Usage
pirateplot(formula = NULL, data = NULL, line.fun = mean, pal = "basel", back.col = gray(1), point.cex = 1, point.pch = 16, point.lwd = 1, cut.min = NULL, cut.max = NULL, width.min = 0.3, width.max = NA, bean.o = NULL, point.o = NULL, bar.o = NULL, inf.o = NULL, line.o = NULL, inf = "hdi", inf.p = 0.95, theme.o = 1, hdi.iter = 1000, jitter.val = 0.03, line.lwd = 4, bean.lwd = 1, bean.lty = 1, inf.lwd = 1, bar.border.lwd = 1, gl.col = NULL, ylim = NULL, xlim = NULL, xlab = NULL, ylab = NULL, main = NULL, yaxt = NULL, xaxt = NULL, point.col = NULL, bar.col = NULL, bean.border.col = NULL, inf.col = NULL, average.line.col = NULL, bar.border.col = NULL, at = NULL, bw = "nrd0", adjust = 1, add = F, sortx = "alphabetical", cex.lab = NULL, cex.axis = 1, bty = "n", evidence = F, family = NULL, inf.band = "wide", ...)
Arguments
formula
(formula) A formula in the form y ~ x1 + x2 + x3 indicating the vertical response variable (y) and up to three independent varaibles
data
(dataframe) A dataframe containing the variables specified in formula.
line.fun
(function) A function that determines how average lines and bar heights are determined (default is mean).
pal
(string) A string indicating the color palette of the plot. Can be a single color, a vector of colors, or the name of a palette in the piratepal() function (e.g.; "basel", "google", "southpark"). To see all the palettes, run piratepal(palette = "all", action = "show")
point.cex, point.pch, point.lwd
(numeric) Numbers indicating the size, pch type, and line width of raw data points.
cut.min, cut.max
(numeric) Optimal minimum and maximum values of the beans.
width.min, width.max
(numeric) The minimum and maximum width of a bean.
bar.o, point.o, inf.o, line.o, bean.o
(numeric) A number between 0 and 1 indicating how opaque to make the bars, points, inference band, average line, and beans respectively. These values override whatever is in the specified theme
inf
(string) A string indicating what types of inference bands to calculate. "ci" means frequentist confidence intervals, "hdi" means Bayesian Highest Density Intervals (HDI).
inf.p
(numeric) A number between 0 and 1 indicating the level of confidence to use in calculating inferences for either confidence intervals or HDIs. The default is 0.95
theme.o
(integer) An integer in the set 0, 1, 2, 3, specifying an opacity theme (that is, specific values of bar.o, point.o, etc.). You can override specific opacity values in a theme by specifying bar.o, inf.o (etc.)
hdi.iter
(integer) An integer indicating how many iterations to run when calculating the HDI. Larger values lead to better estimates, but can be more time consuming.
jitter.val
(numeric) A number indicaing how much to jitter the points horizontally. Defaults to 0.05.
bean.lwd, bean.lty, inf.lwd, line.lwd, bar.border.lwd
(numeric) A vector of numbers customizing the look of beans and lines.
gl.col, back.col
(string) An optional string indicating the color of the horizontal gridlines and plotting background.
point.col, bar.col, bean.border.col, inf.col, average.line.col, bar.border.col
(string) An optional vector of colors specifying the colors of the plotting elements. This will override values in the palette.
at
(numeric) An optional vector specifying the locations of the beans. Especially helpful when adding beans to an existing plot with add = T
bw
(string) The smoothing bandwidth to use for the bean. (see ?density)
adjust
(numeric) Adjustment for the bandwidth (see ?density)
add
(logical) A logical value indicating whether to add the pirateplot to an existing plotting space or not.
sortx
(string) An optional argument indicating how to sort the x values. Can be "sequential" (as they are found in the original dataframe), "alphabetical", or a string indicating a function (i.e.; "mean")
cex.lab, cex.axis
Size of the labels and axes.
bty, xlim, ylim, xlab, ylab, main, yaxt, xaxt
General plotting arguments
evidence
(logical) A logical value indicating whether to show Bayesian evidence (Not currently in use)
family
a font family (Not currently in use)
inf.band
Either "wide" to indicate a fixed width band, or "tight" to indcate a band constrained by the bean
...
other arguments passed on to the plot function (e.g.; main, xlab, ylab, ylim, cex.axis, cex.main, cex.lab)