Species richness estimation with breakaway

breakaway is a wrapper for modern species richness estimation for modern datasets

breakaway(
  input_data,
  cutoff = NA,
  output = NULL,
  plot = NULL,
  answers = NULL,
  print = NULL,
  ...
)

Arguments

input_data

An input type that can be processed by convert()

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.

References

Willis, A. and Bunge, J. (2015). Estimating diversity via frequency ratios. Biometrics, 71(4), 1042–1049.

See also

breakaway_nof1; kemp; apples

Author

Amy Willis

Examples

breakaway(apples)
#> Estimate of richness from method breakaway:
#>   Estimate is 1552
#>  with standard error 304.71
#>   Confidence interval: (1201, 2517)
#> 
breakaway(apples, plot = FALSE, output = FALSE, answers = TRUE)
#> Estimate of richness from method breakaway:
#>   Estimate is 1552
#>  with standard error 304.71
#>   Confidence interval: (1201, 2517)
#>