```
##############################################################################
# Copyright (c) 2017 Russell V. Lenth #
# #
# This file is part of the unrepx package for R (*unrepx*) #
# #
# *unrepx* is free software: you can redistribute it and/or modify #
# it under the terms of the GNU General Public License as published by #
# the Free Software Foundation, either version 2 of the License, or #
# (at your option) any later version. #
# #
# *unrepx* is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with R and *unrepx*. If not, see #
# <https://www.r-project.org/Licenses/> and/or #
# <http://www.gnu.org/licenses/>. #
##############################################################################
### Routine to make "Daniel paper"
# n = number of effects to plot
# lin.div = number of divisions on linear scale (1 + lin.div lines plotted)
# ranks are centered using (i - a) / (n + 1 - 2*a)
# ranks says which axis has the ranks
daniel.paper = function(n.effects = 15, linear = 0:40, a = .375,
rank.axis = c("y", "x"),
type = c("half.normal", "normal"),
theme = "blue", lin.lab, rank.lab)
{
theme = get(paste0(theme, "_thm"))
rank.axis = match.arg(rank.axis)
type = match.arg(type)
x = linear
ranks = seq_len(n.effects)
qtl = (ranks - a) / (n.effects + 1 - 2*a)
y = scores = switch(type,
half.normal = stats::qnorm((1 + qtl)/2),
normal = stats::qnorm(qtl))
major = theme$major
minor = theme$minor
axis = if(is.null(theme$axis)) major else theme$axis
mod.major = c(which(linear %% 5 == 0)[1], 0) # index for starting major ticks
if(missing(lin.lab)) lin.lab = ifelse(type=="normal", "Effects", "Absolute effects")
if(missing(rank.lab)) rank.lab = "Rank"
xlab = lin.lab
ylab = rank.lab
if (rank.axis == "x") { # swap axes and labels
tmp = x; x = y; y = tmp
tmp = xlab; xlab = ylab; ylab = tmp
mod.major = rev(mod.major)
}
plot(range(x), range(y), type = "n",
xlab = xlab, ylab = ylab, axes = FALSE, col.lab = axis$col)
par(usr = c(range(x), range(y))) # makes axis ends same as plot-region ends
for (i in seq_along(x)) {
if (i %% 5 == mod.major[1]) abline(v = x[i], col = major$col, lty = major$lty, lwd = major$lwd)
else abline(v = x[i], col = minor$col, lty = minor$lty)
}
for (i in seq_along(y)) {
if (i %% 5 == mod.major[2]) abline(h = y[i], col = major$col, lty = major$lty, lwd = major$lwd)
else abline(h = y[i], col = minor$col, lty = minor$lty)
}
side = switch(rank.axis, y = 2, x = 1)
sel = which(ranks %% 5 == 0)
axis(side, at = scores[sel], labels = ranks[sel],
lwd = 0, lwd.ticks = axis$lwd, col.ticks = axis$col, col.axis = axis$col)
invisible()
}
blue_thm = list(major = list(col = "blue", lty = 1, lwd = 1),
minor = list(col = "cyan", lty = 1))
bw_thm = list(major = list(col = "black", lty = 1, lwd = 1),
minor = list(col = "black", lty = 3))
gray_thm = list(major = list(col = "black", lty = 1, lwd = 1),
minor = list(col = "gray", lty = 1))
bold_thm = list(major = list(col = "black", lty = 1, lwd = 2),
minor = list(col = "black", lty = 1, lwd = 1))
```

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