Displaying 20 results from an estimated 6000 matches similar to: "lmer p-vales are sometimes too small"
2002 Dec 15
2
Interpretation of hypothesis tests for mixed models
My question concerns the logic behind hypothesis tests for fixed-effect
terms in models fitted with lme. Suppose the levels of Subj indicate a
grouping structure (k subjects) and Trt is a two-level factor (two
treatments) for which there are several (n) responses y from each
treatment and subject combination. If one suspects a subject by
treatment interaction, either of the following models seem
2007 Mar 07
1
Failure to run mcsamp() in package arm
Dear r-helpers,
I can run the examples on the mcsamp help page. For example:
****************************************
> M1 <- lmer (y1 ~ x + (1|group))
> (M1.sim <- mcsamp (M1))
fit using lmer,
3 chains, each with 1000 iterations (first 500 discarded)
n.sims = 1500 iterations saved
mean sd 2.5% 25% 50% 75% 97.5% Rhat n.eff
beta.(Intercept)
2010 Aug 11
1
Growth Curves with lmer
Dear all,
I have some growth curve data from an experiment that I try to fit using
lm and lmer. The curves describe the growth of classification accuracy
with the amount of training data t, so basically
y ~ 0 + t (there is no intercept because y=0 at t0)
Since the growth is somewhat nonlinear *and* in order to estimate the
treatment effect on the growth curve, the final model is
y ~ 0 + t +
2006 Nov 24
2
low-variance warning in lmer
For block effects with small variance, lmer will sometimes
estimate the variance as being very close to zero and issue
a warning. I don't have a problem with this -- I've explored
things a bit with some simulations (see below) and conclude that
this is probably inevitable when trying to incorporate
random effects with not very much data (the means and medians
of estimates are plausibly
2013 Nov 12
1
Getting residual term out of lmer summary table
Hello
I'm working with mixed effects models using lmer() and have some problems to get all variance components of the model's random effects. I can get the variance of the random effect out of the summary and use it for further calculations, but not the variance component of the residual term. Could somebody help me with that problem? Thanks a lot! Below an example.
Aline
## EXAMPLE
2006 May 09
1
trying to use standard notation
Hi, all. In setting up my package for post-processing regression
models, I am trying to use standard notation as much as possible: thus,
I use coef() to access estimated coefficients. I wrote a function
called se.coef() to grab standard errors, and se.fixef() and se.ranef()
to grab se's from coefficients estimated from lmer().
I also need a function to access sigma-hat (the residual sd
2011 May 19
1
lmer with 2 random effects with only two levels
Dear all,
I am analysing a data set based on 6 groups of individuals. Each group is
observed for 10 days. 5 days with one manipulation 5 days with another
manipulation. I therefore have 6 replicate groups (n=6) each with one mean
measurement for manipulation A and manipulation B. Each group consists of a
set of males and females. An independent group of males for each group
replicate, however
2010 Feb 09
1
Missing interaction effect in binomial GLMM with lmer
Dear all,
I was wondering if anyone could help solve a problem of a missing interaction effect!!
I carried out a 2 x 2 factorial experiment to see if eggs from 2 different locations (Origin = 1 or 2) had different hatching success under 2 different incubation schedules (Treat = 1 or 2). Six eggs were taken from 10 females (random = Female) at each location and split between the treatments,
2006 Aug 24
1
help: trouble using lines()
Hi R experts,
I have been using ReML as follows...
model<-lmer(late.growth~mtf+year+treat+hatch.day+hatch.day:year+hatch.day:treat+
mtf:treat+ treat:year+ year:treat:mtf+(1|fybrood), data = A)
then I wanted to plot the results of the three way interaction using
lines() as follows...
tmp<-as.vector(fixef(model))
graph1<-plot(mtf,fitted(f2), xlab=list("Brood Size"),
2011 Nov 15
2
Models with ordered and unordered factors
Hello;
I am having a problems with the interpretation of models using ordered or
unordered predictors.
I am running models in lmer but I will try to give a simplified example
data set using lm.
Both in the example and in my real data set I use a predictor variable
referring to 3 consecutive days of an experiment. It is a factor, and I
thought it would be more correct to consider it ordered.
Below
2007 Nov 12
0
Resid() and estimable() functions with lmer
Hi all,
Two questions:
1. Is there a way to evaluate models from lmer() with a poisson
distribution? I get the following error message:
library(lme4)
lmer(tot.fruit~infl.treat+def.treat+(1|initial.size),family=poisson)->model
plot(fitted(model),resid(model))
Error: 'resid' is not implemented yet
Are there any other options?
2. Why doesn't the function estimable() in gmodels
2006 Jan 10
1
extracting coefficients from lmer
Dear R-Helpers,
I want to compare the results of outputs from glmmPQL and lmer analyses.
I could do this if I could extract the coefficients and standard errors
from the summaries of the lmer models. This is easy to do for the glmmPQL
summaries, using
> glmm.fit <- try(glmmPQL(score ~ x*type, random = ~ 1 | subject, data = df,
family = binomial), TRUE)
> summary(glmmPQL.fit)$tTable
2002 Jul 18
1
sem: incorrect parameter estimates
Hello.
I am getting results from sem that are not correct (that's assuming
that the results from my AMOS 4.0 software are correct). sem does not
vary some of the parameters substantially from their starting values,
and the final estimates of those parameters as well as the model
chisquare value are incorrect. I've attached some code that
replicates the problem. The parameters in
2011 Sep 05
0
glht (multcomp): NA's for confidence intervals using univariate_calpha (fwd)
fixed @ R-forge. New version should appear on CRAN soon.
Thanks for the report!
Torsten
>
> ---------- Forwarded message ----------
> Date: Sat, 3 Sep 2011 23:56:35 +0200
> From: Ulrich Halekoh <Ulrich.Halekoh at agrsci.dk>
> To: "r-help at r-project.org" <r-help at r-project.org>
> Subject: [R] glht (multcomp): NA's for confidence intervals using
2011 Sep 03
0
glht (multcomp): NA's for confidence intervals using univariate_calpha
Hej,
Calculation of confidence intervals for means
based on a model fitted with lmer
using the package multcomp
- yields results for calpha=adjusted_calpha
- NA's for calpha=univariate_calpha
Example:
library(lme4)
library(multcomp)
### Generate data
set.seed(8)
d<-expand.grid(treat=1:2,block=1:3)
e<-rnorm(3)
names(e)<-1:3
d$y<-rnorm(nrow(d)) + e[d$block]
2010 Oct 26
1
lme vs. lmer results
Hello,
and sorry for asking a question without the data - hope it can still
be answered:
I've run two things on the same data:
# Using lme:
mix.lme <- lme(DV ~a+b+c+d+e+f+h+i, random = random = ~ e+f+h+i|
group, data = mydata)
# Using lmer
mix.lmer <- lmer(DV
~a+b+c+d+(1|group)+(e|group)+(f|group)+(h|group)+(i|group), data =
mydata)
lme provided an output (fixed effects and random
2012 Dec 29
1
AIC values with lmer and anova function
Dear colleagues,
I have a data from a repeated measures design that I'm analysing through a
mixed model. Nine independent sampling units (flasks with culture medium
with algae) were randomly divided into 3 groups ("c", "t1", "t2"). There is
no need for inclusion of the random effect of the intercept, because the
nine sample units are homogeneous among each other
2013 Nov 07
1
problem with interaction in lmer even after creating an "interaction variable"
Dear all,
I have a problem with interactions in lmer. I have 2 factors (garden and
gebiet) which interact, plus one other variable (home), dataframe arr. When
I put:
/
lmer (biomass ~ home + garden:gebiet + ( 1|Block), data = arr)/
it writes:
/Error in lme4::lFormula(formula = biomass ~ home + garden:gebiet + (1 | :
rank of X = 28 < ncol(X) = 30/
In the lmer help I found out that if not
2005 Oct 26
1
R-help Digest, Vol 32, Issue 26
r-help at stat.math.ethz.ch on Wednesday, October 26, 2005 at 6:00 AM -0500 wrote:
Ronaldo,
Try Harold's suggestion. The df still won't agree, because lmer (at least in its current version) just puts an upper bound on the df. But that should be OK, because all those t tests are approximations anyways, and you can get better confidence
intervals (credible intervals, whatever) by using the
2006 Oct 20
1
Translating lme code into lmer was: Mixed effect model in R
This question comes up periodically, probably enough to give it a proper
thread and maybe point to this thread for reference (similar to the
'conservative anova' thread not too long ago).
Moving from lme syntax, which is the function found in the nlme package,
to lmer syntax (found in lme4) is not too difficult. It is probably
useful to first explain what the differences are between the