vignettes/vignette-default-settings.R

In r-hyperspec/hyperSpec: Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)

# Plotting settings ==========================================================

# Base plot parameters -------------------------------------------------------
# Note:  more knitr settings further down!
knitr::knit_hooks$set(small.mar = function(before, options, envir) {
  if (before) {
    par(mar = c(4.1, 4.1, 1, .6))
  }
})

knitr::opts_chunk$set(small.mar = TRUE)

# Lattice parameters ---------------------------------------------------------
set_trellis_layout_hw_default <- function() {

  trellis_layout_heights <- list(
    top.padding = 1,
    main = 1,
    main.key.padding = 1,
    key.top = 1,
    xlab.top = 1,
    key.axis.padding = 1,
    axis.top = 1,
    strip = 1,
    panel = 1,
    axis.panel = 1,
    between = 1,
    axis.bottom = 1,
    axis.xlab.padding = 1,
    xlab = 1,
    xlab.key.padding = 0,
    key.bottom = 1,
    key.sub.padding = 1,
    sub = 1,
    bottom.padding = 1
  )

  trellis_layout_widths <- list(
    left.padding = 1,
    key.left = 1,
    key.ylab.padding = 0,
    ylab = 1,
    ylab.axis.padding = 1,
    axis.left = 1,
    axis.panel = 1,
    strip.left = 1,
    panel = 1,
    between = 1,
    axis.right = 1,
    axis.key.padding = 1,
    ylab.right = 1,
    key.right = 1,
    right.padding = 1
  )

  trellis.par.set(layout.heights = trellis_layout_heights)
  trellis.par.set(layout.widths = trellis_layout_widths)
}

set_trellis_layout_hw_custom <- function() {
  trellis_layout_heights <- trellis.par.get("layout.heights")
  trellis_layout_heights[grep("padding", names(trellis_layout_heights))] <- 0
  trellis.par.set(layout.heights = trellis_layout_heights)

  trellis_layout_widths <- trellis.par.get("layout.widths")
  trellis_layout_widths[grep("padding", names(trellis_layout_widths))] <- 0
  trellis.par.set(layout.widths = trellis_layout_widths)
}

set_trellis_layout_hw_custom()

# knitr Settings =============================================================

# Notes on Figure Sizes.
#
# There are (at least) 2 common figure aspect ratios in  the vignettes.
# One is a full width figure, suitable for spectra or spectra-like plots.
# The other is a square plot, desirable for maps.
# Option `sq.fig = TRUE` should be used for square plots.

knitr::opts_hooks$set(sq.fig = function(options) {

  if (isTRUE(options$sq.fig)) {
    options$fig.width  <- 4
    options$fig.height <- 3
  }

  options
})

knitr::opts_chunk$set(
  echo       = TRUE,     # Should blocks with program code be shown in knitted documents?
  eval       = TRUE,     # Should program code be evaluated?
  tidy       = "styler", # Use code output styled in the Tidyverse style
  fig.height = 2.5,      # Default width for plots.
  fig.width  = 6,        # Default height for plots.
  fig.align  = "center", # Default alignment for plots in knitted documents.
  collapse   = TRUE,
  comment    = "#>"
)

# R Settings =================================================================
options("width" = 100, "digits" = 5)
options(rmarkdown.html_vignette.check_title = FALSE) # Vig index entry not document title
set.seed(2020)

# Temporary options ==========================================================
# This option controls if reviewer's/translator's notes are visible in vignettes
options(show_reviewers_notes = FALSE)

# Example (template) of reviever's notes block that could be hidden:

# <!-- ======================================================================= -->
# ```{block, type="note-t", echo=show_reviewers_notes}
# **Reviewer's notes**:
#
# 1. `# FIXME:`{.r} ...
# 2. `# TODO:`{.r} ...
# 3. `# NOTE:`{.r} ...
# ```
# <!-- ======================================================================= -->