fortify.poolaccum: Fortify extrapolated species richness of a species pool

In gavinsimpson/ggvegan: 'ggplot2' Plots for the 'vegan' Package

Fortify extrapolated species richness of a species pool

Description

Prepares a fortified version of results from vegan::poolaccum() objects.

Usage

## S3 method for class 'poolaccum'
fortify(model, data, alpha = 0.05, ...)

Arguments

model	an object of class vegan::poolaccum().
data	original data set. Currently ignored.
alpha	level of quantiles for envelopes shown (default 0.05).
...	additional arguments passed to vegan::summary.poolaccum(), notably display to control which indices should be computed.

Value

A data frame with columns index, size, richness, lower, upper, and std_dev, containing the richness index, permutation richness estimator, sample size, upper and lower 1 - \alpha quantile interval, and standard deviation of permutation estimates, respectively.

Author(s)

Didzis Elferts & Gavin L. Simpson

Examples

data(BCI)
pool <- poolaccum(BCI)
df <- fortify(pool)

ggplot(df, aes(x = size, y = richness, colour = index)) +
    geom_ribbon(aes(ymin = lower, ymax = upper, x = size, fill = index),
                alpha = 0.3, inherit.aes = FALSE) +
    geom_line() +
    facet_wrap(~ index)

gavinsimpson/ggvegan documentation built on July 28, 2023, 9:24 a.m.