ackage:quantreg"), sep = ", ")
will print the list in a form suitable for including in the export()
directive in your NAMESPACE file. Just delete the names that are meant
for internal use only.
Duncan Murdoch
Roger Koenker
r.koen...@ucl.ac.uk<mailto:r.koen...@ucl.ac.uk>
the record: that was Henrik Singmann's suggestion, I just
agreed with it.
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On 30/06/2019 8:08 p.m., Abby Spurdle wrote:
In that case, I was wrong.
And I must apologize...
In saying that, good to see Windows out performing Linux on the command
line...
That's going to set the bees abuzz...
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e in the memory manager. (But see
http://developer.r-project.org/Refcnt.html for some plans. That
document is from about 5 years ago; I don't know the current state.)
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+ 1
+ # browser()
+ x = NextMethod()
+ return(x)
+ }
>
> df <- as.data.frame(matrix(1:20, nrow=5))
> class(df) <- c("MYCLASS","data.frame")
> counttt
[1] 0
So there's something else going on in your system. Maybe post
sessionInfo()?
Duncan Murdoch
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ment view. Do you see this when running R
from the command line?
Duncan Murdoch
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Environment panel. If this concerns you then you
should contact RStudio.
Now I see it!
Duncan Murdoch
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e requesting is listed as having been done in the NEWS
for 3.6.0...
Duncan Murdoch
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t;test"
> iconv(s, to="UTF-16",toRaw=TRUE)
[[1]]
[1] fe ff 00 74 00 65 00 73 00 74
I don't know if SQL Server can handle raw vectors; I'd try to get it to
accept UTF-8 input instead.
Duncan Murdoch
Thanks,
Michael
——
sessionInfo()
#> R version 3.6.1 (2019
kage names?
The tarball names separate the package name from the version number
using an underscore. There is code that is written to assume there is
at most one underscore, e.g. .check_package_CRAN_incoming in
src/library/tools/R/QC.r.
That code could be changed, but so could the propose
2-018/index.html
Looking at the article now, it's not as entertaining as I remember his
presentation was, but it makes good points about the value of consistency.
Duncan Murdoch
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named "FuzzyNumbers.Ext.2", whose tarball is
FuzzyNumbers.Ext.2_3.2.tar.gz, so I think we've already lost that game.
Duncan Murdoch
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On 09/08/2019 4:37 p.m., Gabriel Becker wrote:
Duncan,
On Fri, Aug 9, 2019 at 1:17 PM Duncan Murdoch <mailto:murdoch.dun...@gmail.com>> wrote:
On 09/08/2019 2:41 p.m., Gabriel Becker wrote:
> Note that this proposal would make mypackage_2.3.1 a valid
*package name*,
s) or a newline. I don't
know how many of those there are, but the list would include at least
semicolon, newline, }, ), ], and maybe others.
Duncan Murdoch
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was general agreement that it would be a good idea to add
some warnings. News for R 3.6.0 includes this:
"Experimentally, setting environment variable _R_CHECK_LENGTH_1_LOGIC2_
will lead to warnings (or errors if the variable is set to a ‘true’
value) when && or || encounter and use a
ons in short
scripts. That's how I've always recommended large projects be
organized. You don't want a long script for anything, and you don't
want multiple source files unless they're in a package.
Duncan Murdoch
This question was motivated largely by this discussi
t for anything worth keeping.
Duncan Murdoch
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,
but it appears you have an object new to 3.6.0 that needs something that
doesn't exist in 3.5.0. The solution is probably to use 3.6.x to read
that file, and then save it with "version=2" as an argument. That
should cause it to use the older format.
Duncan Murdoch
Ideally,
On 26/08/2019 1:58 p.m., William Dunlap wrote:
Duncan Murdoch wrote:
> Scripts are for throwaways, not for anything worth keeping.
I totally agree and have a tangentially relevant question about the <<-
operator. Currently 'name <<- value' means to look up the env
t should be a whole number
value (talking about 0, 1, "2 or more", not about what would happen with
options(warn = pi/2), for example.
In older versions, options(warn = pi/2) is treated the same as
options(warn = 1), and in the new version, it is displayed as 1 as well.
Duncan Murdoc
.ch/R-manual/R-devel/doc/html/NEWS.html
And if you want to follow along, you can get it as an RSS feed from
<http://developer.r-project.org/RSSfeeds.html>. If you don't know what
an RSS feed is, see feedly.com.
Duncan Murdoch
On Sun, 2019-09-29 at 08:33 -0400, Duncan Murdoch
kage in Suggests, your package should work (perhaps
with some limitations) without the suggested one. Unfortunately for
you, the limitation "can't rebuild the vignettes" is incompatible with
building the package, but I don't think there's anything you can put in
the DE
Is the documentation out of date? That quote appears to have been
written in 2002.
Duncan Murdoch
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On 01/10/2019 4:58 a.m., Serguei Sokol wrote:
Le 30/09/2019 à 16:17, Duncan Murdoch a écrit :
There's a StackOverflow question
https://stackoverflow.com/q/22024082/2554330 that references this text
from ?missing:
"Currently missing can only be used in the immediate body of the
fun
ed at all unless they want to update Rgui or
R.app or command line R.
Duncan Murdoch
If
iris %>% group_by(Species) %>% summarize(mean_sl = mean(Sepal.Length)) %>%
filter(mean_sl > 5)
were *parsed* as, for example, into
local({
. = group_by(iris, Species)
._
nt. In that case, the `.` binding, if
any, would be restored to its original value in `on.exit()` (or through
unwind-protection if implemented in C).
That makes sense.
Duncan Murdoch
Best,
Lionel
On 6 Oct 2019, at 01:50, Gabriel Becker wrote:
Hi all,
I think there's some nuance
On 07/10/2019 8:38 a.m., Lionel Henry wrote:
On 7 Oct 2019, at 13:47, Duncan Murdoch <mailto:murdoch.dun...@gmail.com>> wrote:
On 07/10/2019 4:22 a.m., Lionel Henry wrote:
Hi Gabe,
There is another way the pipe could go into base R that could not be
done in package space an
f the generic.
----
Duncan Murdoch
I am implementing S3 dispatch for generic methods in environments that are
not
packages. I am trying to emulate the R package namespace mechanism by
having a
“namespace” environment that de
, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘Package2’
It can’t find it. However, it does not seem like the correct thing is to have
R_LIBS_USER=/myHome/libraries
Why not?
Duncan Murdoch
How should I go about this?
Thanks in advance!
[[alternative HTML
on to base R?
I am happy to work with someone from the R core team (if you wish) and
suggest an implementation in C.
That seems like it would sometimes be a useful function, and maybe
someone will point out a package that already contains it. But if not,
why would it belong in
)'s set.seed(324) is bad practice.
Duncan Murdoch
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efore any serious
simulations.)
I think it's pretty common in example code, and that's justifiable. But
it could be avoided by using withr::with_seed() or something equivalent.
Duncan Murdoch
You can fairly easily work around that by saving and restoring .Random.seed. I
wonde
quot;cols"
is defined there as a local variable. The "drop" argument shouldn't be
used until it is. (There's a call to "missing(drop)" early in the
source that doesn't count: it doesn't evaluate "drop", it just checks
whether it is specified by the caller.)
Duncan Murdoch
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On 03/11/2019 6:43 p.m., Rolf Turner wrote:
On 4/11/19 10:31 AM, Duncan Murdoch wrote:
On 03/11/2019 4:11 p.m., Rolf Turner wrote:
I recently tried to write a new method for "[", to be applied to data
frames, so that the object returned would retain (all) attributes of t
tent.
Hadley it right that restoring the original attributes of a vector (list
or atomic) after subsetting is unsafe.
Right, so Rolf should only restore attributes that are ones he added in
the first place. Unknown attributes should be left alone.
Duncan Murdoch
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n(pkgs, ..., force = FALSE) {
if (!force) {
pkgs <- Filter(Negate(requireNamespace), pkgs
utils::install.packages(pkgs, ...)
}
You might want to make this more elaborate, e.g. doing update.packages()
on the ones that exist. But really, isn't the problem with the script
yo
ALSE.
If you didn't change the default, it wouldn't help your example: the
badly written script would run with force=TRUE, and wouldn't benefit at all.
Duncan Murdoch
Package managers like pip (python), conda (python), yum (CentOS), apt
(Ubuntu), and apk (Alpine) are all &
then
use update.packages() all the time instead of install.packages() the
first time and update.packages() subsequent times.
That makes more sense to me than the "force = FALSE" proposal.
Duncan Murdoch
Bill Dunlap
TIBCO Software
wdunlap tibco.com <http://tibco
d script (by deleting
one line) is the solution to the problem, not fixing R with a multistage
series of revisions, tests, etc.
Duncan Murdoch
and more so when installing lots of packages conditionally, e.g.
if (requireNamespace("foo")) install.packages("foo")
if (require
") # Creates an object named t2 of class "trackcurve"
# that contains "track"
inherits(t2, "track") # TRUE
"track" %in% class(t2) # FALSE
I can't think of any examples not involving S4.
Duncan Murdoch
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ar with R history: the current revision of R is 77405. That
particular file has been revised 248 times since rev 2.)
I suspect either nobody has noticed it before, or nobody had the nerve
to touch it.
Duncan Murdoch
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efinitely something you should do. Put this into
NAMESPACE:
S3method(print, my1stclass)
and it should be fine.
Duncan Murdoch
A similar problem has function plot, I don't show it here. It leads to
an error message, when plot.default and xy.coords cannot work with the
object for which t
t there, let us
know, and either someone will give you one, or someone will report it
for you.)
As a workaround, I don't see it happening with extend=FALSE, but of
course that might not suit your needs in general.
Duncan Murdoch
Thank you for your consideration,
Johann
On Mon,
age.)
On the other hand, it comes close to working, and it seems like allowing
frequency=0.2 would be a useful addition. I'm going to keep looking,
and see how hard it would be to get this to work properly. If it
doesn't break other things, I may submit this as an enhancement.
D
I've now posted this as an enhancement request:
https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17669
On 06/12/2019 12:35 p.m., Duncan Murdoch wrote:
To R-devel:
I've sent this to Johann privately already; just in case anyone else is
interested in this issue, here's what
est for the presence of DESCRIPTION in the newly created
location), falling back to a copy if things didn't succeed.
Duncan Murdoch
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be used. If you wanted to use
both, you would need a longer x. For example,
> strsplit(c("1:2", "3:4"), split=c(",", ":"), fixed=TRUE)
[[1]]
[1] "1:2"
[[2]]
[1] "3" "4"
The first element is split using "," --
copy
has been updated: it understands the svn revision numbers recorded in
the patch. (Conflicts cause trouble, but no more than any other time.)
This doesn't work so well if you are adding or moving files.
The patch produced in this way is also suitable for including in a bug
repor
is the case for the vast
majority of R-corers.
When I was building for Windows, the workflow required the build to be
in the source tree. Windows systems weren't assumed to be able to run
configure, so all the work it does was done manually for the Rtools tools.
Duncan Murdoch
, and
var(unlist(simulate(lm(x0~1), 1, 1))) is 2.0064. Shouldn't it be 3
= var(mean(x0)) + var(x0) = (2/2) + 2?
That calculation ignores the uncertainty in the estimation of sigma.
Duncan Murdoch
* In the glm example with x1=1,
var(unlist(simulate(glm(x1~1, poisson), 100
On 27/12/2019 10:31 a.m., Spencer Graves wrote:
On 2019-12-27 04:34, Duncan Murdoch wrote:
On 26/12/2019 11:14 p.m., Spencer Graves wrote:
Hello, All:
The default "simulate" method for lm and glm seems to ignore the
sampling variance of the parameter estimates; see the
h proposal it is. Certainly if you don't get action
(or at least discussion) within a few days, any other proposal will be
forgotten.
Duncan Murdoch
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On 06/01/2020 5:19 p.m., neonira Arinoem wrote:
@steve
Seek for online document named "writing R extensions" chapter 2. It tells
You hardly need to look for it online: it is included with every copy
of R. Just run help.start() in R (or look in the menus for the GUI
versions)
hat I get a different error report; it reports this test instead:
if(class(varlist) == "coxmevar")
That appears in a number of places in the coxme source, and clearly
needs to be updated to use inherits().
Duncan Murdoch
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ould be as simple as replacing n by R_forceint(n) in the
k = n - k step.
I think that would break symmetry: you want choose(n, k) to equal
choose(n, n-k) when n is very close to an integer. So I'd suggest the
replacement whenever R_IS_INT(n) is true.
Duncan Murdoch
-pd
On 14 Ja
On 14/01/2020 10:50 a.m., peter dalgaard wrote:
On 14 Jan 2020, at 16:21 , Duncan Murdoch wrote:
On 14/01/2020 10:07 a.m., peter dalgaard wrote:
Yep, that looks wrong (probably want to continue discussion over on R-devel)
I think the culprit is here (in src/nmath/choose.c)
if (k
rmal_lm())
[1] 532614827
> #> [1] 4163
> save_size_qs(normal_ggplot())
[1] 417967987
> #> [1] 857446
> save_size_rds(normal_ggplot())
[1] 532624477
> #> [1] 12895
Duncan Murdoch
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f its many dependencies haven't been updated).
The default should be TRUE, even though this will lead to some packages
being updated unnecessarily, because the cost of an unnecessary update
is so much less than the cost of missing a necessary update.
Dunc
far more users than tables does, so changing the
name of your special functions or the corresponding regular functions
could be a huge headache.
Perhaps there's a way to set a flag before evaluating the function in
the formula, and generate a warning if survival::strata is called wh
On 29/02/2020 4:19 a.m., Ben Bolker wrote:
I think Robin knows about FAQ 7.31/floating point (author of
'Brobdingnag', among other numerical packages). I agree that this is
surprising (to me).
To reframe this question: is there way to get an *exact* ASCII
representation of a numeric value
ll possible without '2)',
but '2)' would allow to use dput(*, control = "All")
which is somewhat easier to readers & writers.
I think 1) is a good idea, and adding something with the meaning of
AllHex seems useful: but that's not a name I'd choose, since
it's the printing that is inconsistent.
Duncan Murdoch
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. However, setting
options(stringsAsFactors = NULL)
reverts to the same behavior as the old options(stringsAsFactors =
TRUE). Is this intentional?
Duncan Murdoch
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for the filename to write to, and have the example write to
tempdir() instead of the current directory?
Duncan Murdoch
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This sounds promising.
Also remember that user-defined macros are possible, so even if you need
a lot of contortions to enter the code, you can simplify it at the Rd level.
Duncan Murdoch
On 30/04/2020 5:50 a.m., Gábor Csárdi wrote:
You can probably already do this using the \if{html
ut{<tt>src="<url-to-your-site>/mathjax/tex-chtml.js">}}
Duncan Murdoch
Best,
Wolfgang
-Original Message-
From: Gábor Csárdi [mailto:csardi.ga...@gmail.com]
Sent: Thursday, 30 April, 2020 11:51
To: Viechtbauer, Wolfgang (SP)
Cc: r-devel
Subject: Re: [Rd] Use o
The tools package is not for users, it's for functions that R uses in
installing packages, checking them, etc. If you want a function for
users, it would belong in utils. But what's wrong with the digest
package? What's the argument that R Core should take this on?
Duncan Mu
ere, since it
works so well as a contributed package already.
Duncan Murdoch
On 05/05/2020 9:11 a.m., Viechtbauer, Wolfgang (SP) wrote:
Hi All,
After some tinkering, and with support from Duncan, I put together a package
that allows for easy inclusion of MathJax equations in Rd files. The packa
eBin equivalents specific to your library wouldn't be
any harder than creating a connection. For those, you will probably
want to work with an "external pointer" (see Writing R Extensions).
Rcpp probably has support for these if you're working in C++.
Duncan Murdoch
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ws(package = "R-3")
table(R3$Version, R3$Category)
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ow fixed. (The issue was that R-devel
on the news machine didn't have rJava installed; the highlighting of
differences is done by some old Java code.)
Duncan Murdoch
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eally old
function is too hard to accommodate, and they should back it out, maybe
by making a new function with the new signature.
Or you could make a new function with the old signature, and use that
instead of apply().
Duncan Murdoch
On 22/05/2020 6:26 a.m., Lukas Lehnert via R-devel w
function(X,
FUN,
bySI = NULL,
...,
simplify = TRUE) {
?
Yes, that sounds like an ideal solution. The docs can say it is ignored
in old versions and passed on in new ones.
Duncan Murdoch
Henrik
On Fri, May 22, 2020 at 6
e interior of the feasible region, but
the minimum may be on the boundary."
The boundary is not in the interior.
Duncan Murdoch
The help page says
The feasible region is defined by ‘ui %*% theta - ci >= 0’,
but the R code for constrOptim reads
if (any(ui %*% theta - ci &l
se code, I thought I'd pass along the offending code. I've
tested the crash on R 2.11.1 (on Linux and Mac), but not in devel
versions of R.
Thanks for posting that. It does still exist on R-devel, and as you
say, it shouldn't. I'll fix it.
Duncan Murdoch
HTH, Rob
riable in the current function.
Since these are just pointers to the environment, this doesn't take up
much space in memory, but when you save the object to disk, a copy of
the whole environment will be made, and that can end up wasting up a lot
of space if the environment contains a lot of th
sing the infix operator syntax. (I think the description in the R
Language Definition suggests this is not legal, since $$ is not a valid
name, but it does currently work and that's unlikely to change.)
Duncan Murdoch
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cal or the system survival library
when I type search(), and .Autoloaded is NULL.
Could you show us the result of .libPaths(), search(), searchpaths() and
sessionInfo()?
Duncan Murdoch
I'm mystified as to how R decided to use that library, and what it was
trying to pull from it. I
th so Windows can find it (there are other tricks,
but they apply at the Windows level, not at the R level).
I haven't tried this, but can't you use Sys.setenv() to change the PATH
to what you want? Presumably you'll want to change it back afterwar
On 10/07/2010 2:33 PM, Paul Johnson wrote:
On Wed, Jul 7, 2010 at 7:12 AM, Duncan Murdoch wrote:
On 06/07/2010 9:04 PM, julian.tay...@csiro.au wrote:
Hi developers,
After some investigation I have found there can be large discrepancies in
the same object being saved as an external
ronment of a function and what the
pointer in a ‘EXTPTRSXP’ points to) is not included in the
calculation."
If you really want to know how much space an object will take when saved,
probably the only reliable way is to save the object and look at how much space
the file takes.
Duncan Murd
s an environment just as a closure
does. In neither case does the print() method tell you about it --
but ?formula does.
I've just changed the default print method for formulas to display the
environment if it is not globalenv(), which is the rule used for
cl
umbering scheme...
Duncan Murdoch
Locale ID:1033
Additional Information 1: 8772
Additional Information 2: 9431192a7274b0ee769861df31ecee58
Additional Information 3: f768
Additional Information 4: 930d06d3f6aed4162dca7601993082f5
Anyone knows if there anything else I ca
g called "userdump", but never tried it.)
Duncan Murdoch
/Henrik
On Mon, Jul 26, 2010 at 1:30 PM, Duncan Murdoch
wrote:
> On 26/07/2010 5:15 AM, Henrik Bengtsson wrote:
>>
>> Just FYI: Problem remains (on same system) with "R version 2.12.0
>> Under de
is shorter and then R.exe doesn't
crash. This is that working PATH:
Thanks, I can reproduce it now. Should be fixable.
Duncan Murdoch
C:\Program Files\Common Files\Microsoft Shared\Windows
Live;c:\Rtools212\bin;c:\Rtools212\perl\bin;c:\Rtools212\MinGW\bin;c:\Rtools\bin;c:\Rtools\per
On 28/07/2010 11:06 AM, Duncan Murdoch wrote:
On 28/07/2010 9:37 AM, Henrik Bengtsson wrote:
> Hi,
>
> by pure luck, I discovered that it has to do with the number of
> characters (or similar) in the Windows system environment variable
> 'PATH'. I used a custom PATH
/ColorBrewer.R
unlink RColorBrewer/R/ residuals.MCMCglmm.R
xyz
That certainly looks bad. I can't reproduce it on Windows; it doesn't
allow that filename. So I'll have to leave this for a Unix-alike user.
Duncan Murdoch
unlink RColorBrewer/R/residuals.MCMCglmm.R
unlink
)))}
else {return(base::t(x))}}
(This fails because of infinite recursion, but I don't quite understand
why).
You should call base::t.default, not base::t. Then this will work. The
same solution fixes the one below, though you won't even need the base::
prefix on t.default.
Duncan M
HTML)
I think it would not be a good idea to put a stub in place of the NEWS
file. Sometimes the stub would be newer than the source NEWS.Rd file
(depending on how the source had been obtained), and make would skip it:
so we'd have to force it to be made every time, necessary or not.
D
e that the starts, then starts, then end the
paragraph, but the has not ended yet.
I don't really understand in html, but I think the correct way would be
--
save.defaults, save.image.defaults:
see save.
--
Michael
What version are you using? I don't see that in current R patc
On 05/08/2010 5:18 PM, Michael Lachmann wrote:
Duncan Murdoch-2 wrote:
What version are you using? I don't see that in current R patched.
I see this in version 2.11.1.
This is the code I ran to generate it:
page <- utils:::.getHelpFile(?options)
tools::Rd2HTML(page,out="t.h
On 05/08/2010 8:46 PM, David B. Thompson, Ph.D., P.E., D.WRE, CFM wrote:
On Aug 5, 2010, at 5:20 PM, Duncan Murdoch wrote:
On 05/08/2010 7:18 PM, David B. Thompson, Ph.D., P.E., D.WRE, CFM wrote:
I'm running R 2.11.1 (MacBook Pro and OS X 10.6.4) and am trying to set a line
type i
On 06/08/2010 7:52 AM, Duncan Murdoch wrote:
On 05/08/2010 8:46 PM, David B. Thompson, Ph.D., P.E., D.WRE, CFM wrote:
On Aug 5, 2010, at 5:20 PM, Duncan Murdoch wrote:
On 05/08/2010 7:18 PM, David B. Thompson, Ph.D., P.E., D.WRE, CFM wrote:
I'm running R 2.11.1 (MacBook Pro and OS X 1
on" in the signature. Slightly unpleasant, though.
You could use formulas for that. If you pass in
formula = ~ x + y*z
then environment(formula) will be the right evaluation environment, and
formula[[2]] will be the unevaluated x + y*z.
Duncan Murdoch
Standardised, simpler syntax lik
he named chunk. I'd like to drop the option, so
that the default behaviour (which has always been equivalent to "expand
= TRUE") would be the only behaviour.
Duncan Murdoch
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On 19/08/2010 3:17 PM, Marc Schwartz wrote:
On Aug 19, 2010, at 2:07 PM, Duncan Murdoch wrote:
> I am trying to improve the error reporting in Sweave documents, so that if
you have a syntax error in a code chunk, it will tell you which line of your input
file contained the error.
>
On 19/08/2010 4:29 PM, Claudia Beleites wrote:
I never used it.
I got curious, though. What would be a situation that benefits of this option?
When I put it in, I thought it would be for people who were writing
about Sweave.
Duncan Murdoch
Maybe a use case could be found by "
or (syntax error at this point, maybe some other kinds of
error in the future) in the <> chunk, but that
chunk wasn't eval'd, mainloop was eval'd. So the error is going to be
reported as occurring in chunk mainloop, but with a line number from
somewhere else in the file. Is t
sn't taken
advantage of in many places. If that is expanded, my Sweave changes
should take advantage of it automatically.
Duncan Murdoch
In a course on "using R" (for beginners),
I would really like to show warnings that code chunks produce.
Currently, the warnings are printed to the c
On 19/08/2010 5:25 PM, Duncan Murdoch wrote:
On 19/08/2010 5:07 PM, Kevin Coombes wrote:
> I use it, frequently. The idea for it goes back to some of Knuth's
> original literate programming ideas for developing weave and tangle when
> he was writing TeX (the program). I want
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