Error in .local(object, n, verbose, ...) : Update not yet written

On Wed, Apr 27, 2011 at 8:50 AM, Gregory Gilbert
Hello All,

I am running the following code under R.2.11.1 on a Dell PowerEdge 2900 III
running Windows 2003 Server 64-bit OS (Release 2 build 3790) with 48GB RAM.

When I try an get HPD intervals for my model using mcmcsamp() I get the
following error: "Error in .local(object, n, verbose, ...) : Update not yet
written"

I have searched the R-help & R-sig-mixed archives; I have googled the
specific error (and found some threads in R-help dating to 2008-2009
suggesting the author of the code put this message in mcmcsamp to remind him
to finish coding a particular part of mcmcsamp); I have examined the lme4
documentation (and mcmcsamp); I have read the R FAQ; and I have consulted
with my boss PhD biostatistician (he suggested I make a post). As mentioned,
I did run across a number of conversations dating to 2008-2009 regarding
this error, but did not see a suggestion. I did see something to the effect
that it was to remind the programmer he needed to finish some coding. Was
the code ever finished/updated? Is the issue still outstanding? I have tried
installing lm4a from R-forge and ran into the following error:
You didn't tell us about your model.  What is the model?  Is it a
linear mixed-effects model, a generalized linear mixed-effects model,
...?  Does it have only scalar random effects or are there
vector-valued random effects?
install.packages("lma4", repos="http://R-Forge.R-project.org")
Warning: unable to access index for repository
http://R-Forge.R-project.org/bin/windows64/contrib/2.11
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
?package ?lma4? is not available

when I researched this error it was suggested I install "Rccp" from R-forge.
I tried this and received the following error:

install.packages("Rcpp", repos="http://R-Forge.R-project.org")
Warning: unable to access index for repository
http://R-Forge.R-project.org/bin/windows64/contrib/2.11
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
?package ?Rcpp? is not available
The problem with installing the Rcpp package is that recent versions
depend on an R version >= 2.12.0 and you are running version 2.11.
Similarly for the lme4 (which you misspelled as "lma4", although
perhaps you meant "lme4a").

First I would recommend installing R-2.13.0, the most recent version.
Then try installing lme4 from CRAN.  If you want to try lme4a then
install Rcpp, minqa and MatrixModels from CRAN and, finally,

install.packages("lme4a", repos="http://lme4.R-forge.R-project.org/repos")
Where am I going wrong in the process? What have I missed? Is this a problem
with my data? I have run a similar regression with continuous A1c data
(range: 3 to 18) as the dependent variable and had no problems for all my
data (n=700K observations and 5 time points). I also ran the data for 1%,
5%, 10%, and 25% random samples or the data, with a continuous dependent
variable) and had no problems generating CIs. I am not wedded to mcmcsamp()
& HPDinterval(), but I understand it is one of the more robust methods of
generating CIs about beta for mixed effects models. I am happy to use any
approach as long as statistically valid.

Any status or updates would be greatly appreciated.

Thanks in advance.

Greg Gilbert

options(repos="http://lib.stat.cmu.edu/R/CRAN/")
myPackages <- c("lme4", "foreign", "Hmisc")
install.packages(myPackages, dependencies=TRUE)
update.packages(checkBuilt=TRUE, ask=FALSE)
library(foreign)
library(Hmisc)
library(lme4)

cohort <- sasxport.get("//v07.med.va.gov/cha/TREP/___neworganization/workgroups/wg10_06_sampling_gebregziabher/data/PCT01SRS.xpt")
Processing SAS dataset PCT01SRS ? ? ? ? ?..
## time is 1 to 5
cohort$time.ctr.sq <-(cohort$time-3)*(cohort$time-3)
attach(cohort)
## a1cge8 is 0, 1
## id is 4-7 digit number
## age is continuous 18-103
## svcpct is continuous 0 to 100
## all other variables are binary 0, 1
f ?<- a1cge8 ~ ?(1|id) ? + time ? ? ? + time.ctr.sq ? ? +
+ ? ? ? ? ? ? ? ? nhb ? ? ?+ hispanic ? + other ? ? ? ? ? +
+ ? ? ? ? ? ? ? ? male ? ? + age ? ? ? ?+ mstat ? ? ? ? ? +
+ ? ? ? ? ? ? ? ? svcpct ? + urban ? ? ?+
+ ? ? ? ? ? ? ? ? abuse ? ?+ anemia ? ? + cancer ? ? ? ? ?+
+ ? ? ? ? ? ? ? ? cbd ? ? ?+ chf ? ? ? ?+ cvd ? ? ? ? ? ? +
+ ? ? ? ? ? ? ? ? depress ?+ htn ? ? ? ?+ hypothy ? ? ? ? +
+ ? ? ? ? ? ? ? ? liver ? ?+ lung ? ? ? + lytes ? ? ? ? ? +
+ ? ? ? ? ? ? ? ? obese ? ?+ other.dz ? + psych ? ? ? ? ? +
+ ? ? ? ? ? ? ? ? pvd
## finite population correction
population <- 890394
sample ? ? <- ? 9000
fpp ? ? ? ?<- sqrt((population-sample)/(population-1))

fit ? ? ? ?<- lmer(f, family=binomial(link="logit"), data=cohort)

? ?mcmc.ci <- mcmcsamp(fit, 1000)
Error in .local(object, n, verbose, ...) : Update not yet written
ci ? ? ? ? <- HPDinterval(mcmc.ci)
Error: object 'mcmc.ci' not found
Error in HPDinterval(mcmc.ci) :
?error in evaluating the argument 'object' in selecting a method for
function 'HPDinterval'

? ? ? ?[[alternative HTML version deleted]]

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