Displaying 20 results from an estimated 2000 matches similar to: "package installtion"
2011 Dec 16
1
simulation
I'm using an R program (which I did not write) to simulate multilevel data
(subjects in locations) used in power calculations. It uses lmer to fit a
mixed logistic model to the simulated data based on inputs of means,
variances, slopes and proportions:
?
(fitmodel <- lmer(modelformula,data,family=binomial(link=logit),nAGQ=1))
where modelformula is set up in another part of the program.?
2008 Aug 19
1
R vs Stata on generalized linear mixed models: glmer and xtmelogit
Hello,
I have compared the potentials of R and Stata about GLMM, analysing the dataset 'ohio' in the package 'faraway' (the same dataset is analysed with GEE in the book 'Extending the linear model with R' by Julian Faraway).
Basically, I've tried the 2 commands 'glmmPQL' and 'glmer' of R and the command 'xtmelogit' of Stata. If I'm not
2009 Aug 28
1
Help with glmer {lme4) function: how to return F or t statistics instead of z statistics.
Hi,
I'm new to R and GLMMs, and I've been unable to find the answers to my
questions by trawling through the R help archives. I'm hoping someone
here can help me.
I'm running an analysis on Seedling survival (count data=Poisson
distribution) on restoration sites, and my main interest is in
determining whether the Nutrients (N) and water absorbing polymer Gel
(G) additions to the
2008 Aug 25
1
Specifying random effects distribution in glmer()
I'm trying to figure out how to carry out a Poisson regression fit to
longitudinal data with a gamma distribution with unknown shape and
scale parameters.
I've tried the 'lmer4' package's glmer() function, which fits the
Poisson regression using:
library('lme4')
fit5<- glmer(seizures ~ time + progabide + timeXprog +
offset(lnPeriod) + (1|id),
data=pdata,
2008 Jul 06
2
Error: cannot use PQL when using lmer
> library(MASS)
> attach(bacteria)
> table(y)
y
n y
43 177
> y<-1*(y=="y")
> table(y,trt)
trt
y placebo drug drug+
0 12 18 13
1 84 44 49
> library(lme4)
> model1<-lmer(y~trt+(week|ID),family=binomial,method="PQL")
Error in match.arg(method, c("Laplace", "AGQ")) :
'arg' should be one of
2013 Nov 05
2
Error message glmer using R: “ 'what' must be a character string or a function”
I am running a multi-level model. I use the following commands with
validatedRS6 as the outcome, random as the predictor and clustno as the
random effects variable.
new<-as.data.frame(read.delim("BABEX.dat", header=TRUE))
install.packages("lme4")
library(lme4)
model1<- glmer(validatedRS6 ~ random + (1|clustno), data=new,
family=binomial("logit"), nAGQ)
2005 Dec 14
3
Fitting binomial lmer-model, high deviance and low logLik
Hello
I have a problem when fitting a mixed generalised linear model with the
lmer-function in the Matrix package, version 0.98-7. I have a respons
variable (sfox) that is 1 or 0, whether a roe deer fawn is killed or not
by red fox. This is expected to be related to e.g. the density of red
fox (roefoxratio) or other variables. In addition, we account for family
effects by adding the mother
2007 Nov 30
2
lmer and method call
Hello all,
I'm attempting to fit a generalized linear mixed-effects model using lmer
(R v 2.6.0, lmer 0.99875-9, Mac OS X 10.4.10) using the call:
vidusLMER1 <- lmer(jail ~ visit + gender + house + cokefreq + cracfreq +
herofreq + borcur + comc + (1 | code), data = vidusGD, family = binomial,
correlation = corCompSymm(form = 1 | ID), method = "ML")
Although the model fits, the
2011 May 16
4
Problem on glmer
Hi all,
I was trying to fit a Gamma hierarchical model using "glmer", but got weird error message that I could not understand. On the other hand, a similar call to the glmmPQL leads to results that are close to what I expect. I also tried to change tha "nAGQ" argument in "glmer", but it did not solve the problem. The model I was fitting has a simple structure - one
2005 Dec 05
1
extracting p-values from lmer()
Dear R users,
I've been struggling with the following problem: I want to extract the Wald p-value
from an lmer() fit, i.e., consider
library(lme4)
n <- 120
x1 <- runif(n, -4, 4)
x2 <- sample(0:1, n, TRUE)
z <- rnorm(n)
id <- 1:n
N <- sample(20:200, n, TRUE)
y <- rbinom(n, N, plogis(0.1 + 0.2 * x1 - 0.5 * x2 + 1.5 * z))
m1 <- lmer(cbind(y, N - y) ~ x1 + x2 + (1 | id),
2005 Apr 18
1
lmer question
Hi --
I'm using lmer for binomial data. I am trying to
replicate estimates provided by Agresti (2002,
Categorical data analysis, Wiley) using abortion data
in table 10.13 (estimates provided in table 12.3 p.
505).
I fit the same model using these three commands:
a1 <- lmer(resp ~ sex + option1 + option2 + (1|id),
data=abort,family=binomial, method = c("AGQ"))
a2 <-
2023 Dec 02
1
Try reproduce glmm by hand
Dear all,
In order to be sure I understand glmm correctly, I try to reproduce by
hand a simple result. Here is a reproducible code. The questions are in
_________________
Of course I have tried to find the solution using internet but I was not
able to find a solution. I have also tried to follow glmer but it is
very complicated code!
Thanks for any help.
Marc
# Generate set of df with nb
2012 Apr 17
1
random effects using lmer
Hi,
I am trying to run a logistic regression to look at the risk of malaria
infection in individuals. I want to account for intra household correlation
and so want to include a household level random effect. I have been using
the lmer command in lme4 package but am getting some strange results that
are completely different to those I get using STATA.
Can I just check that this is the correct
2016 Apr 15
1
Heteroscedasticity in a percent-cover dataset
Hi,
I am currently trying to do a GLMM on a dataset with percent cover of
seagrass (dep. var) and a suite of explanatory variables including algal
(AC) and epiphyte cover (EC), rainfall, temperature and sunshine hours.
M2=glmer(SG~AC+EC+TP+SS+RF+(1|Location/fSi/fTr),
family=binomial,data=data,nAGQ=1)
As the dependent variable is percent cover, I used a binomial error
structure. I also have a
2005 Nov 30
1
likelihood ratio tests using glmmPQL
I am analysing some binary data with a mixed effects model using
glmmPQL.
I am aware that I cannot use the AIC values to help me find the minimum
adequate model so how do I perform likelihood ratio tests? I need to
fix on the minimum adequate model but I'm not sure of the proper way to
do this.
Thank you very much,
Elizabeth Boakes
Elizabeth Boakes
PhD Student
Institute of Zoology
2006 Jan 03
1
lmer error message
Dear All,
I have the following error message when I fitted lmer to a binary data with the "AGQ" option:
Error in family$mu.eta(eta) : NAs are not allowed in subscripted assignments
In addition: Warning message:
IRLS iterations for PQL did not converge
Any help?
Thanks in advance,
Abderrahim
[[alternative HTML version deleted]]
2005 Nov 02
1
nlminb failed to converge with lmer
Dear all,
I'm building binomial mixed-model using lme4 package.
I'm able to obtain outputs properly except when I include two particular
variables: date (from 23 to 34; 1 being to first sampling day) and Latitude
(UTM/100 000, from 55.42 to 56.53). No "NA" is any of those variables.
In those cases, I get the warning message: "nlminb failed to converge"
I tried to
2007 Dec 31
1
Regd: CentOS 4.4 Installtion Screen Shots
Dear All,
I need CentOS 4.4 Step-by-Step Installation Screen Shots.
Please send me the following Installation Screen Shots Details or link
Regards
-S.Balaji
2012 Jan 23
2
Recompile
Looked at several posts and the installtions docs and still not clear.?
If I compile source codes and then somewhere down the line add
a new package, then I have to recompile my entire installation,
correct?? Seems like this is the sentiment of the emails I read.
2007 Jan 26
2
Using functions within functions (environment problems)
Hi everyone,
I've been having difficulty writing wrapper functions for some
functions where those same functions include other functions with
eval()
calls where the environment is specified. A very simple example using
function lmer from lme4:
lmerWrapper <- function(formula, data, family = gaussian, method =
c("REML",
"ML", "PQL", "Laplace",