Re: [R] Question about proxy setting of R

[Carina Salt via R-help]

As far as I can see, the 'internal' method doesn't work for https mirrors
(on my system, anyway).  However, the http mirrors still exist (try "
http://cloud.r-project.org/; for example) so why not just use one of those?

Cheers,
Carina

On 5 December 2016 at 12:27, jim holtman  wrote:

> You will probably have to check with your network folks to see what is
> possible on your system.
>
>
> Jim Holtman
> Data Munger Guru
>
> What is the problem that you are trying to solve?
> Tell me what you want to do, not how you want to do it.
>
> On Mon, Dec 5, 2016 at 6:33 AM,  wrote:
>
> > Dear Jim,
> >
> > Thanks to your advice, "Proxy Authentification" window showed up,
> however,
> > I couldn't access to the internet. Error messages are as below.
> >
> > -- -- ---
> > > update.packages(ask='graphics',checkBuilt=TRUE)
> > --- Please select a CRAN mirror for use in this session ---
> > Warning: failed to download mirrors file (scheme not supported in URL
> > 'https://cran.r-project.org/CRAN_mirrors.csv'); using local file
> > 'C:/PROGRA~1/R/R-33~1.2/doc/CRAN_mirrors.csv'
> > Warning: unable to access index for repository
> > https://cran.ism.ac.jp/src/contrib:
> >   scheme not supported in URL 'https://cran.ism.ac.jp/src/
> contrib/PACKAGES'
> >
> > Proxy authentication failed:
> > please re-enter the credentials or hit Cancel
> > -- -- ---
> >
> > I assume the proxy server is only available for "http", not "https".
> > What should I do ?
> >
> > J J
> >
> >
> > - Original Message -
> > *From:* jim holtman 
> > *To:* qwertyui_per...@yahoo.co.jp
> > *Date:* 2016/12/2, Fri 09:13
> > *Subject:* Re: [R] Question about proxy setting of R
> >
> > Try this option:
> >
> >  options(download.file.method = "internal")
> >
> >
> >
> >
> >
> > Jim Holtman
> > Data Munger Guru
> >
> > What is the problem that you are trying to solve?
> > Tell me what you want to do, not how you want to do it.
> >
> > On Wed, Nov 30, 2016 at 10:37 PM,  wrote:
> >
> > Hello,
> >
> > I use R 3.0.2 on Win 7 through proxy server using ".Rprofile" in home
> > directory that includes "Sys.setenv(http_proxy=proxy_ server:port)".
> > There has been no problem to access the internet for some years.
> > In this situation, I installed R 3.3.1 and then entered "update.packages
> > ()", however, "Proxy Authentification" window didn't show up and
> > failed to access the internet. Error messages are as below.
> >
> > -- -- ---
> > > update.packages(ask='graphics' ,checkBuilt=TRUE)
> > --- Please select a CRAN mirror for use in this session ---
> > Warning: failed to download mirrors file (cannot open URL
> > 'https://cran.r-project.org/CRAN_mirrors.csv'); using local file
> > 'C:/PROGRA~1/R/R-33~1.2/doc/ CRAN_mirrors.csv'
> > Warning: unable to access index for repository
> > https://cran.ism.ac.jp/src/contrib:
> >   cannot open URL 'https://cran.ism.ac.jp/src/contrib/PACKAGES'
> > Warning: unable to access index for repository
> > http://www.stats.ox.ac.uk/pub/RWin/src/contrib:
> >   cannot open URL 'http://www.stats.ox.ac.uk/
> pub/RWin/src/contrib/PACKAGES
> > '
> > Warning message:
> > In download.file(url, destfile = f, quiet = TRUE) :
> >   cannot open URL 'https://cran.r-project.org/CRAN_mirrors.csv': HTTP
> > status was '407 Proxy Authentication Required'
> >
> > -- -- ---
> >
> > Strange to say, R 3.0.2 is able to access to the internet, and R 3.3.1
> > shows collect proxy setting in ".Rprofile"  by "Sys.getenv("http_proxy")"
> > From internet information, I added "http_proxy_user=ask" to ".Rprofile",
> or
> > " --internet2" to the desktop icon of R 3.3.1, ending up in the same
> > result.
> >
> > Please show me the way of proxy setting of R 3.3.1.
> >
> > __ 
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > 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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>
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[R] Use of 'by' function with FUN=mean

[Carina Salt]

Hi everybody

I'm having some unexpected errors from the 'by' function when using it to
apply the mean function (by a factor) to a dataframe of numerical
variables.  The following piece of toy code demonstrates:

myDataF-warpbreaks
myDataF$X-runif(54) # creating an additional numerical variable in
warpbreaks for purposes of this demo
by(myDataF[,c(X,breaks)],myDataF[,tension],FUN=mean)


In R3.0.1  R3.0.2 (run on Windows 7) this gives the following error

myDataF[, tension]: L
[1] NA
-
myDataF[, tension]: M
[1] NA
-
myDataF[, tension]: H
[1] NA
Warning messages:
1: In mean.default(data[x, , drop = FALSE], ...) :
  argument is not numeric or logical: returning NA
2: In mean.default(data[x, , drop = FALSE], ...) :
  argument is not numeric or logical: returning NA
3: In mean.default(data[x, , drop = FALSE], ...) :
  argument is not numeric or logical: returning NA


In R2.15.2 (again run on Windows 7) the works but gives a warning about a
depreciated function

: L
 X breaks
 0.5705876 36.389
-
: M
 X breaks
 0.5370582 26.389
-
: H
 X breaks
 0.3908149 21.667
Warning messages:
1: mean(data.frame) is deprecated.
 Use colMeans() or sapply(*, mean) instead.
2: mean(data.frame) is deprecated.
 Use colMeans() or sapply(*, mean) instead.
3: mean(data.frame) is deprecated.
 Use colMeans() or sapply(*, mean) instead.

I *think* that in older versions of R (which I no longer have installed)
the use of 'by' in this way worked fine (it seems to appear in old code of
mine, anyway).  This would be consistent with the behavior being caused by
a depreciated function, I guess.

However, the help page for 'by' suggests that the above code should work,
as far as I can tell, so I'm a bit confused - anybody got any ideas what
I'm doing wrong here, please?

Cheers,
Carina

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[R] Fwd: Use of 'by' function with FUN=mean

[Carina Salt]

Hi everybody

Sorry guys, please ignore my previous email regarding the problem I was
having using the 'by' function with FUN=mean.  Just read the given error
properly and realised my (silly) mistake in that you can no longer apply
the mean function to a dataframe regardless of whether its wrapped within
'by' or not, as its depreciated in this context -  I'm obviously a bit too
ready for the weekend!!  ;-)

Cheers,
Carina

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Re: [R] Adding Proxy information in 'R' application

[Carina Salt]

Hi Jose

I faced the same problem at my workplace too - the solution (at least for
us) was to insert the following function into the Rprofile.ste file in the
etc folder in the R install folder - or, if the  .First function already
exists, you could just insert the line beginning Sys.setenv(….) into that
function.  The bit in the speech marks needs to be a suitable web proxy
address and port, and the 'http_proxy_user=ask' bit is telling R to ask for
a username and password.

.First - function() {
Sys.setenv(http_proxy=http://webproxy:8080 http_proxy_user=ask)
}

Hope this works for you!

Cheers,
Carina


On 8 November 2013 17:10, Batista, Jose jose.bati...@nb.com wrote:

 R-Help Mailing List,

 I'm currently working with a user who is actively trying to download 
 install libraries for 'R' on her office PC. While using
 install.packages(packageName, dependencies = TRUE) works without a
 problem on our home PCs, we use a proxy at the firm and therefore it
 doesn't let the application go directly out of the network on port 80.  Is
 there a way to manually set proxy information within the application so
 that it can, indeed, reach the internet when we're trying to download and
 install libraries (and necessary dependencies) from within the application?
  I've gone through some of the options but there's nothing there for it.

 Regards,
 José Emmanuel Batista





 
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Re: [R] survfit number of variables != number of variable names

[Carina Salt]

Hi - I've seen a similar issue going on with survfit when using strata in
the model, although I get a different error message from ge.  If it helps
to track down the problem (rather than confusing things further) here is
some code that should reproduce the issue I've seen.  I'm running R 2.15.2,
with survival version 2.36-14 .

Cheers,
Carina

##

library(survival)

# use aml dataset from survival  create 3 imaginary possible stratas -
strat3 has 3 levels, strat4 has 4 levels, strat5 has 5 levels
aml$strat3-as.factor(rep(c(1:3),length=nrow(aml)))
aml$strat4-as.factor(rep(c(1:4),length=nrow(aml)))
aml$strat5-as.factor(rep(c(1:5),length=nrow(aml)))

# create a counting process format dataset from aml - call this aml2
aml2-survSplit(aml,cut=c(5,10,50),end=time,start=start,event=status,episode=i,id=indiv)

# create a dataset of 4 'new' observations - call this aml.new
aml.new-aml[1:4,]
aml.new$time-c(30,50,70,100)
aml.new$status-1
aml.new$x[1:4]-c(rep(Maintained,2),rep(Nonmaintained,2))
aml.new$strat3[1:4]-1
aml.new$strat4[1:4]-1
aml.new$strat5[1:4]-1

# create a counting process format dataset from aml.new - call this aml2.new
aml2.new-survSplit(aml.new,cut=c(5,10,50),end=time,start=start,event=status,episode=i,id=indiv)

# First a model using no strata - survfit works fine on new dataset
myModel-coxph(Surv(start, time, status) ~ x,data = aml2)
plot(survfit(myModel,aml2.new,id=indiv))

# Now a model using strata = strat4 (which has 4 levels) - survfit again
works fine on new dataset (which has 4 new individuals)
myModel-coxph(Surv(start, time, status) ~ x+strata(strat4),data = aml2)
plot(survfit(myModel,aml2.new,id=indiv))

# Now a model using strata = strat3 (which has 3 levels) - survfit works
here too
myModel-coxph(Surv(start, time, status) ~ x+strata(strat3),data = aml2)
plot(survfit(myModel,aml2.new,id=indiv))

# Now a model using strata = strat5 (which has 5 levels) - survfit now does
not work, with error saying
# Error in survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,  :
#  'names' attribute [5] must be the same length as the vector [4]
myModel-coxph(Surv(start, time, status) ~ x+strata(strat5),data = aml2)
plot(survfit(myModel,aml2.new,id=indiv))

# Now recreate aml.new but with 3 rather than 4 'new' observations
rm(aml.new)
aml.new-aml[1:3,]
aml.new$time-c(30,50,70)
aml.new$status-1
aml.new$x[1:3]-c(rep(Maintained,2),rep(Nonmaintained,1))
aml.new$strat3[1:3]-1
aml.new$strat4[1:3]-1
aml.new$strat5[1:3]-1

# create a counting process format dataset from aml.new
aml2.new-survSplit(aml.new,cut=c(5,10,50),end=time,start=start,event=status,episode=i,id=indiv)


# Survfit on model using strat3 still works
myModel-coxph(Surv(start, time, status) ~ x+strata(strat3),data = aml2)
plot(survfit(myModel,aml2.new,id=indiv))

# But Survfit on model using strat4 doesn't work now
myModel-coxph(Surv(start, time, status) ~ x+strata(strat4),data = aml2)
plot(survfit(myModel,aml2.new,id=indiv))

# Survfit on strat5 model doesn't work either
myModel-coxph(Surv(start, time, status) ~ x+strata(strat5),data = aml2)
plot(survfit(myModel,aml2.new,id=indiv))







On 19 November 2012 17:01, Terry Therneau thern...@mayo.edu wrote:

 I can't reproduce the problem.

 Tell us what version of R and what version of the survival package.
 Create a reproducable example.  I don't know if some variables are numeric
 and some are factors, how/where the surv object was defined, etc.

 Terry Therneau




 On 11/17/2012 05:00 AM, r-help-requ...@r-project.org wrote:

 This works ok:

cox = coxph(surv ~ bucket*(today + accor + both) + activity, data =
 data)
   fit = survfit(cox, newdata=data[1:100,])

 but using strata leads to problems:

cox.s = coxph(surv ~  bucket*(today + accor + both) +
 strata(activity),
   data = data)
   fit.s = survfit(cox.s, newdata=data[1:100,])

 Error in model.frame.default(data = data[1:100, ], formula = ~bucket +  :
number of variables != number of variable names

 Note that the following give rise to the same error:

fit.s = survfit(cox.s, newdata=data)

 Error in model.frame.default(data = data, formula = ~bucket + today +  :
number of variables != number of variable names

 but if I use data implicitly, all is working fine:

   fit.s = survfit(cox.s)

 Any idea on how I could solve this?

 Best, and thank you,

 ge


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[R] Using method = aic with pspline survreg (survival library)

[Carina Salt]

Hi everybody.  I'm trying to fit a weibull survival model with a spline
basis for the predictor, using the survival library.  I've noticed that it
doesn't seem to be possible to use the aic method to choose the degrees of
freedom for the spline basis in a parametric regression (although it's
fine with the cox model, or if the degrees of freedom are specified directly
by the user), and I was wondering if there is some reason for this?


Simple example:

library(survival)
attach(cancer)
# cox model with specified degs of freedom - works fine
fit1 - coxph(Surv(time, status) ~ ph.ecog + pspline(age,3), cancer)
# cox model with aic - works fine
fit1 - coxph(Surv(time, status) ~ ph.ecog + pspline(age,method=aic),
cancer)
# weibull model with specified degs of freedom - works fine
fit1 - survreg(Surv(time, status) ~ ph.ecog + pspline(age,3), cancer,
dist=weibull)
# weibull model with aic - gives an error
fit1 - survreg(Surv(time, status) ~ ph.ecog +
pspline(age,method=aic),dist=weibull, cancer)
Error in (cfun[[1]])(parmlist[[1]], iter, iterlist[[1]], n.eff, pdf[1],  :
  object 'loglik' not found

I also get a similar error about object 'loglik' not found if I try to use
method=aic in the specification of a frailty term in a survreg model.

Thanks for your help - apologies in advance if I'm missing something very
obvious. I'm using R2.13.0 btw, with survival v2.39-9.

Regards
Carina

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