web-dev-qa-db-ja.com

ニットを使用してRMarkdown文書に参考文献を含める

knitcitationsを使用し、R Studioで作成中のR Markdownドキュメントに参考文献を追加しようとしています。私のドキュメントのヘッダーは次のようになります。

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

次のコードを使用して、最後に参考文献を追加します。

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

参照ファイルbibliography.bibのコンテンツは次のとおりです。

@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}
}

ただし、生成された出力は書誌事項としてではなくコメントとして表示されます。 sample entries

ファイルは次のコードでコンパイルされます。

"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

簡潔にするために、パスを_paperおよび_paperに変更しました。

RStudioに参考文献を含める際のアドバイス を追おうとしたとき、ドキュメントは参考文献のエントリなしで作成されました。したがって、私の質問、どこで間違いを犯していますか、RStudioで作業しているときに書誌エントリを強制的に生成するにはどうすればよいですか？

編集

非常に有用なコメントに続いて、理想的には、添付文書で引用された作品を明示的に示すことを避けたいと思います。事実、私はいくつかの引用された作品で構成される参考文献だけでなく、主要な文書に関連しているが、文書内で明示的に参照されていない論文も含めることに興味があります。

rlatexrstudior-markdownbibliography
20
Konrad

pandoc documentation 言います：

実際に本文に引用せずに参考文献にアイテムを含めたい場合は、ダミーのnociteメタデータフィールドを定義し、そこに引用を配置できます。

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

@item3

この例では、ドキュメントにはitem3の引用のみが含まれますが、参考文献にはitem1、item2、item3のエントリが含まれます。

17
Ben Bolker

最小限の作業例を次に示します。

paper.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}
}

コンソール出力

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.pdfenter image description here

18
zx8754

Bibtexファイルにall参照を含める場合は、 frankyan で説明されているように使用できます。

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

@*は、すべての参照のワイルドカードです。

3
Rainer