credibilityIntervals: Plot credibility intervals and central tendency descriptor...

In AndrewLJackson/tRophicPosition: Bayesian Trophic Position Estimation with Stable Isotopes

Plot credibility intervals and central tendency descriptor from posterior distributions of trophic position and/or alpha parameter

Description

This function plots a data frame in ggplot2 format (variables in columns, observations in rows), likely returned by the functions multiModelTP and multiSpeciesTP. This is especially useful when there are several species or communities to compare, and a combined plot is preferred.

Usage

credibilityIntervals(
  df,
  x = "consumer",
  plotAlpha = TRUE,
  legend = NULL,
  legendAlpha = NULL,
  y1 = "mode",
  y1min = "lower",
  y1max = "upper",
  y1lim = NULL,
  y2 = "alpha.mode",
  y2min = "alpha.lower",
  y2max = "alpha.upper",
  xlab = "Bayesian models",
  ylab1 = "Posterior trophic position",
  ylab2 = "Posterior alpha",
  group_by = NULL,
  scale_colour_manual = NULL,
  labels = NULL,
  plot = TRUE,
  ...
)

Arguments

df	data frame with at least 4 columns, a grouping variable, maximum, minimum and a central tendency descriptor (median, mode, etc.).
x	string defining the grouping variable.
plotAlpha	logical. If TRUE it expects that the data frame has at least 7 columns, another descriptor of central tendency, its maximum and minimum.
legend	list, position of the legend if not NULL, e.g. c(0.8, 0.8).
legendAlpha	list, position of the legend for the alpha plot, if not NULL, e.g. c(0.8, 0.8).
y1	string of the column with the central tendency descriptor of trophic position. By default, is the mode.
y1min	lower value plotted for trophic position. For the 95 credibility interval, this value would be 0.025 percentile.
y1max	higher value plotted for trophic position. For the 95 credibility interval, this value would be 0.975 percentile.
y1lim	vector of length 2, with limits of the y axis of trophic position.
y2	string of the column with the central tendency descriptor of alpha.
y2min	lower value plotted for alpha. For the 95 this value would be percentile 0.025.
y2max	higher value plotted for alpha. For the 95 interval, this value would be percentile 0.0975.
xlab	string of the label of the X axis.
ylab1	string of the label of Y1 axis (trophic position).
ylab2	string of the label of Y2 axis (alpha).
group_by	grouping variable (factor) in case of using colours.
scale_colour_manual	a list of colours (ggplot2 syntaxis) to use with group_by.
labels	string, manual labels for the x axis.
plot	logical, by default TRUE. In case of saving the output as a variable, the user can decide not to plot the output.
...	additional parameters passed to credibilityIntervals().

Value

a gtable (if alpha is plotted) with two ggplot2 objects or a ggplot2 object (if alpha is not plotted)

Examples

isotopeData <- generateTPData()
models <- multiModelTP(isotopeData, n.adapt = 200, n.iter = 200,
burnin = 200)
credibilityIntervals(models$gg, x = "model")

AndrewLJackson/tRophicPosition documentation built on Jan. 2, 2023, 12:14 p.m.