Displaying 20 results from an estimated 37 matches for "mer_fin".
2008 Dec 05
1
lme4, error in mer_finalize(ans)
...ckage
library(lme4)
# first fit a linear model with letter position nested in
word length
lm(rt ~ length + length:pos, data=df)
# fit a mixed effects model, with subj (participant) as
random effect
lmer(rt ~ length + length:pos + (1 | subj), data=df)
Using lmer() results in an error: Error in
mer_finalize(ans) : Downdated X'X is not positive
definite, 13. I don't experience any problems using lm().
Does anyone know where things go wrong?
~ Ben Meijering
2013 Jan 18
1
Error in mer_finalize(ans) : Downdated X'X is not positive definite, 8.
...d 4 sets for each radii: 1) with both random effects, 2+3)
only one (each) random effect, and 4) none.
I have tried to model the relationships using glm, glmer and lmer.
The problem is that in the full model (all 7 variables) of some sets with
random effects I get the following error:
*Error in mer_finalize(ans) : Downdated X'X is not positive definite, 8.*
The only record of this error I have found in the internet is for data with
missing observation. This doesn't comply with my data set. I think it
might be a singularity problem but I don't know how to check it, and as a
result,...
2012 Feb 06
1
lmer with spatial and temporal random factors, not nested
...lt;-lmer(Richness~Y+Canopy+Veg_cm+Treatment+(1|Site/Block/Plot)+(1|Year),
family=poisson, REML=FALSE),
where
richness = integer
Y & Treatment = factor
Canopy & Veg_cm = numerical, continous
Site/Block/Plot= factor
Year = integer
I get the following warning message:
Warning messages:
1: In mer_finalize(ans) :
Cholmod warning 'not positive definite' at
file:../Cholesky/t_cholmod_rowfac.c, line 432
2: In mer_finalize(ans) : singular convergence (7)
Is this due to the nature of my fixed/random factors or the way I put
up the random factors?
In lme I could include a component for aut...
2009 Dec 24
1
Multiple CHOLMOD errors when attempting poisson glmm
Hello,
I have been attempting to run a poisson glmm using lme4 for some time now
and have had a lot of trouble. I would say 9 times out of 10 I receive the
following warning:
CHOLMOD warning: %h
Error in mer_finalize(ans) :
Cholmod error `not positive definite' at
file:../Cholesky/t_cholmod_rowfac.c, line 432
My data are counts of microbe colony forming units (CFUs) collected from
termite cuticles and the surrounding environment over a 3 year period. I am
attempting to analyze the effect of severa...
2009 Feb 26
1
error message and convergence issues in fitting glmer in package lme4
...ce, and income structure, poverty=county poverty rate, fastfood=number of fastfood places per 100,000 people in the county, and a county random effect.
>
> If I leave out fastfood, the model gets at least fitted - although it doesn't converge (yet):
>
> Warning message:
> In mer_finalize(ans) : false convergence (8)
>
> I would be grateful for any advice on what the problem could be and how to resolve it.
>
> Thanks,
> Tanja
Tanja Srebotnjak, PhD, MSc, Dipl. Stat.
Postgraduate Fellow
Institute for Health Metrics and Evaluation
University of Washington
230...
2013 Mar 23
1
Non-convergence error for GLMM with LME4?
Hello! I am trying to run a GLMM using LME4, and keep getting the warning message: "In mer_finalize(ans) : false convergence (8)" I am quite new to R, and in looking into this thus far, it appears that there are a variety of reasons why this might occur, such as needing to standardize some parameters or if all subjects in one combination of parameters all have the same outcome. I also...
2009 Jun 28
1
HLM - centering level 2 predictor
....
x2 is the level 2 predictor variable.
id.full is the conditioned variable.
It runs beautifully when only x1 is centered (I subtracted the grand mean from each value). However, when I also centered x2 variable with the same procedure, it gives me the following error message:
Warning message:
In mer_finalize(ans) : singular convergence (7)
I'd appreciate if someone could explain me what it means.
One of the differences between "non-centered values" and "centered values" is that the "centered values" include negative values. Could it be the reason? If so, what...
2010 Feb 02
1
lme4 package and gamma family
...4_0.999375-32.zip; R-2.10.1). According to the information, I
should be able to use a generalized linear mixed model.
However when I try to fit a model with Gamma distribution of the errors, it
gives me the following error
model1<-lmer(Cmic~1+(1|FOREST/DEPTH),data=DATOS,family=Gamma)
Error en mer_finalize(ans) :
General form of glmer_linkinv not yet written
The same occurs with the function glmer, although I have seen in the forum
that other people has been able to implement this type of models.
Does anyone know why is this happening?
Thanks!
Cristina
IRNAS-CSIC
Seville, Spain
--
Vi...
2008 Jul 12
1
a warning message from lmer
...ls(regdat$ObsGender)
[1] "F" "M"
> levels(regdat$WalkerGender)
[1] "F" "M"
the watning is:
>
fit1<-lmer(Agree~Display+Survey+Emotion+WalkerGender+ObsGender+(1|WalkerID)+(1|ObsID),family=binomial(link='logit'),data=regdat)
Warning message:
In mer_finalize(ans, verbose) : gr cannot be computed at initial par
(65)
Does anybody have some hint to solve this problem? I'd very much
appreciate it!
Thanks,
Lan Wei
2008 Oct 30
1
How to increase iteration limit for lmer()?
Dear R users:
I am running lmer(), and I had the following warning message:
"In mer_finalize(ans): iteration limit reached without convergence (9)
What is the default limit for lmer()? And how do I increase the limit?
Many thanks,
Julia
--
View this message in context: http://www.nabble.com/How-to-increase-iteration-limit-for-lmer%28%29--tp20252974p20252974.html
Sent from the R he...
2009 Feb 15
1
GLMM, ML, PQL, lmer
...Breslow and
Clayton 1993 JASA paper. Model 3 of the epileptic dataset has two random
effects, one subject specific, and one observation specific. Thus if we
count random effects, there are more parameters than observations. When I
try to run the following code, I get an error saying: "Error in
mer_finalize(ans) : q = 295 > n = 236".
require (lme4)
require (glmmAK)
data(epilepticBC)
dat = epilepticBC
dat$rand=1:nrow(dat)
dat$V4=dat$visit==4
formula1 = Seizure ~ Base + Trt + I(Trt*Base) + Age + V4
fit=lmer (update (formula1, .~. + (1|id) + (1|rand)), family=poisson,
data=dat, nAGQ=1)
Is...
2011 Jun 24
1
Help with lmer
Hey,
I am having trouble with lmer. I am looking at the presence/absence of water shrews against habitat and other factors e.g
so I used this:
m1<-lmer(Presencebsence~Habitatype*Width+(1|Sitename))summary(m1)
But i keep getting this error up
Error in mer_finalize(ans) : Downdated X'X is not positive definite, 16.> summary(m1)Error in asMethod(object) : matrix is not symmetric [1,2]
What does this mean and now can I fix it?
Sophie
[[alternative HTML version deleted]]
2011 Feb 06
1
random interaction effect in lmer
Hi dears while modeling an interaction random effect in lmer i receive the
instantaneous error message
> ldlM4<-lmer(ldl~rt*cd4+age+rf+pharmac+factor(hcv)+
+ hivdur+(rt:cd4|id),na.action=na.omit,REML=F)
*Warning message:
In mer_finalize(ans) : false convergence (8)
*
I think the matter lies in syntax, 'cause i sistematically receive the same
message even when changing response...
PS: the above model runs quite well in lme and only rarely I recive :
*
Errore in lme.formula(fixed = ldl ~ rt + cd4 + age + rf + pharmac +
fact...
2010 Dec 13
1
Testing an interaction with a random effect in lmer
...and group, as the raw data suggests that different groups may behave differently in different seasons. Is there a way to do this in the lmer package?
When i put it in directly:
model<-lmer(binom~season*group+(1|group/individual),binomial,data=data1)
I get an error messgae:
Warning message:
In mer_finalize(ans) : gr cannot be computed at initial par (65)
The model runs with the following:
modelb<-lmer(binom~season*(1|group)+(1|group/badger),binomial,data=data1)
or
modelb<-lmer(binom~season+(1|group/badger)+(1|group:season),binomial,data=data1)
but here I guess I am modelling it as part...
2008 Sep 24
0
weights option in lmer
...using the weights option.
I am using the
R version 2.7.2 (2008-08-25) and lmer version in lme4_0.999375-26, which I think it is the latest version!
I am getting and error message when I add the
option "weights" in the lmer function. This is the error message I
get "Error en mer_finalize(ans) : Calculated PWRSS for a LMM is negative".
I have been
reading in the last few weeks all the forum questions and answers about this
issue. Certainly this has been discussed MANY times before especially with
older versions of lmer (much less in the newer versions). I have been tr...
2012 Mar 23
3
Using MuMIn - error message
Hello,
I hope that you can bare with me. I am new to models, but I think I have a
pretty godd understanding of how to run them now, including how to use AICc
and Anova. The issue is that I have many factors that I wish to compare so
doing each one at a time would take forever.
I came across the MuMIn package and I was so excited, however I am getting
an error message and i don't know why.
2010 Oct 26
1
lme vs. lmer results
...<- 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 effects coefficients).
lmer gave me an error: Error in mer_finalize(ans) : Downdated X'X is
not positive definite, 10.
I've rerun lmer with - but specifying the random effects for 2 fewer
predictors. This time it ran and provided an output. (BTW, the random
effects of lmer with 2 fewer predictors specified as random were very
close to the output of lme...
2011 Nov 21
2
errors with lme4
...i want to remove
some, but the ideal model:
GLM.1 <-lmer(fledgesucc ~ +lay +hatch +elev +seadist +nnd +npd
+meanterranova +minpengS1 +minpengS2 +wchillpengS1 +wchillpengS2
+(1|territory), family=binomial(logit), data=fledge)
doesn't work because of these errors:
'Warning message: In mer_finalize(ans) : gr cannot be computed at
initial par (65)'.
"matrix is not symmetric [1,2]"
If i delete one or more of the T records (i.e. minpengS2 +wchillpengS2)
the model works...below and example:
GLM.16 <-lmer(fledgesucc ~ lay +hatch +elev +seadist +nnd +npd
+meanterranova +...
2008 Nov 24
1
lme4 and false convergence
...OUNT[min. 1 to max. 37,mean = 10]).
---------------------------------------------------------------------
PROBLEM 1:
I have developed the following GLMM:
mix.1<-glmer(PRES~AG+FOR+OPEN+LDEV+DEV+COUNT+(1|SITE),family=binomial,data=merge1)
I receive the following error:
Warning message:
In mer_finalize(ans) : false convergence (8)
There is model output, but I am worried it might be biased.
I have tried:
-Data transformation of the predictor variables (e.g., log(COUNT)),
which does seem successful in some simpler models, but does not work
consistently.
-The most updated version of lme4...
2010 Jan 04
2
Piecewise regression in lmer
...using this formula in lmer:
m<-lmer(repro ~ OTHER FIXED EFFECTS + age*(age < 2) + age*(age >= 2 &
age < 8) + age*(age >= 8) + (1|id) + (1|yr), data = reproduction,
family = binomial, link = "logit", GHQ = TRUE)
However, this gives the warning:
Warning message:
In mer_finalize(ans) : gr cannot be computed at initial par (65)
which is not apparent if I use just two break points or I implement
the model in glm.
My question is essentially whether anyone can recommend a method for
performing piecewise regression in lmer or another mixed model
framework. Any advi...