for
precision) for alternatives for extended precision calculations.
Ben Bolker
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and provide
response variable?
In general, lme questions should go to the r-sig-mixed-models
mailing list.
Ben Bolker
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-requisites (minqa
and MatrixModels) install fine. So I guess we'll have to find a way to
make it work on 2.12.1 - the version I'm using. GenStat managed to analyse
the same data just fine, so it's not a problem with the data.
Can you send data? Crashing R is by definition a bug ...
Ben
maxsilva mmsilva3 at uc.cl writes:
I generated a glm logit model using a sample of a bigger set, and now I want
to test the model with the bigger set. How can I do this? predict makes
predictions only for a number of rows equal to the sample used. The question
is, how can I use the
people like me doing the hacking ...
Ben Bolker
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are starting from a clean session; (2) perhaps, if
you're up to it, using traceback() and/or options(error=recover)
to try to track the problem a bit farther; (3) contacting
the package maintainer ...
Ben Bolker
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maxsilva mmsilva3 at uc.cl writes:
Thank you for your answer. But I still have the problem; for example, if i
have data for 10 months, estimate the parameters of my logit model using 10
months of data, and then use
predictions-predict(model,data=1monthonly,family = binomial(link =
Federico Bonofiglio bonoricus at gmail.com writes:
You're confused by the formatting differences betwen
columns. The first column uses 'standard' notation, the
second and third use 'scientific' notation -- see comments
inline.
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On 11-02-07 03:56 AM, Martin Maechler wrote:
Ben Bolker bbol...@gmail.com
on Sat, 5 Feb 2011 15:58:09 -0500 writes:
A bug was recently posted to the R bug database (which
probably would better have been posted as a query here
Antje Niederlein niederlein-rstat at yahoo.de writes:
A few day ago, I was looking for an answer to my question but didn't
get one. Anybody who can help now?
Hello,
I tried to use mle to fit a distribution(zero-inflated negbin for
count data). My call is very simple:
I will point
JaFF el.romaro at gmail.com writes:
Hi folks,
I have a dataset from a trial measuring the subjects' pupils. There are many
measurements, all of which must be analysed in a similar fashion; so if I
get the analysis right for one of them, I've got them all. For simplicity,
let us call
Jinsong Zhao jszhao at yeah.net writes:
Hi there,
I have fitted a sample (with size 20) to a normal and/or logistic
distribution using fitdistr() in MASS or fitdist() in fitdistrplus
package. It's easy to get the parameter estimates. Now, I hope to report
the confidence interval for
questions.
good luck,
Ben Bolker
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and provide commented, minimal, self-contained
Cristiano Strieder cstrieder at gmail.com writes:
Hi all,
I have commited a new release of my package and waited for more than
one day. After that
install.packages(tests,repos=http://r-forge.r-projet.org;) still
returns package 'tests' is not available. I have done the local
build
Chris82 rubenbauar at gmx.de writes:
Hello R users,
I have a little problem with a for loop.
Below there is an simple example of my problem.
I want to delet the commas in the character string. Fore this reason I
create a for loop to unpick the string and rebuild him without the
On 02/02/2011 09:29 AM, David Winsemius wrote:
On Feb 2, 2011, at 8:22 AM, Ben Bolker wrote:
Ramya ramya.victory at gmail.com writes:
I have the code for the density plot
j - 8
plot(density(diff_in_sample[,1]), main = list.files()[j])
for(i in 1:25){
lines(density(diff_in_sample[,i
My concern was that it was outside the density function and I thought
the density function would throw an error before it passed anything to
na.omit().
plot(na.omit(density(c(1,1,1,1,1,NA,4,4,4,4))) )
Error in density.default(c(1, 1, 1, 1, 1, NA, 4, 4, 4, 4)) :
'x' contains missing
Ramya ramya.victory at gmail.com writes:
I have the code for the density plot
j - 8
plot(density(diff_in_sample[,1]), main = list.files()[j])
for(i in 1:25){
lines(density(diff_in_sample[,i]))
}
This gives me an error
Error in density.default(diff_in_sample[, i]) :
'x' contains
Eik Vettorazzi E.Vettorazzi at uke.uni-hamburg.de writes:
if you have a homogeneous mc (= a constant transition matrix), your
state at time 10 is given by (chapman-kolmogorov)
p10=p0 %*% tm^(10)
so you need a matrix power function.
There are matrix exponential functions in the Matrix and
are Venables and Ripley (i.e. MASS) and Crawley's
Statistical Data Analysis book.
Ben Bolker
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baptiste auguie baptiste.auguie at googlemail.com writes:
Dear list,
I'm trying to visualise some ellipsoidal shapes in 3D. Their position,
axes, and angular orientation can be arbitrary. I saw an ellipse3d
function in rgl; however it is heavily oriented towards the
statistical concept
Uwe Ligges ligges at statistik.tu-dortmund.de writes:
On 29.01.2011 15:06, martanair wrote:
[snip]
I write:
radon.data- list (n, J, x, y, county)
radon.inits- function (){
list (a=rnorm(J), b=rnorm(1), mu.a=rnorm(1),
sigma.y=runif(1), sigma.a=runif(1))
}
Kostenko, Olga O.Kostenko at nioo.knaw.nl writes:
I have a question about the output of linear mixed model fitted in R
using nlme package. In particular, what are the t-values that are given
in an output, how are they calculated and based on what test? I guess it
cannot be a simple Student
James Meadow jfmeadow at gmail.com writes:
Hi,
I am trying to work with the ape package, and there is one thing I am
struggling with. When calling the *read.GenBank()* function, I can get it
to work with an object created like this:
*x - c(AY395554,AY611035, ...)*
*read.GenBank(x)*
on the boundary, e.g.
if the best estimate of your zero-inflation parameter is zero
or very close to it.
4. Use the pscl package, which has reasonably robust and
efficient built-in functions for fitting zero-inflated (and
hurdle) models.
good luck,
Ben Bolker
before posting.)
One hint for the second question: ?rt
good luck,
Ben Bolker
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and provide
,trim=0.05) #or 0.1 I am not sure
z-sort(x)
#next use either
y-z[-c(1:50,951:1000)] # We want the bottom 5% and top 5% so this
corresponds to the elements that we are taking away.
#or
#y-z[-c(1:100,901:1000)]
mean(y)
--
From: Ben Bolker bbol
it
helps a lot.
I would also suggest going to Google scholar and
searching for 'nls growth curve Bates to find some papers that
have used this approach.
If you need to post again, please read the posting guide and
show us how far you have managed to get on your own.
good luck,
Ben Bolker
Tal Galili tal.galili at gmail.com writes:
Hello Troy.
A tiny question (without answering your question), why did you choose to do
it this way instead of using
?step
or
?stepAIC
?
[snip snip]
My questions are:
Should I be using var.test to run the F-test to decide which
Kostenko, Olga O.Kostenko at nioo.knaw.nl writes:
I have a question about the output of linear mixed model fitted in R
using nlme package. In particular, what are the t-values that are given
in an output, how are they calculated and based on what test? I guess it
cannot be a simple Student
Stuart Luppescu slu at ccsr.uchicago.edu writes:
I want box plots by group to display in order of increasing
mean (or median) of each group but can't seem to figure it out and
couldn't find anything on R-seek, either.
?reorder ... ?
__
fantomas tomas.iesmantas at gmail.com writes:
Hello,
does anybody know another faster function for random multivariate normal
variable simulation? I'm using mvrnorm, but as profiling shows, my algorithm
spends approximately 50 % in executing mvrnorm function.
Maybe some of you knows
(20))
library(coda)
m - mcmc(data=z)
t(apply(m,2,quantile,c(0.025,0.975)))
If that sort of thing doesn't work for you, please
post an example of what doesn't work ...
Ben Bolker
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suggest that you send follow-ups to r-sig-mixed-mod...@r-project.org
and possibly take a look at http://glmm.wikidot.com/faq
cheers
Ben Bolker
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PLEASE do read the posting
Toby Marthews toby.marthews at ouce.ox.ac.uk writes:
Dear R HELP,
ABOUT glmmPQL and the anova command. Here is an example of a
repeated-measures ANOVA focussing on the way
starling masses vary according to (i) roost situation and
(ii) time (two time points only).
[snip]
Samaritan d.harliwich at gmail.com writes:
[snip]
You might want to ask follow-up questions on the R-sig-mixed-models list
At the most basic level, I'm testing the effect of sleep deprivation on
various behaviours (e.g. amount of time spent awake, amount of time spend
expressing
Frodo Jedi frodo.jedi at yahoo.com writes:
Dear all,
I need an help because I am really not able to find over
internet a good example
in R to analyze an unbalanced table with Anova with
repeated measures.
For unbalanced table I mean that the questions are
not answered all by the same
anord andreas.nord at zooekol.lu.se writes:
Dear all,
I'm trying to make multiple comparisons for an lme-object. The data is for
an experiment on parental work load in birds, in which adults at different
sites were induced to work at one of three levels ('treat'; H, M, L). The
[1] 5.2245
Ben Bolker
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and provide commented, minimal, self-contained, reproducible code.
Mihai.Mirauta at bafin.de writes:
Hi,
I want to save the autocorrelation plots resulting out of ACF (acf(ts)), not
just by using the Save as
command in the R Gui but using some sort of code, which allows me to chose the
format and the path.
Thank you,
Mihai
for example:
a -
))
cheers
Ben Bolker
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and provide commented, minimal, self-contained, reproducible code.
Nevil Amos nevil.amos at gmail.com writes:
How do I keep the linking column[s] in a merge()?
I need to use the values again in a further merge.
simple reproducible example please?
(e.g. make up a couple of 4-row datasets that show what you
want, what you are trying, and what you are
Graham Smith myotistwo at gmail.com writes:
I assume this has a proper name, but I don't know what it is and wondered
if anyone knew of a package that might do the following, or something
similar.
As an example, assume I have borrowed and read 10 books on R , and I have
subjectively
of arguments to the function, and the default was supposed to be
TRUE. Because axes *is* in the explicit list of arguments, this
overrides it. I would contact the maintainer [maintainer(xts)] and
ask if this is a bug.
cheers
Ben Bolker
__
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luck
Ben Bolker
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and provide commented, minimal, self-contained, reproducible code.
ATANU ata.sonu at gmail.com writes:
can anyone tell me how can i control the method of estimation (i.e. scoring
method or Newton raphson method) in glm and compute deviance function ?
I don't think you can; you would have to write your own, although you
can take advantage of the framework
Victor F Seabra vseabra at uol.com.br writes:
Please, I wonder if someone knows how to add the
less than or equal to symbol in the plot generated by the code below:
var1-c('age = 3','age = 7','age = 10','age = 11','age = 20','age =
25','age = 30','age = 45','age = 50','age
Berwin A Turlach berwin at maths.uwa.edu.au writes:
G'day H.T.
On Sat, 1 Jan 2011 00:41:10 -0500 (EST)
H. T. Reynolds htr at udel.edu wrote:
When I create a factor with labels in the order I want, write the
data as a text file, and then retrieve them, the factor levels are no
)? -- Reread
the detailed answers you got previously that distinguish the difference
between how the character is stored within R and how it is printed
on the console.
good luck
Ben Bolker
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markdx mrkdennehy at gmail.com writes:
Example from page 29, Chapter 2.3 from Applied Spatial Analysis with R
I am new to R...just trying to replicate the example from the book.
m - matrix(c(0,0,1,1), ncol = 2, dimnames = list(NULL, + c (min,
max)))
Error in +c(min, max) : invalid
Duncan Murdoch murdoch.duncan at gmail.com writes:
As others have said, there are packages that provide caching.
I haven't used them, because I like to keep my projects as
self-contained as possible: adding a dependency on one of those
packages is undesirable[1]. What I do in the case
array chip arrayprofile at yahoo.com writes:
[snip]
I can think of analyzing this data using glm() with the attached dataset:
test-read.table('test.txt',sep='\t')
fit-glm(cbind(positive,total-positive)~treatment,test,family=binomial)
summary(fit)
anova(fit, test='Chisq')
First, is this
RaoulD raoul.t.dsouza at gmail.com writes:
Hi,
I'm a bit stuck and need some help with R code to code a variable F_R based
on a combination of conditions.
The first condition would code F_R as F and would be based on the
min(Date) and Min(Time) for each combination of UniqueID
.
*From:* Ben Bolker bbol...@gmail.com
*To:* r-h...@stat.math.ethz.ch
*Sent:* Tue, December 21, 2010 5:08:34 AM
*Subject:* Re: [R] logistic regression or not?
array chip arrayprofile at yahoo.com http://yahoo.com/ writes:
[snip]
I can think of analyzing
functions in the reshape (or reshape2)
packages (reshape2 may be faster). It may take a bit of work
to get the syntax right (try it out on a small subset of your
data).
Ben Bolker
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).
Thanks,
Stefano
On Sun, Dec 19, 2010 at 10:54 PM, Ben Bolker bbolker at gmail.com wrote:
Stefano Ghirlanda dr.ghirlanda at gmail.com writes:
I am trying to load into R a MATLAB format file (actually, as saved by
octave). The file is about 300kB but R complains with a memory
allocation
Stefano Ghirlanda dr.ghirlanda at gmail.com writes:
I am trying to load into R a MATLAB format file (actually, as saved by
octave). The file is about 300kB but R complains with a memory
allocation error:
library(Rcompression)
library(R.matlab)
Loading required package: R.oo
Loading
David Winsemius dwinsemius at comcast.net writes:
On Dec 18, 2010, at 7:01 AM, e-letter wrote:
Readers,
I am trying to use the function dotchart. The data is:
testdot
category values1 values2 values3 values4
1a 10 27 56 709
2b 4
Ben Bolker bbolker at gmail.com writes:
Mike Marchywka marchywka at hotmail.com writes:
[snip]
The gsl package has this function, apparently -- it agrees with
Mathematica/Wolfram Alpha's Hypergeometric2F1 for a single set of
inputs (2,3,4,0.5), although apparently the algorithm
Alaios alaios at yahoo.com writes:
Hello I have two function in R
like
g(x)=2x-3
and s(x)=5x^2+2
and I want to find the integrafl of the g(x)*s(x) inside the interval of [a,b]
Analytically or numerically?
It sounds like you want the answer analytically, in which case R
can't do
is that you want to answer this question on the Bioconductor
mailing list instead ...
Ben Bolker
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Ben Bolker bbolker at gmail.com writes:
Analytically or numerically?
It sounds like you want the answer analytically, in which case R
can't do it, but it is an easy integral
g(x)*s(x) = 10*x^3-15*x^2+4*x-6
indefinite integral = 10/3*x^4 -15/3*x^3 + 4/2*x^2 - 6*x + C
oops
many years of experience.
Test your objective function with your starting value (it should give
a finite value), with values near your starting value (it should give
similar answers), and with parameter values that you suspect to be worse
(but not crazily worse) (it should give higher values).
Ben
RockO rock.ouimet at gmail.com writes:
Dear R world,
Do you know about a function that would capitalize in the correct manner
first and family names?
I found in the cwhmisc only the CapLeading function, but it just does not do
the job, taking care only to capitalize the first letter of
coordinates.
Ben Bolker
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and provide commented, minimal, self-contained, reproducible code.
Tianchan Niu niu at isis.georgetown.edu writes:
Dear all,
I would like to use cut() to make numerics to factors, the sample codes are as
follows. However, the result is
not what I want, since r[3] = 9 should be in the interval of 8-10% rather
than 2-4%. Maybe cut() is not
the right function
Kurt_Helf at nps.gov writes:
Greetings
In attempting to create a date variable based on month (e.g.,
February, April, etc.) and year (e.g., 2006) data, wherein I converted
Month to a factor with Jan=1...Dec=12, I used the following command:
Steve Sidney sbsidney at mweb.co.za writes:
Dear list
I have quite a small data set in which I need to have the following
values ignored - not used when performing an analysis but they need to
be included later in the report that I write.
Can anyone help with a suggestion as to how
combination of (1) (requested) help to perform
the task asked and (2) (unrequested) advice. Personality, philosophy,
and the degree of perceived unwisdom/danger in the specified activity
determine the mix.
cheers
Ben Bolker
__
R-help@r-project.org
, you could try
binom~season + (season|group/individual)
was the switch from 'individual' above to 'badger' below
a slip?
Thanks for the clear description.
Ben Bolker
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Brian Tsai btsai00 at gmail.com writes:
Hi,
I'm having problems using the 'width' aesthetic attribute for the
geom_errorbarh. This is the same problem reported earlier here, but I'll
try to write the problem more clearly:
http://www.mail-archive.com/r-help at
Craig O'Connell craigpoconnell at gmail.com writes:
I am currently modifying a previously developed predator prey model and
was curious if there was a way to add in a disturbance to the model (let's
say at time t=100). The disturbance can be the introduction of 40 prey
(N=40) and 10
Stavros Macrakis macrakis at alum.mit.edu writes:
read.table gives idiosyncratic results when the input is formatted
strangely, for example:
read.table(textConnection(
a'b\nc'd\n),header=FALSE,
fill=TRUE,sep=,quote=')
= c'd a'b c'd
read.table(textConnection(
a'b\nc'd\nf'\n'\n),
and don't
understand ...
A reproducible example would be nice too.
Ben Bolker
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and provide
wocket deborahmalley at yahoo.co.uk writes:
Hey
So sorry to be a total newbie, but i'm just finding my feet with R.
I heard on the grapevine i could recreate a scanned microarray image, or at
least get a good graphic of it from a just a data file.
I have .txt files for illumina
Romildo Martins romildo.martins at gmail.com writes:
how convert x in xarray (numbers)?
x
[1] 0 - 13
y
[1] 11 - 23
z
[1] 220 - 9
xarray
[1] 0 13
yarray
[1] 11 23
zarray
[1] 220 9
Is
as.numeric(unlist(strsplit(0 - 13,-)))
what you want?
, but
I think you might get a more informed answer on the Bioconductor list ...
Ben Bolker
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Barry Rowlingson b.rowlingson at lancaster.ac.uk writes:
On Thu, Dec 9, 2010 at 4:20 PM, Uwe Wolfram uwwo at in-chemnitz.de wrote:
I am currently working on a project which involves nls-fits of three
dimensional surfaces such as ellipsoids or even more complex. I have
been searching R
Rosario Garcia Gil M.Rosario.Garcia at slu.se writes:
Hello
I hope my question makes sense. It is possible to specify the shape
paramenters in a glm model with family Gamma?
It doesn't look that way, but you can do a Gamma model with
a specified shape parameter (albeit much less
sachinthaka.abeywardana at allianz.com.au writes:
Is it possible to write a program such that it downloads a csv from a given
web address? Would be great if this could be done at a particular time
during the day as well. Say 9AM monday-friday.
downloading a csv file is easy:
x -
Baoqiang Cao bqcaomail at gmail.com writes:
I have a least square fitting problem with linear inequality
constraints. pcls seems capable of solving it so I tried it,
unfortunately, it is stuck with the following error:
M - list()
M$y = Dmat[,1]
M$X = Cmat
M$Ain = as.matrix(Amat)
Joonas - as_trix85 ast_rix85 at hotmail.com writes:
I'm trying to estimate the parameters for GARCH(1,1) process.
Here's my code:
loglikelihood -function(theta) {
h=((r[1]-theta[1])^2)
p=0
for (t in 2:length(r)) {
h=c(h,theta[2]+theta[3]*((r[t-1]-theta[1])^2)+theta[4]*h[t-1])
}
Eduardo Klein eklein at usb.ve writes:
I would like to know how R assigns the numeric code to a set of factors
in a vector.
[snip]
It is indeed alphabetical by default. To get it in order of
appearance you could do something like
set.seed(1001)
x -
Tingting Zhan tingting.zhan at jefferson.edu writes:
Hi all,
I have the output of summary() of an lme object called lme.exp1, for
example
#
summary(lme.exp1)
[snip]
for the common variance parameter sigma. But if I need the
/group/ggplot2 that is probably better than R-help for
ggplot-specific questions.
Ben Bolker
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Timothy_Handley at nps.gov writes:
I'm confused as to the trustworthiness of the dispersion parameters
reported by glm. Any help or advice would be greatly appreciated.
[snip]
Specifics: The summary function says that my fitted GLM has a dispersion
parameter=15.8. On the other hand, the
Jim Silverton jim.silverton at gmail.com writes:
Hello,
I have some discrete pvalues and I would like to sort them. Then add random
noise so that they are ordered the same way as the original pvalues. Off
course I don't want any pvalues less than 0 or greater than 1. Any ideas on
how to do
Jorge Ivan Velez jorgeivanvelez at gmail.com writes:
Hi Romildo,
One possible way would be the following:
index - apply(m, 1, function(row) any(a %in% row))
m[index, ]
HTH,
Jorge
Does the original poster mean
index - apply(m, 1, function(row) all(a %in% row))
m[index, ]
?
Lorenzo Melchor Lorenzo.Melchor at icr.ac.uk writes:
I am trying to run affylmGUI on my mac computer. I have already
installed the Tlc package as well as Bwidgets through ActiveTcl
conversion installing files.
However, when running affylmGUI() on R, I keep getting the message in
the
.
Ben Bolker
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Michael Bedward michael.bedward at gmail.com writes:
Hello Kayce,
My (very basic) understanding is that you can't directly compare the
coefficients across models that have different response variables, nor
could you use AIC and similar metrics of model goodness of fit.
Instead, I think
Francial Giscard LIBENGUE libengue at gmail.com writes:
S'il vous plait, j'ai un problème avec la fonction gamma je n'arrive pas à
bienécrire l'exposant j'ai utilisé ^ et ça ne marche pas.
cordialemont
ici on parle anglais (je ne sais pas s'il y a une autre liste ou on pourrait
poser
Bert Gunter gunter.berton at gene.com writes:
Eh??? Why would you want to do that?? (R isn't C).
So the simple answer is: you can't.
The other answer is, well of course you sort of can via, e.g.
for(i in 0:9) {
z - myMatrix[i+1,]
...
}
But as Josh said, I think this falls
be able to choose better starting conditions. You may be able to pick
an optimization method that is more suitable for your objective function
(see ?optim and the optimx package on r-forge).
Ben Bolker
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R-help@r-project.org mailing list
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cct663 cct663 at gmail.com writes:
I have a few questions relating to overdispersion in a sex ratio data set
that I am working with (note that I already have an analysis with GLMMs for
fixed effects, this is just to estimate dispersion). The response variable
is binomial because nestlings can
Bert Gunter gunter.berton at gene.com writes:
[snip snip snip]
Cheers,
Bert
P.S. Your results look fishy, even for a simulation. The extremely low
standard errors and rank deficiencies strongly suggest to me that your
methodology is faulty and that you are getting a bunch of baloney. I
Alexander Shenkin ashenkin at ufl.edu writes:
Hello All,
I'm trying to run a maximum likelihood analysis using dmultinomial (i'm
avoiding dmultinom as I'd like to run it with vectors for the ML stuff).
However, I'm having a hard time getting even the simplest example
running. Any help
Alaios alaios at yahoo.com writes:
Hello everyone.
I would like to find the sample covariance matrix using R.
So far I read on the wikipedia what a sample_covariance is
http://en.wikipedia.org/wiki/Sample_covariance
according to wikipedia one vector is
enough to calculate the sample
Dickison, Daniel ddickison at carnegielearning.com writes:
The documentation for agrep says it uses the Levenshtein edit distance,
but it seems to get this wrong in certain cases when there is a
combination of deletions and substitutions. For example:
agrep(abcd, abcxyz, max.distance=1)
skan juanpide at gmail.com writes:
How can I get multipanel conditioning graphics with rgl as I do with lattice
|
For example I have three variables x, y, z, w. Where x,y,z are continuous
and w is categorical or discrete.
I want to use plot3d(x,y,z) for each value of w in a panel
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