inst/doc/cotram.R

In cotram: Count Transformation Models

## ----setup, echo = FALSE, results = "hide", message = FALSE, warning = FALSE----
set.seed(290875)

sapply(c("cotram", "tram", "mlt", "lattice"), library, char = TRUE)

trellis.par.set(list(plot.symbol = list(col=1,pch=20, cex=0.7),
                     box.rectangle = list(col=1),
                     box.umbrella = list(lty=1, col=1),
                     strip.background = list(col = "white"), 
                     axis.components = list(top = list(tck = 0),
                                            right = list(tck = 0)))
                )
ltheme <- canonical.theme(color = FALSE)     ## in-built B&W theme
ltheme$strip.background$col <- "transparent" ## change strip bg
lattice.options(default.theme = ltheme)

panel <- function(x, y, ...) {
  panel.abline(h = 1, col = "grey")
  panel.xyplot(x, y, type = "l", col = "black")
}

knitr::opts_chunk$set(echo = TRUE, results = 'markup', error = FALSE,
                      warning = FALSE, message = FALSE,
                      tidy = FALSE, cache = FALSE, size = "small",
                      fig.width = 6, fig.height = 4, fig.align = "center",
                      out.width = NULL, ###'.6\\linewidth', 
                      out.height = NULL,
                      fig.scap = NA)
knitr::render_sweave()  # use Sweave environments
knitr::set_header(highlight = '')  # do not \usepackage{Sweave}

## R settings
opt <- options(prompt = "R> ", continue = "+  ", useFancyQuotes = FALSE, width = 75)  # JSS style
library("colorspace")
col <- diverge_hcl(10, h = c(246, 40), c = 96, l = c(65, 90))
fill <- diverge_hcl(10, h = c(246, 40), c = 96, l = c(65, 90), alpha = .3)

## ----citation, echo = FALSE----------------------------------------------
year <- substr(packageDescription("cotram")$Date, 1, 4)
version <- packageDescription("cotram")$Version

## ----DVC-data, echo = FALSE, results = "hide", message = FALSE-----------
obs <- NULL
if (!file.exists("analysis/DVC.rda")) {
    op <- options(timeout = 120)
    dwnfl <- try(download.file("https://zenodo.org/record/17179/files/DVC.tgz", "DVC.tgz"))
    options(op)
    if (!inherits(dwnfl, "try-error")) {
        untar("DVC.tgz", file = "analysis/DVC.rda")
        load("analysis/DVC.rda")
    }
} else {
    load("analysis/DVC.rda")
}

## ----fail, results = "asis", echo = FALSE--------------------------------
if (is.null(obs)) {
    cat("Downloading data from zenodo failed, stop processing.", "\\end{document}\n")
    knitr::knit_exit()
}