Ostats_plot  R Documentation 
This function plots the overlap of traits among species for each community. If there are multiple traits, each trait is plotted separately in onedimensional space.
Ostats_plot( plots, sp, traits, overlap_dat = NULL, use_plots = NULL, n_col = 1, scale = "fixed", colorvalues = NULL, alpha = 0.5, adjust = 2, bin_width = 1, limits_x = NULL, legend = FALSE, name_x = "trait value", name_y = "probability density", normalize = TRUE, means = FALSE, circular = FALSE, discrete = FALSE, circular_args = list() )
plots 
Site identity: a vector of names of each community. 
sp 
Taxon identity: a vector of species or taxa names. 
traits 
A vector of trait measurements for each individual, or a matrix or data frame with rows representing individuals and columns representing traits. 
overlap_dat 
Optional: an object containing the output of 
use_plots 
a vector of sites to plot. If NULL, the function will plot all the sites. 
n_col 
Number of columns for layout of individual panels. Default is 1. 
scale 
If you want the scale of x, y or both x and y axis to be independent,
set the argument to "free_x", "free_y" or "free" respectively.
Default = "fixed" which uses the same scale across all sites.
See 
colorvalues 
Vector of color values for the density polygons. Defaults to a viridis palette if none provided. 
alpha 
defines the transparency level for the density polygons. Default is 0.5. 
adjust 
the bandwidth adjustment of the density polygons. Default is 2.
See 
bin_width 
the width of each bin of the histograms. Default is 1.
Only used if 
limits_x 
Vector of length 2, with multiplicative factor to apply to the minimum
and maximum values of each trait to expand the limits of the x axis.
Default is 
legend 
Whether to include a legend. Defaults to 
name_x 
xaxis label. Default is 'trait value' 
name_y 
yaxis label. Default is 'probability density' 
normalize 
if 
means 
if 
circular 
if 
discrete 
if 
circular_args 
optional list of additional arguments to pass to

Density plots of species trait distributions plotted together
for each community to show how they overlap each other. Each community
is plotted on a separate panel within a multipanel figure.
The overlap value obtained as output from Ostats
is labelled on each community graph, if provided by the user.
If trait values are discrete rather than continuous, histograms are plotted instead of kernel density plots.
If trait values are circular, a circular kernel density estimate for each species is plotted on a polar coordinate plot. If trait values are both circular and discrete, a "sunburst" plot is returned.
The class of the returned object is Ostats_plot_object
. Calling
print
on this object will draw the plot using
grid.draw
.
If more than one trait is provided, a list of objects of class
Ostats_plot_object
will be returned.
Ostats
to Calculate Ostatistics (communitylevel
pairwise niche overlap statistics)
# set the arguments: plots < small_mammal_data$siteID sp < small_mammal_data$taxonID traits < log10(small_mammal_data$weight) # to plot only selected sites: use_plots < c('BART','KONZ','JORN') Ostats_plot(plots = plots, sp = sp, traits = traits, overlap_dat = small_mammal_Ostats, use_plots = use_plots, means = TRUE)
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