Functions to estimate entropy and diversity share many arguments, whose default value is generally the best choice. They are explained here.
estimator
Each function comes with several estimators that correspond to the state of the art. Asymptotic entropy and diversity are calculated according to the chosen estimator.
level
level allows estimating entropy or diversity at a chosen
level, that may be a number of individuals (at least 1) of a sample
coverage (between 0 and 1) that is first converted to a number of
indidivuals by coverage_to_size().
If level is not NULL,
estimator is ignored.
The unveiled estimators, whose names start with Unveil,
rely on the estimation of the distribution of probabilities of the
species (i.e. the probability for an individual to belong to each
species). They require several arguments, that are ignored if another
estimator is chosen.
probability_estimator
The probability estimators allow estimating the actual probability of species from the observed abundances.
unveiling
The unveiling technique sets the distribution of the unobserved
species. If unveiling is “none”, they are ignored.
jack_alpha and jackmax
If richness_estimator is jackknife,
jackmax is the maximum order allowed.
jack_alpha is the risk level of the confidence interval of
the estimation.
The estimation starts at order \(k=0\). If the estimate of order \(k+1\) is out of the confidence interval of the estimate of order \(k\), then \(k\) is incremented and the test is repeated until the optimal order is found.