[Rd] Windows build not running on r-forge

2011-03-27 Thread S Ellison
Please forgive any mis-post, and do feel free to point me to a more appropriate list if this isn't properly R-dev. I have a package on R-forge that shows correct linux and other *nix builds, but no windows build. The log for the patched version shows the error below, which appears to be due to a

[Rd] Windows build not running on r-forge

2011-03-28 Thread S Ellison
Please forgive any mis-post, and do feel free to point me to a more appropriate list if this isn't properly R-dev. I have a package on R-forge that shows correct linux and other *nix builds, but no windows build. The log for the patched version shows the error below, which appears to be due to a

Re: [Rd] Windows build not running on r-forge

2011-03-28 Thread S Ellison
you what the R-forge log told me. Steve Ellison Prof Brian Ripley rip...@stats.ox.ac.uk 28/03/2011 05:32 On Mon, 28 Mar 2011, S Ellison wrote: Please forgive any mis-post, and do feel free to point me to a more appropriate list if this isn't properly R-dev. I have a package on R-forge

Re: [Rd] median and data frames

2011-04-28 Thread S Ellison
This seems trivially fixable using something like median.data.frame - function(x, na.rm=FALSE) { sapply(x, function(y, na.rm=FALSE) if(is.factor(y)) NA else median(y, na.rm=na.rm), na.rm=na.rm) } Paul Johnson pauljoh...@gmail.com 28/04/2011 06:20 On Wed, Apr 27, 2011 at 12:44 PM, Patrick

Re: [Rd] Unexpected email address change - again...

2011-07-01 Thread S Ellison
Further apologies to the list, but emails are still not getting to folk. Duncan, you should have had a diff from me yesterday - if not, they've fouled it up again... -- View this message in context:

Re: [Rd] Package (PR#13475)

2009-04-10 Thread S Ellison
I had the same normalizePath error recently on a new laptop, with a fresh install of R 2.8.1 and an attempt to install lme4. First attempt: package 'Matrix' successfully unpacked and MD5 sums checked Error in normalizePath(path) : path[1]: The system cannot find the file specified Second

Re: [Rd] Inconsistency in as.data.frame.table for stringsAsFactors

2010-01-22 Thread S Ellison
Some of us (including me) have strongly argued on several occasions that global options() settings should *not* have an effect on anything computing ... ... Global options are less of a problem where a function allows them to be overridden by the user or programmer. If something is affected

Re: [Rd] Why is there no c.factor?

2010-02-05 Thread S Ellison
c() should have been put on the deprecated list a couple of decades ago Don't you dare! Back to reality phew! had me worried there. c() is no problem at all for lists, Dates and most simple vector types; why deprecate something solely because it doesn't behave for something it doesn't claim

[Rd] One for the wish list - var.default etc

2007-05-09 Thread S Ellison
I was working on a permutation-like variant of the bootstrap for smaller samples, and wanted to be able to get summary stats of my estimator conveniently. mean() is OK as its a generic, so a mean.oddboot function gets used automatically. But var, sd and others are not originally written as

Re: [Rd] One for the wish list - var.default etc

2007-05-09 Thread S Ellison
Brian, If we make functions generic, we rely on package writers implementing the documented semantics (and that is not easy to check). That was deemed to be too easy to get wrong for var(). Hard to argue with a considered decision, but the alternative facing increasing numbers of package

[Rd] Boxplot issues (formerly posted to R-help in error)

2007-06-22 Thread S Ellison
Boxplot and bxp seem to have changed behaviour a bit of late (R 2.4.1). Or maybe I am mis-remembering. An annoying feature is that while at=3:6 will work, there is no way of overriding the default xlim of 0.5 to n+0.5. That prevents plotting boxes on, for example, interval scales - a useful

Re: [Rd] boxplot and bxp do not respect xlim by default (PR#9756)

2007-06-26 Thread S . Ellison
What is mystifying is that the issue was not present in previous versions, = so appropriate code already existed. However, I agree that there seem to be a couple of additional issues that = I had missed. =20 I am perfectly happy to look at this again myself, though, and provide = extended code;

Re: [Rd] boxplot and bxp do not respect xlim by default (PR#9754)

2007-07-02 Thread S Ellison
Brian, Note that ?bxp quite carefully says which graphical pars it does and does not accept, and 'xlim' is one it does not accept. In my version at the time, bxp did not list which plot parameters it does not accept. xlim was simply not mentioned at all. I can't easily see lack of a mention

Re: [Rd] formula(CO2)

2007-07-16 Thread S Ellison
CO2 is apparently a groupedData object; the formula attribute is described by Pinheiro and Bates as a 'display formula'. Perhaps reference to the nlme package's groupedData help would be informative? Gabor Grothendieck [EMAIL PROTECTED] 16/07/2007 16:18:37 Yes. That's what I was referring

Re: [Rd] Specifying a function as not being and S3 Class function

2012-04-24 Thread S Ellison
Is it possible to keep from triggering the following warning when I check the package? summary: function(object, ...) summary.agriculture: function(x, analyte.names, results.col, analyte.col, by, det.col, [clip] Part of the solution is to add ... to the legacy function; that is

Re: [Rd] Milestone: 4000 packages on CRAN

2012-08-24 Thread S Ellison
of the world's best statisticians and a system entirely under their control does not guarantee an unambiguous count. Anyone out there still think statistics are easy? Even so, 4000 plus or minus a few says a great deal for the R project's impact S Ellison *with limited accuracy but some entertainment

[Rd] Is there an automatic method for updating an existing CRAN package from R-forge?

2012-10-01 Thread S Ellison
-project.org/web/packages/policies.html for FTP upload? S Ellison *** This email and any attachments are confidential. Any use...{{dropped:8}} __ R-devel@r-project.org mailing list https

Re: [Rd] Is there an automatic method for updating an existing CRAN package from R-forge? - resolved

2012-10-03 Thread S Ellison
a clash with an existing package name but a clash with an existing version number. Probable explanation: I have failed to update my DESCRIPTION file. Apologies for wasting folks' time. Again. S Ellison *** This email and any attachments

Re: [Rd] Request: Documentation of formulae

2008-06-03 Thread S Ellison
Rather than transport quantities of the Introduction to R (a perfectly sensible title for a very good starting point, IMHO) would it not be simpler and involve less maintenance to include a link or cross-reference in the 'formula' help page to the relevant part of the Introduction? If nothing

[Rd] savePlot() no longer automatically adds an extension to the filename.

2008-06-03 Thread S Ellison
Plaintive squeak: Why the change? Some OS's and desktops use the extension, so forgetting it causes trouble. The new default filename keeps a filetype (as before) but the user now has to type a filetype twice (once as the type, once as extension) to get the same effect fo rtheir own filenames.

Re: [Rd] savePlot() no longer automatically adds an extension to the filename.

2008-06-04 Thread S Ellison
Michael Prager [EMAIL PROTECTED] 06/04/08 4:28 AM There is much to be said for consistency (across platforms and functions) and stability (across versions) in software. I could not agree more. But while consistency is an excellent reason for making the patch consistent across platforms, it

Re: [Rd] savePlot() no longer automatically adds an extension to the filename.

2008-06-04 Thread S Ellison
default were suggestions for possible future tidying-up in subsequent releases. Steve E S Ellison [EMAIL PROTECTED] 06/04/08 12:44 PM Michael Prager [EMAIL PROTECTED] 06/04/08 4:28 AM There is much to be said for consistency (across platforms and functions) and stability (across versions

[Rd] Is text(..., adj) upside down? (Or am I?)

2008-07-22 Thread S Ellison
?text says 'adj' allows _adj_ustment of the text with respect to '(x,y)'. Values of 0, 0.5, and 1 specify left/bottom, middle and right/top, respectively. But it looks like 0, 1 specify top, bottom respectively in the y direction. plot(1:4) text(2,2, adj=c(0,0), adj=c(0,0))

Re: [Rd] Is text(..., adj) upside down? (Or am I?)

2008-07-22 Thread S Ellison
Yup; you're all right - it IS consistent (and I'd even checked the x-adj and it did what I expected!!). It's just that ?text is talking about the position of the 'anchor' point in the text region rather than the subsequent location of the centre of the text. Anyway; if anyone is considering a

Re: [Rd] Q-Q plot scaling in plot.lm(); bug or thinko?

2013-10-17 Thread S Ellison
of prior weights the scaled residuals are expected to be IID Normal (under the normality assumption for a linear model) and without scaling they aren't IID, so a Q-Q plot would be meaningless without scaling. S Ellison *** This email

[Rd] Possible tweak to R intro - was RE: [R] Subseting a data.frame -

2013-10-18 Thread S Ellison
Transferred from R-help: From: S Ellison Subsetting using subset() is perhaps the most natural way of subsetting data frames; perhaps a line or two and an example could usefully be included in the 'Working with data frames' section of the R Intro? From: Bert Gunter [mailto:gunter.ber

[Rd] Maintainer NOTE in R CMD Check

2014-03-08 Thread S Ellison
and that removes the above Note*, but I then get a Note warning of maintainer change. Is either Note going to get in the way of CRAN submission? (And if one of them will, which one?) S Ellison *A minor aside: I couldn't find any documented reason for that, or indeed any restriction on the format

Re: [Rd] [RFC] A case for freezing CRAN

2014-03-20 Thread S Ellison
or dependency lists is a good idea that individual package maintainers could relatively easily manage, but I think freezing CRAN as a whole or adopting single release cycles for CRAN would be thoroughly impractical. S Ellison

Re: [Rd] Advice on package design for handling of dots in a formula

2014-10-15 Thread S Ellison
This seems to be a common approach in other packages. However, one of my testers noted that if he put formula=y~. then w, ID, and site showed up in the model where they weren't supposed to be. This is the documented behaviour for '.' in a formula - it means 'everything else in the data

Re: [Rd] No error when assigning values to an empty vector/matrix/array

2014-10-24 Thread S Ellison
to at least look at and either to fix or to at least warn of in documentation. S Ellison *** This email and any attachments are confidential. Any use, copying or disclosure other than by the intended recipient is unauthorised

Re: [Rd] 'vapply' not returning list element names when returned element is a length-1 list

2015-08-05 Thread S Ellison
'. Whether that is inconsistent is something of a matter of perspective. Simplification applied as far as possible will always depend on what simplification is possible for the particular return values, so different return values provide different behaviour. S Ellison

Re: [Rd] authorship and citation

2015-10-08 Thread S Ellison
so. So ask before removing someone from your citation. If they say 'no', don’t remove them. S Ellison *** This email and any attachments are confidential. Any use, copying or disclosure other than by the intended recipient is

Re: [Rd] authorship and citation

2015-10-07 Thread S Ellison
> > Is there a point at which the original developer should not stay on the > > author > list? > > Authorship is not just about code. For example, there are functions in R > which > have been completely recoded, but the design and documentation remain. > Copyright can apply to designs and

Re: [Rd] authorship and citation

2015-10-06 Thread S Ellison
ticularly one that starts small but is subsequently refactored in growth - there may be no code left that was contributed by the original developer. Is there a point at which the original developer should not stay on the author list?

Re: [Rd] row names of 'rowsum()'

2016-09-19 Thread S Ellison
' section of the help page says " A numeric or complex array of suitable size, or a vector if the result is one-dimensional. For the first four functions the 'dimnames' (or 'names' for a vector result) are taken from the original array

Re: [Rd] ifelse() woes ... can we agree on a ifelse2() ?

2016-11-26 Thread S Ellison
er a single logical (that could be used with 'if') nor a vector that can be readily replicated to the desired length with 'rep'? If not, I'd drop the attempt to generate new ifelse-like functions. S Ellison *** This email and a

[Rd] Wayback and related questions (was: RE: I have corrected a dead link ...)

2017-09-01 Thread S Ellison
ut that's a personal opinion. If these really are serious issues, somebody needs to work up a consistent policy for R projects; otherwise we'll all be walking on eggshells. S Ellison *** This email and any attachments are confide

Re: [Rd] side-effect of calling functions via `::`

2017-09-01 Thread S Ellison
t; either the generic or the class. > > I agree... (and typically it does "own" the class) If that is true and a good general guide, is it worth adding something to that effect to 1.5.2 of "Writing R extensions"? At present, nothing in 1.5.2 requires or recommends

Re: [Rd] RFC: make as.difftime more consistent or convenient

2018-08-03 Thread S Ellison
intain in the long term. So if you want to do something that will readily convert all combinations of things like '12 w', '12W', '12wks', '3m 2d', 1wk 2d', '18d' etc, write that as a stand-alone routine that converts those 'simple' formats directly to difftime objects and call i

Re: [Rd] invisible functions

2018-10-17 Thread S Ellison
ed library version of a function rather than (say) a 'source'd user-space version that is under development. Being non-specific (ie omitting foo:::) means that test code would pick up the development version in the current user environment by default. That's handy for small

Re: [Rd] Documentation examples for lm and glm

2018-12-17 Thread S Ellison
> From: Thomas Yee [mailto:t@auckland.ac.nz] > > Thanks for the discussion. I do feel quite strongly that > the variables should always be a part of a data frame. This seems pretty much a decision for R core, and I think it's useful to have raised the issue. But I, er, feel strongly

Re: [Rd] Documentation examples for lm and glm

2018-12-14 Thread S Ellison
FWIW, before all the examples are changed to data frame variants, I think there's fairly good reason to have at least _one_ example that does _not_ place variables in a data frame. The data argument in lm() is optional. And there is more than one way to manage data in a project. I personally

Re: [Rd] Unexpected argument-matching when some are missing

2018-11-29 Thread S Ellison
> > plot(x=1:10, y=) > > plot(x=1:10, y=, 10:1) > > > > In both cases, 'y=' is ignored. In the first, the plot is for y=NULL (so not > 'missing' y) > > In the second case, 10:1 is positionally matched to y despite the > > intervening > 'missing' 'y=' > > > > So it isn't just 'missing'; it's

Re: [Rd] Unexpected argument-matching when some are missing

2018-11-29 Thread S Ellison
> When trying out some variations with `[.data.frame` I noticed some (to me) > odd behaviour, Not just in 'myfun' ... plot(x=1:10, y=) plot(x=1:10, y=, 10:1) In both cases, 'y=' is ignored. In the first, the plot is for y=NULL (so not 'missing' y) In the second case, 10:1 is positionally

Re: [Rd] Unexpected argument-matching when some are missing

2018-11-30 Thread S Ellison
> Yes, I think all of that is correct. But y _is_ missing in this sense: > > plot(1:10, y=) > > ... > Browse[2]> missing(y) Although I said what I meant by 'missing' vs 'not present', it wasn't exactly what missing() means. My bad. missing() returns TRUE if an argument is not specified in the

Re: [Rd] Documentation for sd (stats) + suggestion

2019-02-19 Thread S Ellison
> As far as I can tell, the manual help page for ``sd`` > > ?sd > > does not explicitly mention that the formula for the standard deviation is > the so-called "Bessel-corrected" formula (divide by n-1 rather than n). See Details, where it says "Details: Like 'var' this uses denominator n

[R-pkg-devel] Is S3 class registration essential for CRAN?

2016-07-12 Thread S Ellison
to be fixed for _some_, or doesn't need to be changed (the present version on cran is running without apparent issues, but was submitted before the checks expanded to pick this up). S Ellison *** This email and any attachments

Re: [R-pkg-devel] Mis-spelled word with winbuilder

2016-09-22 Thread S Ellison
> I have googled 'piecewise' and it seems to be > widely used with that spelling. ... because that is the only correct spelling of 'piecewise' in English... Butu I see Duncan Murdoch has explained why it was flagged; not all English words appear in all English dictionaries. In fact, not all