* Working example of org-ref in action?
@ 2014-07-01 11:37 Rainer M Krug
2014-07-01 12:30 ` Joseph Vidal-Rosset
[not found] ` <854myzon2h.fsf@andrew.cmu.edu>
0 siblings, 2 replies; 3+ messages in thread
From: Rainer M Krug @ 2014-07-01 11:37 UTC (permalink / raw)
To: emacs-orgmode
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Hi
I must say org-ref looks really useful to me - I am organising my
references with Mendeley which can zync to a bibtex file, so this is
perfect for me.
I am trying to get into org-ref, but as I haven't used any pure LaTeX
that often, I am struggling with a few things and have two questions:
1) I have a managed to export to html, but I want to use LaTeX - what do
I have to add to the .org file to be able to do this?
2) Is there somewhere a small working example which uses the different
citation formats and exports to LaTeX but also html?
Cheers,
Rainer
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa
Tel : +33 - (0)9 53 10 27 44
Cell: +33 - (0)6 85 62 59 98
Fax : +33 - (0)9 58 10 27 44
Fax (D): +49 - (0)3 21 21 25 22 44
email: Rainer@krugs.de
Skype: RMkrug
PGP: 0x0F52F982
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* Re: Working example of org-ref in action?
2014-07-01 11:37 Working example of org-ref in action? Rainer M Krug
@ 2014-07-01 12:30 ` Joseph Vidal-Rosset
[not found] ` <854myzon2h.fsf@andrew.cmu.edu>
1 sibling, 0 replies; 3+ messages in thread
From: Joseph Vidal-Rosset @ 2014-07-01 12:30 UTC (permalink / raw)
To: Rainer M Krug, John Kitchin; +Cc: Liste-emacs-orgmode@gnu.org
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Hi Rainer, hi John and the list,
In your thread I add this remark for John: when I use jmax starter-kit in
directory different from my usual .emacs.d/ , org-ref seems to work
correctly, but I meet difficulty to add what I'm using : org-article class
for example, and so on. This starter-kit apart, I am unable to install, to
load and to use correctly org-ref . I do not know exactly where I have to
put the org-ref files and how I must configure my init.el , and I do not
want to break my usual .emacs.d configuration just in order to use org-ref.
So, I would be happy to get a solution, because it is true that org-ref
seems to have attractive features. John's work is very impressive, and I
regret to be at the moment unable to enjoy it really.
Best wishes
Jo.
2014-07-01 13:37 GMT+02:00 Rainer M Krug <Rainer@krugs.de>:
> Hi
>
> I must say org-ref looks really useful to me - I am organising my
> references with Mendeley which can zync to a bibtex file, so this is
> perfect for me.
>
> I am trying to get into org-ref, but as I haven't used any pure LaTeX
> that often, I am struggling with a few things and have two questions:
>
> 1) I have a managed to export to html, but I want to use LaTeX - what do
> I have to add to the .org file to be able to do this?
>
> 2) Is there somewhere a small working example which uses the different
> citation formats and exports to LaTeX but also html?
>
> Cheers,
>
> Rainer
>
> --
> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
> Biology, UCT), Dipl. Phys. (Germany)
>
> Centre of Excellence for Invasion Biology
> Stellenbosch University
> South Africa
>
> Tel : +33 - (0)9 53 10 27 44
> Cell: +33 - (0)6 85 62 59 98
> Fax : +33 - (0)9 58 10 27 44
>
> Fax (D): +49 - (0)3 21 21 25 22 44
>
> email: Rainer@krugs.de
>
> Skype: RMkrug
>
> PGP: 0x0F52F982
>
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^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: Working example of org-ref in action?
[not found] ` <854myzon2h.fsf@andrew.cmu.edu>
@ 2014-07-02 16:54 ` Rainer M Krug
0 siblings, 0 replies; 3+ messages in thread
From: Rainer M Krug @ 2014-07-02 16:54 UTC (permalink / raw)
To: John Kitchin; +Cc: emacs-orgmode
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I cc this this to the org mailing list as I have forgotten this the last time.
John Kitchin <jkitchin@andrew.cmu.edu> writes:
> Rainer M Krug <Rainer@krugs.de> writes:
>
> I am not sure I understand what you are asking. To export to LaTeX, you
> just use the regular latex export, e.g. C-c C-e C-b l L will show a
> buffer of the body converted to LaTeX.
Sorry for not being clear. I can export to LaTeX / pdf, but the
references are not found. I am using
latexmk -pvc -pdf ./reftest.tex
to compile the tex file.
I assume I am missing some LaTeX headers which I have to add in org.
reftest.org is as follow:
--8<---------------cut here---------------start------------->8---
# -*- mode: org ; mode:visual-line; -*-
#+TITLE: reftest
#+DATE: \today
#+AUTHOR: Rainer M. Krug
#+EMAIL: Rainer@krugs.de
#+OPTIONS: ':nil *:t -:t ::t <:t H:3 \n:nil ^:t arch:headline
#+OPTIONS: author:t c:nil creator:comment d:(not "LOGBOOK") date:t
#+OPTIONS: e:t email:nil f:t inline:t num:t p:nil pri:nil prop:nil
#+OPTIONS: stat:t tags:t tasks:t tex:t timestamp:t toc:t todo:t |:t
#+DESCRIPTION:
#+KEYWORDS:
#+LANGUAGE: en
#+SELECT_TAGS: export
#+EXCLUDE_TAGS: noexport
#+CREATOR: Emacs 24.3.1 (Org mode beta_8.3)
#+LATEX_CLASS: article
#+LATEX_CLASS_OPTIONS:
#+LATEX_HEADER:
#+LATEX_HEADER_EXTRA:
* Introduction
** Here comes the test
Some test refs ([[cite:Vallet2011,Paquette2011,Lebourgeois2013,Forrester2013]]). And one more [[cite:Vila2013]], plus one more [[cite:Charru2011]].
* References
[[bibliography:~/Documents/Projects/IFN/ProductivityMixedStands/prodMixStands.bib]]
* File Local Variables :noexport:
# Local Variables:
# org-ref-default-bibliography: ~/Documents/Projects/IFN/ProductivityMixedStands/prodMixStands.bib
# reftex-default-bibliography: ~/Documents/Projects/IFN/ProductivityMixedStands/prodMixStands.bib
# End:
--8<---------------cut here---------------end--------------->8---
I attach the .bib file and the resulting pdf
Thanks for any suggestions,
Rainer
>
> E.g.
>
> cite:armiento-2014-high,daza-2014-carbon-dioxid
>
> autocite:daza-2014-carbon-dioxid
>
> [[bibliography:~/Dropbox/bibliography/references.bib]]
>
>
>
> exports to this:
> \cite{armiento-2014-high,daza-2014-carbon-dioxid}
>
> \autocite{daza-2014-carbon-dioxid}
>
> \bibliography{~/Dropbox/bibliography/references}
>
> The rest of the setup is the same as in org-mode, you need to say what
> the Latex class is, what packages to use, etc...
>
>> Hi
>>
>> I must say org-ref looks really useful to me - I am organising my
>> references with Mendeley which can zync to a bibtex file, so this is
>> perfect for me.
>>
>> I am trying to get into org-ref, but as I haven't used any pure LaTeX
>> that often, I am struggling with a few things and have two questions:
>>
>> 1) I have a managed to export to html, but I want to use LaTeX - what do
>> I have to add to the .org file to be able to do this?
>>
>> 2) Is there somewhere a small working example which uses the different
>> citation formats and exports to LaTeX but also html?
>>
>> Cheers,
>>
>> Rainer
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa
Tel : +33 - (0)9 53 10 27 44
Cell: +33 - (0)6 85 62 59 98
Fax : +33 - (0)9 58 10 27 44
Fax (D): +49 - (0)3 21 21 25 22 44
email: Rainer@krugs.de
Skype: RMkrug
PGP: 0x0F52F982
[-- Attachment #1.2: reftest.pdf --]
[-- Type: application/pdf, Size: 69664 bytes --]
[-- Attachment #1.3: reftest.tex --]
[-- Type: application/x-tex, Size: 1045 bytes --]
% Created 2014-07-02 Wed 18:50
\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{fixltx2e}
\usepackage{graphicx}
\usepackage{longtable}
\usepackage{float}
\usepackage{wrapfig}
\usepackage{rotating}
\usepackage[normalem]{ulem}
\usepackage{amsmath}
\usepackage{textcomp}
\usepackage{marvosym}
\usepackage{wasysym}
\usepackage{amssymb}
\usepackage{hyperref}
\tolerance=1000
\usepackage{color}
\usepackage{listings}
\author{Rainer M. Krug}
\date{\today}
\title{reftest}
\hypersetup{
pdfkeywords={},
pdfsubject={},
pdfcreator={Emacs 24.3.1 (Org mode beta_8.3)}}
\begin{document}
\maketitle
\tableofcontents
\section{Introduction}
\label{sec-1}
\subsection{Here comes the test}
\label{sec-1-1}
Some test refs (\cite{Vallet2011,Paquette2011,Lebourgeois2013,Forrester2013}). And one more \cite{Vila2013}, plus one more \cite{Charru2011}.
\section{References}
\label{sec-2}
\bibliography{~/Documents/Projects/IFN/ProductivityMixedStands/prodMixStands}
% Emacs 24.3.1 (Org mode beta_8.3)
\end{document}
[-- Attachment #1.4: prodMixStands.bib --]
[-- Type: application/octet-stream, Size: 10889 bytes --]
Automatically generated by Mendeley Desktop 1.11
Any changes to this file will be lost if it is regenerated by Mendeley.
BibTeX export options can be customized via Preferences -> BibTeX in Mendeley Desktop
@article{Forrester2013,
abstract = {Interactions between plant species can be dynamic, changing spatially and temporally with variability in climatic, soil and stand conditions. We examined how inter- and intra-specific interactions between Abies alba Mill. and Picea abies (L.) Karst. varied with climate, site quality and stand density in the Black Forest of south-western Germany, using spatially explicit neighbourhood indices. The mixing response, a measure of complementarity, was quantified as the increase in growth of individual trees in a mixed-species neighbourhood compared to a mono-specific neighbourhood. Both species benefited from growing in mixed-species neighbourhoods, but this complementarity effect (−60\% to >200\%) depended on climatic conditions, site quality and stand density. Complementarity increased for A. alba with increasing mean maximum temperatures in August, those for P. abies increased with mean minimum temperatures in May and site quality, and in each case the magnitude of the effect was amplified with increasing stand density. Complementarity is often considered to become more important in less productive ecosystems, but this study showed that for the given pair of species, complementarity effects can increase as growing conditions improve. A simple model is proposed that describes how relationships between productivity and complementarity change depending on the resources limiting productivity.},
author = {Forrester, David I. and Kohnle, Ulrich and Albrecht, Axel T. and Bauhus, J\"{u}rgen},
doi = {10.1016/j.foreco.2013.04.038},
file = {:Users/rainerkrug/Documents/Mendeley/Files/Forrester et al/Forrester et al.\_2013\_Complementarity in mixed-species stands of Abies alba and Picea abies varies with climate, site quality and stand.pdf:pdf},
issn = {03781127},
journal = {Forest Ecology and Management},
keywords = {Competition index,Competitive reduction,Individual tree model,Plant–plant interactions},
month = sep,
pages = {233--242},
publisher = {Elsevier B.V.},
title = {{Complementarity in mixed-species stands of Abies alba and Picea abies varies with climate, site quality and stand density}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0378112713002831 http://www.sciencedirect.com/science/article/pii/S0378112713002831},
volume = {304},
year = {2013}
}
@article{Lebourgeois2013,
abstract = {In most dendroecological studies, climate–tree growth relationships are established for trees growing on pure stands. However, response to climate may be affected by inter-species interactions and local constraints, which beg the question of the effect of mixture on tree growth response under various ecological conditions. To assess these effects, climate–tree growth relationships of pure Abies alba stands were compared to those of three different mixtures: A. alba with Fagus sylvatica, with Picea abies and with both species. 151 stands (456 A. alba trees) were sampled in the Vosges mountains in north-eastern France under three contrasted climates, from low altitude and dry conditions (mean precipitation in July <85mm and altitude <600m) to high altitude and humid conditions (P July >115mm and alt. >900m). We sampled adult trees and homogeneous stand conditions to clearly assess differences in sensitivity to climate. Climate–tree growth relationships were evaluated from 12 A. alba chronologies (four mixtures×three climatic conditions) through pointer years and response function analyses. Late previous summer conditions and current summer soil water deficit and temperature played a major role on A. alba growth. Results showed greater sensitivity to temperature at high elevation, and to summer drought at low altitude and under dry conditions. Mixture allowed maintaining a higher level of A. alba growth during extreme climatic events and reduced A. alba response to summer drought especially under the driest contexts. Different facilitation processes may explain mixture effects such as changes in rooting depth, water input by stemflow and rainfall interception. This differentiated functioning of mixed forests highlights their importance for adapting forest management to climate change.},
author = {Lebourgeois, F. and Gomez, N. and Pinto, P. and M\'{e}rian, P.},
doi = {10.1016/j.foreco.2013.04.003},
file = {:Users/rainerkrug/Documents/Mendeley/Files/Lebourgeois et al/Lebourgeois et al.\_2013\_Mixed stands reduce Abies alba tree-ring sensitivity to summer drought in the Vosges mountains, western Europe.pdf:pdf},
issn = {03781127},
journal = {Forest Ecology and Management},
keywords = {Abies alba,Climate–tree growth relationships,Drought,Mixed stand,Temperate forests,Tree-ring},
month = sep,
pages = {61--71},
publisher = {Elsevier B.V.},
title = {{Mixed stands reduce Abies alba tree-ring sensitivity to summer drought in the Vosges mountains, western Europe}},
url = {http://www.sciencedirect.com/science/article/pii/S0378112713002090 http://linkinghub.elsevier.com/retrieve/pii/S0378112713002090},
volume = {303},
year = {2013}
}
@article{Vallet2011,
author = {Vallet, Patrick and P\'{e}rot, Thomas},
file = {:Users/rainerkrug/Documents/Mendeley/Files/Vallet, P\'{e}rot/Vallet, P\'{e}rot\_2011\_Silver fir stand productivity is enhanced when mixed with Norway spruce evidence based on large-scale inventory data.pdf:pdf;:Users/rainerkrug/Documents/Mendeley/Files/Vallet, P\'{e}rot/Vallet, P\'{e}rot\_2011\_Silver fir stand productivity is enhanced when mixed with Norway spruce evidence based on large-scale inventory data.doc:doc;:Users/rainerkrug/Documents/Mendeley/Files/Vallet, P\'{e}rot/Vallet, P\'{e}rot\_2011\_Silver fir stand productivity is enhanced when mixed with Norway spruce evidence based on large-scale inventory d(2).doc:doc;:Users/rainerkrug/Documents/Mendeley/Files/Vallet, P\'{e}rot/Vallet, P\'{e}rot\_2011\_Silver fir stand productivity is enhanced when mixed with Norway spruce evidence based on large-scale inventory d(3).doc:doc},
issn = {11009233},
journal = {Journal of Vegetation Science},
keywords = {abies alba,basal area growth model,mixed-,modelling,over-yielding,picea,species stand},
month = oct,
number = {5},
pages = {932--942},
title = {{Silver fir stand productivity is enhanced when mixed with Norway spruce: evidence based on large-scale inventory data and a generic modelling approach}},
url = {http://doi.wiley.com/10.1111/j.1654-1103.2011.01288.x},
volume = {22},
year = {2011}
}
@article{Vila2013,
abstract = {BACKGROUND: Despite empirical support for an increase in ecosystem productivity with species diversity in synthetic systems, there is ample evidence that this relationship is dependent on environmental characteristics, especially in structurally more complex natural systems. Empirical support for this relationship in forests is urgently needed, as these ecosystems play an important role in carbon sequestration.
METHODOLOGY/PRINCIPAL FINDINGS: We tested whether tree wood production is positively related to tree species richness while controlling for climatic factors, by analyzing 55265 forest inventory plots in 11 forest types across five European countries. On average, wood production was 24\% higher in mixed than in monospecific forests. Taken alone, wood production was enhanced with increasing tree species richness in almost all forest types. In some forests, wood production was also greater with increasing numbers of tree types. Structural Equation Modeling indicated that the increase in wood production with tree species richness was largely mediated by a positive association between stand basal area and tree species richness. Mean annual temperature and mean annual precipitation affected wood production and species richness directly. However, the direction and magnitude of the influence of climatic variables on wood production and species richness was not consistent, and vary dependent on forest type.
CONCLUSIONS: Our analysis is the first to find a local scale positive relationship between tree species richness and tree wood production occurring across a continent. Our results strongly support incorporating the role of biodiversity in management and policy plans for forest carbon sequestration.},
author = {Vil\`{a}, Montserrat and Carrillo-Gavil\'{a}n, Amparo and Vayreda, Jordi and Bugmann, Harald and Fridman, Jonas and Grodzki, Wojciech and Haase, Josephine and Kunstler, Georges and Schelhaas, Martjan and Trasobares, Antoni},
doi = {10.1371/journal.pone.0053530},
file = {:Users/rainerkrug/Documents/Mendeley/Files/Vil\`{a} et al/Vil\`{a} et al.\_2013\_Disentangling biodiversity and climatic determinants of wood production.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
keywords = {Biodiversity,Climate,Europe,Models, Biological,Species Specificity,Trees,Trees: growth \& development,Wood,Wood: growth \& development},
month = jan,
number = {2},
pages = {e53530},
pmid = {23437038},
title = {{Disentangling biodiversity and climatic determinants of wood production.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3577818\&tool=pmcentrez\&rendertype=abstract},
volume = {8},
year = {2013}
}
@article{Paquette2011,
author = {Paquette, Alain and Messier, Christian},
doi = {10.1111/j.1466-8238.2010.00592.x},
file = {:Users/rainerkrug/Documents/Mendeley/Files/Paquette, Messier/Paquette, Messier\_2011\_The effect of biodiversity on tree productivity from temperate to boreal forests.pdf:pdf},
issn = {1466822X},
journal = {Global Ecology and Biogeography},
keywords = {biodiversity and ecosystem functioning,boreal forests,canada,diversity,ecosystem,fertility gradient,forest biomes,functional diversity,phylogenetic,services,temperate forests,tree productivity},
month = jan,
number = {1},
pages = {170--180},
title = {{The effect of biodiversity on tree productivity: from temperate to boreal forests}},
url = {http://doi.wiley.com/10.1111/j.1466-8238.2010.00592.x},
volume = {20},
year = {2011}
}
@article{Charru2011,
author = {Charru, Marie and Seynave, Ingrid and Morneau, Fran\c{c}ois and Rivoire, Micha\"{e}l and Bontemps, Jean-Daniel},
doi = {10.1007/s13595-011-0149-0},
file = {:Users/rainerkrug/Documents/Mendeley/Files/Charru et al/Charru et al.\_2011\_Significant differences and curvilinearity in the self-thinning relationships of 11 temperate tree species assessed f.pdf:pdf},
issn = {1286-4560},
journal = {Annals of Forest Science},
month = nov,
number = {2},
pages = {195--205},
title = {{Significant differences and curvilinearity in the self-thinning relationships of 11 temperate tree species assessed from forest inventory data}},
url = {http://link.springer.com/10.1007/s13595-011-0149-0},
volume = {69},
year = {2011}
}
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2014-07-01 11:37 Working example of org-ref in action? Rainer M Krug
2014-07-01 12:30 ` Joseph Vidal-Rosset
[not found] ` <854myzon2h.fsf@andrew.cmu.edu>
2014-07-02 16:54 ` Rainer M Krug
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