[R] could not find function "Varcov" after upgrade of R?

[Mark Difford]

Hi Zhu,

>> could not find function "Varcov" after upgrade of R?

Frank Harrell (author of Design) has noted in another thread that Hmisc has
changed... The problem is that functions like anova.Design call a function
in the _old_ Hmisc package called Varcov.default. In the new version of
Hmisc this is called something else (vcov.default).

The best way to fix this is to install the new (i.e. current) version of
Hmisc and Frank's replacement for his Design package, which is called rms
(Regression Modeling Strategies).

Regards, Mark.


zhu yao wrote:
> 
> 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 at 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 at 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 at 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
>>
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at 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.
> 
> 

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