Displaying 20 results from an estimated 700 matches similar to: "coxme for random effects only model"
2010 Aug 22
2
coxme AIC score and p-value mismatch??
Hi,
I am new to R and AIC scores but what I get from coxme seems wrong. The AIC
score increases as p-values decrease.
Since lower AIC scores mean better models and lower p-values mean stronger
effects or differences then shouldn't they change in the same direction? I
found this happens with the data set rats as well as my own data. Below is
the output for two models constructed with the rats
2006 Jun 29
2
help with coxme
Hi there,
I have a question on fitting data by coxme. In particular I want to fit a
random intercept and random slope cox model. Using the rats dataset as an
example, I generated another covariate x2 and want to specify a random slope
for x2. Here is my code:
x2=matrix(rep(runif(50), 3), 50, 3)
x2=as.vector(t(x2))
rats2=cbind(rats, x2)
But when I used the coxme function as follows, it gave
2012 Sep 14
1
Correlation between random effects in the package coxme
Hello,
Why the correlation between the random effects is negative?
library(coxme)
rats1 <- coxme(Surv(time, status) ~ (1|litter), rats)
random.effects(rats1)[[1]] #one value for each of the 50 litters
print(rats1)
rats2 <- lmekin(time ~ (1|litter), rats)
fixed.effects(rats2)
random.effects(rats2)[[1]] #one value for each of the 50 litters
print(rats2)
2012 Feb 03
1
coxme with frailty--variance of random effect?
Dear all,
This probably stems from my lack of understanding of the model, but I
do not understand the variance of the random effect reported in coxme.
Consider the following toy example:
#------------------------------- BEGINNING OF CODE
------------------------------------------------
library(survival)
library(coxme)
#--- Generate toy data:
d <- data.frame(id = c(1:100), #
2008 Dec 28
1
Random coefficients model with a covariate: coxme function
Dear R users:
I'm new to R and am trying to fit a mixed model
Cox regression model with coxme function.
I have one two-level factor (treat) and one
covariate (covar) and 32 different groups
(centers). I'd like to fit a random coefficients model, with treat and covar
as fixed factors and a random intercept, random
treat effect and random covar slope per center.
I haver a couple of
2008 Mar 05
1
coxme - fitting random treatment effect nested within centre
Dear all,
I am using "coxme" function in Kinship library to fit random treatment effect nested within centre. I got 3 treatments (0,1,2) and 3 centres. I used following commands, but got an error.
> ugroup=paste(rep(1:3,each=3),rep(0:2,3),sep='/')
> mat1=bdsmatrix(rep(c(1,1,1,1,1,1,1,1,1),3),blocksize=rep(3,3),dimnames=list(ugroup,ugroup))
>
2012 Feb 19
1
coxme: model simplification using LR-test?
Hi
I'm encountering some problems with coxme
My data:
I'm looking at the survival of animals in an experiment with 3 treatments,
which came from 4 different populations, two of which were infected with a
parasite and two of which were not. I'm interested if infected animals
differe from uninfected ones across treatments.
Factor 1: treatment (3 levels)
Factor 2: infection state
2011 Jan 25
1
coxme and random factors
Hi
I would really appreciate some help with my code for coxme...
My data set
I'm interested in survival of animals after an experiment with 4
treatments, which was performed on males and females. I also have two
random factors:
Response variable: survival (death)
Factor 1: treatment (4 levels)
Factor 2: sex (male / female)
Random effects 1: person nested within day (2 people did
2011 Aug 02
2
Extract p value from coxme object
Dear R experts;
I am trying to extract the p values from a coxme object (package coxme). I
can see the value in the model output, but I wanted to have the result with
a higher number of decimal places.
I have searched the mailing list and followed equivalent suggestions for
nlme/lme objects, but I wasn't successful.
Thanks;
Catarina
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2007 Apr 20
1
Approaches of Frailty estimation: coxme vs coxph(...frailty(id, dist='gauss'))
Dear List,
In documents (Therneau, 2003 : On mixed-effect cox
models, ...), as far as I came to know, coxme penalize
the partial likelihood (Ripatti, Palmgren, 2000) where
as frailtyPenal (in frailtypack package) uses the
penalized the full likelihood approach (Rondeau et al,
2003).
How, then, coxme and coxph(...frailty(id,
dist='gauss')) differs? Just the coding algorithm, or
in
2007 Dec 05
4
coxme frailty model standard errors?
Hello,
I am running R 2.6.1 on windows xp
I am trying to fit a cox proportional hazard model with a shared
Gaussian frailty term using coxme
My model is specified as:
nofit1<-coxme(Surv(Age,cen1new)~ Sex+bo2+bo3,random=~1|isl,data=mydat)
With x1-x3 being dummy variables, and isl being the community level
variable with 4 levels.
Does anyone know if there is a way to get the standard error
2012 Oct 07
1
variances of random effects in coxme
Dear R users,
I'm using the function coxme of the package coxme in order to build Cox
models with complex random effects. Unfortunately, I sometimes get
surprising estimations of the variances of the random effects.
I ran models with different fixed covariates but always with the same 3
random effects defined by the argument
varlist=coxmeMlist(list(mat1,mat2,mat3), rescale = F, pdcheck = F,
2007 Apr 20
1
Hiding "Warning messages" in coxme output
Dear list,
I have been trying to use coxme in R 2.3.1.
When I use coxme in the following data sim.fr1, i get
"Warning messages: using 'as.environment(NULL)' is
deprecated"
Why does it occur?
How can I hide such warning message,
especially when coxme is under a loop?
Mohammad Ehsanul Karim (Institute of Statistical
Research and Training, University of Dhaka)
>
2006 Mar 30
1
Random Coefficients using coxme
Hello, I was hoping someone could answer a question for me that may
either be statistical or script related. I don't come from a statistics
background, so I am not positive if I am using the correct nomenclature
or even the correct procedure. Is it possible to model "random
coefficients" in a mixed effects cox-regression using coxme from the
Kinship package? For example, using
2011 Jan 16
1
Help in Coxme
I am a relative newbie to survival analysis and R in general, but
would like to use the coxme package to analyse some data I currently
have.
The data is relative to survival times of drosophila melanogaster
populations to infection with pathogens, and has the variables:
Time,
Status,
Treatment (4 treatments + 2 controls)
Population
Replicate
?and I'm currently using the following call
2010 Aug 04
5
Question regarding significance of a covariate in a coxme survival model
Hi,
I am running a Cox Mixed Effects Hazard model using the library coxme. I
am trying to model time to onset (age_sym1) of thought problems (e.g.
hearing voices) (sym1). As I have siblings in my dataset, I have
decided to account for this by including a random effect for family
(famid). My covariate of interest is Mother's diagnosis where a 0 is
bipolar, 1 is control, and 2 is major
2012 Jun 30
1
How do I extract coefficient standard errors /CI for a "coxme" model
Hello, and thanks for your time
I'm trying to extract standard errors to produce confidence intervals from a
multivariable coxme model object so I can write a function that will print
a summary for some reproducible research. As far as I can glean, the SE is
produced on-the-fly by the print method. I'll dig into the source code if I
have to, but I'd rather not have to.
Any help
2013 Jul 05
1
multcomp on significant interaction in coxme model
Dear R community
I currently try to get post hoc multiple comparisons with the package
multcomp from a cox mixed-effects model, where the survival is explained
by two variables (cover with levels: nocover and cover; treatment with
levels: tx, uv, meta), whose interaction is significant.
I read Hothorn, T. 2011: Additional multcomp Examples and there is an
example involving a two-way ANOVA with
2006 Jul 05
0
Problem with coxme
------------- Begin Forwarded Message -------------
Date: Wed, 5 Jul 2006 09:09:14 -0500 (CDT)
From: Terry Therneau <therneau at mayo.edu>
Subject: RE: Problem with coxme
To: jhz22 at medschl.cam.ac.uk
Cc: R-help at stat.mat.ethz.ch, liulei at virginia.edu, spencer.graves at pdf.com
Content-MD5: BXKVsHtW/1I9mIUqrXBU0g==
The original question involved a strange error message from coxme
2012 Sep 06
1
How to extract p value from the lmekin object obtained by fitting mixed model with function lmekin() in package coxme?
Hi, R experts
I am currently using lmekin() function in coxme package to fit a
mixed effect model for family based genetic data. How can I extract the p
value from a lmekin object? When I print the object in R console, I can
see the p value and Z value are just over there. But I can not extract them
by the coef() function. kinfit$coefficient$fixed (kinfit is the name of the
lmekin object)