setup.Rnw

<<setup-child,include=FALSE,cache=FALSE,purl=FALSE>>=
library(knitr)
if (!exists("params")) params <- list()
opts_chunk$set(
  cache=TRUE,
  cache.path=paste("tmp","cache",as.character(params$prefix),sep="/"),
  comment=NA,
  echo=TRUE,
  eval=TRUE,
  dev='CairoPNG',
  dev.args=list(bg='transparent'),
  dpi=300,
  error=FALSE,
  fig.align='center',
  fig.height=4,fig.width=6.83,
  fig.lp="fig:",
  fig.path=paste("tmp","figure",as.character(params$prefix),sep="/"),
  fig.pos="h!",
  fig.show='asis',
  highlight=TRUE,
  include=TRUE,
  message=FALSE,
  progress=TRUE,
  prompt=FALSE,
  purl=TRUE,
  results="markup",
  size='small',
  strip.white=TRUE,
  tidy=FALSE,
  warning=FALSE
  )

options(
  width=60, # number of characters in R output before wrapping
  keep.source=TRUE,
  encoding="UTF-8"
)

library(ggplot2)
theme_set(theme_bw())

knit_hooks$set(
  document = function (x) {
    sub('\\usepackage[]{color}','\\usepackage{xcolor}',x,fixed=TRUE)
  }
)

registerS3method(
  "knit_print",
  "data.frame",
  function (x, ...) {
    print(x,row.names=FALSE)
  }
)
@