The untransformed weighted linear regression estimator for species richness estimation

Source: R/richness_wlrm_ut.R

This function implements the untransformed version of the species richness estimation procedure outlined in Rocchetti, Bunge and Bohning (2011).

wlrm_untransformed(
  input_data,
  cutoff = NA,
  print = NULL,
  plot = NULL,
  answers = NULL
)

Arguments

input_data

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

cutoff

Maximum frequency count to use

print

Deprecated; only for backwards compatibility

plot

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

This estimator is based on the negative binomial model and for that reason generally produces poor fits to microbial data. The result is usually artificially low standard errors. Caution is advised.

References

Rocchetti, I., Bunge, J. and Bohning, D. (2011). Population size estimation based upon ratios of recapture probabilities. Annals of Applied Statistics, 5.

Author

Amy Willis

Examples


wlrm_untransformed(apples)
#> Estimate of richness from method wlrm_untransformed:
#>   Estimate is 1330
#>  with standard error 77
#>   Confidence interval: (1210, 1518)
#>   Cutoff:  33