply(Mat, MARGIN=2, FUN=nnzero)
}
But it
Hello Hugo,
Thank you for your reply.
This is a snap shot of what my data looks like:
Presencebsence
Habitatype
Substratetype
Width
Banktype
BankIncline
Bankheight
Waterdepth
0
Lake
Rocksgravel
600
Earth
0.45
less1
greater2
0
Lake
Hi everyone.
My problem: I've 4 distributions: A, B, C and D:
#A
mA=16.6
sA=3.0
#B
mB=18.9
sB=3.2
#C
mC=20.3
sC=2.1
#D
mD=24
sD=0.8
###Graphiques ensembles
plot(function(x) dnorm(x,mA,sA),0,40,col=orange,ylim=c(0,0.5))
plot(function(x) dnorm(x,mB,sB),0,40,add=T,col=green)
Dear R members
Could someone tell me how to simulate Likert-type data using the rnorm
function.
Let's say, 200*15 random numbers in a variable that goes from 1 to 4 in
steps of
1 (i.e., 1, 2, 3, 4) belonging to a normal distribution?
random.data â matrix(rnorm(200 * 15), nrow = 200, ncol
?sample
Date: Sun, 26 Jun 2011 02:26:10 -0700
From: wjca...@hotmail.com
To: r-help@r-project.org
Subject: [R] how to simulate Likert-type data using R
Dear R members
Could someone tell me how to simulate Likert-type data using the rnorm
function.
Let's say, 200*15 random numbers in a
Hello
My data.frame (dat) contains many variables named var.names and others
named var.names_var.id
For example
var.name - c(gdp,inf,unp)
var.id - c(w,i)
x - paste(var.name, rep(var.id, each=length(var.name)), sep=_)
How can I access variables in the dama.frame by names listed in x, for
Dimitris,
Thanks for the great code. When the number of rows of X and mu are large, it
is probably faster due to R's vectorization. Thanks again.
--
View this message in context:
http://r.789695.n4.nabble.com/Multivariate-normal-density-in-C-for-R-tp3624602p3625857.html
Sent from the R help
Duncan,
it isn't really that difficult to diagnose. A google search for
ss11=sample(x1, n1, replace=TRUE)
turned up this documented R-script
ttp://www2.latech.edu/~dcahoy/TwoSampleEqualVarTest.R
as a likely source for his fragmented and mangled post; other variable
names
Thanks everyone!
Now it became difficult to decide. I will give feedback soon.
Caveman
On Sat, Jun 25, 2011 at 9:59 PM, Tobias Verbeke
tobias.verb...@openanalytics.eu wrote:
Hi Caveman,
On 06/25/2011 11:18 AM, Orvalho Augusto wrote:
I need a way to send R objects and call R functions
Corect me if this is not the right place to post this.
I have a mdbdriver.jar (to access an MSAccess file) under Linux. I bought
the license from http://www.csv-jdbc.com/ guys. The driver work fine when
tested with DBVisualizer or another JDBC thing.
The problem is that driver needs 3 other more
Thank you all for the answering.
Sorry I did not state the problem clearly. I want to take the integration
with respect to mu, not x.
For example, f1 should have been a function of x after integrating mu out of
f(x, mu) which is the following:
f(x, mu)=dnorm(x, mean=mu, sd=1)*dnorm(mu, mean=2,
Hi All
I have a symmetric matrix of genes ( 100x100 matrix). I also have a matrix
(100x2) of two columns where column 1 has the gene names and column 2 has
the cluster it belongs to (they are sorted and grouped based on the cluster
no).
I would like to order the rows and columns of the 100x 100
On Jun 26, 2011, at 2:56 AM, Alexander Engelhardt wrote:
Hey,
I just read another post about calling R from C. Someone on
stackoverflow (DWin makes me suspect its David W.?) referenced this: http://www.math.univ-montp2.fr/~pudlo/R_files/call_R.pdf
Which made me think: Why is a loop in R
Hi there,
Does anyone know how to extract data from a function that prints out two or
more summaries? In the function below (the whole code is provided) we get 5
different tables of data. I would like to split each of these tables in a
separate file (while the function itself shouldn't be
As a start, run matchit() for a test dataset and look at:
names(m.out)
and
names(summary(m.out))
You can save those named components in the usual ways.
Sarah
On Sun, Jun 26, 2011 at 10:06 AM, Ana Kolar annako...@yahoo.com wrote:
Hi there,
Does anyone know how to extract data from a function
Dear all, I have following kind of character vector:
Vec - c(344426, dwjjsgcj, 123sgdc, aagha123, sdh343asgh, 123jhd51)
Now I want to split each element of this vector according to numeric and string
element. For example in the 1st element of that vector, there is no string
element. Therefore
On Sun, Jun 26, 2011 at 10:54 AM, Megh Dal megh700...@yahoo.com wrote:
Dear all, I have following kind of character vector:
Vec - c(344426, dwjjsgcj, 123sgdc, aagha123, sdh343asgh,
123jhd51)
Now I want to split each element of this vector according to numeric and
string element. For
On 2011-06-26 06:34, li li wrote:
Thank you all for the answering.
Sorry I did not state the problem clearly. I want to take the
integration with respect to mu, not x.
For example, f1 should have been a function of x after integrating mu
out of f(x, mu) which is the following:
f(x, mu)=dnorm(x,
summary(m.out) is a list with items with those names. Once you know
the names, you can extract them in the same way as you'd extract any
element from a list: by name, by position, etc.
On Sun, Jun 26, 2011 at 10:48 AM, Ana Kolar annako...@yahoo.com wrote:
Thank you Sarah!
But
On Jun 26, 2011, at 10:54 AM, Megh Dal wrote:
Dear all, I have following kind of character vector:
Vec - c(344426, dwjjsgcj, 123sgdc, aagha123, sdh343asgh,
123jhd51)
Now I want to split each element of this vector according to numeric
and string element. For example in the 1st element
On Sun, Jun 26, 2011 at 11:00 AM, Gabor Grothendieck
ggrothendi...@gmail.com wrote:
On Sun, Jun 26, 2011 at 10:54 AM, Megh Dal megh700...@yahoo.com wrote:
Dear all, I have following kind of character vector:
Vec - c(344426, dwjjsgcj, 123sgdc, aagha123, sdh343asgh,
123jhd51)
Now I want to
IIRC, package mvtnorm will allow an X matrix, but requires mu to be a vector,
so although it's close, it won't do it all...but all suggestions are well
received.
Dimitrius, you don't happen to have the multivariate t form of that
function, do you?
--
View this message in context:
Combine the two matrices into one data.frame and order them
Example done using data.frames rather than matrices but just use use
data.frame(x,y) to convert to a data.frame
bmat - data.frame(matrix(1:25,5))
smat - data.frame(aa= LETTERS[1:25],
bb = rep(c(a,b,c, d, e),5))
df1 -
On 6/26/2011 5:53 PM, zerfetzen wrote:
IIRC, package mvtnorm will allow an X matrix, but requires mu to be a vector,
so although it's close, it won't do it all...but all suggestions are well
received.
Dimitrius, you don't happen to have the multivariate t form of that
function, do you?
Well,
The package lmomco gives the L-moments ratio diagram for some
distributions. It is important to have the TL-moments ration diagrams
also. Does anyone know how to get this diagrams. thank you
--
Osama Abdelaziz Hussien
Department of Statistics
Faculty of Commerce
Alexandria University
Egypt
Peter, Thank you very much!
2011/6/26 Peter Ehlers ehl...@ucalgary.ca
On 2011-06-26 06:34, li li wrote:
Thank you all for the answering.
Sorry I did not state the problem clearly. I want to take the
integration with respect to mu, not x.
For example, f1 should have been a function of x
Hi:
What about
colSums(mymat != 0)
?
# Example:
x - matrix(sample(c(-1, 0, 1, 2), 100, replace = TRUE, prob = c(0.1,
0.8, 0.07, 0.03)),
nrow = 25)
which(x != 0) # 17 nonzero elements in this matrix
[1] 9 17 27 32 36 41 44 45 49 50 62 67 68 72 76 78 82
colSums(x != 0)
[1] 2 8 4
Hi R users:
How can I obtain an italic font only
for one of the two strips in a xyplot?
library(lattice)
t-rep(seq(0,10,5),4)
logCFU-c(2,2.5,3,4,4.5,1.5,2,2.5,3,3.4,2,2.5)
microorg-factor(rep(c(E. coli,L. monocytogenes),each=6))
tratam-factor(rep(c(t1,t2),6))
I am trying generate a sample for a truncated multivariate normal
distribution via the rtmvnorm function in the {tmvtnorm} package.
Why does the following produce NaNs?
rtmvnorm(1, mean = rep(0, 2), matrix(c(0.06906084, -0.07463565, -0.07463565,
0.08078086),2),c(-0.4316738, 0.8283240),
Sophie,
sorry for any possibly duplicate email, my email client currently does not
work correctly. I understand this snapshot as being a subset of your data only.
But I do miss the factor Sitename, which appears in your lmer model as a
random factor. Also, by looking at the subset,
Hi,
I am new to R. Is there a R package for HP-UX Itanium 64 bits server available?
Thanks very much for your help!
Hong
Hong Zhou, MS, MIS
Senior Systems Analyst
Center for Outcomes Research
The Children's Hospital of Philadelphia
3535 Market St. Suite 1029
Philadelphia, PA 10104
Tel: (215)
I´m not an expert either, but from my own experience with those annoying
messages, I can suggest you some precautions you should take:
- First of all, make sure, in your .txt file, that you are using dots for
separating decimals, NOT commas.
- Before writing your model, test each of
On Jun 26, 2011, at 00:10 , David Winsemius wrote:
On Jun 25, 2011, at 4:33 PM, peter dalgaard wrote:
I.e., an unevaluated formulae expression (as in quote(y~x)) is class call,
as is an unclassed formula object. So it is pretty easy to have objects of
class formula very similar to
This is what I have now so far.
p=ggplot(data = test, aes(x = YEAR, y = TOTAL, colour = TREATMENT)) +
geom_point() + geom_smooth(method = lm, se=FALSE) + facet_wrap(~COUNTRY)
p +scale_x_continuous(limits=c(1,4))
http://r.789695.n4.nabble.com/file/n3626510/graph.gif
I would also like to:
1.)
I was glad to see the new rpart.plot package by Stephen Milborrow. I was
however a bit concerned that Stephen distributed a dataset I created, and
renamed the dataset (from titanic3 to ptitanic) in the process [with some
justification, as some variables were omitted]. Fortunately Stephen
On Jun 26, 2011, at 1:10 PM, Zhou, Hong wrote:
Hi,
I am new to R. Is there a R package for HP-UX Itanium 64 bits server
available?
Questions about obscure Unix systems generally get directed to the r-
devel mailing list.
I'm assuming you are asking if it is possible to compile R from
Hi all,
I used bwplot in lattice to create a 6-panel boxplot grouped by a
conditioning variable (param) that displays concentration (conc) in
response to treatment (trtmnt). Here is the functional part of my
code followed by my three questions:
library(lattice);
I was wrong about this. The dataset is small. Most of the space is taken up
by a nice tutorial on rpart.plot. Still I would favor linking to datasets
rather than duplicating part of them.
Thanks
Frank
Frank Harrell wrote:
I was glad to see the new rpart.plot package by Stephen Milborrow. I
On 2011-06-26 11:33, Kenneth Roy Cabrera Torres wrote:
Hi R users:
How can I obtain an italic font only
for one of the two strips in a xyplot?
library(lattice)
t-rep(seq(0,10,5),4)
logCFU-c(2,2.5,3,4,4.5,1.5,2,2.5,3,3.4,2,2.5)
microorg-factor(rep(c(E. coli,L. monocytogenes),each=6))
Just to start things off:
var.name - c(gdp,inf,unp)
var.id - c(w,i)
x - paste(var.name, rep(var.id, each=length(var.name)), sep=_)
x
[1] gdp_w inf_w unp_w gdp_i inf_i unp_i
Now the three differences:
gdp_w - gdp_i
inf_w - inf_i
unp_w - unp_i
Can be got using
dwi - dat[, x[1:3]] -
Thank you very much!
That was exactly what I need!
The answer was not obvious as I thought.
El dom, 26-06-2011 a las 14:36 -0700, Peter Ehlers escribió:
On 2011-06-26 11:33, Kenneth Roy Cabrera Torres wrote:
Hi R users:
How can I obtain an italic font only
for one of the two strips in
Oh. Fantastic! Many thanks for this, Sarah!
Have a great week!
Ana
From: Sarah Goslee sarah.gos...@gmail.com
To: Ana Kolar annako...@yahoo.com; r-help r-help@r-project.org
Sent: Sunday, 26 June 2011, 17:06
Subject: Re: [R] how to extract data from a function
My ignorance! I managed to connect doing:
library(RJDBC)
cp - c(
/opt/DbVisualizer-7.1.1/jdbc/mdb/log4j.jar,
/opt/DbVisualizer-7.1.1/jdbc/mdb/commons_lang.jar,
/opt/DbVisualizer-7.1.1/jdbc/mdb/commons_logging.jar
)
.jinit(classpath=cp)
drv - JDBC(jstels.jdbc.mdb.MDBDriver,
Em 26/6/2011 17:43, Frank Harrell escreveu:
I was glad to see the new rpart.plot package by Stephen Milborrow. I was
however a bit concerned that Stephen distributed a dataset I created, and
renamed the dataset (from titanic3 to ptitanic) in the process [with some
justification, as some
Hello,
my name is Carsten. This ist my first post to R-help mailing list.
I estimate densities with the function density out of the package
stats.
A simplified example:
#generation of test data
n=10
z = rnorm(n)
#density estimation
- Forwarded Message -
From: Ungku Akashah kasla...@yahoo.com
To: r-help@r-project.org r-help@r-project.org
Sent: Friday, June 24, 2011 3:15 PM
Subject:
hi dear R crew.
may i request the script for volcano plot.
if able, pls include any tips about volcano plot.
thank you.
Hi, I can not estimate the zero inflated mixed model parameters successfully.
If it is possible, would you please help me write the code? In my case, I
consider the location as a random effect. My data are:
location y x1 x2 x3
1
1
1
2
2
2
3
3
3
Thank you very much.
Yours,
Xiongqing
Dear Sir,
Just started using R. I want to plot x-1:20, for example, in the colour
blue. How do I do this?
Regards,
Ivo
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R-help@r-project.org mailing list
- Forwarded Message -
From: Ungku Akashah kasla...@yahoo.com
To: r-help@r-project.org r-help@r-project.org
Sent: Friday, June 24, 2011 3:15 PM
Subject:
hello.
I need some help about this R software. I've been searching for volcano plot
script for long, but still not found.
May i
hello.
I need some help about this R software. I've been searching for volcano
plot(statistic) script for long, but still not found.
May i request the script for volcano plot. If able, pls include any tips about
volcano plot.
thank you.
[[alternative HTML version deleted]]
Hi Ungku,
Check
?persp
?volcano
in the R console.
HTH,
Jorge
On Sun, Jun 26, 2011 at 9:22 PM, Ungku Akashah wrote:
- Forwarded Message -
From: Ungku Akashah
To: r-help@r-project.org
Sent: Friday, June 24, 2011 3:15 PM
Subject:
hello.
I need some help about this R
plot(1:20,col='blue')
On Mon, Jun 27, 2011 at 9:40 AM, gwanme...@aol.com wrote:
Dear Sir,
Just started using R. I want to plot x-1:20, for example, in the colour
blue. How do I do this?
Regards,
Ivo
[[alternative HTML version deleted]]
You can find the volcano script (along with a lot of others) at the
following site:
http://addictedtor.free.fr/graphiques/thumbs.php
On Mon, Jun 27, 2011 at 11:49 AM, Jorge Ivan Velez
jorgeivanve...@gmail.com wrote:
Hi Ungku,
Check
?persp
?volcano
in the R console.
HTH,
Jorge
On
Hello,
I am having errors when I try to install RSPerl-0.92 under fedora 14.
I have the following rpms installed:
R-devel-2.13.0-1.fc14.x86_64
R-core-2.13.0-1.fc14.x86_64
perl-5.12.3-143.fc14.x86_64
perl-devel-5.12.3-143.fc14.x86_64
perl-ExtUtils-* (all of them from yum)
Now I get the following
Hi
On Sun, Jun 26, 2011 at 4:21 PM, Sigrid s.stene...@gmail.com wrote:
This is what I have now so far.
p=ggplot(data = test, aes(x = YEAR, y = TOTAL, colour = TREATMENT)) +
geom_point() + geom_smooth(method = lm, se=FALSE) + facet_wrap(~COUNTRY)
p +scale_x_continuous(limits=c(1,4))
On Mon, Jun 27, 2011 at 2:35 AM, Saalem Adera saalemad...@gmail.com wrote:
Hi all,
I used bwplot in lattice to create a 6-panel boxplot grouped by a
conditioning variable (param) that displays concentration (conc) in
response to treatment (trtmnt). Here is the functional part of my
code
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