Re: [Rd] establishing a Code of Conduct for R
On 13 September 2017 at 13:22, Brian G. Peterson wrote: > I am not an official representative of the R team, so this is only my > opinion. > Thank you. > It seems to me that you are trying to create a solution to a problem > which does not exist. I am not trying to create any solution and not my decision if this is really needed for r-project. It was just a naive suggestion, c.f, https://opensource.guide/code-of-conduct/#why-do-i-need-a-code-of-conduct https://www.contributor-covenant.org/ Best Mehmet __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] vcov and survival
Dear Terry, Even the behaviour of lm() and glm() isn't entirely consistent. In both cases, singularity results in NA coefficients by default, and these are reported in the model summary and coefficient vector, but not in the coefficient covariance matrix: > mod.lm <- lm(Employed ~ GNP + Population + I(GNP + Population), + data=longley) > summary(mod.lm) Call: lm(formula = Employed ~ GNP + Population + I(GNP + Population), data = longley) Residuals: Min 1Q Median 3Q Max -0.80899 -0.33282 -0.02329 0.25895 1.08800 Coefficients: (1 not defined because of singularities) Estimate Std. Error t value Pr(>|t|) (Intercept) 88.93880 13.78503 6.452 2.16e-05 *** GNP 0.063170.01065 5.933 4.96e-05 *** Population -0.409740.15214 -2.693 0.0184 * I(GNP + Population) NA NA NA NA --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Residual standard error: 0.5459 on 13 degrees of freedom Multiple R-squared: 0.9791,Adjusted R-squared: 0.9758 F-statistic: 303.9 on 2 and 13 DF, p-value: 1.221e-11 > vcov(mod.lm) (Intercept) GNP Population (Intercept) 190.0269691 0.1445617813 -2.0954381 GNP 0.1445618 0.0001133631 -0.0016054 Population -2.0954381 -0.0016053999 0.0231456 > coef(mod.lm) (Intercept) GNP Population I(GNP + Population) 88.93879831 0.06317244 -0.40974292 NA > > mod.glm <- glm(Employed ~ GNP + Population + I(GNP + Population), + data=longley) > summary(mod.glm) Call: glm(formula = Employed ~ GNP + Population + I(GNP + Population), data = longley) Deviance Residuals: Min1QMedian3Q Max -0.80899 -0.33282 -0.02329 0.25895 1.08800 Coefficients: (1 not defined because of singularities) Estimate Std. Error t value Pr(>|t|) (Intercept) 88.93880 13.78503 6.452 2.16e-05 *** GNP 0.063170.01065 5.933 4.96e-05 *** Population -0.409740.15214 -2.693 0.0184 * I(GNP + Population) NA NA NA NA --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for gaussian family taken to be 0.2980278) Null deviance: 185.0088 on 15 degrees of freedom Residual deviance: 3.8744 on 13 degrees of freedom AIC: 30.715 Number of Fisher Scoring iterations: 2 > coef(mod.glm) (Intercept) GNP Population I(GNP + Population) 88.93879831 0.06317244 -0.40974292 NA > vcov(mod.glm) (Intercept) GNP Population (Intercept) 190.0269691 0.1445617813 -2.0954381 GNP 0.1445618 0.0001133631 -0.0016054 Population -2.0954381 -0.0016053999 0.0231456 Moreoever, lm() has a singular.ok() argument that defaults to TRUE, but glm() doesn't have this argument: > mod.lm <- lm(Employed ~ GNP + Population + I(GNP + Population), + data=longley, singular.ok=FALSE) Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : singular fit encountered In my opinion, singularity should at least produce a warning, both in calls to lm() and glm(), and in summary() output. Even better, again in my opinion, would be to produce an error by default in this situation, but doing so would likely break too much existing code. I prefer NA to 0 for the redundant coefficients because it at least suggests that the decision about what to exclude is arbitrary, and of course simply excluding coefficients isn't the only way to proceed. Finally, the differences in behaviour between coef() and vcov() and between lm() and glm() aren't really sensible. Maybe there's some reason for all this that escapes me. Best, John -- John Fox, Professor Emeritus McMaster University Hamilton, Ontario, Canada Web: socserv.mcmaster.ca/jfox > -Original Message- > From: R-devel [mailto:r-devel-boun...@r-project.org] On Behalf Of > Therneau, Terry M., Ph.D. > Sent: Wednesday, September 13, 2017 6:19 PM > To: r-devel@r-project.org > Subject: [Rd] vcov and survival > > I have just noticed a difference in behavior between coxph and lm/glm: > if one or more of the coefficients from the fit in NA, then lm and glm > omit that row/column from the variance matrix; while coxph retains it > but sets the values to zero. > >Is this something that should be "fixed", i.e., made to agree? I > suspect that doing so will break other packages, but then NA coefs are > rather rare so perhaps not. > > Terry Therneau > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/l
[Rd] vcov and survival
I have just noticed a difference in behavior between coxph and lm/glm: if one or more of the coefficients from the fit in NA, then lm and glm omit that row/column from the variance matrix; while coxph retains it but sets the values to zero. Is this something that should be "fixed", i.e., made to agree? I suspect that doing so will break other packages, but then NA coefs are rather rare so perhaps not. Terry Therneau __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] y label for X11 graphics
In the following plot, the y label is missing if it is too long. x11(type="Xlib") plot(1:5, 1:5, ylab="Do, a deer, a female deer") # missing label plot(1:5, 1:5, ylab="Do") # label is present All is well for x11(type="cairo") This is true both under R devel 2017-09-01 on xubuntu (my desktop), and 3.4.1 on Centos 6.9 (department servers). A minor question is why my locally compiled version defaults to Xlib rather than cairo, since both work as explicit arguments to the x11() command. Terry T. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] establishing a Code of Conduct for R
On Wed, 2017-09-13 at 12:54 +0200, Suzen, Mehmet wrote: > Dear Colleagues/Developers/R enthusiasts, > > Would it be possible to develop a code of conduct (CoC) document for > R lists, CRAN submissions that all developers/maintainers to follow? > This may help all of us to better communicate and move forward > together. > There is a similar effort from Python community, here are the links: > > * https://mail.python.org/pipermail/scipy-dev/2017-August/022044.html > * https://opensource.guide/code-of-conduct/ > I am not an official representative of the R team, so this is only my opinion. It seems to me that you are trying to create a solution to a problem which does not exist. All the R mailing lists have posting guides. The mailing list community is largely self-policing to unwelcome behavior and corrects it quickly. In over 15 years as an active part of this community, it has always appeared to me that the community as a whole already conducts itself in a spirit of professionalism and cooperation. So I don't see the point in asking already overworked volunteers to take on and police more formal policies that really seem unnecessary. Regards, Brian -- Brian G. Peterson http://braverock.com/brian/ Ph: 773-459-4973 IM: bgpbraverock __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] establishing a Code of Conduct for R
Dear Colleagues/Developers/R enthusiasts, Would it be possible to develop a code of conduct (CoC) document for R lists, CRAN submissions that all developers/maintainers to follow? This may help all of us to better communicate and move forward together. There is a similar effort from Python community, here are the links: * https://mail.python.org/pipermail/scipy-dev/2017-August/022044.html * https://opensource.guide/code-of-conduct/ Kind regards, Mehmet __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] unpackPkgZip: "unable to move temporary installation" due to antivirus
Hi,
Me and an office colleague on Microsoft Windows 10 PCs are having
difficulty installing any package. This is a recent issue for us, and
we suspect our McAfee antivirus has modified by our IT department.
Let's take, for example, install.packages("mypackage"), here is the
output:
package ‘mypackage’ successfully unpacked and MD5 sums checked
Warning in install.packages :
unable to move temporary installation
‘C:\Users\mtoews\Documents\R\win-library\3.3\file382064842da2\mypackage’
to ‘C:\Users\mtoews\Documents\R\win-library\3.3\mypackage’
Debugging, I found the issue around here:
https://github.com/wch/r-source/blob/980c15af89d99c04e09a40708512a57c49d1c6ee/src/library/utils/R/windows/install.packages.R#L173-L174
> ## To avoid anti-virus interference, wait a little
> Sys.sleep(0.5)
As indicated by an answer
(https://stackoverflow.com/a/44256437/327026), debugging slows down
the function to allow the package to be installed. A simple fix is to
increase the sleep time to a time that is longer than 0.5 seconds.
(I've tried testing new times, but I can't seem to overload this
function). Or use a different strategy, such as using a few attempts
with increasing wait times, or using a custom unlink function.
Happy to help out or test more on this issue. Also, if any R Core
member could add me to R's Bugzilla members, that would be convenient
for me.
Cheers,
Mike
R version 3.3.3 (2017-03-06) -- "Another Canoe"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
__
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[Rd] CRAN incoming checks / winbuilder on demand results for R-devel
Dear package developers, given some very recent changes in R-devel, many packages under R-devel have to be reinstalled. Due to maintainance work on CRAN we probably won't process submissions today. R-devel results from winbuilder will be flaky at least during the next 10 hours. Best, Uwe Ligges __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
