[Rd] stats::screeplot suggestion
Hi
Here is a suggestion/request for stats::screeplot
* Please allow to change xlab and ylab. The attached file does that, and maintains current
behavior. Reason: strictly speaking, ylab should be "Variance" (singular). It would also
be better to have an explicit label for the X axis: "Component"
In the would-be-nice-if category, I suggest addition of a type="cumulative" chart, a line
graph of cumulative % of variance, labeled "% Variance" by default.
-Michael
- screeplot.default.R -
screeplot.default <- function (x, npcs = min(10, length(x$sdev)),
type = c("barplot", "lines"),
xlab = "",
ylab = "Variances",
main = deparse(substitute(x)), ...)
{
main
type <- match.arg(type)
pcs <- x$sdev^2
xp <- seq_len(npcs)
dev.hold()
on.exit(dev.flush())
if (type == "barplot")
barplot(pcs[xp], names.arg = names(pcs[xp]), main = main,
ylab = ylab, ...)
else {
plot(xp, pcs[xp], type = "b", axes = FALSE, main = main,
xlab = xlab, ylab = ylab, ...)
axis(2)
axis(1, at = xp, labels = names(pcs[xp]))
}
invisible()
}
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept. & Chair, ASA Statistical Graphics Section
York University Voice: 416 736-2100 x66249 Fax: 416 736-5814
4700 Keele StreetWeb: http://www.datavis.ca | @datavisFriendly
Toronto, ONT M3J 1P3 CANADA
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[Rd] re-submission of package after CRAN-pretest notes
It used to be the case that when I submitted a package and it gave notes or warnings in the CRAN checks, I was required to bump the package version before re-submission. I hope this is no longer the case. I recently submitted a package that gave one fairly trivial NOTE, fixed that, and would like to re-submit. -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. & Chair, ASA Statistical Graphics Section York University Voice: 416 736-2100 x66249 4700 Keele StreetWeb: http://www.datavis.ca | @datavisFriendly Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] passing extra arguments to devtools::build
This question was posed on SO :
https://stackoverflow.com/questions/58118495/passing-extra-argumenets-to-devtoolsbuild
but there has been no useful reply.
Something seems to have changed in the |devtools|package, so that the
following commands, that used to run now give an error I can't decipher:
|>Sys.setenv(R_GSCMD="C:/Program
Files/gs/gs9.21/bin/gswin64c.exe")>devtools::build(args
=c('--resave-data','--compact-vignettes="gs+qpdf"'))The
filename,directory name,or volume label syntax is incorrect. Error
in(function(command =NULL,args =character(),error_on_status
=TRUE,:System command error|
I've tried other alternatives with other |devtools| commands, like just
passing a single argument, but still get the same error
|args ='--compact-vignettes="gs+qpdf"'devtools::check_win_devel(args=args)|
I'm using devtools 2.2.0, under R 3.5.2
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept. & Chair, ASA Statistical Graphics Section
York University Voice: 416 736-2100 x66249
4700 Keele StreetWeb: http://www.datavis.ca | @datavisFriendly
Toronto, ONT M3J 1P3 CANADA
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[Rd] packages: Examples with CPU or elapsed time > 10s
I am perplexed about NOTEs I get from Win Builder on my genridge
package, https://github.com/friendly/genridge.
It shows, e.g.,
Examples with CPU or elapsed time > 10s
user system elapsed
plot3d.ridge 12.4 0.05 12.45
However, if I run *exactly the same code* in my console with
system.time(), I get
user system elapsed
0.95 0.16 1.17
What could be the explanation for this?
Second, the .log file from Win Builder shows only the *first example*
with > 10s time.
I have been able to reduce the time by wrapping part of the example in
\donttest{}.
I run Win Builder again, and the NOTE appears for another file. Very
annoying.
It would be far more helpful to see these all together, rather than
having to do this incrementally.
-Michael
-- Michael Friendly Email: friendly AT yorku DOT ca Professor,
Psychology Dept. & Chair, Quantitative Methods York University Voice:
416 736-2100 x66249 Fax: 416 736-5814 4700 Keele Street
Web:http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA
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Re: [Rd] Installing/updating packages on a lab network
On 7/28/2015 1:32 PM, Uwe Ligges wrote: Just add the line R_LIBS_SITE=F:/R/library to the file R_HOME/etc/x64/Renviron.site Thanks, Uwe I have no way to test this and our IT people who do the installation know nothing of R, so follow-up questions: * There is no R_HOME/etc/x64/Renviron.site file, but there is a R_HOME/etc/Rprofile.site I can modify and ask them to install. Would the equivalent in Rprofile.site be Sys.setenv(R_LIBS_SITE=F:/R/library) * Does this require that the R_LIBS_SITE folder exist and be writable by the user? Here is what I see in the current version: .libPaths(), the library trees where R looks for packages gives: [1] G:/uitapps/HEBB_R_LIB2/library [2] C:/Program Files/R/R/R-3.1.1/library If I try to install a new package, e.g., install.packages(rockchalk) I get G:/uitapps/HEBB_R_LIB2/library is not writeable. Use a personal library instead?, followed by a popup window, Create ~R/library? (y/n) This then installs the package, but to C:/Users/friendly/Desktop/~R/library. In the current login session, .libPaths() will then have this path, so in a new R session, load(rockchalk) will work. However, once I logout, all that disappears, so I have to start over again to install or update a package. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb:http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] update.packages(checkBuilt=TRUE, ask=FALSE): possible bug
On 7/19/2015 3:50 AM, peter dalgaard wrote: For some, but not allI repositories I get the error message below: Error in install.packages(update[instlib == l, Package], l, contriburl = contriburl, : specifying 'contriburl' or 'available' requires a single type, not type = both Is it a bug? I think that what Jose is referring to is this error message from install.packages(), even though he set options(pkgType='binary') Isn't that a bug? Moreover, in a fresh R 3.2.1 session [Platform: x86_64-w64-mingw32/x64 (64-bit)], I see getOption(pkgType) [1] both I think this is somehow related to the fact that install.packages() will now tell you if a more current source package exists and ask if you want to install from source. But this would require RTools to be installed to work. IMHO, I consider this a major infelicity or design flaw, that will cause problems for naive and even experienced users. install.packages(foo) should always work unless package foo cannot cannot be found in getOption(repos) -Michael __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Installing/updating packages on a lab network
I'm the faculty member in my department who advises our IT staff on the details of installing R for students and faculty on our Windows 7 lab network. We are about to upgrade from R 3.1.1 to R 3.2.1, and once that is done, this version of R and all installed packages will be frozen in the image that appears in C:/Program Files/R/R-3.2.1/ on every lab computer, and this image is refreshed on each computer at each new login. Every user has a persistent home directory across all university lab computers, typically their F:/ drive (students) and/or X:/ drive (faculty). I need to give instructions to our IT staff for how to arrange for a personal library, say F:/~R/library to be be set automatically, and included in .libPaths() so that install.packages() and update.packages() will work using that path. At present, there is no file R_HOME/etc/Renviron.site and R_HOME/etc/Rprofile.site is the vanilla version with everything commented out, including # set a site library # .Library.site - file.path(chartr(\\, /, R.home()), site-library) Environmental variables set for users include HOMEDRIVE=F: HOMEPATH=\ HOMESHARE=\\vfadmin.yorku.yorku.ca\HH\HOME\friendly with the latter mapped to the X: drive What is the code to be added to Rprofile.site to make this work? thanks, -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb:http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] 'library' or 'require' call not declared from: 'rgl'
I'm checking a new release of vcdExtra via win builder with R-devel 2014-10-29 r66897 and have run into a Warning I don't know how to fix. I have one S3 generic, mosaic3d() that uses rgl and don't want to have rgl always loaded via Depends:. Instead, the mosaic3d.default() method includes if (!require(rgl)) stop(rgl is required) This always worked in the past, but in this testing cycle, I got a slew of no visible global function definition for ... all rgl functions. I revised DESCRIPTION to include: Imports: rgl and NAMESPACE: import(rgl) All the no visible global function definition ... went away, but I'm stuck with * checking dependencies in R code ... WARNING 'library' or 'require' call not declared from: 'rgl' See the information on DESCRIPTION files in the chapter 'Creating R packages' of the 'Writing R Extensions' manual. How can I solve this? -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb:http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] 'library' or 'require' call not declared from: 'rgl'
On 10/30/2014 4:19 PM, Simon Urbanek wrote: Did you intend rgl to be optional? If so, then you should use Suggests: instead. When you use Imports: it will load rgl automatically so require() does't make sense (since it will be always TRUE). I always had it as Suggests: rgl before. But R-devel now gave be all those no visible global function definition for ... messages. Achim suggested using explicitly rgl:: everywhere. That's quite ugly, but seems to work. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb:http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] no visible binding for global variable for data sets in a package
On 8/27/2014 5:24 AM, Martin Maechler wrote:
Michael Friendly frien...@yorku.ca
on Tue, 26 Aug 2014 17:58:34 -0400 writes:
I'm updating the Lahman package of baseball statistics to the 2013
release. In addition to
the main data sets, the package also contains several convenience
functions that make use
of these data sets. These now trigger the notes below from R CMD check
run with
Win builder, R-devel. How can I avoid these?
* using R Under development (unstable) (2014-08-25 r66471)
* using platform: x86_64-w64-mingw32 (64-bit)
...
* checking R code for possible problems ... NOTE
Label: no visible binding for global variable 'battingLabels'
Label: no visible binding for global variable 'pitchingLabels'
Label: no visible binding for global variable 'fieldingLabels'
battingStats: no visible binding for global variable 'Batting'
battingStats: no visible global function definition for 'mutate'
playerInfo: no visible binding for global variable 'Master'
teamInfo: no visible binding for global variable 'Teams'
One such function:
## function for accessing variable labels
Label - function(var, labels=rbind(battingLabels, pitchingLabels,
fieldingLabels)) {
wanted - which(labels[,1]==var)
if (length(wanted)) labels[wanted[1],2] else var
}
and you are using the data sets you mentioned before,
(and the checking has been changed recently here).
This is a bit subtle:
Your data sets are part of your package (thanks to the default
lazyData), but *not* part of the namespace of your package.
Now, the reasoning goes as following: if someone uses a function
from your package, say Label() above,
by
Lahman::Label(..)
and your package has not been attached to the search path,
your user will get an error, as the datasets are not found by
Label().
If you consider something like Lahman::Label(..)
for a bit and the emphasis we put on R functions being the
primary entities, you can understand the current, i.e. new,
R CMD check warnings.
Thanks for this explicit explanation. Now I understand why this occurs.
I see the following two options for you:
1) export all these data sets from your NAMESPACE
For this (I thinK), you must define them in Lahman/R/ possibly via a
Lahman/R/sysdata.rda
Not sure I quite understand how this would work. My NAMESPACE currently
exports
the few functions in this package:
# all the rest is data
export(battingStats,
playerInfo,teamInfo,
Label
)
Do you mean to simply add all the data sets ('globals') that are
referred to in these functions?
# all the rest is data
export(battingStats,
playerInfo,teamInfo,
Label,
battingLabels, pitchingLabels, fieldingLabels,
Batting, Master, Teams
)
That seems a bit odd. Can you actually export data? Maybe there is a
need for a
separate NAMESPACE declaration, that might be called either of
exportdata()
globaldata()
2) rewrite your functions such that ensure the data sets are
loaded when they are used.
2) actually works by adding
stopifnot(require(Lahman, quietly=TRUE))
as first line in Label() and other such functions.
It works in the sense that Lahman::Label(yearID) will
work even when Lahman is not in the search path,
but R-devel CMD check will still give the same NOTE,
though you can argue that that note is actally a false positive.
So, this would be version 1 of 2):
Label - function(var, labels) {
stopifnot(require(Lahman, quietly=TRUE))
if(missing(labels)) labels - rbind(battingLabels, pitchingLabels,
fieldingLabels)
wanted - which(labels[,1]==var)
if (length(wanted)) labels[wanted[1],2] else var
}
And this would be version 2, using data():
Label - function(var, labels) {
stopifnot(require(Lahman, quietly=TRUE))
if(missing(labels)) {
data(battingLabels); data(pitchingLabels); data(fieldingLabels)
labels - rbind(battingLabels, pitchingLabels, fieldingLabels)
}
wanted - which(labels[,1]==var)
if (length(wanted)) labels[wanted[1],2] else var
}
Not sure about another elegant way to make 2) work, apart from
using data() on each of the datasets inside the
function. As I haven't tried it, that may *still* give a
(false) NOTE..
This is a somewhat interesting problem, and I wonder if everyone
else has solved it with '1)' rather than a version of '2)'.
Martin
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept. Chair, Quantitative Methods
York University Voice: 416 736-2100 x66249 Fax: 416 736-5814
4700 Keele StreetWeb:http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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Re: [Rd] no visible binding for global variable for data sets in a package
On 8/27/2014 9:29 AM, Michael Friendly wrote:
It works in the sense that Lahman::Label(yearID) will
work even when Lahman is not in the search path,
but R-devel CMD check will still give the same NOTE,
though you can argue that that note is actally a false positive.
So, this would be version 1 of 2):
Label - function(var, labels) {
stopifnot(require(Lahman, quietly=TRUE))
if(missing(labels)) labels - rbind(battingLabels, pitchingLabels,
fieldingLabels)
wanted - which(labels[,1]==var)
if (length(wanted)) labels[wanted[1],2] else var
}
And this would be version 2, using data():
Label - function(var, labels) {
stopifnot(require(Lahman, quietly=TRUE))
if(missing(labels)) {
data(battingLabels); data(pitchingLabels); data(fieldingLabels)
labels - rbind(battingLabels, pitchingLabels, fieldingLabels)
}
wanted - which(labels[,1]==var)
if (length(wanted)) labels[wanted[1],2] else var
}
Just to follow up: R-devel likes this less than it does my initial
version. I still get no visible binding NOTES, and complaint about
using data() in a function:
* checking R code for possible problems ... NOTE
Label: no visible binding for global variable 'battingLabels'
Label: no visible binding for global variable 'pitchingLabels'
Label: no visible binding for global variable 'fieldingLabels'
battingStats: no visible binding for global variable 'Batting'
battingStats: no visible global function definition for 'mutate'
playerInfo: no visible binding for global variable 'Master'
teamInfo: no visible binding for global variable 'Teams'
Found the following calls to data() loading into the global environment:
File 'Lahman/R/Label.R':
data(battingLabels)
data(pitchingLabels)
data(fieldingLabels)
See section 'Good practice' in '?data'.
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Re: [Rd] no visible binding for global variable for data sets in a package
On 8/27/2014 10:41 AM, peter dalgaard wrote:
Using data() in a package with lazyloaded data seems like asking for trouble to
me. But you're making me curious (and I'm too lazy[*] to set up for rebuilding
the package myself):
Did you actually try putting battingLabels friends in the namespace? What
happened?
Well, I tried this, with NAMESPACE as
# all the rest is data, except we try to export the data sets used
globally in these functions
export(battingStats,
playerInfo,teamInfo,
Label,
battingLabels, pitchingLabels, fieldingLabels,
Batting, Master, Teams
)
R CMD check was even more unhappy, failing immediately, so the attempted
cure was worse than the original disease.
* checking whether package 'Lahman' can be installed ...Warning: running
command 'C:/R/R-3.0.3/bin/x64/Rcmd.exe INSTALL -l
C:/eclipse/Lahman2013.Rcheck --no-html
C:\DOCUME~2\WORKSP~1\LAHMAN~1' had status 1
ERROR
Installation failed.
See 'C:/eclipse/Lahman2013.Rcheck/00install.out' for details.
00install.out said:
Error in namespaceExport(ns, exports) :
undefined exports: battingLabels, pitchingLabels, fieldingLabels,
Batting, Master, Teams
Error: loading failed
Execution halted
My conclusions so far are:
- These are just NOTEs, so I will ignore them for now. But they will
probably trigger the CRAN
maintainers to notice them when I resubmit and I will have to plead
guilty with an explanation. This makes more useless work for all involved.
- Peter Dalgaard noted the change in R-devel, and nobody so far has
suggested a working remedy, so a clean solution
seems warranted. It mentions 'now by default' -- is there a switch for
this?
The change would seem to be this
\item \command{R CMD check} now by default checks code usage
directly on the package namespace without loading and attaching
the package and its suggests and enhances.
and perhaps the remedies could be stated more clearly?
Alternatively, it isn't common, but it is by no means rare for package
functions to need to use data sets
in the package, so some mechanism to declare these, perhaps in NAMESPACE
is needed.
A workaround could be to use rbind(Lahman::battingLabels,) which runs a bit
against the grain for me.
I think the right answer _is_ to export the lazy data; the question is how to do it.
There's nothing particularly strange about exporting non-functions (letters
would be an example, save for the special status of package:base). If you attach the
package, the lazyloaded data appear in the same environment as the exported function so
they are de facto already in the namespace for the purposes of library() and `::`. So I
agree, something like exportData() would be useful. (Or some other mechanism. You might
want to be able to export data selectively.)
- pd
[*] Burdened with pressing obligations, if you like.
On 27 Aug 2014, at 16:07 , Michael Friendly frien...@yorku.ca wrote:
On 8/27/2014 9:29 AM, Michael Friendly wrote:
It works in the sense that Lahman::Label(yearID) will
work even when Lahman is not in the search path,
but R-devel CMD check will still give the same NOTE,
though you can argue that that note is actally a false positive.
So, this would be version 1 of 2):
Label - function(var, labels) {
stopifnot(require(Lahman, quietly=TRUE))
if(missing(labels)) labels - rbind(battingLabels, pitchingLabels,
fieldingLabels)
wanted - which(labels[,1]==var)
if (length(wanted)) labels[wanted[1],2] else var
}
And this would be version 2, using data():
Label - function(var, labels) {
stopifnot(require(Lahman, quietly=TRUE))
if(missing(labels)) {
data(battingLabels); data(pitchingLabels); data(fieldingLabels)
labels - rbind(battingLabels, pitchingLabels, fieldingLabels)
}
wanted - which(labels[,1]==var)
if (length(wanted)) labels[wanted[1],2] else var
}
Just to follow up: R-devel likes this less than it does my initial version. I
still get no visible binding NOTES, and complaint about
using data() in a function:
* checking R code for possible problems ... NOTE
Label: no visible binding for global variable 'battingLabels'
Label: no visible binding for global variable 'pitchingLabels'
Label: no visible binding for global variable 'fieldingLabels'
battingStats: no visible binding for global variable 'Batting'
battingStats: no visible global function definition for 'mutate'
playerInfo: no visible binding for global variable 'Master'
teamInfo: no visible binding for global variable 'Teams'
Found the following calls to data() loading into the global environment:
File 'Lahman/R/Label.R':
data(battingLabels)
data(pitchingLabels)
data(fieldingLabels)
See section 'Good practice' in '?data'.
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Professor, Psychology Dept
[Rd] no visible binding for global variable for data sets in a package
I'm updating the Lahman package of baseball statistics to the 2013
release. In addition to
the main data sets, the package also contains several convenience
functions that make use
of these data sets. These now trigger the notes below from R CMD check
run with
Win builder, R-devel. How can I avoid these?
* using R Under development (unstable) (2014-08-25 r66471)
* using platform: x86_64-w64-mingw32 (64-bit)
...
* checking R code for possible problems ... NOTE
Label: no visible binding for global variable 'battingLabels'
Label: no visible binding for global variable 'pitchingLabels'
Label: no visible binding for global variable 'fieldingLabels'
battingStats: no visible binding for global variable 'Batting'
battingStats: no visible global function definition for 'mutate'
playerInfo: no visible binding for global variable 'Master'
teamInfo: no visible binding for global variable 'Teams'
One such function:
## function for accessing variable labels
Label - function(var, labels=rbind(battingLabels, pitchingLabels,
fieldingLabels)) {
wanted - which(labels[,1]==var)
if (length(wanted)) labels[wanted[1],2] else var
}
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept. Chair, Quantitative Methods
York University Voice: 416 736-2100 x66249 Fax: 416 736-5814
4700 Keele StreetWeb:http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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Re: [Rd] listof
An interesting topic, but I'll only respond with my own experience, and that is, while 'listof' could be usefully extended there was not enough meat on the bones to want to do so. I think this is a limitation of the S3 class/method structure, as I see it. In several packages (effects, heplots, candisc, vcdExtra) I/we deal with lists of objects of a given class, and want to define methods for plot(), summary(), print(), etc. In these cases, the simplest solution was to designate a new class, e.g., 'efflist' for a list of effects in a univariate lm/glm/polr/ ... model or 'candiscList' for a list of candisc objects. Methods for the *list class could then use an apply() construct over the list items. Most recently, in the effects package, we implemented some effects plot methods for multivariate linear models. This is essentially a two-way collection of effects for terms x responses, but how to represent this in the class structure to re-use the existing code for a single effect of a given response variable? The solution used here was to define a new class, 'mlm.efflist', with new methods for this class. This works within the current S3 class scheme, but doesn't provide an extendible semantics. -Michael On 7/29/2014 11:20 PM, Adrian Baddeley wrote: Dear R developers A question about the class 'listof', defined in package 'stats'. Other than its definition and use in the code for 'anova', we can't see that the class 'listof' is used for anything else (in recommended packages, or elsewhere). In the spatstat package we have been using a 'listof' to represent a list of spatial objects of the same class (such as point patterns, or pixel images) and we've defined a plot method. Is it OK for us to hijack an existing class in this way, or is this a violation of some future plans/ design feature of R ? We're about to publish a book on spatstat so I would much appreciate advice if we need to change it. regards Adrian Prof Adrian Baddeley FAA University of Western Australia __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] historical significance of Pr(Chisq) 2.2e-16
Where does the value 2.2e-16 come from in p-values for chisq tests such as those reported below? Anova(cm.mod2) Analysis of Deviance Table (Type II tests) Response: Freq LR Chisq Df Pr(Chisq) B 11026.2 1 2.2e-16 *** W 7037.5 1 2.2e-16 *** Age 886.6 8 2.2e-16 *** B:W 3025.2 1 2.2e-16 *** B:Age 1130.4 8 2.2e-16 *** W:Age 332.9 8 2.2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Historical NA question
On 03/05/2014 12:39 PM, Hadley Wickham wrote: Can anyone tell me what the significance of 1954 is in R's NA? Just ask R: 2*(1-pnorm(1954)) [1] 0 2*(1-pnorm(1954)) %in% NA [1] 0 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] version numbers for CRAN submissions that give warnings/notes
It often happens that I submit a new revision of a package, say mypkg-1.0-10, from R-Forge to CRAN after running R CMD check locally and looking at the log files on R-Forge. But R-Forge has the devel checks disabled, and I get an email from CRAN pointing out some new warning or note I'm asked to correct. OK, I correct this and commit a new rev to R-Forge. But, is it still required to bump the version number to mypkg-1.0-11 before resubmitting to CRAN, even though mypkg-1.0-10 did not make it there? To do so means also modifying the DESCRIPTION, NEWS and mypkg-package.Rd files even for a minor warning or note. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] forking a CRAN project
There is a CRAN package licensed just as GPL, say, XX, I want to use in a book. But I've needed to modify the package to make it do what I need for expository purposes. The package author(s) are amenable to my modifications, but probably unlikely to incorporate them into the CRAN version any time soon. Am I allowed, under GPL, to create a new version of the package, say XX2, in a public repository such as R-Forge or github? I would, of course, maintain their authorship, though perhaps take over the maintainer role. For my purposes in the book, I don't necessarily need to release my version to CRAN; just a public repo a reader could download from. -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] proposal: stats::as.matrix.ftable method
Following some discussion on R-help, I'd like to propose that an
as.matrix method be added
to those available for ftable objects. The reason for this is that
there are a variety of situations
where one needs to flatten a 3+ way table, but then use that for
analysis as a matrix, not just for
pretty-printing. There is an as.table method to turn the result back to
a table, but an as.matrix
method is missing.
methods(class=ftable)
[1] as.data.frame.ftable* as.table.ftable* format.ftable*
[4] head.ftable* print.ftable tail.ftable*
Non-visible functions are asterisked
The function below was proposed by William Dunlop:
# as.matrix method for flattened tables
# modified from Willaim Dunlop, wdun...@tibco.com, R-Help, 01-09-2014
as.matrix.ftable - function(x, sep=_, ...) {
makeDimNames - function(vars) {
structure(
list(do.call(paste, c(rev(expand.grid(rev(vars))),
list(sep=sep,
names = paste(collapse=sep, names(vars))
)
}
structure(
unclass(x),
dimnames=c(makeDimNames(attr(x, row.vars)),
makeDimNames(attr(x, col.vars))),
row.vars=NULL,
col.vars=NULL)
}
Some test cases:
UCB - UCBAdmissions
as.matrix(ftable(Dept ~ Admit + Gender, data=UCB))
Dept
Admit_GenderA B C D E F
Admitted_Male 512 353 120 138 53 22
Admitted_Female 89 17 202 131 94 24
Rejected_Male 313 207 205 279 138 351
Rejected_Female 19 8 391 244 299 317
as.matrix(ftable(Dept ~ ., data=UCB))
Dept
Admit_GenderA B C D E F
Admitted_Male 512 353 120 138 53 22
Admitted_Female 89 17 202 131 94 24
Rejected_Male 313 207 205 279 138 351
Rejected_Female 19 8 391 244 299 317
as.matrix(ftable(Admit + Gender ~ Dept, data=UCB))
Admit_Gender
Dept Admitted_Male Admitted_Female Rejected_Male Rejected_Female
A 512 89 313 19
B 353 17 207 8
C 120 202 205 391
D 138 131 279 244
E53 94 138 299
F22 24 351 317
as.matrix(ftable(Admit ~ ., data=UCB))
Admit
Gender_Dept Admitted Rejected
Male_A512 313
Male_B353 207
Male_C120 205
Male_D138 279
Male_E 53 138
Male_F 22 351
Female_A 89 19
Female_B 178
Female_C 202 391
Female_D 131 244
Female_E 94 299
Female_F 24 317
Related functions: The vcd package defines a more extensive suite of
similar structable functions,
including as.matrix.structable; however that function doesn't supply
appropriate dimnames for
the dimensions. Given as.matrix.ftable(), that is easy to correct:
# use as.matrix.ftable, but
# need to remove other attributes: dnames, split_vertical
library(vcd)
as.matrix.structable - function(x, sep=_, ...) {
structure(
as.matrix.ftable(x, sep, ...),
dnames = NULL,
split_vertical = NULL
)
}
Test:
as.matrix(structable(Gender ~ Admit + Dept, data=UCB))
Gender
Admit_Dept Male Female
Admitted_A 512 89
Admitted_B 353 17
Admitted_C 120202
Admitted_D 138131
Admitted_E 53 94
Admitted_F 22 24
Rejected_A 313 19
Rejected_B 207 8
Rejected_C 205391
Rejected_D 279244
Rejected_E 138299
Rejected_F 351317
as.matrix(structable(Gender + Admit ~ Dept, data=UCB))
Gender_Admit
Dept Male_Admitted Male_Rejected Female_Admitted Female_Rejected
A 512 313 89 19
B 353 207 17 8
C 120 205 202 391
D 138 279 131 244
E53 138 94 299
F22 351 24 317
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept. Chair, Quantitative Methods
York University Voice: 416 736-2100 x66249 Fax: 416 736-5814
4700 Keele StreetWeb: http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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[Rd] bug/infelicity in citation(base)
utils::citation() offers the option auto=(NULL|TRUE) to obtain the
citations for a package from the package
DESCRIPTION file or a CITATION file, as described below:
|auto|
a logical indicating whether the default citation auto-generated from
the package 'DESCRIPTION' metadata should be used or not, or |NULL|
(default), indicating that a 'CITATION' file is used if it exists, or an
object of class |packageDescription
http://127.0.0.1:11936/library/utils/help/packageDescription| with
package metadata (see below).
This presents a problem when citation() is used in functions such as
bibtex::write.bib() and
knitr::write_bib(), because the base package is treated specially in
citation() and does not
allow auto=TRUE
citation(base,auto=TRUE)
Error in citation(base, auto = TRUE) :
broken installation, no CITATION file in the base package.
This is a strange and misleading message, since the base package,
presumably by design
has no CITATION file. It requires a workaround in functions like
knitr::write_bib when given
a list of packages,
bib = sapply(x, function(pkg) {
cite = citation(pkg, auto = if (pkg == base)
NULL
else TRUE)
entry = toBibtex(cite)
entry[1] = sub(\\{,$, sprintf({R-%s,, pkg), entry[1])
gsub(, , entry)
}, simplify = FALSE)
Is there some reason why citation() can't simply ignore auto=TRUE
(perhaps with a message)
for the base package?
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept. Chair, Quantitative Methods
York University Voice: 416 736-2100 x66249 Fax: 416 736-5814
4700 Keele StreetWeb: http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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Re: [Rd] declaring package dependencies
On 9/13/2013 12:15 PM, John Fox wrote: If I understand this thread, Michael's package doesn't use loglm() -- it provides methods for objects produced by loglm() and hence Enhances the package. Well, here's the rub: vcdExtra uses MASS::loglm() in examples, and also in R code, where it provides new S3 methods for loglm objects. And, this whole problem only arose after vcd (on which I Depend), modified its Imports to: Imports: utils, MASS, grDevices, colorspace where, previously, MASS had been a Depends (or Suggests?) there. For my examples, the old Suggests: MASS worked, but now I've used require(MASS) in each of those examples. However, the use in R code also triggered an error on loglm, even when I added Enhances: MASS to DESCRIPTION. OK, so I switched to using Imports: MASS but even that doesn't cure the problem alone. I then got: * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: 'MASS' All declared Imports should be used. See the information on DESCRIPTION files in the chapter 'Creating R packages' of the 'Writing R Extensions' manual. but then an Error when an example using the function which called loglm() directly was run. ### ** Examples data(Titanic, package=datasets) # variables are in the order Class, Sex, Age, Survived tt - seq_loglm(Titanic) 1 model.string: = Class Error in eval(expr, envir, enclos) : could not find function loglm Calls: seq_loglm - eval - eval Execution halted So, as several people have suggested, I changed to use MASS::loglm() in code, though it still perplexes me why this is necessary. At any rate, this now passes R devel. Whew! Thanks to a suggestion from Mattew Dowle, I'm now using winbuilder (thx, Uwe for this!) and can get rather quick ( 30 min.) feedback on an R-devel build, whereas the R-Forge build cycle often takes a day. So, my workflow is now - R CMD check on local version in StatET - If OK, send to winbuilder, http://win-builder.r-project.org/upload.aspx - If OK, commit to R-Forge, and perhaps submit to CRAN if this is the final rev in a development cycle. But I still feel like I'm spending too much time on satisfying the unknown, new requirements of CRAN checks. As Dirk said (also deserving to be a fortune), Absent a time machine or psychic powers, I do not see how package developers can reasonably be expected to cope with this. The effort by R Core members that goes into R and CRAN is certainly herculean and I appreciate it very much. Like Dirk, I'm just looking for a little more predictability as CRAN evolves. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] declaring package dependencies
I received the following email note re: the vcdExtra package A vcd update has shown that packages TIMP and vcdExtra are not declaring their dependence on colorspace/MASS: see http://cran.r-project.org/web/checks/check_results_vcdExtra.html But, I can't see what to do to avoid this, nor understand what has changed in R devel. Sure enough, CRAN now reports errors in examples using MASS::loglm(), using R Under development (unstable) (2013-09-11 r63906) Caesar.mod0 - loglm(~Infection + (Risk*Antibiotics*Planned), data=Caesar) Error: could not find function loglm In DESCRIPTION I have Depends: R (= 2.10), vcd, gnm (= 1.0.3) Suggests: ca,gmodels,Fahrmeir,effects,VGAM,plyr,rgl,lmtest,MASS,nnet,ggplot2,Sleuth2,car and the vcd DESCRIPTION has Depends: R (= 2.4.0), grid, stats Suggests: KernSmooth, mvtnorm, kernlab, HSAUR, coin Imports: utils, MASS, grDevices, colorspace so, in an R 3.0.0 console, library(vcdExtra) loads vcd and its dependencies: library(vcdExtra) Loading required package: vcd Loading required package: MASS Loading required package: grid Loading required package: colorspace Loading required package: gnm Warning messages: 1: package ‘vcd’ was built under R version 3.0.1 2: package ‘MASS’ was built under R version 3.0.1 Note: these CRAN errors do not occur on R-Forge, using R version 3.0.1 Patched (2013-08-21 r63645) and the latest devel version (0.5-11) of vcdExtra. -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] packages with Sweave and knitr vignettes?
Now that R 3.0.0+ supports non-Sweave vignettes, R-exts \S 1.4.2 seems
to imply that
it is possible to include both Sweave and knitr vignettes in a single
package.
I'm wondering
if anyone has tried this and/or if there are some hidden gotchas putting
this into practice,
and concerned about creating problems with CRAN checks if I try this.
Consider two vignettes:
pkg/vignettes/vign1.Rnw, containing:
% !Rnw weave = Sweave
%\VignetteEngine{Sweave}
...
pkg/vignettes/vign2.Rnw, containing:
% !Rnw weave = knitr
%\VignetteEngine{knitr::knitr}
...
both are .Rnw files, distinguished only by \VignetteEngine. vign1.Rnw is
currently in my
package, and vign2.Rnw compiles OK outside it, using knitr in an R
console or RStudio.
R-exts implies that the DESCRIPTION file must include (minimally):
VignetteBuilder: Sweave, knitr
Suggests: knitr
Is anything more/different required? Does a package exist that does this?
TIA
-Michael
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept. Chair, Quantitative Methods
York University Voice: 416 736-2100 x66249 Fax: 416 736-5814
4700 Keele StreetWeb: http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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[Rd] Confusion about Depends:, Imports:, Enhances:, import(), inportFrom()
In checking my vcdExtra package, the following NOTE newly appeared (R-Forge, using R version 3.0.1 Patched (2013-08-20 r63635)) Package in Depends field not imported from: ‘gnm’ These packages needs to imported from for the case when this namespace is loaded but not attached. In the DESCRIPTION file, I have Depends: R (= 2.10), vcd, gnm (= 1.0.3) In NAMESPACE: # we are a vcd extension import(vcd) I've read 1.1.1 of R-Exts, but it is not clear to me whether I should also import gnm or change the DESCRIPTION file to use Imports: vcd, gnm (= 1.0.3) R-Exts says: The ‘Imports’ field lists packages whose namespaces are imported from (as specified in the NAMESPACE file) but which do not need to be attached, but how can I tell if gnm needs to be attached? Also, what is the difference between Imports: in DESCRIPTION and imports() in NAMESPACE? -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] legitimate use of :::
On 8/22/2013 7:45 AM, Uwe Ligges wrote: On 22.08.2013 07:45, Yihui Xie wrote: Hi, So now R CMD check starts to warn against :::, but I believe sometimes it is legitimate to use it when developing R packages. For example, I have some utils functions that are not exported but I want to share them across the packages that I maintain. I do not need to coordinate with other authors about these internal functions since I'm the only author and I know clearly what I'm doing, and I want to avoid copying and pasting the code across packages just to avoid the NOTE in R CMD check. What should I do in this case? Nothing. The way you describe above seems to be a reasonable usage, iff you are the same maintainer who knows what is going on. Other maintainers should not use one of your not exported (hence non API) functions, of course. Uwe Ligges Related to this is the use of other-package unexported utility functions that don't pass Uwe's iff test, but I, as maintainer, want to use in my package. Cases in point: in heplots, I had used stats:::Pillai, stats:::Wilks, stats:::Roy and stats:::LH for calculation in one of my functions. Similarly, I had a need to use car:::df.terms, also unexported, but don't want to ask John Fox to export it just for my use. Uwe's reply suggests that I should not be using car:::df.terms, however. To avoid the NOTEs (which often triggers a 'pls fix' upon submission to CRAN), I simply copied/pasted these functions to my package, but this seems wasteful. -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] probable bugs in stats::loglin calculation of pearson chisq
In running the following example of a loglinear model for the Titanic data, I was surprised to see NaN reported for the Pearson chisq loglin(Titanic, margin=list(1:3, 4)) 2 iterations: deviation 2.273737e-13 $lrt [1] 671.9622 $pearson [1] NaN $df [1] 15 $margin $margin[[1]] [1] Class Sex Age $margin[[2]] [1] Survived Tracing it back, this occurs because there are zeros in the fitted/expected frequencies for children among the Crew. # get fitted (expected) values fitted - loglin(Titanic, margin=list(1:3, 4), fit=TRUE)$fit 2 iterations: deviation 2.273737e-13 fitted[Class=Crew,,Age=Child,] Survived Sex No Yes Male0 0 Female 0 0 I certainly understand the difference between sampling zeros and structural zeros, and this distinction seems properly implemented in loglin() via the start= argument, but only in the calculation of Pearson chisq, not for LRT. I think this is a code bug, but if there is a reason for the difference, it should be documented in the help for loglin. Another probable bug is that the calculation of of the LRT chisq also takes zero fitted values into account, while the calculation of the Pearson chisq does not, and leads to the NaN result for my example. It occurs in the following portion of the code for loglin: fit - z$fit attributes(fit) - attributes(table) observed - as.vector(table[start 0]) expected - as.vector(fit[start 0]) pearson - sum((observed - expected)^2/expected) observed - as.vector(table[table * fit 0]) expected - as.vector(fit[table * fit 0]) lrt - 2 * sum(observed * log(observed/expected)) I don't understand the reasons for the different calculations of observed expected for pearson lrt. FWIW, below is how I calculate these in my mosaics.sas program start chisq(obs, fit); *-- Find Pearson and likelihood ratio chisquares; gf = sum ( (obs - fit)##2 / ( fit + (fit=0) ) ); lr = 2 # sum ( obs # log ( (obs+(obs=0)) / (fit + (fit=0)) ) ); return (gf // lr); finish; -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] vignettes: problems with PDF compaction
On 4/22/2013 5:51 PM, Uwe Ligges wrote:
But this doesn't do anything, not even changing the timestamp on the
file, because the file size doesn't change enough.
Either you changed it or not, there is no not enough.
I meant that the code in tools::compact compares the sizes of the old
and new files and only replaces the old file if the change in size is
sufficient:
if (new/old 0.9 new old - 1) {
file.copy(tf, p, overwrite = TRUE)
}
At any rate, with R_GSCMD now fixed (Thx: Henrik), tools::compactPDF,
with gs_quality=ebook,
still does not reduce the size of my HE-examples.pdf file.
I tried the same on my Ubuntu system (R 2.15.2 also), and there I get
tools::compactPDF(HE-examples.pdf, gs_quality=ebook)
compacted 'HE-examples.pdf' from 739Kb to 366Kb
So, I can now copy the compacted file back to my development tree
on Windows; however, as I understand things, vignettes are re-built
by R CMD build and --compact-vignettes=gs+qpdf has no effect.
So my Ubuntu-compacted file will be overwritten.
It's somewhat maddening to have to spend so much time to save ~373Kb
in order to avoid a CRAN warning.
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept. Chair, Quantitative Methods
York University Voice: 416 736-2100 x66249 Fax: 416 736-5814
4700 Keele StreetWeb: http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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Re: [Rd] vignettes: problems with PDF compaction
On 4/21/2013 1:28 PM, Michael Friendly wrote: [Env: OS: Win Xp; R 2.15.2; IDE: eclipse/StatET] Each time I update my heplots package, I get warnings from R CMD check on R-Forge, * checking sizes of PDF files under ‘inst/doc’ ... WARNING ‘gs+qpdf’ made some significant size reductions: compacted ‘HE-examples.pdf’ from 739Kb to 366Kb To follow up my own post, I did some more checking of whether/how to compact PDFs on my own system. My conclusion is that that I am unable to comply with the request from CRAN maintainers, even though I would like to. Once again, I wonder why this cannot be handled on the CRAN side automatically. qpdf: running it from a cmd prompt (using the options from tools::compactPDF) doesn't do very much compression C:\R\testqpdf --stream-data=compress --object-streams=generate HE-examples.pdf HE-examples-comp.pdf C:\R\testdir HE-examples* 04/22/2013 10:55 AM 699,191 HE-examples-comp.pdf 04/22/2013 10:28 AM 756,624 HE-examples.pdf gs: I have gs installed at C:\Program Files\gs\gs9.07\bin\gswin32.exe, but the gs installer doesn't put itself on the path, so tools::compactPDF sees gs_cmd as empty: gs_cmd = Sys.getenv(R_GSCMD, ) [1] so it can't run gs+qpdf. OK, so I try to do it manually: Sys.setenv(R_GSCMD = C:/Program Files/gs/gs9.07/bin/gswin32.exe) setwd(test) tools::compactPDF(HE-examples.pdf) tools::compactPDF(HE-examples.pdf, gs_quality=ebook) But this doesn't do anything, not even changing the timestamp on the file, because the file size doesn't change enough. C:\R\testdir HE-examples.pdf 04/22/2013 10:28 AM 756,624 HE-examples.pdf -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] vignettes: problems with PDF compaction
[Env: OS: Win Xp; R 2.15.2; IDE: eclipse/StatET] Each time I update my heplots package, I get warnings from R CMD check on R-Forge, * checking sizes of PDF files under ‘inst/doc’ ... WARNING ‘gs+qpdf’ made some significant size reductions: compacted ‘HE-examples.pdf’ from 739Kb to 366Kb and upon submission to CRAN, a message from maintainers: On CRAN now: but again there were warnings about significant size reductions in PDF compaction, which should really be fixed on your end. however, I am unable to find what to do to fix this on my end. In my package directory, I have the vignette sources all under vignettes/, with copies of the .pdf and .Rnw under inst/doc for historical reasons. [Q: can I now safely delete the copies under inst/doc ?] inst/doc/ HE-examples.pdf HE-examples.Rnw vignettes/ HE-examples.pdf HE-examples.Rnw HE-examples.bib fig/ ... I have qpdf installed: Sys.which(Sys.getenv(R_QPDF, qpdf)) qpdf c:\\Rtools\\bin\\qpdf.exe but, if I try to run it on the vignettes/HE-examples.pdf file, nothing happens: tools::compactPDF(C:/Documents/workspace/heplots/vignettes/HE-examples.pdf) Since vignettes are re-built from sources and then installed into inst/doc, I don't see why PDF compaction cannot be run as part of the build process. That is, if R CMD check --as-cran detects a problem, shouldn't there be some option for R CMD build that would run gs+qpdf to correct it? The idea of vignettes for R packages is a good thing, but, this problem (and others with vignettes) discourages me from using vignettes in packages, a bad thing. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] vignettes: problems with PDF compaction
On 4/21/2013 1:47 PM, Uwe Ligges wrote: Since vignettes are re-built from sources and then installed into inst/doc, I don't see why PDF compaction cannot be run as part of the build process. That is, if R CMD check --as-cran detects a problem, shouldn't there be some option for R CMD build that would run gs+qpdf to correct it? Yes, see R CMD build --help that tells you --compact-vignettes= try to compact PDF files under inst/doc: no (default), qpdf, gs, gs+qpdf, both I meant that perhaps R-Forge and CRAN could *automatically* do the compaction. I *do* run R CMD build on my machine with options --compact-vignettes=qpdf --keep-empty-dirs --resave-data giving the log info: * checking for file 'C:/Documents/workspace/heplots/DESCRIPTION' ... OK * preparing 'heplots': * checking DESCRIPTION meta-information ... OK * installing the package to re-build vignettes * creating vignettes ... OK * compacting vignettes and other PDF files * checking for LF line-endings in source and make files * checking for empty or unneeded directories * looking to see if a 'data/datalist' file should be added * re-saving image files * building 'heplots_1.0-9.tar.gz' However: (a) the heplots_1.0-9.tar.gz source package is built outside of the workspace source tree I sync with R-Forge (b) when I examine the heplots_1.0-9.tar.gz source package, the file heplots/inst/doc/HE-examples has not been modified in size. So, I still don't know how to correct this on my end. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] assignInNamespace to create a setwd() replacement: how to use unlockBinding()?
Thanks, Uwe Yes, that was evil, but like other evil practices, it worked for many R generations. Your suggestion wasn't hard to implement and makes my .Rprofile healthier happier. -Michael On 2/8/2013 9:17 AM, Uwe Ligges wrote: Replacing base functionality is bad practice, since some packages may rely on the actual functionality from base. Why not provide such functions in a private package that masks the base functionality for your interactive work only (and keeps base clean to be used by other packages). Finally, you can load that package in your startup code. Best, Uwe Ligges -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] assignInNamespace to create a setwd() replacement: how to use unlockBinding()?
In my .Rprofile for Windows, I had the following functions defined to
mirror a few features
I miss from linux:
(a) replace setwd() with a version that stashes the current directory so
it can be easily restored
(b) writes a short version of the current R directory to the Windows
title bar: I can always see where I am,
with multiple Rgui windows.
(c) creates a cd() shorthand for setwd(), but with the difference that
cd() acts like cd - under the tcsh shell,
returning to the previously stored directory.
setwd-new.R ##
# .Rprofile functions to set current directory in WindowTitle
#==
# setwd() replacement functions
#==
oldsetwd - base::setwd
utils::assignInNamespace(setwd,
function(dir) {
.lastdir - oldsetwd(dir)
utils::setWindowTitle( short.path(base::getwd()) )
.lastdir
}, base)
# setwd replacement, allowing cd() to be like 'cd -' on unix (return to
last dir)
cd - function(dir) {
if(missing(dir)) dir - .lastdir
.lastdir - base::setwd(dir)
utils::setWindowTitle( short.path(base::getwd()) )
}
short.path - function(dir, len=2) {
np -length(parts - unlist(strsplit(dir, '/')))
parts -rev( rev(parts)[1:min(np,len)] )
dots - ifelse (nplen, '...', '')
paste(dots,paste(parts, '/', sep='', collapse=''))
}
These all worked for all R versions up to R 2.15.0, where it began to
break as follows:
source(setwd-new.R)
Error in utils::assignInNamespace(setwd, function(dir) { :
locked binding of ‘setwd’ cannot be changed
I understand what the error means, and I think that unlockBinding()
somewhere in my code gives a solution,
but I don't see where or how.
I should also add that in my actual .Rprofile, I source these functions
into a local environment attach
so they are always available, but don't clutter up ls()
.my.env - local({
# all my local definitions
})
attach(.my.env)
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept. Chair, Quantitative Methods
York University Voice: 416 736-2100 x66249 Fax: 416 736-5814
4700 Keele StreetWeb: http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
__
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https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] CRAN task views: markdown? better .CSS?
CRAN task views are useful, but they seem difficult to write and maintain because the XML format is rather limited (no sectioning) and the packagelist must be maintained manually. They are also difficult to read because the generated html and .css used are extremely basic, giving an overly dense page. Are there any markdown-like tools for writing a CTV? Is it possible to apply a custom .css to a CTV? -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] CRAN task views: markdown? better .CSS?
On 1/31/2013 12:01 PM, Achim Zeileis wrote: Michael: CRAN task views are useful, but they seem difficult to write and maintain because the XML format is rather limited (no sectioning) What type of sectioning would you like to have? In the HTML part, you can use the usual structuring tools like h*, p, etc. It's not OK. I think you mean the info ... /info section, where I failed to read the vignette sufficiently closely, which talks about using HTML. and the packagelist must be maintained manually. Yes, but I recently started adding tools to help checking this. Hopefully I'll also get round to add some more convenience features for this. Something simple might be a tool to scan the info ... /info section for pkg ... /pkg mentions and just print a new packagelist section to the console. This would avoid having to remember what you added recently and manually add to the packagelist -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Declaring/importing non-exported functions [car] in another package
A new function in my heplots package wants to use a non-exported utility function in the car package, df.terms, but this depends on other non-exported functions. From the Writing R extensions manual, I thought I could do this via (in my NAMESPACE) importFrom(car, car:::df.terms, car:::df.terms.default, car:::is.aliased) but I get: ** preparing package for lazy loading Error : objects 'car:::df.terms', 'car:::df.terms.default', 'car:::is.aliased' are not exported by 'namespace:car' ERROR: lazy loading failed for package 'heplots' \S 1.6.1 of the manual says regarding importFrom(): Using |foo:::f| instead of |foo::f| allows access to unexported objects. This is generally not recommended, as the semantics of unexported objects may be changed by the package author in routine maintenance. Questions: 1. Why doesn't this work? 2. Is my only alternative to copy these functions to my package, also unexported? thx, -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Declaring/importing non-exported functions [car] in another package
On 1/16/2013 11:40 AM, Duncan Murdoch wrote: \S 1.6.1 of the manual says regarding importFrom(): Using |foo:::f| instead of |foo::f| allows access to unexported objects. This is generally not recommended, as the semantics of unexported objects may be changed by the package author in routine maintenance. Questions: 1. Why doesn't this work? I think you misread the manual. It is talking about ways to access functions other than by using importFrom. You can use car:::df.terms in your functions. Thanks for the clarification, but I blame the manual. Could I suggest a change in the manual to make this clearer: Using |foo:::f| directly in a function instead of |foo::f| allows access to unexported objects (rather than in importsFrom()). ... -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Declaring/importing non-exported functions [car] in another package
On 1/16/2013 11:40 AM, Duncan Murdoch wrote:
2. Is my only alternative to copy these functions to my package, also
unexported?
Using car:::df.terms explicitly is another option.
Another possibility is for the car maintainer (John Fox) to export
that function from car.
Hmm. It turns out that this is a bit more complicated, since
car::df.terms is an S3 generic,
relying on car:::df.terms.default().
In my function, I am now using car::: explicitly--
# determine size of intervals [perhaps need importFrom(car,
car:::df.terms, ...) in NAMESPACE?]
if(is.null(df)) {
df - if (Scheffe) sum(car:::df.terms(object)) else 2
}
However, when I removed the definitions of the subsidiary
df.terms.default from my package, R CMD check
complains bitterly:
coefplot(mod, add=TRUE, Scheffe=TRUE, fill=TRUE)
Error in UseMethod(df.terms) :
no applicable method for 'df.terms' applied to an object of class
c('mlm', 'lm')
Calls: coefplot - coefplot.mlm - Anonymous
Execution halted
So, the semantics of importFrom() do not allow non-exported functions (I
still wonder why), and my only direct option is to
copy these functions to my package.
-Michael
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept. Chair, Quantitative Methods
York University Voice: 416 736-2100 x66249 Fax: 416 736-5814
4700 Keele StreetWeb: http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
__
R-devel@r-project.org mailing list
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Re: [Rd] Declaring/importing non-exported functions [car] in another package
On 1/16/2013 12:26 PM, John Fox wrote: Dear Duncan and Michael, My initial reaction is that I'd rather not export these functions from the car package since the package already has many exported functions and the functions in question perform low-level operations that won't be of interest to end users. I recognize, however, the functions (and possibly some others) may be useful in other packages, such as heplots, so I'll think about this some more. This is why I wrote directly to R-devel rather than to you. It is low-level, and doesn't need to be exported. OTOH, it provides an elegant way to provide Sheffe-type intervals ellipses as you do in car::confidenceEllipse, which I copied. best, -Michael Following up on Michael's subsequent message in this thread, I find the current text in Sec. 1.6.1 (Specifying imports and exports) of Writing R Extensions reasonably clear. Best, John On Wed, 16 Jan 2013 11:40:37 -0500 Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-01-16 11:25 AM, Michael Friendly wrote: A new function in my heplots package wants to use a non-exported utility function in the car package, df.terms, but this depends on other non-exported functions. From the Writing R extensions manual, I thought I could do this via (in my NAMESPACE) importFrom(car, car:::df.terms, car:::df.terms.default, car:::is.aliased) but I get: ** preparing package for lazy loading Error : objects 'car:::df.terms', 'car:::df.terms.default', 'car:::is.aliased' are not exported by 'namespace:car' ERROR: lazy loading failed for package 'heplots' \S 1.6.1 of the manual says regarding importFrom(): Using |foo:::f| instead of |foo::f| allows access to unexported objects. This is generally not recommended, as the semantics of unexported objects may be changed by the package author in routine maintenance. Questions: 1. Why doesn't this work? I think you misread the manual. It is talking about ways to access functions other than by using importFrom. You can use car:::df.terms in your functions. 2. Is my only alternative to copy these functions to my package, also unexported? Using car:::df.terms explicitly is another option. Another possibility is for the car maintainer (John Fox) to export that function from car. Duncan Murdoch -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD check: better diagnosis for non-ASCII characters
On 11/28/2012 6:02 AM, Martin Maechler wrote: In any case, I support your suggestion (replacing ::: by :: !) and would definitely volunteer to accept patches and then put such an improvement into R. Thanks, Martin. If you can point me to the source where this is carried out, I can attempt a patch. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] stumped on re-building package vignette
[Env: Win Xp / StatET 2.0 / R 2.15.0] In my heplots package I extended the HE-examples.Rnw vignette under inst/doc. The package passes R CMD check on my machine: * using log directory 'C:/eclipse-3.7/heplots.Rcheck' * using R version 2.15.0 (2012-03-30) * using platform: i386-pc-mingw32 (32-bit) ... * checking sizes of PDF files under 'inst/doc' ... OK * checking installed files from 'inst/doc' ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... 'HE-examples.Rnw' ... OK 'repeated.Rnw' ... OK ... However, on R-Forge and on CRAN, the following error/warning is generated: Mon Jun 4 20:18:22 2012: Checking package heplots (SVN revision 136) ... * using log directory ‘/mnt/building/build_2012-06-04-20-02/RF_PKG_CHECK/PKGS/heplots.Rcheck’ * using R version 2.15.0 Patched (2012-06-03 r59505) * using platform: x86_64-unknown-linux-gnu (64-bit) ... * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘HE-examples.Rnw’ ... [4s/4s] OK ‘repeated.Rnw’ ... [4s/4s] OK [9s/9s] OK * checking re-building of vignette PDFs ... NOTE Error in re-building vignettes: ... Loading required package: car Loading required package: MASS Loading required package: nnet Error: processing vignette 'HE-examples.Rnw' failed with diagnostics: cannot open file 'fig/plot-plastic1.pdf' Execution halted * checking PDF version of manual ... OK I am unable to determine why the file fig/plot-plastic1.pdf cannot be opened. It is in my inst/doc/fig directory is regenerated by the .Rnw file. What could cause this? Second, I have tried manually running tools::compactPDF(HE-examples.pdf) on the .pdf file under inst/doc in the package, but no change is made to the .pdf file. I can't see any way to correct this. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] setting global options for a package
This may be elementary, but I can't find an answer: How can I set up
global options for
some specific arguments to functions in a package which can be easily
changed by the user?
This question relates to the selection of colors used in functions in
several packages (heplots,
genridge), where I want to provide reasonable default values for plots,
but allow users to
change those defaults globally for all plots produced with my functions.
One solution is to use palette() for the default, as in
foo - function(x, col=palette(), ...) {}
but the standard palette is not appropriate for my use, and I'd rather
not hijack more typical uses
Another is to use an explicit list of colors for default, as in
bar - function(x, col=c('red', 'blue', 'brown', 'darkgreen', ...), ...) {}
but this must be overridden each time by someone to wants to change the
defaults.
options() seems like the way to go, but I'm not sure how to implement
this. If I use
a .onLoad function to set some options, will these be created in the
global environment?
If not, how to make them so?
.onLoad - function() {
options(heplot.colors =
c(red, blue, black, darkgreen, darkcyan,magenta,
brown,darkgray))
}
My function could then use
foo - function(x, getOption(heplot.colors), ...) {}
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele StreetWeb: http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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Re: [Rd] uncompressed saves warning
On 3/21/2012 1:22 PM, Uwe Ligges wrote: What is the equivalent R command to compress these files in my project tree? Michael, if you use R CMD build --resave-data to build the tar archive, the versions therein are recompressed. But AFAIK, in StatET, R CMD build builds a separate .tar.gz file under c:/eclipse, and does not affect the project directory where these files are stored and sync'd with R-Forge. Otherwise, you can also open the files and resave them via save() and appropriate arguments. I exported the .rda files to c:/R/data and ran load(gfrance.rda) load(gfrance85.rda) save(gfrance, file=gfrance.RData, compress=xz) Error in xzfile(file, wb, compression = 9) : cannot open the connection In addition: Warning message: In xzfile(file, wb, compression = 9) : cannot initialize lzma encoder, error 5 Why doesn't this work? save(gfrance, file=gfrance.RData, compress=TRUE) The above works, but only compresses a 300K file to 299K Or use resaveRdaFiles() in package tools to runn it on a whole folder automatically. sessionInfo() R version 2.14.1 (2011-12-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] p3d_0.02-4 mgcv_1.7-13 car_2.0-12 nnet_7.3-1 rgl_0.92.798 vcd_1.2-13 colorspace_1.1-1 MASS_7.3-17 loaded via a namespace (and not attached): [1] lattice_0.20-6 Matrix_1.0-4 nlme_3.1-103 tools_2.14.1 -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] uncompressed saves warning
[Env: Windows XP Pro / R 2.14.1 / StatET / R-Forge] A package of mine now generates a Warning under R 2.15.0 beta on CRAN checks: * checking data for ASCII and uncompressed saves ... WARNING Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress gfrance.rda 300Kb179Kb xz gfrance85.rda295Kb176Kb xz What is the equivalent R command to compress these files in my project tree? -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R-devel now triggers nags on notes from vignettes
I recently submitted a minor update to a CRAN package that passed all CRAN checks ~ two weeks ago. Now, I get the response below from the CRAN-check-daemon R-devel reports * checking installed files from ‘inst/doc’ ... NOTE The following files are already in R: ‘jss.cls’ Please remove them from your package. The following files should probably not be installed: ‘sfheaders.sty’ The following directories should probably not be installed: ‘fig’ Consider the use of a .Rinstignore file: see ‘Writing R Extensions’, or move the vignette sources from ‘inst/doc’ to ‘vignettes’. Please fix. I added a .Rinstignore file to my project, (at top level, same as DESCRIPTION) containing inst/doc/fig/ inst/doc/jss.cls inst/doc/sfheaders.sty and re-submitted to CRAN, but the same nag notes return again. How to fix? And, why has the CRAN-check-daemon suddenly gotten so picky about NOTEs, particularly from vignettes? -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb:http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] nobs() and logLik()
On 1/20/2012 1:42 AM, Berwin A Turlach wrote: One reason that I can see for people to use zero weights rather than 'subset' is that fitted() and predict() in the former case readily produce fitted values for the observations that received a zero weight. Another is that including the case of zero weights naturally allows a variety of simple robust methods via a weight function that descends to 0. A discontinuity at 0 in the handling of weights prevents this use. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R package BibTex entries: looking for a more general solution
On 12/19/2011 2:02 AM, Renaud Gaujoux wrote: Hi, I actually adapted and integrated this feature into Achim's -- nice -- function (posted on r-help). Romain included it a couple of weeks ago into the bibtex package as function write.bib, and submitted the update to CRAN, but some NOTEs in the check delayed its availability on CRAN. You can still install and try out the new version with: install.packages(bibtex, repos=http://R-Forge.R-project.org;) Keys for multiple citations are generated as pkgname%i, which might not be ideal, but works ok though. It might be better not number the first (main) citation. Romain, I think I will submit a patch for this. Hope this helps. Thanks, Renaud I now have a working function, Rpackages.bib() that is roughly equivalent to your write.bib() and other related material at http://euclid.psych.yorku.ca/SCS/Private/Rbibs/ Also, see the document http://euclid.psych.yorku.ca/SCS/Private/Rbibs/Rpkg-test.pdf which reports some problems perl fixes for the generated bibentries. These might be incorporated into the functions to make the resulting bibtex files directly usable. Your bibtex package seems the most natural place for this. Also, write.bib() doesn't seem to work unless you pass a list of package names. write.bib() Error in is(entry, bibentry) : argument entry is missing, with no default write.bib(NULL) Error in write.bib(NULL) : Invalid argument `entry`: expected a bibentry object or a character vector of package names. best, -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R package BibTex entries: looking for a more general solution
Back in 2010 I raised this issue, and there was some discussion,
https://stat.ethz.ch/pipermail/r-devel/2010-November/058987.html
The goal, then, as now is to have a way to produce a bibtex-clean .bib
file (i.e., not requiring
manual editing except in unusual circumstances) reflecting installed
packages
for use in writing where one often needs/wants to cite all packages used
in a given article.
Achim wrote the function below which largely does this job, quite
nicely now that most
DESCRIPTION files now contain Authors@R fields. However, something
changed since
R 2.11.1 when I tried this last, so that the function no longer
generates keys for packages
which contain *more than one citation*.
I've tried debugging with browser(), but can't figure out how to make
the lines around FIXME
work. Can someone help?
You can see the result from this at
http://euclid.psych.yorku.ca/SCS/Private/Rbibs/Rpackages-2.14.0.bib
The function is also at:
# Original code by Achim Zeileis, 16 Dec 2009, R-help
# Added: support header and preamble
Rpackages.bib - function(filename = paste(Rpackages-,getRversion(),
.bib, sep=),
header=TRUE, preamble=NULL, suppress.warnings=TRUE, verbose = TRUE)
{
## installed packages
pkgs - unique(installed.packages()[,1])
if (suppress.warnings) warn - options(warn=-1)
bibs - lapply(pkgs, function(x) try(toBibtex(citation(x
if (suppress.warnings) options(warn)
n.installed - length(bibs)
## omit failed citation calls
ok - !(sapply(bibs, class) == try-error)
pkgs - pkgs[ok]
bibs - bibs[ok]
n.converted - sum(ok)
## unify to list of Bibtex
bibs - lapply(bibs, function(x) if(inherits(x, Bibtex)) list(x)
else x)
## FIXME: add bibtex keys to each entry [the line below does not work!!]
pkgs - lapply(seq_along(pkgs), function(i) if(length(bibs[[i]]) 1)
paste(pkgs[i], 1:length(bibs[[i]]), sep = ) else pkgs[i])
pkgs - do.call(c, pkgs)
bibs - do.call(c, bibs)
for(i in seq_along(pkgs)) bibs[[i]][1] -
gsub({,, paste({, pkgs[i], ,, sep = ), bibs[[i]][1], fixed
= TRUE)
if(header) header - gsub(^, %, toLatex(sessionInfo()))
output - file(filename, a)
cat(header, preamble, sep='\n', file=output, append=TRUE)
## write everything to a single .bib file
writeLines(do.call(c, lapply(bibs, as.character)), con=output)
close(output)
if(verbose) cat(Converted, n.converted, of, n.installed,
package citations to BibTeX,
\nResults written to file, filename, \n)
## return Bibtex items invisibly
invisible(bibs)
}
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele StreetWeb: http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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Re: [Rd] How to deal with package conflicts
On 11/25/2011 9:10 AM, Terry Therneau wrote: The ridge() function was put into the survival package as a simple example of what a user could do with penalized functions. It's not a serious function, and I'd be open to any suggestions for change. Actually, for any L2 penalty + Cox model one is now better off using coxme as the maximization process is much better thought out there. I'd be happy to remove ridge from survival -- except that there are bound to be lots of folks using the function and any such changes (even good ones) to the survival package are fraught with peril. Duncan provided one suggestion: make ridge() an S3 generic, and rename ridge() to ridge.coxph(), but this won't work, since you use ridge() inside coxph() and survreg() to add a penalty term in the model formula. Another idea might be simply to not export ridge(), but I have the feeling this will break your R CMD checks. Alternatively, my particular problem (wanting to use car::vif in my package documentation) would be solved if John Fox considered making making survival a Suggests: package rather than a Depends: one. This might work, since survival is only referenced in car by providing Anova() methods for coxph models. I think all of this raises a general issue of unintended consequences of package bloat, where (a) Depends: packages are forced to load by require()/library(), whether they are really needed or not; (b) There is nothing like require(car, depends=FALSE) to circumvent this; (c) Once a require()'d package is loaded, it cannot be unloaded; (d) AFAIK, there is no way for a package author to override the masking of functions or data provided by other other packages, except by using mypackage::myfun() calls. To me this seems to be a flaw in the namespace mechanism. best, -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] How to deal with package conflicts
In my genridge package, I define a function ridge() for ridge
regression, creating objects of class 'ridge'
that I intend to enhance.
In a documentation example, I want to use some functions from the car
package. However, that package
requires survival, which also includes a ridge() function, for coxph
models. So, once I require(car)
my ridge() function is masked, which means I have to use the awkward
form below in my .Rd files.
ridgemod - genridge::ridge(...)
I tried to detach survival, but that doesn't work:
detach(package:survival)
Error: package ‘survival’ is required by ‘car’ so will not be detached
I don't see any solution to this, other than
(a) renaming my ridge() to something else -- don't want to do this
(b) use \dontrun{} for the examples that use car
Or, is there some other way?
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele StreetWeb: http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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[Rd] NAMESPACES for data only packages
the NEWS file for R-devel says * Even data-only packages without *R* code need a namespace and so may need to be installed under *R* 2.14.0 or later. but what should this contain? Can it simply be an empty NAMESPACE file? I assume that data does not have to be exported. -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] CRAN: How to list a non-Sweave doc under Vignettes: on package page?
On 11/6/2011 7:41 PM, Henrik Bengtsson wrote:
Hi,
is it possible to have non-Sweave vignettes(*) in inst/doc/ be listed
under 'Downloads' on CRAN package pages? For instance, in my R.rsp
package I have a inst/doc/report.pdf (part of the source *.tar.gz)
that is not detected/listed. The PDF is not based on a Sweave
vignette but an *.tex.rsp vignette that is dynamically created via
inst/doc/Makefile. It is listed
(*) BTW, can the term vignette be used for any inst/doc/ document,
or should it be reserved for Sweave+LaTeX-based documents?
I have a related problem/question and a request to R-Core to consider
relaxing the requirements for vignettes when, for one reason or another,
they cannot be built entirely via Sweave. In such cases, perhaps
package authors can provide alternative metadata in the form of an
00index.html or something similar to allow such vignettes to be
more visible.
Those who face this problem would then be able to figure out a
Makefile or manual way to maintain the metadata file. What would be
required to implement this?
In my case, my Guerry package has a vignette, inst/doc/MultiSpat.pdf,
originally built entirely with Sweave. However, the vignette require()d
a package only on R-Forge, which the author does not wish
to release to CRAN. At some point, ~ R 2.10, this triggered a
WARNING/ERROR from the CRAN check daemon, in spite of the fact that the
vignette .Rnw file contained the following hack designed to make sure
that all necessary packages were available anywhere:
\subsection{Installation and loading of required packages}
Several packages must be installed to run the different analyses:
ni0, fig=F, eval=TRUE, echo=TRUE, debug=TRUE, results=hide, include
=FALSE, width=7, height=7=
pkg - c(maptools,spdep,ade4,Guerry,spacemakeR)
inst.pkg - row.names(installed.packages())
pkg2inst - pmatch(pkg,inst.pkg)
if(any(is.na(pkg2inst[1:4])))
install.packages(pkg[which(is.na(pkg2inst[1:4]))],repos=http://cran.at.r-project.org;)
if(is.na(pkg2inst[5]))
install.packages(spacemakeR, repos=http://R-Forge.R-project.org;)
library(maptools)
library(ade4)
library(spdep)
library(spacemakeR)
library(Guerry)
@
However, this hack was deemed unacceptable for a CRAN package vignette.
In the end, the only solution that would satisfy the CRAN check daemon
was to delete the source inst/doc/MultiSpat.Rnw file from the package.
Consequently, the .pdf vignette remains in the package, but it is not
listed as a vignette on CRAN, nor found via vignette()
best,
-Michael
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele StreetWeb: http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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Re: [Rd] NOTE: unstated dependencies in examples
On 10/13/2011 11:34 AM, Uwe Ligges wrote:
I looked at the code and since this is not that trivial to change, I
think we can well live with typing
grep -r gplots ./man
which is not too hard to run on the source package, I believe.
Best wishes,
Uwe
Yes, that's quite easy, if I wanted to search for files mentioning
gplots. However, the NOTE was misleading:
'library' or 'require' calls not declared from:
gplots sp
suggesting that I had used a function from those packages somewhere
without a library() or require(). It turned out that I had just omitted
those packages from the Suggests: line in DESCRIPTION. So,
perhaps it would be more informative to say:
'library' or 'require' calls not declared in Depends: or Suggests: from:
gplots sp
-Michael
On 13.10.2011 03:00, Yihui Xie wrote:
You have this in Jevons.Rd:
# show as balloonplots
if (require(gplots)) {
and this in Snow.Rd:
%\dontrun{
library(sp)
It will certainly be helpful if R CMD check can provide more
informative messages (in this case, e.g, point out the Rd files).
Regards,
Yihui
--
Yihui Xiexieyi...@gmail.com
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA
On Wed, Oct 12, 2011 at 11:33 AM, Michael Friendlyfrien...@yorku.ca
wrote:
Using R 2.13.1, I am now getting the following NOTE when I run R CMD
check
on my HistData
package
* checking for unstated dependencies in examples ... NOTE
'library' or 'require' calls not declared from:
gplots sp
Under R 2.12.x, I didn't get these notes.
I have ~ 25 .Rd files in this package, and AFAICS, every example uses
library or require for the
functions used; the DESCRIPTION file has the long list of Suggests,
which
previously was sufficient
for packages used in examples.
Suggests: gtools, KernSmooth, maps, ggplot2, proto, grid, reshape, plyr,
lattice, ReadImages, car
But I have no way to find the .Rd file(s) that triggered this note.
What is the tool used in R CMD check to make this diagnosis? It would be
better
if this reported the .Rd file(s) that triggered this note.
Is it possible that this note could be specious?
-Michael
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street Web: http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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--
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Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele StreetWeb: http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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[Rd] NOTE: unstated dependencies in examples
Using R 2.13.1, I am now getting the following NOTE when I run R CMD check on my HistData package * checking for unstated dependencies in examples ... NOTE 'library' or 'require' calls not declared from: gplots sp Under R 2.12.x, I didn't get these notes. I have ~ 25 .Rd files in this package, and AFAICS, every example uses library or require for the functions used; the DESCRIPTION file has the long list of Suggests, which previously was sufficient for packages used in examples. Suggests: gtools, KernSmooth, maps, ggplot2, proto, grid, reshape, plyr, lattice, ReadImages, car But I have no way to find the .Rd file(s) that triggered this note. What is the tool used in R CMD check to make this diagnosis? It would be better if this reported the .Rd file(s) that triggered this note. Is it possible that this note could be specious? -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R license for a derived data-only package
I'm looking for guidance or advice about the R license to use in preparing a package containing the Baseball Database from http://baseball1.com/statistics/ My main purpose is to make it available to students in a course, and to develop it with others I'd like to put it on R-Forge, and then perhaps make it public on CRAN. However, the page above bears a very restrictive copyright notice and limited license: This database is copyright 1996-2010 by Sean Lahman. A license is granted for individual use for research purposes. It may not be re-distributed without permission. Any commercial use, or other dissemination of the database in part or in whole is prohibited. Use of this database constitutes acceptance of these terms. I've written several times to the author asking permission for my intended wider use, but have received no reply. What makes this perplexing is that I am apparently free to distribute this by sending links in an email or posting them on a web page, so that others actually download them for personal use. The R package, however would be considered a derived work, I think, since it contains .RData files I created and .Rd documentation. Does the original limited license apply to this? AFAICS, none of the R licenses described at: http://www.r-project.org/Licenses/ seem to cover this situation, although they seem to apply to the R package, not the data on which it is based. The TeX archive CTAN defines a wider range of licenses, including a bunch of non-free ones, http://ctan.mirror.rafal.ca/help/Catalogue/licenses.html But I don't know if any of these are acceptable in R packages (e.g., will pass R CMD check). I'd rather not have to consult a lawyer, so any guidance is welcome. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] CRAN packages maintained by you
It is A Good Thing to regularize Authors and Maintainers of packages, particularly for citation() and toBibTex(). Could I add a suggested TODO item for the maintainer of package.skeleton and friends to help reinforce this for new packages: - Please add appropriate templates for Author@R in the skeleton DESCRIPTION file generated, indicating the proper format as well as the use of role= to signal the creator and maintainer. - a comment to see ?person for descriptions of fields wouldn't hurt either best, -Michael On 8/8/2011 9:46 AM, Kurt Hornik wrote: Dear maintainers, This concerns the packages CITAN ENmisc Formula MSBVAR RExcelInstaller RcmdrPlugin.mosaic Rd2roxygen Rz SGP betareg expectreg fastcluster glmc gptk heplots pxR sideChannelAttack sp spacetime trapezoid vcd maintained by one of you. I see that you have added Author@R fields providing enhanced information on package authors to your DESCRIPTION files, which since R 2.12.0 is used for auto-generating citations. In current r-devel, we have finally added functionality for also auto-generating package DESCRIPTION Author and Maintainer fields from the enhanced information if needed [i.e., existing fields will not be overwritten]. However, in the process of this the field was renamed to 'Authors@R', so please change your DESCRIPTION files accordingly. In doing so, pls note that to auto-generate Maintainer fields the Authors@R fields need to provide authors with a maintainer (cre) role and an email address. Currently, packages CITAN MSBVAR SGP fastcluster glmc gptk heplots sideChannelAttack sp spacetime trapezoid do not specify the package maintainer in their Authors@R field. (Note that to take advantage of the new auto-generation functionality, you need to rename to Authors@R, remove the DESCRIPTION Author and Maintainer fields in the package sources, and then run R CMD build from a current version of r-devel.) Best -k -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Consistency of messages from R CMD {check,build,install}
A minor gripe/request: Could all R CMD package tools not at the very least be consistent in indicating when they are done, as in * DONE (packagename) or at least * DONE R CMD build leaves one hanging, not knowing whether it has completed or it is time to get another coffee. * checking for file 'C:/Documents/workspace/heplots/DESCRIPTION' ... OK * preparing 'heplots': * checking DESCRIPTION meta-information ... OK * installing the package to re-build vignettes * creating vignettes ... OK * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building 'heplots_0.9-8.tar.gz' Some checking/building processes take a while, so it would also be nice if more of the info lines ended with ... OK tia, -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] system.file() to read a text file from a vignette
[Env: R 2.12.2, WinXp] In a vignette for the vcdExtra package, I had a text file, tv.dat under data/, that I used in the vignette as tv1,results=verbatim= tv.data-read.table(system.file(data,tv.dat,package=vcdExtra)) head(tv.data,5) @ I was told that this now generates a warning for non-Rdata files in R CMD check. But I'm now confused about where to put this and how to use system.file() in the vignette to read it. The R-exts.pdf says The R working directory for all vignette tests in R CMD check is the installed version of the ‘doc’ subdirectory. Make sure all files needed by the vignette (data sets, . . . ) are accessible by either placing them in the ‘inst/doc’ hierarchy of the source package, or using calls to system.file(). So, I moved this file to inst/doc/extdata/tv.dat, and changed the vignette to tv1,results=verbatim= tv.data-read.table(system.file(inst,doc,extdata,tv.dat,package=vcdExtra)) head(tv.data,5) @ But I get the error: Error: processing vignette 'vcd-tutorial.Rnw' failed with diagnostics: chunk 23 (label=tv1) Error in read.table(system.file(inst, doc, extdata, tv.dat, package = vcdExtra)) : no lines available in input How can I fix this? -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] system.file() to read a text file from a vignette
On 3/23/2011 10:21 AM, Duncan Murdoch wrote: Everything in the inst directory is moved up a level when it is installed. So you shouldn't mention inst in its path. I discovered this by error-and-trial. ?system.file is mute on this. Perhaps R-ext.pdf could make this explicit by saying The R working directory for all vignette tests in R CMD check is the installed version of the doc subdirectory. Make sure all files needed by the vignette (data sets, . . . ) are accessible by either placing them in the inst/doc hierarchy of the source package, or using calls to system.file(), *noting that the inst directory is moved up a level when it is installed and should not be mentioned in the path used in system.file().* -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] aperm() should retain class of input object
* contourplot.array* dotplot.array* [7] duplicated.arraylevelplot.array*unique.array -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb:http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] aperm() should retain class of input object
aperm() was designed for multidimensional arrays, but is also useful for
table objects, particularly
with the lattice, vcd and vcdExtra packages. But aperm() was designed
and implemented before other
related object classes were conceived, and I propose a small tune-up to
make it more generally useful.
The problem is that aperm() always returns an object of class 'array',
which causes problems for methods
designed for table objects. It also requires some package writers to
implement both .array and .table
methods for the same functionality, usually one in terms of the other.
Some examples of unexpected, and initially perplexing results (when only
methods for one class are implemented)
are shown below.
library(vcd)
pairs(UCBAdmissions, shade=TRUE)
UCB - aperm(UCBAdmissions, c(2, 1, 3))
# UCB is now an array, not a table
pairs(UCB, shade=TRUE)
There were 50 or more warnings (use warnings() to see the first 50)
# fix it, to get pairs.table
class(UCB) - table
pairs(UCB, shade=TRUE)
Of course, I can define a new function, tperm() that does what I think
should be the expected behavior:
# aperm, for table objects
tperm - function(a, perm, resize = TRUE) {
result - aperm(a, per, resize)
class(result) - class(a)
result
}
But I think it is more natural to include this functionality in aperm()
itself. Thus, I propose the following
revision of base::aperm(), at the R level:
aperm - function (a, perm, resize = TRUE, keep.class=TRUE)
{
if (missing(perm))
perm - integer(0L)
result - .Internal(aperm(a, perm, resize))
if(keep.class) class(result) - class(a)
result
}
I don't think this would break any existing code, except where someone
depended on coercion to an array.
The drop-in replacement for aperm would set keep.class=FALSE by default,
but I think TRUE is more
natural.
FWIW, here are the methods for table and array objects
from my current (non-representative) session.
methods(class=table)
[1] as.data.frame.table barchart.table* cloud.table*
contourplot.table* dotplot.table*
[6] head.table* levelplot.table*pairs.table*
plot.table* print.table
[11] summary.table tail.table*
Non-visible functions are asterisked
methods(class=array)
[1] anyDuplicated.array as.data.frame.array as.raster.array*
barchart.array* contourplot.array* dotplot.array*
[7] duplicated.arraylevelplot.array*unique.array
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele StreetWeb:http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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Re: [Rd] warning creating an as.array method in a package
I found a solution to this problem, but don't understand why it was necessary. In a clean workspace, I get: methods(as.array) [1] as.array.default showMethods(as.array) Function as.array: not a generic function So, I just added the generic definition to my package, making with warnings go away. as.array - function(x, ...) UseMethod(as.array) as.array.loddsratio - function (x, log=x$log, ...) drop(array(coef(x, log = log), dim = dim(x), dimnames=dimnames(x))) Yet, help(as.array) says: as.array is a generic function for coercing to arrays. The default method does so by attaching a dim attribute to it. It also attaches dimnames if x has names. Is this a documentation error? sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.11.1 On 12/9/2010 10:05 AM, Michael Friendly wrote: I posted on this topic to r-help, but never got a sufficient answer, so I'm reposting here. [Env: R 2.11.1, Win Xp, using Eclipse/StatET] In a package I'm working on, I want to create as.matrix() and as.array() methods for a particular kind of object (log odds ratios). These are returned in a loddsratio object as the $coefficients component, a vector, but really reflect an underlying (R-1)x(C-1)xstrata array, whose attributes are contained in other components. These are all properly declared in the NAMESPACE as S3 methods, ... S3method(dim, loddsratio) S3method(dimnames, loddsratio) S3method(print, loddsratio) S3method(vcov, loddsratio) S3method(as.matrix, loddsratio) S3method(as.array, loddsratio) Yet, when I run R CMD check, R CMD build, etc. or even load the package, I get the warning, library(vcdExtra) Loading required package: vcd Loading required package: MASS Loading required package: grid Loading required package: colorspace Loading required package: gnm Warning message: found an S4 version of ‘as.array’ so it has not been imported correctly showMethods(as.array) Function: as.array (package base) x=ANY x=Matrix But as.array does show up as a method for my class: methods(class=loddsratio) [1] as.array.loddsratio* as.data.frame.loddsratio* [3] as.matrix.loddsratio* coef.loddsratio* [5] confint.loddsratio* dim.loddsratio* [7] dimnames.loddsratio* print.loddsratio* [9] vcov.loddsratio* Non-visible functions are asterisked Is there some work-around so I can have an S3 as.array() method in my package and avoid this warning? -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] warning creating an as.array method in a package
I posted on this topic to r-help, but never got a sufficient answer, so I'm reposting here. [Env: R 2.11.1, Win Xp, using Eclipse/StatET] In a package I'm working on, I want to create as.matrix() and as.array() methods for a particular kind of object (log odds ratios). These are returned in a loddsratio object as the $coefficients component, a vector, but really reflect an underlying (R-1)x(C-1)xstrata array, whose attributes are contained in other components. These are all properly declared in the NAMESPACE as S3 methods, ... S3method(dim, loddsratio) S3method(dimnames, loddsratio) S3method(print, loddsratio) S3method(vcov, loddsratio) S3method(as.matrix, loddsratio) S3method(as.array, loddsratio) Yet, when I run R CMD check, R CMD build, etc. or even load the package, I get the warning, library(vcdExtra) Loading required package: vcd Loading required package: MASS Loading required package: grid Loading required package: colorspace Loading required package: gnm Warning message: found an S4 version of ‘as.array’ so it has not been imported correctly showMethods(as.array) Function: as.array (package base) x=ANY x=Matrix But as.array does show up as a method for my class: methods(class=loddsratio) [1] as.array.loddsratio* as.data.frame.loddsratio* [3] as.matrix.loddsratio* coef.loddsratio* [5] confint.loddsratio* dim.loddsratio* [7] dimnames.loddsratio* print.loddsratio* [9] vcov.loddsratio* Non-visible functions are asterisked Is there some work-around so I can have an S3 as.array() method in my package and avoid this warning? -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Request: kronecker to get a sep= argument
kronecker, with make.dimnames=TRUE uses a hardwired sep=: in the line
tmp - outer(dnx[[i]], dny[[i]], FUN = paste, sep = :)
For an application in which dimnames arise from an n-way array, where
different dimensions have
different roles, and I would like to be able to use kronecker in the form
kronecker(A, B, make.dimnames=TRUE, sep='/')
All this requires is to change the following two lines:
kronecker - function (X, Y, FUN = *, make.dimnames = FALSE, sep=: ...)
{
...
tmp - outer(dnx[[i]], dny[[i]], FUN = paste, sep = sep)
}
Otherwise, I have to reproduce the logic inside kronecker() in my
application function.
-Michael
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele StreetWeb: http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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[Rd] R package BibTex entries: looking for a more general solution
== Summary ==
* Problem: BibTeX entries extracted from R packages via citation()
require too much manual editing to be
of general use.
* Proposal: Date: fields should be made mandatory in package DESCRIPTION
files, perhaps
beginning with warnings from R CMD check
* Proposal: Package authors should be encouraged to use a (new)
Contributors: field in the DESCRIPTION file
rather than packing all information into the Author: field, which at
present cannot often be parsed by BibTeX.
* Files: All test files referred to here can be found at
http://euclid.psych.yorku.ca/SCS/Private/Rbibs/
== Details ==
Around 16 Dec. 2009, I queried R-help about automating the extraction of
citation()s from R packages. The stimulus
was that some journals, notably JSS, now require a reference and
citation of every R package mentioned,
and it is a pain to create these manually, no less maintain them for
current versions.
The result of that query was a function, Rpackage.bibs() by Achim
Zeileis that I have been using ever since.
Code in: http://euclid.psych.yorku.ca/SCS/Private/Rbibs/Rpackages.bib.R
On one current system I get the following:
Rpackage.bibs(file=Rpackages-R.2.11.1.bib)
Converted 230 of 230 package citations to BibTex
Results written to file Rpackages-R.2.11.1.bib
Warning messages:
1: In citation(x) :
no date field in DESCRIPTION file of package 'codetools'
2: In citation(x) :
no date field in DESCRIPTION file of package 'gridBase'
3: In citation(x) : no date field in DESCRIPTION file of package 'iplots'
See:
http://euclid.psych.yorku.ca/SCS/Private/Rbibs/Rpkg-test.pdf
for the result of processing this .bib file with latex/bibtex using the
jss.bst bibliography style
I'm writing to R-Devel because the DESCRIPTION and inst/CITATION files
in R packages provide the
basic data used in citation() and any methods based on this, and yet the
information in these files is
often insufficient to generate well-formed BibTeX entries for use in
vignettes and publications.
One easy case is illustrated above, where 3 packages have no Date: field
so the BibTeX gets no
year = {},
and references get printed as Murrell, P () for gridBase. (In my
original test under R 2.9.1, there where
~ 20 such warnings.) Thus, I propose that Date: be a required field in
DESCRIPTION files, and
R CMD check complain if this is not found.
The more difficult case has to do with the Author: field in the
DESCRIPTION file (when no CITATION file is present)
People can write whatever they want here, and the result looks sort of
OK when printed by citation(), but confuses
BibTeX mightly. One example:
citation(akima)
To cite package ‘akima’ in publications use:
Fortran code by H. Akima R port by Albrecht Gebhardt aspline function
by Thomas Petzoldt petzo...@rcs.urz.tu-dresden.de enhancements and
corrections by Martin Maechler (2009). akima: Interpolation of
irregularly spaced data. R package version 0.5-4.
http://CRAN.R-project.org/package=akima
A BibTeX entry for LaTeX users is
@Manual{,
title = {akima: Interpolation of irregularly spaced data},
author = {Fortran code by H. Akima R port by Albrecht Gebhardt aspline
function by Thomas Petzoldt petzo...@rcs.urz.tu-dresden.de
enhancements and corrections by Martin Maechler},
year = {2009},
note = {R package version 0.5-4},
url = {http://CRAN.R-project.org/package=akima},
}
ATTENTION: This citation information has been auto-generated from the
package DESCRIPTION file and may need manual editing, see
‘help(citation)’ .
Yes, the ATTENTION note does say that manual editing may be necessary,
but I think a worthy goal would be
to try to reduce the need for this.
One simple way to do that would be to support an extra Contributions:
field in the DESCRIPTION file,
so that Authors: can be more cleanly separated for the purpose of
creating well-structured BibTeX.
Perhaps others have better ideas.
-Michael
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele StreetWeb:http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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