Chao1 species richness estimator

Source: R/richness_chao1.R

This function implements the Chao1 richness estimate, which is often mistakenly referred to as an index.

chao1(input_data, output = NULL, answers = NULL)

Arguments

input_data

An input type that can be processed by convert() or a phyloseq object
output

Deprecated; only for backwards compatibility
answers

Deprecated; only for backwards compatibility

Value

An object of class alpha_estimate, or alpha_estimates for phyloseq objects

Note

The authors of this package strongly discourage the use of this estimator. It is only valid when you wish to assume that every taxa has equal probability of being observed. You don't really think that's possible, do you?

Author

Amy Willis

Examples



chao1(apples)
#> Estimate of richness from method chao1:
#>   Estimate is 1241
#>  with standard error 38.05
#>   Confidence interval: (1016, 4716)
#>