add_singletons: Add singletons

Description Usage Arguments Value

View source: R/add_singletons.R

Description

Modifies an SAD to add rare species that may have been missed during sampling. Takes the difference between the number of species estimated by the bias-corrected Chao and ACE estimators (as implemented in vegan::estimateR) and the observed number of species. Adds the average of these two differences to the observed dataframe, with each added species getting one individual each. use_max is an option to use a high estimate (estimated mean + estimated standard error) from the estimators before calculating the mean difference. Returns the original SAD with added records for the estimated rare species.

Usage

1
add_singletons(dat, use_max = F)

Arguments

dat

dataframe with columns rank, abund, site, dat, singletons, sim, and source. This is the format you will get if you use load_dataset and filter to a single site

use_max

use estimated richness + standard error? Defaults F, but T is used in pipelines.

Value

dataframe with additional records for estimated rare species


diazrenata/scadsanalysis documentation built on May 14, 2021, 6:59 p.m.