Nothing
includeChapter <- 1:7 %in% (1:7) # [-6]
includeApp <- 1:4 %in% 1:3
require(MASS) # make sure this comes before dplyr loads
require(Matrix) # make sure this comes before mosaic loads
require(fastR2)
require(mosaic)
theme_set(theme_bw())
require(knitr)
require(xtable)
options(xtable.floating = FALSE)
opts_knit$set(width=74)
opts_knit$set(self.contained=FALSE)
opts_chunk$set(
digits = 3,
dev="pdf", # don't need EPS files anymore
dev.args=list(colormodel="cmyk"),
comment="##",
prompt=FALSE,
size="small",
cache=TRUE,
cache.path='cache/c-',
cache.lazy=FALSE,
tidy=FALSE,
fig.width=8*.45,
fig.height=6*.45,
fig.show="hold",
fig.align="center",
out.width=".47\\textwidth",
# background="gray88",
# background="white",
# background="transparent",
boxedLabel=TRUE
)
opts_template$set(fig3 = list(fig.height = 7*.40, fig.width = 8*.40, out.width=".31\\textwidth"))
opts_template$set(figtall = list(fig.height = 8*.45, fig.width = 8*.45, out.width=".47\\textwidth"))
opts_template$set(fig1 = list(fig.height = 3*0.9, fig.width = 8 * 0.9, out.width=".95\\textwidth"))
opts_template$set(figbig = list(fig.height = 9*0.9, fig.width = 12*0.9, out.width=".95\\textwidth"))
knit_hooks$set(seed = function(before, options, envir) {
if (before) set.seed(options$seed)
})
knit_hooks$set(digits = function(before, options, envir) {
if (before) {
options(digits = options$digits)
} else {
options(digits = 3)
}
})
knit_hooks$set(
document = function(x) {
sub('\\usepackage[]{color}', '\\usepackage{xcolor}', x, fixed = TRUE)
gsub(
"\\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}",
"\\definecolor{shadecolor}{gray}{0.8}", x, fixed = TRUE)
}
)
knit_hooks$set(chunk = function (x, options) {
if ( !is.null(options$boxedLabel) && options$boxedLabel &&
! grepl("unnamed-chunk", options$label) &&
(is.null(options$echo) || options$echo) ) {
labeling <- paste0(
"\\endgraf\\nobreak\\null\\endgraf\\penalty-2\\kern-.5\\baselineskip",
"\n\n",
"\\hfill \\makebox[0pt][r]{\\fbox{\\tiny ",
options$label,
"}}",
"\\endgraf",
"\\kern-4.5ex\n\n")
} else {
labeling <- ""
}
ai = knitr:::output_asis(x, options)
col = if (!ai)
paste(knitr:::color_def(options$background),
if (!knitr:::is_tikz_dev(options)) "\\color{fgcolor}",
sep = "")
k1 = paste(col, "\\begin{kframe}\n", sep = "")
k2 = "\\end{kframe}"
x = knitr:::.rm.empty.envir(paste(k1, labeling, x, k2, sep = ""))
size = if (options$size == "normalsize")
""
else sprintf("\\%s", options$size)
if (!ai)
x = sprintf("\\begin{knitrout}%s\n%s\n\\end{knitrout}",
size, x)
if (options$split) {
name = knitr:::fig_path(".tex", options)
if (!file.exists(dirname(name)))
dir.create(dirname(name))
cat(x, file = name)
sprintf("\\input{%s}", name)
}
else x
}
)
blackAndWhite = TRUE
fastRlty = rep(1,20)
fastRlty = c(1,2,5,6,1,2,5,6,1,2,5,6)
trellis.par.set(theme=col.whitebg())
# trellis.par.set(theme=col.fastR(bw=blackAndWhite),lty=fastRlty)
trellis.par.set(theme=col.fastR())
# options(width=70)
options(continue=" ")
options(str = strOptions(strict.width = "wrap"))
options(show.signif.stars=FALSE)
options(digits=3)
# # omit some of the output from summary( lm( ) )
# print.summary.lm <-
# function (x, digits = max(3L, getOption("digits") - 3L), symbolic.cor = x$symbolic.cor,
# signif.stars = getOption("show.signif.stars"), ...)
# {
# output <- capture.output( stats:::print.summary.lm(x, digits=digits, symbolic.cor = symbolic.cor,
# signif.stars=signif.stars, ...) )
# l <- sapply( output, nchar )
# w1 <- min( grep("Call", output) )
# w2 <- min( grep("Resid", output) )
# w3 <- min( grep("Coef", output) )
# rows <- 1:length(output)
# keep <- (rows >= w1 & rows < w2) | (rows >=w3)
# cat( paste(output[keep], collapse="\n") )
# return(invisible(x))
# }
#
# print.summary.glm <-
# function (x, digits = max(3L, getOption("digits") - 3L), symbolic.cor = x$symbolic.cor,
# signif.stars = getOption("show.signif.stars"), ...)
# {
# output <- capture.output( stats:::print.summary.glm(x, digits=digits, symbolic.cor = symbolic.cor,
# signif.stars=signif.stars, ...) )
# l <- sapply( output, nchar )
# w1 <- min( grep("Call", output) )
# w2 <- min( grep("Resid", output) )
# w3 <- min( grep("Coef", output) )
# rows <- 1:length(output)
# keep <- (rows >= w1 & rows < w2) | (rows >=w3)
# cat( paste(output[keep], collapse="\n") )
# return(invisible(x))
# }
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