Displaying 20 results from an estimated 100 matches similar to: "Extracting SD of random effects from lme object"
2007 Jul 31
1
Extracting random parameters from summary lme and lmer
LS,
I'm estimating multilevel regression models, using the lme-function
from the nlme-package. Let's say that I estimated a model and stored
it inside the object named 'model'. The summary of that model is
shown below:
Using summary(model)$tTable , I receive the following output:
> summary(model)$tTable
Value Std.Error DF t-value
2007 Jul 30
1
Extract random part of summary nlme
Dear helpers,
I'm estimating multilevel regression models, using the lme-function
from the nlme-package. Let's say that I estimated a model and stored
it inside the object named 'model'. The summary of that model is
shown below:
Using summary(model)$tTable , I receive the following output:
> summary(model)$tTable
Value Std.Error DF t-value
2007 Jan 06
1
help with gls
Hello R-users,
I am using gls function in R to fit a model with certain correlation
structure.
The medol as:
fit.a<-gls(y~1,data=test.data,correlation=corAR1(form=~1|aa),method="ML")
mu<-summary(fit.a)$coefficient
With the toy data I made to test, the estimate of mu is exactly equal to
the overall mean of y which can not be true.
But, if I make a toy data with y more than two
2008 Feb 19
1
Matrix inversion
Howdy,
I am trying to invert a matrix for the purposes of least squares. I
have tried a number of things, and the variety of results has me
confused.
1. When I try solve() I get the following:
>Error in solve.default(t(X) %*% X) : system is computationally
singular: reciprocal condition number = 3.76391e-20
2. When I try qr.solve(), I get:
>Error in qr.solve(t(X) %*% X) : singular matrix
2010 Jul 26
1
Problem upgrading to 2.11
Hello,
I am trying to upgrade to 2.11 from 2.10 in the hopes of gaining
TCL/TK capabilities (let's pretend for the moment that this should
work). I've added "deb http://cran.stat.ucla.edu/bin/linux/ubuntu
lucid/" to /etc/apt/sources.list as described in the guide and have
run
apt-get update
apt-get install r-base r-base-dev
Things seem to work. When I look at the installed
2007 Jun 25
3
Bug in getVarCov.gls method (PR#9752)
Hello,
I am using R2.5 under Windows.
Looks like the following statement
vars <- (obj$sigma^2)*vw
in getVarCov.gls method (nlme package) needs to be replaced with:
vars <- (obj$sigma*vw)^2
With best regards
Andrzej Galecki
Douglas Bates wrote:
>I'm not sure when the getVarCov.gls method was written or by whom. To
>tell the truth I'm not really sure what
2008 Aug 29
3
extract variance components
HI,
I would like to extract the variance components estimation in lme function
like
a.fit<-lme(distance~age, data=aaa, random=~day/subject)
There should be three variances \sigma_day, \sigma_{day %in% subject } and
\sigma_e.
I can extract the \sigma_e using something like a.fit$var. However, I cannot
manage to extract the first two variance components. I can only see the
results in
2007 Jun 20
2
Linear Mixed Models with nlme, more than one random effect
Hi, I' trying to learn how to use lme for Linear Mixed Models and I have a
problem when I have to include more than one random effect in my model. I
know that this could be a stupid question to ask, but I'm not able to solve
it by myself... One example: if my model is
response = operator + block + day
with operator and block as fixed effects and day as random effect, I use
res.lme
2004 Dec 29
3
gls model and matrix operations
Dear List:
I am estimating a gls model and am having to make some rather unconventional modifications to handle a particular problem I have identified. My aim is to fit a GLS with an AR1 structure, obtain the variance-covariance matrix (V), modify it as needed given my research problem, and then reestimate the GLS by brute force using matrix operations. All seems to be working almost perfectly,
2006 Mar 07
1
lme and gls : accessing values from correlation structure and variance functions
Dear R-users
I am relatively new to R, i hope my many novice questions are welcome.
I have problems accessing some objects (specifically the random effects, correlation structure and variance function) from an object of class gls and lme.
I used the following models:
yah <- gls (outcome~ -1 + as.factor(Trial):as.factor(endpoint)+
2008 Mar 10
1
Mimicking SPSS weighted least squares
Howdy,
In SPSS, there are 2 ways to weight a least squares regression:
1. You can do it from the regression menu.
2. You can set a global weight switch from the data menu.
These two options have no, in my experience, been equivalent.
Now, when I run lm in R with the weights= switch set accordingly, I
get the same set of results you would see with option #1 in SPSS.
Does anybody know how to
2008 Aug 06
1
Warning when using survey:::svyglm
Howdy,
Referencing the below exchange:
https://stat.ethz.ch/pipermail/r-help/2006-April/103862.html
I am still getting the same warning ("non-integer #successes in a
binomial glm!") when using svyglm:::survey. Using the API data:
library(survey)
data(api)
#stratified sample
dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
2010 Jan 15
1
'nlme' library - lme function results
Dear R-helpers
I am running a simple mixed effects model using lme(). The call looks
like this:
fit <- lme(Analyte~Sample, data=Data, random=~1 | Run)
I am particularly interested in the estimated random effects. When I
print the 'fit' object, it looks something like example below:
(...)
Random effects:
Formula: ~1 | Run
(Intercept) Residual
StdDev: 3.483794 3.637523
2002 May 29
1
Extracting intercept and residual std dev from lme results
Greetings-
I need to extract, programatically, the standard deviations of the
intercept and residuals from an lme model. These are presented by
print.lme as:
...
(Intercept) Residual
StdDev: 1.410635 0.7800512
...
(data taken from ?lme's examples section)
I can get the residuals with x$sigma where x is the fitted lme object. I
can't find the intercept, though. The closest
2006 Jun 30
1
lme and SAS Proc mixed
I am trying to use lme to fit a mixed effects model to get the same
results as when using the following SAS code:
proc mixed;
class refseqid probeid probeno end;
model expression=end logpgc / ddfm=satterth;
random probeno probeid / subject=refseqid type=cs;
lsmeans end / diff cl; run;
There are 3 genes (refseqid) which is the large grouping factor, with
2 probeids nested within each refseqid,
2005 Jan 20
3
Constructing Matrices
Dear List:
I am working to construct a matrix of a particular form. For the most
part, developing the matrix is simple and is built as follows:
vl.mat<-matrix(c(0,0,0,0,0,64,0,0,0,0,64,0,0,0,0,64),nc=4)
Now to expand this matrix to be block-diagonal, I do the following:
sample.size <- 100 # number of individual students
I<- diag(sample.size)
bd.mat<-kronecker(I,vl.mat)
This
2003 Mar 04
2
How to extract R{i} from lme object?
Hi, lme() users,
Can some one tell me how to do this.
I model Orthodont with the same G for random
variables, but different R{i}'s for boys and girls, so
that I can get sigma1_square_hat for boys and
sigma2_square_hat for girls.
The model is Y{i}=X{i}beta + Z{i}b + e{i}
b ~ iid N(0,G) and e{i} ~ iid N(0,R{i}) i=1,2
orth.lme <- lme(distance ~ Sex * age, data=Orthodont,
random=~age|Subject,
2006 May 26
2
lme, best model without convergence
Dear R-help list readers,
I am fitting mixed models with the lme function of the nlme package.
If I get convergence depends on how the method (ML/REM) and which (and
how much) parameters will depend randomly on the cluster-variable.
How get the bist fit without convergence?
I set the parameters msVerbose and returnObject to TRUE:
lmeControl(maxIter=50000, msMaxIter=200, tolerance=1e-4,
2004 Aug 03
2
lme fitted correlation of random effects: where is it?
The print method for lme *prints out* the fitted correlation matrix for
the random effects. Is there any way to get these values as an object in
R? I have examined the components of the lme object (called "junk" in the
example below) and the components of summary(junk) without finding these
numbers.
(How I did this: I dumped the entire lme object to a text file and then
used egrep to
2016 Jun 13
2
Samba 4 Member server show diferent UID than Ad Server
Hello friends, I come to ask for a hand.
I have an AD server with Samba 4.1 and added a Member Server 4.4 without
problems.
The only problem I'm having is that the UID of users in the Member Server
are different from the AD server.
Ad Server
KENNEDY\florenciaelmone:*:3000679:100:Florencia Elmone
Domingues:/home/KENNEDY/florenciaelmone:/bin/false
Member Server