plot_abu: Plot distributions of species abundance

In MoBiodiv/mobr: Measurement of Biodiversity

Plot distributions of species abundance

Description

Plot distributions of species abundance

Usage

plot_abu(
  mob_in,
  group_var,
  ref_level = NULL,
  type = "sad",
  scale = "gamma",
  col = NULL,
  lwd = 3,
  log = "",
  leg_loc = "topleft"
)

Arguments

mob_in	a 'mob_in' class object produced by 'make_mob_in'
group_var	String that specifies which field in mob_in$env the data should be grouped by
ref_level	String that defines the reference level of group_var to which all other groups are compared with, defaults to NULL. If NULL then the default contrasts of group_var are used.
type	either 'sad' or 'rad' for species abundance vs rank abundance distribution, defaults to 'sad'.
scale	character string either 'alpha' for sample scale or 'gamma' for group scale. Defaults to 'gamma'.
col	optional vector of colors.
lwd	a number which specifies the width of the lines
log	a string that specifies if any axes are to be log transformed, options include 'x', 'y' or 'xy' in which either the x-axis, y-axis, or both axes are log transformed respectively
leg_loc	a string that specifies the location of the legend, options include: 'lowerleft', 'topleft', 'loweright','topright'

Examples

data(inv_comm)
data(inv_plot_attr)
inv_mob_in <- make_mob_in(inv_comm, inv_plot_attr, coord_names = c('x', 'y'))
plot_abu(inv_mob_in, 'group', 'uninvaded', type='sad', log='x')
plot_abu(inv_mob_in, 'group', 'uninvaded', type='rad', scale = 'alpha', log='x')

MoBiodiv/mobr documentation built on Oct. 26, 2024, 10:51 a.m.