R help - Sep 2009 - could not find function "Varcov" after upgrade of R?

After upgrading R to 2.9.2, I can't use the anova() fuction.
It says "could not find function "Varcov" ".
What's wrong with my computer? Help needed, thanks!

Yao Zhu
Department of Urology
Fudan University Shanghai Cancer Center
No. 270 Dongan Road, Shanghai, China

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I uses the Design library.

take this example:

library(Design)
n <- 1000
set.seed(731)
age <- 50 + 12*rnorm(n)
label(age) <- "Age"
sex <- factor(sample(c('Male','Female'), n,
              rep=TRUE, prob=c(.6, .4)))
cens <- 15*runif(n)
h <- .02*exp(.04*(age-50)+.8*(sex=='Female'))
dt <- -log(runif(n))/h
label(dt) <- 'Follow-up Time'
e <- ifelse(dt <= cens,1,0)
dt <- pmin(dt, cens)
units(dt) <- "Year"
dd <- datadist(age, sex)
options(datadist='dd')
Srv <- Surv(dt,e)

f <- cph(Srv ~ rcs(age,4) + sex, x=TRUE, y=TRUE)
cox.zph(f, "rank")             # tests of PH
anova(f)
# Error in anova.Design(f) : could not find function "Varcov"



Yao Zhu
Department of Urology
Fudan University Shanghai Cancer Center
No. 270 Dongan Road, Shanghai, China


2009/9/12 Ronggui Huang <ronggui.huang@gmail.com>
> I cannot reproduce the problem you mentioned.
>
> >  ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
> >  trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
> >   group <- gl(2,10,20, labels=c("Ctl","Trt"))
> >   weight <- c(ctl, trt)
> >   anova(lm.D9 <- lm(weight ~ group))
> > sessionInfo()
> R version 2.9.2 (2009-08-24)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=Chinese (Simplified)_People's Republic of
> China.936;LC_CTYPE=Chinese (Simplified)_People's Republic of
> China.936;LC_MONETARY=Chinese (Simplified)_People's Republic of
> China.936;LC_NUMERIC=C;LC_TIME=Chinese (Simplified)_People's Republic
> of China.936
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> 2009/9/12 zhu yao <mailzhuyao@gmail.com>:
> > After upgrading R to 2.9.2, I can't use the anova() fuction.
> > It says "could not find function "Varcov" ".
> > What's wrong with my computer? Help needed, thanks!
> >
> > Yao Zhu
> > Department of Urology
> > Fudan University Shanghai Cancer Center
> > No. 270 Dongan Road, Shanghai, China
> >
> >        [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>
>
> --
> HUANG Ronggui, Wincent
> Doctoral Candidate
> Dept of Public and Social Administration
> City University of Hong Kong
> Home page: http://asrr.r-forge.r-project.org/rghuang.html
>
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On Sep 12, 2009, at 5:24 AM, zhu yao wrote:
> After upgrading R to 2.9.2, I can't use the anova() fuction.
> It says "could not find function "Varcov" ".
> What's wrong with my computer? Help needed, thanks!
You have not given us very much information but from the naming  
conventions I would guess that you need to reinstall the Design/Hmisc  
combination of packages after having updated your R from an an earlier  
version of R that was different in the "second digit". The libraries  
for the 2.9 series of R versions is stored in a different directory  
than the 2.8 or 2.7 versions. There is a simple command to the  
update.packages function that will reinstall updated versions of the  
packages you had previously installed. My practice, unnecessarily  
incremental, has been to reinstall each of the packages from scratch.

The automatic method would be:

update.packages()  # which will ask you to confirm eachnpackage

# or

update.packages(ask=FALSE) # which will not ask

-- 

David Winsemius, MD
Heritage Laboratories
West Hartford, CT