[R] 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 [[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.
Re: [R] could not find function Varcov after upgrade of R?
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.hu...@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 mailzhu...@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
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] could not find function Varcov after upgrade of R?
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 __ 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.
Re: [R] could not find function Varcov after upgrade of R?
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.hu...@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 mailzhu...@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
[[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.
--
View this message in context:
http://www.nabble.com/could-not-find-function-%22Varcov%22-after-upgrade-of-R--tp25412881p25414017.html
Sent from the R help mailing list archive at Nabble.com.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] could not find function Varcov after upgrade of R?
Did you type library(Hmisc,T) before loading Design?
Carlos
--
From: David Freedman 3.14da...@gmail.com
Sent: Saturday, September 12, 2009 8:26 AM
To: r-help@r-project.org
Subject: Re: [R] could not find function Varcov after upgrade of R?
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.hu...@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 mailzhu...@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
[[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.
--
View this message in context:
http://www.nabble.com/could-not-find-function-%22Varcov%22-after-upgrade-of-R--tp25412881p25414017.html
Sent from the R help mailing list archive at Nabble.com.
__
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.
__
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.
Re: [R] could not find function Varcov after upgrade of R?
I am unable to reproduce that problem, either. Have both of you
updated both the Design and Hmisc packages? Varcov is in Hmisc.
--
David Winsemius
On Sep 12, 2009, at 8:26 AM, 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.hu...@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 mailzhu...@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
--
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
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
__
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.
Re: [R] could not find function Varcov after upgrade of R?
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.hu...@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 mailzhu...@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
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] could not find function Varcov after upgrade of R?
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.hu...@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 mailzhu...@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
[[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.
--
View this message in context:
http://www.nabble.com/could-not-find-function-%22Varcov%22-after-upgrade-of-R--tp25412881p25414257.html
Sent from the R help mailing list archive at Nabble.com.
__
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.
Re: [R] could not find function Varcov after upgrade of R?
Thanks for the reminder - actually I think I've become sloppy about the 'T'
(and the order of loading the Hmisc and Design packages), but that doesn't
seem to be the problem. Also, all of my packages have been updated
david
Carlos Alzola wrote:
Did you type library(Hmisc,T) before loading Design?
Carlos
--
From: David Freedman 3.14da...@gmail.com
Sent: Saturday, September 12, 2009 8:26 AM
To: r-help@r-project.org
Subject: Re: [R] could not find function Varcov after upgrade of R?
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.hu...@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 mailzhu...@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
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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@r-project.org mailing list
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
--
View this message in context:
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and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
--
View this message in context:
http://www.nabble.com/could-not-find-function-%22Varcov%22-after-upgrade-of-R--tp25412881p25416444.html
Sent from the R help mailing list archive at Nabble.com.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] could not find function Varcov after upgrade of R?
David Freedman wrote:
Thanks for the reminder - actually I think I've become sloppy about the 'T'
(and the order of loading the Hmisc and Design packages), but that doesn't
seem to be the problem. Also, all of my packages have been updated
Note that Frank Harrell already answered that there is a Hmisc - Design
issue which will be fixed early next week.
You had the unfortune to be too up to date and got the bug that was
introduced very recently (and most people who answered had not so recent
packages).
Uwe Ligges
david
Carlos Alzola wrote:
Did you type library(Hmisc,T) before loading Design?
Carlos
--
From: David Freedman 3.14da...@gmail.com
Sent: Saturday, September 12, 2009 8:26 AM
To: r-help@r-project.org
Subject: Re: [R] could not find function Varcov after upgrade of R?
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.hu...@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 mailzhu...@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
[[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.
--
View this message in context:
http://www.nabble.com/could-not-find-function-%22Varcov%22-after-upgrade-of-R--tp25412881p25414017.html
Sent from the R help mailing list archive at Nabble.com.
__
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.
__
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.
__
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.
