使用 knitcitations 在 RMarkdown 文档中包含参考书目
Including Bibliography in RMarkdown document with use of the knitcitations
我正在尝试使用 knitcitations 并将参考书目添加到我在 R Studio 中起草的 R Markdown 文档中。我文档的 header 如下所示：
---
title: "Some Title"
author: "Me"
date: "September 2015"
bibliography: bibliography.bib
output:
pdf_document:
highlight: tango
number_sections: yes
toc: yes
---
我想使用以下代码在最后添加参考书目：
```{r generateBibliography, echo=FALSE, eval=TRUE, message=FALSE, warning=FALSE}
require("knitcitations")
cleanbib()
options("citation_format" = "pandoc")
read.bibtex(file = "bibliography.bib")
```
参考文件bibliography.bib具有以下内容：
@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}
}
但是，生成的输出显示为注释，而不是书目条目：
文件是用这段代码编译的：
"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
为简洁起见，我将路径更改为 _paper 和 _paper。
当我试图遵循 advice on including bibliography in RStudio 时，生成的文档根本没有书目条目。因此我的问题是，我在哪里犯了错误以及在 RStudio 中工作时如何强制生成书目条目？
编辑
根据非常有用的评论，理想情况下我想避免在附件中明确指出引用的作品。事实上，我有兴趣包括参考书目，其中包括一些被引用的作品以及与主要文档相关但未在文档中明确引用的论文。
这是最小的工作示例：
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}
}
控制台输出
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.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
If you want to include items in the bibliography without actually citing them in the body text, you can define a dummy nocite metadata field and put the citations there:
---
nocite: |
@item1, @item2
...
@item3
In this example, the document will contain a citation for item3 only, but the bibliography will contain entries for item1, item2, and item3.
上面的整个块（从 --- 到 ...）可以放在代码中的任何位置。 @abichat 更喜欢将其放在 YAML 之后或参考部分中。
如果你想在bibtex文件中包含所有引用，你可以使用frankyan这里提到的
---
title: 'My Title'
author: "Me me me me!"
output: pdf_document
bibliography: references.bib
nocite: '@*'
---
@* 是所有引用的通配符。
要获取书目条目而不是类似 "comment" 的样式，请在块头中使用 results="asis"，即
```{r generateBibliography, results="asis", echo=FALSE}
require("knitcitations")
cleanbib()
options("citation_format" = "pandoc")
read.bibtex(file = "bibliography.bib")
```
我正在尝试使用 knitcitations 并将参考书目添加到我在 R Studio 中起草的 R Markdown 文档中。我文档的 header 如下所示：
---
title: "Some Title"
author: "Me"
date: "September 2015"
bibliography: bibliography.bib
output:
pdf_document:
highlight: tango
number_sections: yes
toc: yes
---
我想使用以下代码在最后添加参考书目：
```{r generateBibliography, echo=FALSE, eval=TRUE, message=FALSE, warning=FALSE}
require("knitcitations")
cleanbib()
options("citation_format" = "pandoc")
read.bibtex(file = "bibliography.bib")
```
参考文件bibliography.bib具有以下内容：
@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}
}
但是，生成的输出显示为注释，而不是书目条目：
文件是用这段代码编译的：
"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
为简洁起见，我将路径更改为 _paper 和 _paper。
当我试图遵循 advice on including bibliography in RStudio 时，生成的文档根本没有书目条目。因此我的问题是，我在哪里犯了错误以及在 RStudio 中工作时如何强制生成书目条目？
编辑
根据非常有用的评论，理想情况下我想避免在附件中明确指出引用的作品。事实上，我有兴趣包括参考书目，其中包括一些被引用的作品以及与主要文档相关但未在文档中明确引用的论文。
这是最小的工作示例：
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}
}
控制台输出
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.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
If you want to include items in the bibliography without actually citing them in the body text, you can define a dummy nocite metadata field and put the citations there:
---
nocite: |
@item1, @item2
...
@item3
In this example, the document will contain a citation for item3 only, but the bibliography will contain entries for item1, item2, and item3.
上面的整个块（从 --- 到 ...）可以放在代码中的任何位置。 @abichat 更喜欢将其放在 YAML 之后或参考部分中。
如果你想在bibtex文件中包含所有引用，你可以使用frankyan这里提到的
---
title: 'My Title'
author: "Me me me me!"
output: pdf_document
bibliography: references.bib
nocite: '@*'
---
@* 是所有引用的通配符。
要获取书目条目而不是类似 "comment" 的样式，请在块头中使用 results="asis"，即
```{r generateBibliography, results="asis", echo=FALSE}
require("knitcitations")
cleanbib()
options("citation_format" = "pandoc")
read.bibtex(file = "bibliography.bib")
```