the - Incluyendo la bibliografía en el documento de RMarkdown con el uso de las prendas de punto

r markdown tutorial pdf

Question

Estoy intentando usar knitcitations y agregar bibliografía al documento R Markdown que estoy redactando en R Studio. El encabezado de mi documento se ve así:

---
title: "Some Title"
author: "Me"
date: "September 2015"
bibliography: bibliography.bib
output:
  pdf_document: 
    highlight: tango
    number_sections: yes
    toc: yes
---

Quiero agregar la bibliografía al final usando el siguiente código:

```{r generateBibliography, echo=FALSE, eval=TRUE, message=FALSE, warning=FALSE}
require("knitcitations")
cleanbib()
options("citation_format" = "pandoc")
read.bibtex(file = "bibliography.bib")
```

El archivo de referencia bibliography.bib tiene el siguiente contenido:

@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}
}

Sin embargo, la salida producida aparece como comentarios, no como entrada bibliográfica:

El archivo se compila con este código:

"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 

Por brevedad, cambié los caminos a _paper y _paper .

Cuando intenté seguir los consejos sobre la inclusión de bibliografía en RStudio, el documento se produjo sin entradas bibliográficas. De ahí mi pregunta, ¿ dónde estoy cometiendo el error y cómo puedo forzar la generación de entradas bibliográficas cuando trabajo en RStudio?

Editar

Siguiendo comentarios muy útiles, idealmente me gustaría evitar indicar explícitamente los trabajos citados en el documento adjunto. De hecho, estoy interesado en incluir bibliografía que constará de algunos trabajos citados, pero también de artículos que son relevantes para el documento principal pero que no se mencionan explícitamente en el documento.

Answer 1

Aquí está el ejemplo de trabajo mínimo:

papel.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

referencias.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}
}

Salida de consola

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

papel.pdf

Answer 2

La documentación pandoc dice:

Si desea incluir elementos en la bibliografía sin citarlos en el texto del cuerpo, puede definir un campo de metadatos nocite ficticios y colocar las citas allí:

---
nocite: |
  @item1, @item2
...

@item3

En este ejemplo, el documento contendrá solo una cita para el artículo 3, pero la bibliografía contendrá entradas para el artículo 1, el artículo 2 y el artículo 3.

Answer 3

Si desea incluir todas las referencias en el archivo bibtex, puede usar, como lo menciona frankyan aquí

---
title: ''My Title''
author: "Me me me me!"
output: pdf_document
bibliography: references.bib
nocite: ''@*''
---

El @* es un comodín para todas las referencias.