Łącznie z bibliografią w dokumencie RMarkdown przy użyciu podarków

Question

Próbuję użyć knitcitations i dodać bibliografię do dokumentu R Markdown, który kreślę w R Studio. Nagłówek mojego dokumentu wygląda następująco:

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

chcę dodać bibliografii na końcu za pomocą następującego kodu:

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

Plik odniesienia bibliography.bib ma następującą zawartość:

@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} 
} 

Jednak uzyskane wyniki są wyświetlane jako komentarze, a nie jako pozycje bibliograficzne:

plik jest skompilowany z tym kodem:

"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 

Dla zwięzłości, zmieniłem ścieżkę do _paper i _paper.

---

Kiedy próbowałem śledzić advice on including bibliography in RStudio dokument został wyprodukowany bez pozycji bibliograficznych w ogóle. Stąd moje pytanie, , gdzie popełniam błąd i jak mogę wymusić generowanie wpisów bibliograficznych podczas pracy w RStudio?

Edit

Po bardzo użytecznych uwag, idealnie chciałbym uniknąć wyraźnie wskazuje cytowane prace w załączonym dokumencie. W rzeczywistości interesuje mnie uwzględnienie bibliografii, która będzie składać się z cytowanych prac, ale także dokumentów, które są istotne dla głównego dokumentu, ale nie są wyraźnie wymienione w dokumencie.

Answer 1

pandoc documentation mówi:

Jeśli chcesz zawierać elementy w bibliografii bez faktycznie przytaczając je w tekście, można zdefiniować obojętne pola metadanych nocite i umieścić tam cytatów:

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

@item3 

W tym przykładzie Dokument będzie zawierał cytat tylko dla pozycji 3, ale bibliografia będzie zawierała pozycje dla pozycji 1, pozycji 2 i pozycji 3.

Answer 2

Oto minimalne przykład roboczych:

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} 
} 

wyjście 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 

papier.pdf