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

[Frank E Harrell Jr]

I apologize for this change in the Hmisc package which breaks the 
current version of Design in CRAN.  Design should be updated by early 
next week. In the meantime there are two solutions:

1. Install the rms package which is a replacement for Design with better 
graphics, and note the few changes you would need to make in your code 
as described in http://biostat.mc.vanderbilt.edu/Rrms (the main change 
is for plot(fit object)), or

2. Run source('http://biostat.mc.vanderbilt.edu/tmp/Varcov.r') to define 
the Varcov functions until Design is updated

Frank


David Freedman wrote:
> I've had the same problem with predict.Design, and have sent an email to the
> maintainer of the Design package at Vanderbilt University.  I wasn't even
> able to run the examples given on the help page of predict.Design - I
> received the same error about Varcov that you did.  
> 
> I *think* it's a problem with the package, rather than R 2.9.2, and I hope
> the problem will soon be fixed.  I was able to use predict.Design with 2.9.2
> until I updated the Design package a few days ago.
> 
> david freedman
> 
> 
> 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
>>>

-- 
Frank E Harrell Jr   Professor and Chair           School of Medicine
                      Department of Biostatistics   Vanderbilt University