Estou tentando usarknitcitations e adicione bibliografia ao documento R Markdown que estou escrevendo no R Studio. O cabeçalho do meu documento fica assim:

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

Quero adicionar a bibliografia no final usando o seguinte código:

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

O arquivo de referênciabibliography.bib tem o seguinte conteúdo:

@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}
}

No entanto, a saída produzida aparece como comentários, não como entrada bibliográfica:

O arquivo é compilado com 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 uma questão de brevidade, mudei os caminhos para_paper e_paper.

Quando tentei seguir oconselhos sobre como incluir bibliografia no RStudio o documento foi produzido sem entradas bibliográficas. Daí minha pergunta,onde estou cometendo o erro e como forçar a geração de entradas bibliográficas ao trabalhar no RStudio?

Editar

Após comentários muito úteis, idealmente, gostaria de evitar indicar explicitamente os trabalhos citados no documento em anexo. De fato, estou interessado em incluir bibliografia que consistirá em alguns trabalhos citados, mas também em documentos relevantes para o documento principal, mas que não sejam explicitamente referenciados no documento.