Displaying 20 results from an estimated 1000 matches similar to: "mcmcsamp and variance ratios"
2010 Jan 31
2
lmer, mcmcsamp, coda, HPDinterval
Hi,
I've got a linear mixed model created using lmer:
A6mlm <- lmer(Score ~ division + (1|school), data=Age6m)
(To those of you to whom this model looks familiar, thanks for your patience
with this & my other questions.) Anyway, I was trying this to look at the
significance of my fixed effects:
A6post <- mcmcsamp(A6mlm, 50000)
library(coda)
HPDinterval(A6post)
..but I got this
2009 Feb 24
2
lmer, estimation of p-values and mcmcsamp
(To the list moderator: I just subscribed to the list. Apologies for not
having done so longer before trying to post.)
Hi all,
I am currently using lmer to analyze data from an experiment with a
single fixed factor (treatment, 6 levels) and a single random factor
(block). I've been trying to follow the online guidance for estimating
p-values for parameter estimates on these and other
2008 Jun 30
1
Coda not providing summary on mcmc object
The object is a mcmc sample from lmer. I am using R v2.7.1. Please let me
know what additional information I can provide, hopefully I am just making a
simple mistake. Thanks in advance!
> data(ratdrink, package = 'faraway')
> rd.er <- lmer(wt ~ weeks*treat + (1 | subject), data = ratdrink)
> rd.mc <- mcmcsamp(rd.er, 10000)
> library(coda)
Loading required package:
2006 Jun 09
1
binomial lmer and fixed effects
Hi Folks,
I think I have searched exhaustively, including, of course R-help (D.
Bates, S. Graves, and others) and but I remain uncertain about
testing fixed effects with lmer(..., family=binomial).
I gather that mcmcsamp does not work with Do we rely exclusively on z
values of model parameters, or could we use anova() with likelihood
ratios, AIC and BIC, with (or without)
2007 Apr 03
2
HPDinterval problem
Hi,
Can anyone tell me why I am not getting the correct intervals for
fixed effect terms for the following generalized linear mixed model
from HPDinterval:
> sessionInfo()
R version 2.4.1 (2006-12-18)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
2006 Aug 08
1
fixed effects following lmer and mcmcsamp - which to present?
Dear all,
I am running a mixed model using lmer. In order to obtain CI of
individual coefficients I use mcmcsamp. However, I need advice which
values that are most appropriate to present in result section of a
paper. I have not used mixed models and lmer so much before so my
question is probably very naive. However, to avoid to much problems with
journal editors and referees addicted to
2008 Aug 12
1
tilde on a spanish keyboard?
I was trying to help someone who used a spanish keyboard on a PC
running Windows. he discovered that he had no tilde key. Does anyone
know of any simple work-arounds?
Thanks,
Hank
Dr. Hank Stevens, Associate Professor
338 Pearson Hall
Botany Department
Miami University
Oxford, OH 45056
Office: (513) 529-4206
Lab: (513) 529-4262
FAX: (513) 529-4243
http://www.cas.muohio.edu/~stevenmh/
2013 Aug 23
1
How to view the source of code?
Hi all R mailing listers:
I am using the coda package. I tried to view the source of HPDinterval code
by typing fix(HPDinterval), it dispalys as follows:
function (obj, prob = 0.95, ...)
UseMethod("HPDinterval")
Then I search the answers about this case (see below), it still failed.
Thank you in advance!
David
> getAnywhere('HPDinterval')2 differing objects matching
2007 Jun 11
1
Package update announcements
Hi Folks,
I was wondering what everyone thought about adding a sentence to each
package update announcement that described what the package did. R
extensions are so numerous that it is difficult to keep up with them.
Would it be appropriate to ask package developers to add a brief
sentence about what the package does, when they announce updates?
I would benefit from such descriptions.
2013 May 08
1
How to calculate Hightest Posterior Density (HPD) of coeficients in a simple regression (lm) in R?
Hi!
I am trying to calculate HPD for the coeficients of regression models
fitted with lm or lmrob in R, pretty much in the same way that can be
accomplished by the association of mcmcsamp and HPDinterval functions for
multilevel models fitted with lmer. Can anyone point me in the right
direction on which packages/how to implement this?
Thanks for your time!
R.
[[alternative HTML version
2007 May 31
2
Different fonts on different axes
Hi Folks,
How do I get red bold font on my y axis and black standard font on my
x axis?
plot(runif(10), ylab="Red, Bold?", xlab="Black, standard?")
Any pointers or examples would be great.
Thanks!
Hank
Dr. Hank Stevens, Assistant Professor
338 Pearson Hall
Botany Department
Miami University
Oxford, OH 45056
Office: (513) 529-4206
Lab: (513) 529-4262
FAX: (513) 529-4243
2005 Oct 14
1
lattice with predicted values
Dear lattice wizards,
I am trying to figure out how to plot predicted values in xyplot,
where the intercept, but not the slope, varies among conditioning
factor levels. I am sure it involves the groups, but I have been
unsuccessful in my search in Pinhiero and Bate, in the help files, or
in the archive, or in my attempts on my own.
My example follows:
FACT is a factor with levels a,b,c
2007 Jan 15
1
Conflict in .Rprofile documentation FAQ vs. Help?
Hi folks,
I note that in the general FAQ's we have
7.25 Why did my .Rprofile stop working when I updated R?
Did you read the NEWS file? For functions that are not in the base
package you need to specify the correct package namespace, since the
code will be run before the packages are loaded. E.g.,
ps.options(horizontal = FALSE)
help.start()
needs to be
2005 Oct 26
2
changing memory limits to speed up lsoda
Hi All,
I am running R 2.2.0 on Mac OS 10.4.2, dual G5 processors with 8 Gig
RAM.
I am running a simulation with lsoda that requires ~378 s to complete
one set of time intervals. I need to optimize the parameters, and so
need to considerably speed up the simulation.
I have tried to figure out how to change the appropriate memory
allocation and have search R help and Introductory
2007 Mar 12
2
Lmer Mcmc Summary and p values
Dear R users
I am trying to obtain p-values for (quasi)poisson lmer models, including
Markov-chain Monte Carlo sampling and the command summary.
>
> My problems is that p values derived from both these methods are
totally different. My question is
(1) there a bug in my code and
>
(2) How can I proceed, left with these uncertainties in the estimations of
> the p-values?
>
> Below
2005 Oct 10
3
Under-dispersion - a stats question?
Hello all:
I frequently have glm models in which the residual variance is much
lower than the residual degrees of freedom (e.g. Res.Dev=30.5, Res.DF
= 82). Is it appropriate for me to use a quasipoisson error
distribution and test it with an F distribution? It seems to me that
I could stand to gain a much-reduced standard error if I let the
procedure estimate my dispersion factor (which
2006 Jun 14
2
lmer binomial model overestimating data?
Hi folks,
Warning: I don't know if the result I am getting makes sense, so this
may be a statistics question.
The fitted values from my binomial lmer mixed model seem to
consistently overestimate the cell means, and I don't know why. I
assume I am doing something stupid.
Below I include code, and a binary image of the data is available at
this link:
2006 May 17
1
nlme model specification
Hi folks,
I am tearing my hair out on this one.
I am using an example from Pinheiro and Bates.
### this works
data(Orange)
mod.lis <- nlsList(circumference ~ SSlogis(age, Asymp, xmid, scal),
data=Orange )
### This works
mod <- nlme(circumference ~ SSlogis(age, Asymp, xmid, scal),
data=Orange,
fixed = Asymp + xmid + scal ~ 1,
start =
2007 Mar 13
1
lme4 and mcmcamp
Dear R users
I am trying to obtain p-values for (quasi)poisson lmer models, using
Markov-chain Monte Carlo sampling and the command summary.
>
> My problems is that p values derived from both these methods are
totally different. My question is
(1) there a bug in my code and
>
(2) How can I proceed, left with these uncertainties in the estimations of
> the p-values?
>
> Below is
2007 Feb 12
1
lmer and estimation of p-values: error with mcmcpvalue()
Dear all,
I am currently analyzing count data from a hierarchical design, and I?ve
tried to follow the suggestions for a correct estimation of p-values as
discusssed at R-Wiki
(http://wiki.r-project.org/rwiki/doku.php?id=guides:lmer-tests&s=lme%20and%20aov).
However, I have the problem that my model only consists of parameters
with just 1 d.f. (intercepts, slopes), so that the