Я пытаюсь использовать knitcitations и добавить библиографию к документу R Markdown, который я создаю в R Studio. Заголовок моего документа выглядит так:

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

Я хочу добавить библиографию в конце, используя следующий код:

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

Ссылочный файл bibliography.bib имеет следующее содержание:

@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}
}

Однако полученный вывод отображается в виде комментариев, а не в виде библиографической записи:

Файл скомпилирован с этим кодом:

"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 

Для краткости я изменил пути к _paper и _paper.

---

Когда я пытался следовать совету по включению библиографии в RStudio, документ был составлен без библиографических записей вообще. Отсюда мой вопрос: где я делаю ошибку и как заставить генерировать библиографические записи при работе в RStudio?

Изменить

После очень полезных комментариев, в идеале, я бы хотел избежать явного указания цитируемых работ в прилагаемом документе. На самом деле, я заинтересован в том, чтобы включить библиографию, которая будет состоять из некоторых цитируемых работ, а также статей, которые относятся к основному документу, но на которые нет явной ссылки в документе.