Displaying 20 results from an estimated 2000 matches similar to: "Help with lme and correlated residuals"
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)+
2006 Mar 02
0
Help with lme code
Dear R - Users
I have some problems fitting a linear mixed effects model using the lme function (from the library nlme). A sample data is as shown at the bottom of this mail. I fit my linear mixed model using the following R code:
bmr <-lme (outcome~ -1 + as.factor(endpoint)+ as.factor(endpoint):trt, data=datt,
random=~-1 + as.factor(endpoint) +
2006 Jan 18
2
Help with mixed effects models
Dear R-users
I have problems using lme
The model i want to fit can be viewed as a two-level bivariate model
Two-level bivariate: bivariate (S coded as -1,T coded as 1) endpoint within trial
OR
It can equivalently be considered as a three-level model.Three-level: endpoint within patient, patient within trial.
My code tries to model the levels through a RANDOM statement and a
2006 Jan 30
5
Help with R: functions
Hello R-users
I am new to R and trying to write some functions. I have problems writing functions that takes a data set as an arguement and uses variables in the data. I illustrate my problem with a small example below:
sample data #------------------
visual24<-rnorm(30,3,5)
visual52<-rt(30,7)
dats<- data.frame(cbind(visual24,visual52))
remove(visual24, visual52)
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
2008 Dec 06
1
Questions on the results from glmmPQL(MASS)
Dear Rusers,
I have used R,S-PLUS and SAS to analyze the sample data "bacteria" in
MASS package. Their results are listed below.
I have three questions, anybody can give me possible answers?
Q1:From the results, we see that R get 'NAs'for AIC,BIC and logLik, while
S-PLUS8.0 gave the exact values for them. Why? I had thought that R should
give the same results as SPLUS here.
2010 Sep 17
1
lmer() vs. lme() gave different variance component estimates
Hi, I asked this on mixed model mailing list, but that list is not very active,
so I'd like to try the general R mailing list. Sorry if anyone receives the
double post.
Hi, I have a dataset of animals receiving some eye treatments. There are 8
treatments, each animal's right and left eye was measured with some scores
(ranging from 0 to 7) 4 times after treatment. So there are
2009 Oct 15
2
plotting/examining residuals of a mixed generalised linear model
Dear R users,
I'm hoping that more experienced users will be able to assist me in
examining the model fit of a mixed generalised linear model. The example
using the data 'bacteria' within the MASS package will hopefully illustrate
what I would like to acheive;
library(MASS)
library(nlme)
attach(bacteria) # y being output and the trt - treatment group being an
explanatory variable.
2004 Feb 05
2
Incomplete Factorial design
Hello,
I am planning a study with the main point to evaluate the interaction of two treatments,
but for ethical reasons one cell is empty, that with patients receaving no treatment at all
Treatment B
2005 Nov 09
8
Element-by-element multiplication operator?
Is there an element-by-element multiplication in R, like the .* operator in Matlab?
eg: A (2x3)
B (2x3)
C=A.*B
C (2x3)
C = [[a11*b11 a12*b12 a13*b13]; [a21*b21 a22*b22 a23*b23]]
I can't find one...
Thanks
-Mike Gates
2009 Mar 03
1
R - need more memory, or rejection sampling algorithm doesn't work?
Hi all,
I am trying to run rejection sampling for the quantity z11 in the function
below. Unfortunately I can't simplify the function further so that z11 only
appears once.
Whenever I run the algorithm, R looks as if it is running it (no error
messages or anything), but then nothing happens for minutes...how long
should it take to run something like this in R? I have tried in in both
linux
2009 Jun 01
4
stock openjdk vs. epel
If you have the epel repo installed and enabled during a yum update, you
get java-1.6.0-openjdk-1.6.0.0-1.0.b12.el5.2 instead of the stock .b09
version. Is this intentional and desirable? I thought epel generally
did not replace stock components with newer versions.
--
Les Mikesell
lesmikesell at gmail.com
2006 Feb 07
1
post-hoc comparisons following glmm
Dear R community,
I performed a generalized linear mixed model using glmmPQL (MASS
library) to analyse my data i.e : y is the response with a poisson
distribution, t and Trait are the independent variables which are
continuous and categorical (3 categories C, M and F) respectively, ind
is the random variable.
mydata<-glmmPQL(y~t+Trait,random=~1|ind,family=poisson,data=tab)
Do you think it
2011 Feb 20
2
concatenate vector after strsplit()
ls is a list of character vectors created by strsplit()
I want to concatenate the 1st 4 character elements of each list item as a new vector called file. I admit to being confused about list syntax even after numerous readings.
Here's what I tried:
ls <- list(c("Focused", "10k", "A12", "t04.tif", "+", "µm"),
2009 May 19
4
nlrwr package. Error when fitting the optimal Box-Cox transformation with two variables
Dear all:
I'm trying to fit the optimal Box-Cox
transformation related to nls (see the code
below) for the demand of money data in Green (3th
Edition) but in the last step R gives the next
error message.
Error en
`[.data.frame`(eval(object$data), ,
as.character(formula(object)[[2]])[2]) :
undefined columns selected.
?Any idea to solve the problem?
Thanks in advance,
2006 Aug 24
1
how to constrast with factorial experiment
Hello, R users,
I have two factors (treat, section) anova design experiment where
there are 3 replicates. The objective of the experiment is to test if
there is significant difference of yield between top (section 9 to 11)
and bottom (section 9 to 11) of the fruit tree under treatment. I
found that there are interaction between two factors. I wonder if I
can contrast means from levels of
2011 May 03
3
ANOVA 1 too few degrees of freedom
I'm running an ANOVA on some data for respiration in a forest. I am having a
problem with my degrees of freedom. For one of my variables I get one fewer
degrees of freedom than I should.
I have 12 plots and I therefore expected 11 degrees of freedom, but instead
I got 10.
Any ideas?
I have some code and output below:
> class(Combined.Plot)
[1] "character"
>
2011 Mar 07
5
Parsing question, partly comma separated partly underscore separated string
Dear R-list,
I have a partly comma separated partly underscore separated string that I am trying to parse into R.
Furthermore I have a bunch of them, and they are quite long. I have now spent most of my Sunday trying to figure this out and thought I would try the list to see if someone here would be able to get me started.
My data structure looks like this,
(in a example.txt file)
Subject
2007 Mar 14
1
How to transform matrices to ANOVA input datasets?
Hello, R experts,
I have a list called dataHP which has 30 elements (m1, m2, ..., m30).
Each element is a 7x6 matrix holding yield data from two factors
experimental design, with treatment in column, position in row. For
instance, the element 20 is:
dataHP[[20]]
col1 col2 col3 trt1 trt2 trt3
[1,] 22.0 20.3 29.7 63.3 78.5 76.4
[2,]
2008 Oct 15
2
Network meta-analysis, varConstPower in nlme
Dear Thomas Lumley, and R-help list members,
I have read your article "Network meta-analysis for indirect treatment
comparisons" (Statist Med, 2002) with great interest. I found it very
helpful that you included the R code to replicate your analysis;
however, I have had a problem replicating your example and wondered if
you are able to give me a hint. When I use the code from the