Inclure la bibliographie dans le document RMarkdown avec l'utilisation des tricotages
J'essaie d'utiliser knitcitations et d'ajouter une bibliographie au document R Markdown que je rédige dans R Studio. L'en-tête de mon document ressemble à ceci:
---
title: "Some Title"
author: "Me"
date: "September 2015"
bibliography: bibliography.bib
output:
pdf_document:
highlight: tango
number_sections: yes
toc: yes
---
Je veux ajouter la bibliographie à la fin en utilisant le code suivant:
```{r generateBibliography, echo=FALSE, eval=TRUE, message=FALSE, warning=FALSE}
require("knitcitations")
cleanbib()
options("citation_format" = "pandoc")
read.bibtex(file = "bibliography.bib")
```
Le fichier de référence bibliography.bib a le contenu suivant:
@article{debarsy_testing_2010,
title = {Testing for spatial autocorrelation in a fixed effects panel data model},
volume = {40},
issn = {0166-0462},
url = {http://www.sciencedirect.com/science/article/pii/S0166046210000451},
doi = {10.1016/j.regsciurbeco.2010.06.001},
abstract = {The aim of this paper is to assess the relevance of spatial autocorrelation in a fixed effects panel data model and in the affirmative, to identify the most appropriate spatial specification as this appears to be a crucial point from the modeling perspective of interactive heterogeneity. Several {LM} test statistics as well as their {LR} counterparts, which allow discriminating between endogenous spatial lag versus spatially autocorrelated errors, are therefore proposed. Monte Carlo experiments show their good finite sample performance. Finally, an empirical application is provided in the framework of the well-known Feldstein–Horioka puzzle.},
pages = {453--470},
number = {6},
journaltitle = {Regional Science and Urban Economics},
shortjournal = {Regional Science and Urban Economics},
author = {Debarsy, Nicolas and Ertur, Cem},
urldate = {2015-10-01},
date = {2010-11},
keywords = {Panel data, Spatial autocorrelation, Test statistics},
file = {complex_zotero_path}
}
@article{lamichhane_spatial-temporal_2015,
title = {Spatial-Temporal Modeling of Neighborhood Sociodemographic Characteristics and Food Stores},
volume = {181},
issn = {0002-9262, 1476-6256},
url = {http://aje.oxfordjournals.org/content/181/2/137},
doi = {10.1093/aje/kwu250},
abstract = {The literature on food stores, neighborhood poverty, and race/ethnicity is mixed and lacks methods of accounting for complex spatial and temporal clustering of food resources. We used quarterly data on supermarket and convenience store locations from Nielsen {TDLinx} (Nielsen Holdings N.V., New York, New York) spanning 7 years (2006–2012) and census tract-based neighborhood sociodemographic data from the American Community Survey (2006–2010) to assess associations between neighborhood sociodemographic characteristics and food store distributions in the Metropolitan Statistical Areas ({MSAs}) of 4 {US} cities (Birmingham, Alabama; Chicago, Illinois; Minneapolis, Minnesota; and San Francisco, California). We fitted a space-time Poisson regression model that accounted for the complex spatial-temporal correlation structure of store locations by introducing space-time random effects in an intrinsic conditionally autoregressive model within a Bayesian framework. After accounting for census tract–level area, population, their interaction, and spatial and temporal variability, census tract poverty was significantly and positively associated with increasing expected numbers of supermarkets among tracts in all 4 {MSAs}. A similar positive association was observed for convenience stores in Birmingham, Minneapolis, and San Francisco; in Chicago, a positive association was observed only for predominantly white and predominantly black tracts. Our findings suggest a positive association between greater numbers of food stores and higher neighborhood poverty, with implications for policy approaches related to food store access by neighborhood poverty.},
pages = {137--150},
number = {2},
journaltitle = {American Journal of Epidemiology},
shortjournal = {Am. J. Epidemiol.},
author = {Lamichhane, Archana P. and Warren, Joshua L. and Peterson, Marc and Rummo, Pasquale and Gordon-Larsen, Penny},
urldate = {2015-10-01},
date = {2015-01-15},
langid = {english},
pmid = {25515169},
keywords = {food availability, food stores, intrinsic conditionally autoregressive model, neighborhood characteristics, Poverty, sociodemographic factors, spatial-temporal modeling, supermarkets},
file = {complex_zotero_path}
}
Cependant, la sortie produite apparaît sous forme de commentaires et non comme entrée bibliographique: 
Le fichier est compilé avec ce code:
"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS _paper.md --to latex
--from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures
--output _paper.pdf --filter pandoc-citeproc --table-of-contents --toc-depth 2 --template "path_\latex\default.tex"
--number-sections --highlight-style tango --latex-engine pdflatex --variable "geometry:margin=1in" --bibliography bibliography.bib
Par souci de concision, j'ai changé les chemins d'accès en _paper et _paper.
Quand j'ai essayé de suivre les conseils pour inclure la bibliographie dans RStudio le document a été produit sans aucune entrée bibliographique. D'où ma question, où je fais l'erreur et comment puis-je forcer la génération d'entrées bibliographiques lorsque je travaille dans RStudio?
Éditer
Après des commentaires très utiles, je voudrais idéalement éviter d'indiquer explicitement les œuvres citées dans le document ci-joint. En fait, je suis intéressé à inclure une bibliographie qui comprendra certains ouvrages cités mais aussi des articles qui sont pertinents pour le document principal mais qui ne sont pas explicitement référencés dans le document.
Le documentation pandoc dit:
Si vous souhaitez inclure des éléments dans la bibliographie sans les citer réellement dans le corps du texte, vous pouvez définir un champ de métadonnées factices nocites et y placer les citations:
---
nocite: |
@item1, @item2
...
@item3
Dans cet exemple, le document contiendra une citation pour l'élément3 uniquement, mais la bibliographie contiendra des entrées pour l'élément1, l'élément2 et l'élément3.
Voici un exemple de travail minimal:
papier.Rmd
---
title: 'My Title'
author: "Me me me me!"
output: pdf_document
bibliography: references.bib
---
Application written in the R programming language [@RCoreTeam] using the Shiny framework [@Chang2015].
# REFERENCES
references.bib
@Misc{Chang2015,
Title = {shiny: Web Application Framework for R. R package version 0.12.1},
Author = {Chang, W. and Cheng, J. and Allaire, JJ. and Xie, Y. and McPherson, J. },
Year = {2015},
Type = {Computer Program},
Url = {http://CRAN.R-project.org/package=shiny}
}
@Article{RCoreTeam,
Title = {R: A Language and Environment for Statistical Computing},
Author = {{R Core Team}},
Year = {2015},
Type = {Journal Article},
Url = {http://www.R-project.org}
}
Sortie console
processing file: paper.Rmd
"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS paper.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures --output paper.pdf --filter pandoc-citeproc --template "C:\Users\tdadaev\Documents\R\win-library\3.2\rmarkdown\rmd\latex\default.tex" --highlight-style tango --latex-engine pdflatex --variable "geometry:margin=1in" --bibliography references.bib
output file: paper.knit.md
Output created: paper.pdf
paper.pdf 
Si vous souhaitez inclure toutes les références dans le fichier bibtex, vous pouvez utiliser, comme mentionné par frankyan ici
---
title: 'My Title'
author: "Me me me me!"
output: pdf_document
bibliography: references.bib
nocite: '@*'
---
Le @* est un caractère générique pour toutes les références.