Fortify extrapolated species richness of a species pool

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

Usage

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

# S3 method for class 'poolaccum'
tidy(x, data, alpha = 0.05, ...)

Arguments

model, x: 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

Gavin L. Simpson & Didzis Elferts

Examples


library("vegan")
library("ggplot2")
data(BCI)
pool <- poolaccum(BCI)
df <- fortify(pool)
df
#> # A tibble: 240 × 6
#>    index  size richness lower upper std_dev
#>    <fct> <dbl>    <dbl> <dbl> <dbl>   <dbl>
#>  1 S         3     139.  125.  150.    6.78
#>  2 S         4     151.  140.  161.    5.43
#>  3 S         5     159.  147   171.    5.74
#>  4 S         6     165.  155.  176     5.26
#>  5 S         7     170.  162.  180.    4.84
#>  6 S         8     175.  166.  185.    5.32
#>  7 S         9     178.  170   188.    5.27
#>  8 S        10     181.  172.  193.    5.59
#>  9 S        11     184.  175.  196.    5.34
#> 10 S        12     187.  177.  198.    5.29
#> # ℹ 230 more rows

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)