Dear Friends,
I am seeking for any help on an error message in lme
functions. I use mixed model to analyze a data with
compound symmetric correlation structure. But I get an
error message: Error in corMatrix.corCompSymm(object) :
NA/NaN/Inf in foreign function call (arg 1). If I change
the
Dear R-help,
How could a cross-correlation plot be optimized such that the relationship
between seasonal time-series can be studied?
We are working with strong seasonal time-series and derived a
cross-correlation plot to study the relationship between time-series. The
seasonal variation however
On Mon, 31 Oct 2005, Olaf Schenk wrote:
Dear R users,
I would like to use several R functions from a C-code and I have read
the Introduction to the .C Interface to R. Unfortunately, my shared
library with the C-code works only in cases where I use R-routines that
are defined Rmath.h, eg.
On Mon, 31 Oct 2005, Romain Francois wrote:
Le 31.10.2005 11:22, Robert a écrit :
I have two groups of data and want to test how the
mean of one group is significant different from the
mean of the other group of data.
which R function can be used?
Thanks.
t.test if you assume normality
Le 31.10.2005 13:45, Prof Brian Ripley a écrit :
On Mon, 31 Oct 2005, Romain Francois wrote:
Le 31.10.2005 11:22, Robert a écrit :
I have two groups of data and want to test how the
mean of one group is significant different from the
mean of the other group of data.
which R function can
I use the lme function from the nlme library (or alternatively from the
Matrix library) to estimate a random effects model. Both functions return
the covariance matrix of the estimated parameters. I have the following
question:
Is it possible to retrieve the information matrix of such a model
I have defined a function to compute the value of a
beta distribution of the second kind (the existing
beta distribution of th stats package is the beta
distribution of the first kind). It works perfectly
for a single value, but I want to apply it to a vector
of 22 000 values. I can use a loop for
Florent
have a look at:
help(sapply)
On Mon, 31 Oct 2005, Florent Bresson wrote:
I have defined a function to compute the value of a
beta distribution of the second kind (the existing
beta distribution of th stats package is the beta
distribution of the first kind). It works perfectly
for a
I just have a try with sapply. The problem is that my
function pbeta2 has two parameters z and p (wich is a
vector of two parameters). If I use sapply , R returns
a message incicating that parameter p is missing. It
is a problem since both z and p are varying along my
data.frame.
Florent
have a
On Mon, 31 Oct 2005, Florent Bresson wrote:
I just have a try with sapply. The problem is that my
function pbeta2 has two parameters z and p (wich is a
vector of two parameters). If I use sapply , R returns
a message incicating that parameter p is missing. It
is a problem since both z and p are
I wish to obtain the right-most n characters of a character string? What is
the appropriate function?
-
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
On Mon, 31 Oct 2005, Thomas Lumley wrote:
On Mon, 31 Oct 2005, Florent Bresson wrote:
I just have a try with sapply. The problem is that my
function pbeta2 has two parameters z and p (wich is a
vector of two parameters). If I use sapply , R returns
a message incicating that parameter p is
You should then try apply. See ?apply.
For instance:
a - matrix(c(1:10), 5, 2)
apply(a, 1, function(x) x[1] + 100 * x[2])
This way you can disaggregate the components of your input (that is not a
singleton) and use them inside your function separately.
Carlos J. Gil Bellosta
Dear R list,
I'm having some problems with font encodings when using R+Sweave+Latex in my
native language: Portuguese.
My environment:
Kubuntu 5.10 Linux
$ uname -a
Linux nassa 2.6.12-9-686 #1 Mon Oct 10 13:25:32 BST 2005 i686 GNU/Linux
R R.version
_
platform
?nchar
?substr
rightmost - function(x, y){substr(x, start=nchar(x) - (y - 1),
stop=nchar(x))}
x - c(asfef, qwerty, yuiop[, b, stuff.blah.yech)
rightmost(x, 2)
[1] ef ty p[ b ch
rightmost(x, 3)
[1] fef rty op[ b ech
t c wrote:
I wish to obtain the right-most n characters of a
t c wrote:
I wish to obtain the right-most n characters of a character string? What is
the appropriate function?
See ?nchar ?substr
k - 2
x - abcdef
nc - nchar(x)
substr(x, nc - k + 1, nc)
HTH,
--sundar
__
R-help@stat.math.ethz.ch mailing
t c wrote:
I wish to obtain the right-most n characters of a character string? What is
the appropriate function?
You could make one yourself:
rightmostn - function(x, n){
res - substr(x, nchar(x)-n+1, nchar(x))
return(res)
}
magic - hocuspocus
rightmostn(magic, 5)
[1] pocus
HTH,
t c [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
I wish to obtain the right-most n characters of a character string? What
is the appropriate function?
substr will work:
x - c(abcd, xyz)
N - 2
substr(x, nchar(x)-N+1, nchar(x))
[1] cd yz
N - 3
substr(x, nchar(x)-N+1,
It works really faster with mapply. I just had to
change my fonction from pbeta2(z,p) with p=c(p1,p2) to
pbeta2(z,p1,p2). Thanks for the tip.
--- Thomas Lumley [EMAIL PROTECTED] a écrit :
On Mon, 31 Oct 2005, Florent Bresson wrote:
I just have a try with sapply. The problem is that
my
Hi,
I have a binary (o/1 - coded) data set and want to test it's autocorrelation
structure. Is that function implemented in R?
Can I use the ACF - funtion with binary data?
Thanks for your help,
Daniel
__
R-help@stat.math.ethz.ch mailing list
Note that this one can be slightly simplified by using sub instead of gsub
(since you only will have one match anyways) and the $ is not needed
since .* will consume the maximal matching string:
sub(.*(..), \\1, mystring)
On 10/31/05, Carlos J. Gil Bellosta [EMAIL PROTECTED] wrote:
Hi,
I use write.table() to write a file to an external xls file. the column names
left-shift one position in output file. I check with col.names() row.names(),
the file is fine. How to prevent the shifting?
I71 I111I304I307I305I306I114I72
On Mon, 31 Oct 2005 16:46:24 +0100,
Luís Torgo (LT) wrote:
Dear R list,
I'm having some problems with font encodings when using R+Sweave+Latex in
my
native language: Portuguese.
My environment:
Kubuntu 5.10 Linux
$ uname -a
Linux nassa 2.6.12-9-686 #1 Mon Oct 10 13:25:32
Hello R-users,
I am a relatively new user of R and I have a question regarding glm. I want
to run the function GLM on multiple individuals separately and then get
means for summary statistics such as AIC and coef. Is there a way to do this
in R without separately going through each individual
Prof Brian Ripley [EMAIL PROTECTED] writes:
Sorry, no. The Wilcoxon test does NOT test a difference in means: its
null hypothesis is that the two samples came from the same continuous
distribution, a much narrower assumption. (It is sensitive to
differences in variances, for example, and is
You are using UTF-8 and declaring latin1. It is your use of UTF-8
that will have changed, not R.
On Mon, 31 Oct 2005, Luís Torgo wrote:
Dear R list,
I'm having some problems with font encodings when using R+Sweave+Latex in my
native language: Portuguese.
My environment:
Kubuntu 5.10 Linux
$
Dear Group,
I am a novice R programmer with little statistical
background. I am a molecular biologist by training.
I generated a correlation matrix (157 X 157) for 157
variables.
I want to selection only the unique values (values
that are either side of the diagnol). I want these
unique
Have you received a reply to this? I haven't seen one. I just tried
several things with RSiteSearch. Searching for ordered logit produced
70 hits. One of the first 10 indicate, The CRAN package MCMCpack has
at least ordered probit.
This will give you a matrix with the row/column names of the respective
values. Not sure what you meant by a list, but you can convert the matrix to
a list.
m2
a b c d e
A 1 5 9 13 17
B 2 6 10 14 18
C 3 7 11 15 19
D 4 8 12 16 20
cbind(row=rownames(m2)[row(m2)[lower.tri(m2)]],
+
Hi Jim,
Thanks for the tip, but I really need the same polar chart but over a
line no in a circle. I didn't find it on the plotrix package.
Regards, EKS
Jim Lemon wrote:
Eduardo Klein wrote:
Hi,
I'm looking for the way to make vector plot over a time line. This
plot, similar to the
Not sure if this is what you are looking for but check out:
http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=80
On 10/31/05, Eduardo Klein [EMAIL PROTECTED] wrote:
Hi Jim,
Thanks for the tip, but I really need the same polar chart but over a
line no in a circle. I didn't find it
Hi, I have no experience with R and I'm finding the manuals a bit obtuse
and written as if I already understood R.
I'm trying to import a csv file from a floppy and it's not working. The
code I'm using is
read.table(F:\GEORGIA\species_richness\SR_use.csv, sep=,, header =
TRUE, row.names = 1)
On Mon, 31 Oct 2005, Jeffrey Stratford wrote:
Hi, I have no experience with R and I'm finding the manuals a bit obtuse
and written as if I already understood R.
I'm trying to import a csv file from a floppy and it's not working. The
code I'm using is
On Mon, 31 Oct 2005, Jeffrey Stratford wrote:
Hi, I have no experience with R and I'm finding the manuals a bit obtuse
and written as if I already understood R.
I'm trying to import a csv file from a floppy and it's not working. The
code I'm using is
On Mon, 31 Oct 2005, Jeffrey Stratford wrote:
Hi, I have no experience with R and I'm finding the manuals a bit obtuse
and written as if I already understood R.
I'm trying to import a csv file from a floppy and it's not working. The
code I'm using is
If you mean you want to test that there is no autocorrelation,
then there is some information on using the Ljung-Box test on
such data in the working paper 'Robustness of the Ljung-Box
test and its rank equivalent' on the Burns Statistics website.
The executive summary is that the test seems to
On 10/31/2005 1:31 PM, Jeffrey Stratford wrote:
Hi, I have no experience with R and I'm finding the manuals a bit obtuse
and written as if I already understood R.
I'm trying to import a csv file from a floppy and it's not working. The
code I'm using is
Try this:
# test data
mm - cor(iris[,-5])
mm
# get upper triangle from matrix
mm[lower.tri(mm)]
# if you want it as a data frame with columns for row and column names
as.data.frame.table(mm)[lower.tri(mm),]
In either of the cases above you could substitute row(mm) col(mm)
for lower.tri(mm)
Hi,
Recently I was told by users of some of the function I wrote that they
experience crashes in places where logical vector was passed to sum
function. However on my computer those functions work just fine. After
closer look at documentation of function 'sum', I realized that it is
defined only
On 10/31/2005 2:00 PM, Tuszynski, Jaroslaw W. wrote:
Hi,
Recently I was told by users of some of the function I wrote that they
experience crashes in places where logical vector was passed to sum
function. However on my computer those functions work just fine. After
closer look at
Hello everybody,
I have been recently using reshape to convert long data to wide
data. Everything was going well until I reached some problematic
datasets. It has taken me a couple of weeks to finally figure out
what might be happening.
The problem is reproducible with test cases, and on two
Dear Jeff,
One way to do this is with by():
summaries - by(example, Individual, function(data){
mod - glm(Type~Dwater+Habitat, data=data, family=binomial)
list(AIC=AIC(mod), coef=coef(mod))
})
sapply(summaries, function(x) x$coef)
rowMeans(sapply(summaries, function(x) x$coef))
I am having trouble with try and tryCatch.
I have read the documentation but I just don't get it.
Here is what I am trying to do. I am testing a function which has a number
of parameters. I want to test it for different values of the parameters
and I have some loops, in the middle of which is
Dear R-users,
Running R 2.1.1 in WindowsXP, there seems to be a 'bug' in sd()
If
x-c(1,2,3,NA,5)
mean(x)
[1] NA
But
sd(x)
Or
var(x)
give
Error in var(x, na.rm = na.rm) : missing observations in cov/cor
There are obvious work-rounds, like
sd(x, is.na(x)==F)
which gives the result (with error
Try:
sd (x,na.rm=TRUE)
[1] 1.707825
Jarek
\
Jarek Tuszynski, PhD. o / \
Science Applications International Corporation \__,|
(703) 676-4192 \
[EMAIL PROTECTED]
Hello to all,
I am try to build a package, I do the follow commands: R CMD check pack,
R CMD pack build and run OK, no errors. I put my shared library in package
subdirectory R, src, but it is not put a shared library .so in directory
/usr/lib/R/library/pack/lib. Below is my code :
It sounds like you want `try` with the argument `silent = TRUE`. This
will allow you to keep running your program without errors. If you want
to check if the line had an error, you can error control by seeing if
the class of the resulting object is try-error. For example, let's say
I wanted to
The behavior is actually documented in the var() help file (?var), although
it's not clear that this would be the behavior if you just read ?sd. sd()
does call var if you look at the code, so the behavior should not be
unexpected.
--Matt
-Original Message-
From: [EMAIL PROTECTED]
Dear WizaRds,
I would like to fit a curve to ten points with nls() for one
unknown parameter gamma in the Kahnemann/ Tversky function, but somehow
it won't work and I am unable to locate my mistake.
p.kum - seq(0.1,1, by=0.1)
felt.prob.kum - c(0.16, 0.23, 0.36, 0.49, 0.61, 0.71, 0.85,
Roger Dungan wrote:
[snip]
There are obvious work-rounds, like
sd(x, is.na(x)==F)
which gives the result (with error message)
[1] 1.707825
Warning message:
the condition has length 1 and only the first element will be used in:
if (na.rm) complete.obs else all.obs
What you are doing
Hi,
This is a newbie question. I have been using glm to perform some logistic
regression. However, if I take the fitted parameters (as part of the glm
object) and pass them on the glm.predict function, for some test cases I
am getting predicted values that are a little over 1. This is a bit
Mark,
The parameter of your model (gamma) should not be a part of the dataframe.
In addition, the start argument should be a named list.
Something like this works
nls.dataframe - data.frame(p.kum,felt.prob.kum)
nls.kurve - nls( formula = felt.prob.kum ~
If you left the type argument to the predict method then your predictions
are on the log-odds scale. Try using the type='response' in the predict
method for glm.
--Matt
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Rohit Singh
Sent: Monday, October
On 31-Oct-05 Rohit Singh wrote:
Hi,
This is a newbie question. I have been using glm to perform some
logistic regression. However, if I take the fitted parameters (as
part of the glm object) and pass them on the glm.predict function,
for some test cases I am getting predicted values that
Hey, all. Quick question. I'm attempting to use some of the great
graphs generated in R for an upcoming talk that I'm writing in
Powerpoint. Copying and pasting (I'm using OSX) yields graphs that
look great in Powerpoint - until I resize them. Then fonts, points,
and lines all become quite
Hi Ted,
So here's what I'm doing:
This is my call to predict.glm:
pY - predict.glm(from69.fin.glm, newdata=d.tab, type=response)
This is what the fitted glm object looks like:
from69.fin.glm
Call: glm(formula = TR ~ z1 + e12_div_p_n + z2 + p_n, data = j2.tab)
Coefficients:
(Intercept)
Hi Rohit:
On 31-Oct-05 Rohit Singh wrote:
Hi Ted,
So here's what I'm doing:
This is my call to predict.glm:
pY - predict.glm(from69.fin.glm, newdata=d.tab, type=response)
This is what the fitted glm object looks like:
from69.fin.glm
Call: glm(formula = TR ~ z1 + e12_div_p_n +
On Mon, 31 Oct 2005, Jarrett Byrnes wrote:
Hey, all. Quick question. I'm attempting to use some of the great
graphs generated in R for an upcoming talk that I'm writing in
Powerpoint. Copying and pasting (I'm using OSX) yields graphs that
look great in Powerpoint - until I resize them.
Note that a simple logistic with a saturation level of 1 seems
to do quite well. Below we have removed the last point in order
to avoid the singularity:
x - p.kum[-10]
y - felt.prob.kum[-10]
plot(log(y/(1-y)) ~ x)
abline(lm(log(y/(1-y)) ~ x), col = red)
On 10/31/05, Mark Hempelmann [EMAIL
Background:
OS: Linux Mandrake 10.1
release: R 2.1.1
editor: GNU Emacs 21.3.2
front-end: ESS 5.2.3
-
Colleagues
Does anyone know how to get rid of the grid in balloonplot? I have read the
help file.
tt - seq(1,10)
tt2 - tt+20
tt3 -tt*1.5
balloonplot(tt, tt2, tt3)
Get the gplots:::balloonplot.default source and remove
the two abline lines.
On 11/1/05, McClatchie, Sam (PIRSA-SARDI)
[EMAIL PROTECTED] wrote:
Background:
OS: Linux Mandrake 10.1
release: R 2.1.1
editor: GNU Emacs 21.3.2
front-end: ESS 5.2.3
-
Colleagues
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