credibilityIntervals | R Documentation |
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.
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, ... )
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(). |
a gtable (if alpha is plotted) with two ggplot2 objects or a ggplot2 object (if alpha is not plotted)
isotopeData <- generateTPData() models <- multiModelTP(isotopeData, n.adapt = 200, n.iter = 200, burnin = 200) credibilityIntervals(models$gg, x = "model")
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.