references.bib.bak

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@Manual{boettiger2014knitcitations,
  Title                    = {knitcitations: Citations for knitr markdown files},
  Author                   = {Carl Boettiger},
  Note                     = {R package version 1.0.5},
  Year                     = {2014},

  Url                      = {http://CRAN.R-project.org/package=knitcitations}
}

@Manual{2014gitbook,
  Title                    = {Gitbook: Build beautiful interactive books using GitHub/Git and Markdown},
  Author                   = {Samy Pesse and Aaron O'Mullan},
  Year                     = {2014},

  Url                      = {http://www.gitbook.io/}
}

@Article{Ray2000,
  Title                    = {Genetic epidemiology of hepatitis C virus throughout egypt.},
  Author                   = {Ray, S. C. and Arthur, R. R. and Carella, A. and Bukh, J. and Thomas, D. L.},
  Journal                  = {J Infect Dis},
  Year                     = {2000},

  Month                    = {Sep},
  Number                   = {3},
  Pages                    = {698--707},
  Volume                   = {182},

  __markedentry            = {[simon:6]},
  Abstract                 = {Hepatitis C virus (HCV) infection is a major health problem in Egypt, where the seroprevalence is 10-20-fold higher than that in the United States. To characterize the HCV genotype distribution and concordance of genotype assessments on the basis of multiple genomic regions, specimens were obtained from blood donors in 15 geographically diverse governorates throughout Egypt. The 5' noncoding, core/E1, and NS5B regions were amplified by reverse transcription-polymerase chain reaction and analyzed by both restriction fragment length polymorphism (RFLP) and phylogenetic tree construction. For the 5' noncoding region, 122 (64\%) of 190 specimens were amplified and analyzed by RFLP: 111 (91\%) were genotype 4, 1 (1\%) was genotype 1a, 1 (1\%) was genotype 1b, and 9 (7\%) could not be typed. Phylogenetic analyses of the core/E1 and NS5B regions confirmed the genotype 4 preponderance and revealed evidence of 3 new subtypes. Analysis of genetic distance between isolates was consistent with the introduction of multiple virus strains 75-140 years ago, and no clustering was detected within geographic regions, suggesting widespread dispersion at some time since then.},
  Doi                      = {10.1086/315786},
  Institution              = {Division of Infectious Diseases, Baltimore, MD 21205, USA. sray@jhmi. edu},
  Keywords                 = {Blood Donors; Egypt, epidemiology; Genotype; Hepacivirus, genetics; Hepatitis C, epidemiology/genetics; Humans; Phylogeny; Polymorphism, Restriction Fragment Length; RNA Replicase, genetics; Reverse Transcriptase Polymerase Chain Reaction; Seroepidemiologic Studies; Viral Envelope Proteins, genetics; Viral Nonstructural Proteins, genetics},
  Language                 = {eng},
  Medline-pst              = {ppublish},
  Owner                    = {simon},
  Pii                      = {JID000477},
  Pmid                     = {10950762},
  Timestamp                = {2015.05.22},
  Url                      = {http://dx.doi.org/10.1086/315786}
}

@Manual{wickham2015devtools,
  Title                    = {devtools: Tools to Make Developing R Packages Easier},
  Author                   = {Hadley Wickham and Winston Chang},
  Note                     = {R package version 1.7.0},
  Year                     = {2015},

  Url                      = {http://CRAN.R-project.org/package=devtools}
}

@Manual{xie2015knitr,
  Title                    = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
  Author                   = {Yihui Xie},
  Note                     = {R package version 1.10},
  Year                     = {2015},

  Url                      = {http://yihui.name/knitr/}
}