kemp {breakaway} | R Documentation |
Species richness estimation with Kemp-type models
Description
This function implements the species richness estimation procedure outlined in Willis & Bunge (2015). The diversity estimate, standard error, estimated model coefficients, model details and plot of the fitted model are returned.
Usage
kemp(
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
code |
A category representing algorithm behaviour. ‘code=1’ indicates no nonlinear models converged and the transformed WLRM diversity estimate of Rocchetti et. al. (2011) is returned. ‘code=2’ indicates that the iteratively reweighted model converged and was returned. ‘code=3’ indicates that iterative reweighting did not converge but a model based on a simplified variance structure was returned (in this case, the variance of the frequency ratios is assumed to be proportional to the denominator frequency index). Please peruse your fitted model before using your diversity estimate. |
name |
The “name” of the selected model. The first integer represents the numerator polynomial degree and the second integer represents the denominator polynomial degree of the model for the frequency ratios. See Willis & Bunge (2015) for details. |
para |
Estimated model parameters and standard errors. |
est |
The estimate of total (observed plus unobserved) diversity. |
seest |
The standard error in the diversity estimate. |
full |
The chosen nonlinear model for frequency ratios. |
ci |
An asymmetric 95% confidence interval for diversity. |
Author(s)
Amy Willis
References
Willis, A. and Bunge, J. (2015). Estimating diversity via frequency ratios. Biometrics, 71(4), 1042–1049.
Rocchetti, I., Bunge, J. and Bohning, D. (2011). Population size estimation based upon ratios of recapture probabilities. Annals of Applied Statistics, 5.
See Also
breakaway
; breakaway_nof1
; apples
Examples
kemp(apples)
kemp(apples, plot = FALSE, output = FALSE, answers = TRUE)