Displaying 20 results from an estimated 3000 matches similar to: "Automating citations in Sweave"
2011 Dec 16
2
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
2009 Dec 11
1
Creating bibtex file of all installed packages?
Hi
is there an easy and fast way, to generate a BibTeX file of all installed /
loaded packages and R?
I know about toBibtex(citation()) to extract the BibTeX for a single
package, but how can I generate a file containg citations for all installed
/ loaded packages?
Cheers,
Rainer
--
NEW GERMAN FAX NUMBER!!!
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology,
UCT),
2012 Nov 22
2
BibTeX entries in CITATION file
Dear List,
While trying to define a customised CITATION file for a package,
following R-exts, I realised that if I use only one 'citEntry' I got
both a text description and a BibTex entry for the package, as for the
'nlme' package:
--------------------------
citation('nlme')
To cite package 'nlme' in publications use:
Jose Pinheiro, Douglas Bates, Saikat
2010 Nov 03
3
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
2007 Feb 05
1
Build error with last R-devel tarball
Hi,
On Windows, with last R-devel tarball (r40647) from
ftp://ftp.stat.math.ethz.ch/Software/R/R-devel_2007-02-04.tar.gz
I get the following build error:
E:\biocbld\bbs-2.0-bioc\R\src\gnuwin32> make
...
...
---------- Making package utils ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
installing R files
Error in namespaceExport(ns, exports) :
2013 Oct 04
0
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
2008 Nov 17
1
CITATION file with multiple citEntry(): no BibTeX produced by citation()
[Using R 2.8.0 / Win XP / ]
I just added a CITATION file to the heplots package--- appended below.
From the document ion for ?CITATION, there can be *one or more* calls to
citEntry() within the CITATION file, and each should produce an object
of class "citation".
With just a single citEntry(), citation produces the expected output,
with BibTeX entry:
>
2012 Aug 06
1
bibtex::read.bib -- extracting bibentry keys
I have two versions of a bibtex database which have gotten badly out of
sync. I need to find find all the entries in
bib2 which are not contained in bib1, according to their bibtex keys.
But I can't figure out how to extract a list of the bibentry keys in
these databases.
A minor question: Is there someway to prevent read.bib from ignoring
entries that do not contain all required fields?
2014 Mar 14
1
Problems building package vignette: Sweave requires multiple passes to build document.
Dear R-devel,
Question:
How can I get Sweave to recognize that the \thebibliography section
is already created and generate the vignette pdf with a single pass? Or
is there a way to let R CMD build know that Sweave needs to be run twice?
If (1) is not possible, any suggestions how to auto-generate a
crude generic bibtex .bib file from my existing document?
Background:
I maintain
2019 May 29
0
Making a package CITATION file from BibTeX
On Thu, 30 May 2019, Dr Gregory Jefferis wrote:
> Dear Colleagues,
>
> I would like to provide a CITATION file for my package nat.nblast [1].
>
> I have the correct citation in BibTeX format [2]. How can I convert this
> BibTeX to the format needed by R for a package CITATION file (I have a
> lot of other packages needing citations ...).
(1) You can use read.bib() from the
2013 Jan 22
1
file.system() in packages
Hello. R-devel, r61697.
I am having difficulty interpreting section 1.4 "Writing package
vignettes" of the R-exts manual. Specifically, I want to use
system.file() in some of my packages to locate a bib file,
uncertainty.bib, which is part of the emulator package. I only want
to maintain a single .bib file.
R-exts says: "All other files needed to re-make the vignette PDFs
(such
2019 May 29
3
Making a package CITATION file from BibTeX
Dear Colleagues,
I would like to provide a CITATION file for my package nat.nblast [1].
I have the correct citation in BibTeX format [2]. How can I convert this
BibTeX to the format needed by R for a package CITATION file (I have a
lot of other packages needing citations ...).
I think what I need is the opposite of RefManageR::toBiblatex [3]. This
seems like it should be a common need, so I
2008 Oct 28
1
Sweave, Bibtex, package references
Dear all,
I'm a big fan and happy user of the Sweave package for routine reporting.
From inside a .Rnw script, I'd like to produce the references in bibtex
format for each package loaded in the environment, write them in a .bib
file and load them back from the
\bibliography{bibliography} statement.
Is this feasible?
Any help would be greatly appreciated!
Thanks in advance,
Paolo
2009 Sep 08
1
makefile for sweave
Hello, I have the following makefile. The problem is that the bibliography
doesn t work. Any help would be appreciated! I really don t don t what to
do..:-(
# The sources of the report (tex, Rnw and other files (e.g. bib, idx))
TEX_CMPS = Report problem
RNW_CMPS = prop1 prop2 ExeExps
OTHER = Report.bib
# The name of the report to produce
all: Report.pdf
code: $(RNW_CMPS:=.R)
clean:
rm
2017 Sep 08
0
post_processor in rmarkdown not working
That is strange. Another function in the same package
(INBOmd::inbo_rapport) uses the same trick. I actually started by copying
the post_processor() from that function. INBOmd::inbo_rapport() works both
with and without BibTex. Working examples are source/inbo_rapport and
source/inbo_rapport_basic from https://github.com/inbo/inbomd_examples.
Note that you need some extra work after installing
2006 Jan 29
1
Citation of R packages
The bibtex citations provided by citation() do not
work all that well in cases where there is no printed
document to reference:
(1) A version field is needed, as the note field is
required for other purposes, currently trying to
sort out nuances that cannot be sorted out in the
author list (author, compiler, implementor of R version,
contributor, ...) and maybe giving a cross-reference
to a book
2017 Sep 07
2
post_processor in rmarkdown not working
On 07/09/2017 2:04 PM, Duncan Murdoch wrote:
> On 07/09/2017 10:11 AM, Thierry Onkelinx wrote:
>> Dear Duncan,
>>
>> Thanks for chiming in. Could you explain how you set debug() on
>> post_processor()? I've tried adding debug(post_processor) to
>> rsos_article() or adding debug(post_processor) when after post_processor
>> was defined in the debugger.
2002 Jul 17
1
editing Sweave files in xemacs with ess (noweb), auctex and reftex
I am having some trouble getting reftex, in particular the bibtex
related features, to work properly in xemacs when editing text in Sweave
files. I have added
(defun Rnw-mode ()
(noweb-mode)
(if (fboundp 'R-mode)
(setq noweb-default-code-mode 'R-mode)))
(add-to-list 'auto-mode-alist '("\\.Rnw\\'" . Rnw-mode))
(add-to-list 'auto-mode-alist
2010 Jun 28
2
How to run Bibtex with pdfLatex in StatEt/MikTex on Windows ?
Hello,
I'm running R2.10, Eclipse, StatEt and MikTex 2.8 to create Sweave
documents, and everything seems to work great, until today...
I was trying to add citations from a Bibtex file, but I just got [?]
citations. However, if I open the .tex file that StatEt created in
MikTex and run the latex+bibtex+pdflatex command, the citations are present.
Does anyone know how to either configure
2009 Dec 11
12
Literature analysis
Dear all,
i am new in R. I am writing a review paper about batteries. However, i
am interested in analyzing all the papers by keywords, author,
references and year.
This could be done by "refviz" a software, which is only running on
windows machines and which is not free.
So my question to you is, is it somehow possible to write a script that
can do all of this work?
And if yes, with