To whom it may concern:
I have a question about how to appropriately conduct an lmer analysis for
negative binomially distributed data. I am using R 2.2.1 on a windows machine.
I am trying to conduct an analysis using lmer (for non-normally distributed
data and both random and
On Thu, 27 Jul 2006, [EMAIL PROTECTED] wrote:
Dear all,
I am reading the data using read.table. However, there are a few rows I
want to skip. How can I do that in an easy way? Suppose I know the row
number that I want to skip. Thanks so much!
The easy way is to read the whole data frame
Hi all,
I have a square (a x a) matrix with values in a range. For example:
[,1] [,2] [,3] [,4]
[1,] -5 -13 -4
[2,] -404 -3
[3,] -315 -2
[4,] -22 -5 -1
I want to take any number smaller than -4 (in this example -5) and
replace it with -4 and
Hi
two solutions, your best option depends on the level
of generality you need.
(i)
M[M -4] - -4
M[M 3] - 3
(ii)
M - pmax(pmin(M,3),-4)
HTH
rksh
On 28 Jul 2006, at 07:44, Kartik Pappu wrote:
Hi all,
I have a square (a x a) matrix with values in a range. For example:
apply is your friend:
fn - function (x, a, b) {
if (x a) return(a) else
if (x b) return(b) else
x
}
apply(mat, c(1,2), fn, -4, 3)
[,1] [,2] [,3] [,4]
[1,] -4 -13 -4
[2,] -403 -3
[3,] -313 -2
[4,] -22 -4 -1
HTH,
Simon.
Kartik
Hello,
I'm an absolut beginner with R and now I got a 2D vector with numbers. I would
like to mirror this vector now by the rows (so that the first row becomes last,
second becomes one before last, ...).
I don't know if there is any method I can use to do this.
Could you please help me?
Antje
mat - matrix(1:16,4,4)
mat
[,1] [,2] [,3] [,4]
[1,]159 13
[2,]26 10 14
[3,]37 11 15
[4,]48 12 16
apply(mat,2,rev)
[,1] [,2] [,3] [,4]
[1,]48 12 16
[2,]37 11 15
[3,]26 10 14
[4,]159
Hi Antje
use the fact that n:1 counts backwards from n, and then use this as
a row index:
m - matrix(1:30,5,6)
m[nrow(m):1,]
[,1] [,2] [,3] [,4] [,5] [,6]
[1,]5 10 15 20 25 30
[2,]49 14 19 24 29
[3,]38 13 18 23 28
[4,]27 12 17
Hi
Not that there's anything wrong with Jacques's answer, but
the List might be interested in the following gotcha:
m - matrix(1:30,5,6)
apply(m,2,rev)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,]5 10 15 20 25 30
[2,]49 14 19 24 29
[3,]38 13 18 23
Jacques VESLOT wrote:
mat - matrix(1:16,4,4)
mat
[,1] [,2] [,3] [,4]
[1,]159 13
[2,]26 10 14
[3,]37 11 15
[4,]48 12 16
apply(mat,2,rev)
[,1] [,2] [,3] [,4]
[1,]48 12 16
[2,]37 11 15
[3,]2
I think you should use glmm.admb.
library(glmmADMB)
?glmm.admb
glmm.admb package:glmmADMB R Documentation
Generalized Linear Mixed Models using AD Model Builder
Description:
Fits mixed-effects models to count data using Binomial, Poisson or
negative
Hi Andy,
I'm using R (windows) version 2.1.1, randomForest version 4.15.
^
Never seen such a version...
Ooops! I meant 4.5-15
I then save each tree to a file so I can combine them all
afterwards. There are no memory
Another approach is:
mat[nrow(mat):1, ]
Patrick Burns
[EMAIL PROTECTED]
+44 (0)20 8525 0696
http://www.burns-stat.com
(home of S Poetry and A Guide for the Unwilling S User)
Jacques VESLOT wrote:
mat - matrix(1:16,4,4)
mat
[,1] [,2] [,3] [,4]
[1,]159 13
[2,]26
Dear Claire
Thank you for providing an example, but it is not totally clear
to me how you want to transform your data. For example in row 1,
you have value 1 in column f and n, but the results after
transformation are not similar A G and A A. Similar problem
for column h and i. They transform
## While in R v. 2.3.1 (the mid-July patch for Windows)
## on a Windows XP machine, this call to order() works fine...
order(1:10,decreasing = TRUE)
## [1] 10 9 8 7 6 5 4 3 2 1
## ...however, the argument name 'decreasing'
## must be typed in toto (note the missing 'g'
## in the
G'day John,
JT == Thaden, John J [EMAIL PROTECTED] writes:
JT Isn't is standard practice to have R base functions accept
JT truncated argument names as long as they are unambiguous?
No. :)
The help page of order states:
Usage:
order(..., na.last = TRUE, decreasing = FALSE)
Hello,
I calculate splines from messured points(x,y) of an unknown function f(x).
e.g.
x - c(0.004115, 0.012345, 0.037037, 0.10, 0.30, 1.00)
y - c(37, 50, 45, 60, 50, 66)
w - c(0.8540541, 0.832, 0.882, 0.798, 0.822, 0.8151515) as
weights
f - smooth.spline(x,y,w)
Now I
Dear mailing list,
I have a big data frame and each element in the matrix has two alphabets. I
want to split those alphabets into two so each element will have one
alphabet and the number of my columns will be doubled . So can some one help
with the code?
Example of what I want is to split them.
x
V1 V2 V3
1 GG AG AG
2 CC CC CC
3 CC CC CC
4 AG AG AG
5 GG GG GG
6 TT TT CT
t(apply(x,1,function(z)do.call('cbind',strsplit(z,''
[,1] [,2] [,3] [,4] [,5] [,6]
1 G G A G A G
2 C C C C C C
3 C C C C C C
4 A G A G A G
5 G G G G G G
6 T T T T C T
On 7/28/06,
The vegan package has non-metric multidimensional scaling in addition to a
variety of other ordination techniques.
Regards,
Helen Mills Poulos
Yale University
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE
Good afternoon,
I am a master student. I am currently doing an internship.
I would like to get some advices about the following issue: I have 2
data sets, both containing the same variables, but the data were
measured using two different procedures. I want to know if the two
procedures are
Ah I see, I did not read your story well enough.
You want to sort after applying table()
Well, the idea I suggested was to keep the real numbers in,
because the fractions are sorted as characters strings (alphabetically),
which is not what you want. So, now I suggest the following:
# First apply
Greetings,
I modified an existing R program (now it is larger than the previous
version), and when I attempt to perform a BUILD using the command
R CMD BUILD --binary --force RAGG the build fails.
It outputs a totally bogus message when it fails; not related at all to
the true problem.
I
Fabien Lebugle wrote:
I am a master student. I am currently doing an internship. I would
like to get some advices about the following issue: I have 2 data
sets, both containing the same variables, but the data were measured
using two different procedures. I want to know if the two
Gunther Höning a écrit :
Hello,
I calculate splines from messured points(x,y) of an unknown function f(x).
e.g.
x - c(0.004115, 0.012345, 0.037037, 0.10, 0.30, 1.00)
y - c(37, 50, 45, 60, 50, 66)
w - c(0.8540541, 0.832, 0.882, 0.798, 0.822, 0.8151515) as
On 7/27/06, Frank E Harrell Jr [EMAIL PROTECTED] wrote:
Tony Lachenbruch has written some about this, also see my book (it's web
page is biostat.mc.vanderbilt.edu/rms). I don't know about the power of
interaction tests, but for main effect tests in the absence of
interaction, the Wilcoxon
From: Eleni Rapsomaniki
Hi Andy,
I'm using R (windows) version 2.1.1, randomForest version 4.15.
^
Never seen such a version...
Ooops! I meant 4.5-15
I then save each tree to a file so I can combine them all
On 7/26/06, Bill Shipley [EMAIL PROTECTED] wrote:
Hello. Douglas Bates has explained in a previous posting to R why he does
not output residual degrees of freedom, F values and probabilities in the
mixed model (lmer) function: because the usual degrees of freedom (obs -
fixed df -1) are not
I am using R in an environment where the HTTP proxy server blocks
browsers that do not send User-Agent strings. Through some testing,
we have determined that R, by default (2.3.1) does not send a string
when performing the chooseCRANmirror() function. Is there a setting
that allows us to
install.packages(gam)
Warning in install.packages(gam) : argument 'lib' is missing: using
/usr/local/lib/R/site-library
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/gam_0.97.tar.gz'
Content type
On Friday 28 July 2006 13:31, Cuvelier Etienne wrote:
Gunther Höning a écrit :
Hello,
I calculate splines from messured points(x,y) of an unknown function
f(x). e.g.
x - c(0.004115, 0.012345, 0.037037, 0.10, 0.30, 1.00)
y - c(37, 50, 45, 60, 50, 66)
w - c(0.8540541,
This has a stats question and a R question. I am sure there are many
core statisticians here how would know the answer to this simple
question. In determining the significant comparisons using the methods
in multcomp, the ones that are designated as significant are the ones
that do not intersect
What OS is this?
If Windows, see the rw-FAQ Q2.19.
Otherwise, see ?download.file and choose a different download method,
or look at the source code (src/modules/internet/nanohttp.c) and submit a
patch.
On Fri, 28 Jul 2006, James P. Howard, II wrote:
I am using R in an environment where the
Tracy Feldman tracysfeldman at yahoo.com writes:
To whom it may concern:
I have a question about how to appropriately conduct an lmer analysis for
negative binomially distributed
data. I am using R 2.2.1 on a windows machine.
I am trying to conduct an analysis using lmer (for
Dear R-helpers,
In the case of two categorical factors, say a and b, once I have
fixed the constrasts, the model matrix is set according to these
contrasts with lm, and the t-tests for the significance of the
parameters provided by summary indeed concern the comparison of the
model with each
Dear Collegues,
it seems like there is a problem with the image()-method in the package arules.
Using an ordninary matrix works fine:
image(matrix(rnorm(200), 10, 20), axes = FALSE, col=brewer.pal(9, Blues) )
delivers an image with blue colors and no axes.
Using an object of the class
Markus:
it seems like there is a problem with the image()-method in the package
arules.
For problems with packages, please contact the maintainer or at least have
im Cc as the posting guide tells you.
Using an ordninary matrix works fine:
image(matrix(rnorm(200), 10, 20), axes = FALSE,
Dear All,
I'm trying to get a heatmap for my n*m matrix, I want to cluster the
m samples (columns) using kmeans with manhattan distance. I was able
to use hclust method to cluster the m samples, but failed to figure
out how to use kmeans. Any suggestion is very welcome!
Best,
Cao
John,
You need to supply a lot more information if you wish to receive any useful
assistance. You have not told us your operating system, version of R, or the
error message you received. You are convinced that the problem is too many
lines of code, but I have seen many postings where people
Dear R-users,
likely there is a simple solution for this problem, but I currently
cannot see it.
I basically would like to get from a matrix values in particular
positions which are the rows of another matrix, without using a
for-loop.
In other words: is there any way to avoid the for-loop in
Yes, by matrix indexing:
R M1[M2]
[1] 1 2 13 15 8
R v
[1] 1 2 13 15 8
Andy
From: Camarda, Carlo Giovanni
Dear R-users,
likely there is a simple solution for this problem, but I currently
cannot see it.
I basically would like to get from a matrix values in particular
positions
On 7/26/06, Bill Shipley [EMAIL PROTECTED] wrote:
Hello. Douglas Bates has explained in a previous posting to R why he does
not output residual degrees of freedom, F values and probabilities in the
mixed model (lmer) function: because the usual degrees of freedom (obs -
fixed df -1) are not
$ apt-get install r-base-dev
and you should get the required dependencies, in this case for
Blas/Atlas.
Hth, Dirk
On Fri, Jul 28, 2006 at 07:04:13AM -0700, xingwang ye wrote:
install.packages(gam)
Warning in install.packages(gam) : argument 'lib' is missing: using
I am new to R, so please forgive me if there is an obvious answer to
this question. I have done fairly extensive searching through R docs,
google and a few R users and have not found an answer to my question.
Is there a way to create a non-interpreted string object in R?
For example, I am using
Enter this at the console
x - scan(what = )
and after pressing the enter after the right paren,
do a paste and then press enter twice.
On 7/27/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
I am new to R, so please forgive me if there is an obvious answer to
this question. I have done
Or even easier,
x - scan(clipboard, what = )
at least on Windows.
On 7/28/06, Gabor Grothendieck [EMAIL PROTECTED] wrote:
Enter this at the console
x - scan(what = )
and after pressing the enter after the right paren,
do a paste and then press enter twice.
On 7/27/06, [EMAIL
Greetings,
We recently obtained a new computer in our lab with a Pentium 4 3.86 GHz
processor and 4 gb of ram running windows xp with service pack 2. After
installing R on this machine, I ran a bit of code and found that the
execution time was actually significantly slower than a machine
Unless there is another level of complexity that i didn't see here,
wouldn't it be a simply application of sapply as follow,
sapply( 1:dim(M2)[[1]], function(x) M1[M2[x,1], M2[x,2]] )
Hope this helps.
Horace
Camarda, Carlo Giovanni [EMAIL PROTECTED] 7/28/2006 9:40 AM
Dear R-users,
likely
Hi all,
I have a dataframe of rownames that I would like to extract from a
larger matrix to form a new matrix. I have tried to use subset, in
this manner
x-subset(largematrix, rownames$names=largematrix$rownames)
where largematrix is the larger matrix and rownames$names is the
dataframe with
try:
x-subset(largematrix, rownames$names %in% largematrix$rownames)
On 7/28/06, Wade Wall [EMAIL PROTECTED] wrote:
Hi all,
I have a dataframe of rownames that I would like to extract from a
larger matrix to form a new matrix. I have tried to use subset, in
this manner
actually the other way around:
x-subset(largematrix, largematrix$rownames %in% rownames$names )
On 7/28/06, jim holtman [EMAIL PROTECTED] wrote:
try:
x-subset(largematrix, rownames$names %in% largematrix$rownames)
On 7/28/06, Wade Wall [EMAIL PROTECTED] wrote:
Hi all,
I have a
List:
I have 2 related questions:
(1) first I have x-y-z data, where x y are the geographic locations of
point values, z. I need to perform a normal score transform on the
z-values and maintain their geographic location. So, how do I go from
columns x-y-z to x-y-z-t (or x-y-t), where the
Hi Tom,
I do not know about R but you might take a look at the GSLIB codes. It has
executables for both tasks using a simplfied GEOEAS format. I recently did some
Normal Score Kriging and use a combination of GSLIB, GEOEAS, and R (for the
contouring of the resulting grid). BTW I used GEOEAS
Be careful not to use clock speed as a measure of computer performance.
Pentium 4s (and the comparable Xeons) were intended to be run very fast,
but never managed it. So a 2.4GHz P4 proved to be slower than a 1GHz
PIII.
Unless you are running Windows 64, the chip having some 64-bit
Hi Andy, Thank you very much for your previous tip.
However, I am running into another problem now.
previously, in my tab-delim file I had only two
columns. now I added another column. and I want the
pairs value to go into the matrix instead of 1.
pair (Apple, S) value 10.
tb #
Ben Bolker bolker at ufl.edu writes:
...
I haven't tried it, but you could also consider using
a Poisson-lognormal (rather than neg binomial, which is Poisson-gamma)
distribution, which might make this all work rather well
in lmer:
www.cefe.cnrs.fr/esp/TBElston_Parasitology2001.pdf
Dear useRs,
I'd like to produce some scatter plots where N units on the X axis are
equal to N units on the Y axis (as measured with a ruler, on screen or
paper). This approach
x - sample(10:200,40) ; y - sample(20:100,40)
windows(width=max(x),height=max(y))
plot(x,y)
is better than
Try:
plot(x, y, asp = 1)
--sundar
bogdan romocea wrote:
Dear useRs,
I'd like to produce some scatter plots where N units on the X axis are
equal to N units on the Y axis (as measured with a ruler, on screen or
paper). This approach
x - sample(10:200,40) ; y - sample(20:100,40)
Dear JeeBee and all,
It is nice. Thanks you very much.
I must learn much more about ?as.fractions, ?as.numeric, ?as.character
and ?table functions.
Best wishes, Muhammad Subianto
On 7/28/06, JeeBee [EMAIL PROTECTED] wrote:
Ah I see, I did not read your story well enough.
You want to sort
I have one addition to Rolf's thorough advice: if your goal is to try
to find evidence that the two procedures are equivalent then the
tests that you should consider are called equivalence tests. These do
not come from lm.
The most popular test is TOST, the two one-sided test, and it doesn't
hello everybody,
I have some code which looks like:
dyn.load(lpSolve.so)
res - lp(some.parameters)
and everything runs fine.
What lp() does, it's just calling a C function which is in lpSolve.so
If I call lp() a large number of times:
for(1 in 1:5000){
gc(verbose=TRUE)
res -
Hi all,
I have a set of points (1...n) each of them defined on a 3D space
(i.e. for each point I do have x,y,z coordinates), and I would like
to generate a mean pairwise geometrical distance between them. Is
there anyway I can do this with R?
Conceptually is really simple. First I have to
Sundar Dorai-Raj sundar.dorai-raj at pdf.com writes:
Try:
plot(x, y, asp = 1)
--sundar
or eqscplot from the MASS package.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting
hi,
using articial data, i'm supposed to estimate model
y(t) = beta(1) + beta(2)*x(t) + u(t), u(t) = gamma*u(t-1) + v(t), t =
1,...,100
which is correctly specified in two ways: ML ommiting the first observation,
and ML using all 100 observation.
since i'm still learning how to use R, i would
Hi, all,
I have a question about random effects model. I am dealing with a
three-factor experiment dataset. The response variable y is modeled
against three factors: Samples, Operators, and Runs. The experimental
design is as follow:
4 samples were randomly chosen from a large pool of test
Hi, all,
I have a question about random effects model. I am dealing with a
three-factor experiment dataset. The response variable y is modeled
against three factors: Samples, Operators, and Runs. The experimental
design is as follow:
4 samples were randomly chosen from a large pool of
On Fri, 28 Jul 2006, johan Faux wrote:
hello everybody,
I have some code which looks like:
dyn.load(lpSolve.so)
res - lp(some.parameters)
and everything runs fine.
What lp() does, it's just calling a C function which is in lpSolve.so
If I call lp() a large number of times:
for(1 in
*hi,*
*using articial data, i'm supposed to estimate model*
*y(t) = beta(1) + beta(2)*x(t) + u(t), u(t) = gamma*u(t-1) + v(t), t =
1,...,100*
*which is correctly specified in two ways: ML ommiting the first
observation, and ML using all 100 observation.*
*since i'm still learning how to use R,
Have a look at readTable() in the R.utils package. It can do quite a
few thinks like reading subsets of rows, specify colClasses by column
names etc. Implementation was done so that memory usage is as small
as possible. Note the note on the help page: WARNING: This method is
very much in an
Dear All:
I have been struggling to run the conditional logistic regression on a
dataset. I am using clogit function in survival package. Here is how the
data is generated. I tried to shorted the data by using the second count
variable but still the clogit did not run. Why I am not able to run
On 7/28/06, Ben Bolker [EMAIL PROTECTED] wrote:
Sundar Dorai-Raj sundar.dorai-raj at pdf.com writes:
Try:
plot(x, y, asp = 1)
--sundar
or eqscplot from the MASS package.
or
library(lattice)
xyplot(y ~ x, aspect = iso)
-Deepayan
Hi.
I'm a student in a graduate program at Simon Fraser University in Canada.
I am trying to run a simple screening experiment with some simulated data.
I simply want to do an ANOVA of an experiemnt with 5 factors (4 have 2
levels, the last has 3 levels) and 48 runs (ie, full factorial).
The
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