breakaway {breakaway} | R Documentation |
Species richness estimation with breakaway
Description
breakaway is a wrapper for modern species richness estimation for modern datasets
Usage
breakaway(
input_data,
cutoff = NA,
output = NULL,
plot = NULL,
answers = NULL,
print = NULL,
...
)
Arguments
input_data |
An input type that can be processed by |
cutoff |
The maximum frequency count to use for model fitting |
output |
Deprecated; only for backwards compatibility |
plot |
Deprecated; only for backwards compatibility |
answers |
Deprecated; only for backwards compatibility |
print |
Deprecated; only for backwards compatibility |
... |
Additional arguments will be ignored; this is for backward compatibility |
Value
An object of class alpha_estimate
Note
‘breakaway’ presents an estimator of species richness that is
well-suited to the high-diversity/microbial setting. However, many microbial
datasets display more diversity than the Kemp-type models can permit. In
this case, the log-transformed WLRM diversity estimator of Rocchetti et. al.
(2011) is returned. The authors' experience suggests that some datasets that
require the log-transformed WLRM contain “false” diversity, that is,
diversity attributable to sequencing errors (via an inflated singleton
count). The authors encourage judicious use of diversity estimators when the
dataset may contain these errors, and recommend the use of
breakaway_nof1
as an exploratory tool in this case.
Author(s)
Amy Willis
References
Willis, A. and Bunge, J. (2015). Estimating diversity via frequency ratios. Biometrics, 71(4), 1042–1049.
See Also
Examples
breakaway(apples)
breakaway(apples, plot = FALSE, output = FALSE, answers = TRUE)