setup.Rnw

<<setup-child,include=FALSE,cache=FALSE,purl=FALSE>>=
library(knitr)
opts_chunk$set(
  cache=TRUE,
  cache.path="tmp/cache/",
  comment=NA,
  echo=TRUE,
  eval=TRUE,
  include=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="tmp/figure/",
  fig.pos="h!",
  fig.show='asis',
  highlight=TRUE,
  message=FALSE,
  progress=TRUE,
  prompt=FALSE,
  purl=TRUE,
  results="markup",
  size='small',
  strip.white=TRUE,
  tidy=FALSE,
  warning=FALSE
  )

library(ggplot2)
theme_set(theme_bw())

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

str_opt <- getOption("str")
str_opt$strict.width <- "cut"
options(
  width=65, # number of characters in R output before wrapping
  keep.source=TRUE,
  encoding="UTF-8",
  str=str_opt
)


myround<- function (x, digits = 1) {
  # taken from the broman package
  if (digits < 1) 
    stop("This is intended for the case digits >= 1.")
  if (length(digits) > 1) {
    digits <- digits[1]
    warning("Using only digits[1]")
  }
  tmp <- sprintf(paste("%.", digits, "f", sep = ""), x)
  zero <- paste0("0.", paste(rep("0", digits), collapse = ""))
  tmp[tmp == paste0("-", zero)] <- zero
  tmp
}


mysummary <- function (x, digits = max(3L, getOption("digits") - 3L), se = TRUE, print.call=FALSE,print.sigma=TRUE,loglik=TRUE,coef.label=TRUE){
  if(print.call) cat("\nCall:", deparse(x$call, width.cutoff = 75L), "", sep = "\n")
    if (length(x$coef)) {
        if(coef.label) cat("Coefficients:\n")
        coef <- round(x$coef, digits = digits)
        if (se && NROW(x$var.coef)) {
            ses <- rep.int(0, length(coef))
            ses[x$mask] <- round(sqrt(diag(x$var.coef)), digits = digits)
            coef <- matrix(coef, 1L, dimnames = list(NULL, names(coef)))
            coef <- rbind(coef, s.e. = ses)
        }
        print.default(coef, print.gap = 2)
    }
    cm <- x$call$method
    if (is.null(cm) || cm != "CSS") {
      if(print.sigma)cat("\nsigma^2 estimated as ", myround(x$sigma2, digits = digits))
      if(loglik)cat("\nlog likelihood = ", myround(x$loglik, 2), 
        ",  aic = ", format(round(x$aic, 2L)), "\n", sep = "")
      } else cat("\nsigma^2 estimated as ", myround(x$sigma2, digits = digits), 
        ":  part log likelihood = ", myround(round(x$loglik, 2)), 
        "\n", sep = "")
    invisible(x)
}

@