Species richness estimators {wiqid}

Species richness estimators

Description

Functions to estimate species richness, based on samples from one or more surveys (quadrats, sites, occasions, ...) as included in EstimateS. See Details for individual estimators.

EstimateS no longer runs under Windows 10 or later and is effectively defunct. See https://www.robertkcolwell.org/pages/estimates.

Usage

richACE(cntVec, threshold = 10)
richICE(incMat, threshold = 10)
richChao1(cntVec, correct = FALSE, ci = 0.95)
richChao2(incMat, correct = FALSE, ci = 0.95)
richJack1(incMat)
richJack2(incMat)
richJackA1(cntVec)
richJackA2(cntVec)
richBoot(incMat)
richMM(incMat)
richRenLau(cntVec)

Arguments

cntVec

a vector of species counts (abundances) with one element for each species. A matrix of counts, species x sites, may also be provided and will be converted to a vector with rowSums. Zeros are allowed, but not missing values; non-integers are rounded.

incMat

a 1/0 matrix of species incidence (presence), species x sites. A matrix of counts may also be provided and will be converted to 1/0 after rounding.

threshold

the definition of rare or infrequent species: species with threshold or smaller counts (ACE) or incidences (ICE) are rare or infrequent.

correct

if TRUE, bias-corrected estimates are calculated.

ci

the required confidence interval.

Details

richACE and richICE calculate Anne Chao's Abundance-based and Incidence-based Coverage Estimators of species richness respectively (Chao et al, 2000).

richChao1 and richChao2 calculate Anne Chao's Chao 1 (abundance-based) and Chao 2 (incidence-based) estimators (Chao 1984, 1987).

richJack1 and richJack2 calculate first and second order incidence-based jackknife estimators of species richness (Smith & van Belle, 1984).

richBoot calculates a bootstrap estimator of species richness (Smith & van Belle, 1984).

richMM calculates the asymptotic species richness from a Michaelis-Menten curve fitted to the species rarefaction curve (Colwell et al. 2004).

The following were not included in EstimateS v.8.2:

richJackA1 and richJackA2 calculate first and second order abundance-based jackknife estimators of species richness (Gotelli & Colwell 2011).

richRenLau calculates Rennolls & Laumonier's (2006) 'shadow species' abundance-based estimator of richness.

Value

richChao1 and richChao2 return a vector with a point estimate, upper and lower confidence limits, and standard deviation.

The other functions return a scalar.

Benchmarks

Output for estimators included in EstimateS 8.2 has been checked against EstimateS for the seedbank and killarneyBirds data sets. EstimateS results are often 0.01 lower, as EstimateS appears to truncate rather than rounding.

Author(s)

Mike Meredith

References

Chao, A. 1984. Non-parametric estimation of the number of classes in a population. Scandinavian Journal of Statistics 11, 265-270.

Chao, A. 1987. Estimating the population size for capture-recapture data with unequal capture probabilities. Biometrics 43:783-791.

Chao, A., W.-H. Hwang, Y.-C. Chen, and C.-Y. Kuo. 2000. Estimating the number of shared species in two communities. Statistica Sinica 10:227-246.

Colwell, R. K., C. X. Mao, & J. Chang. 2004. Interpolating, extrapolating, and comparing incidence-based species accumulation curves. Ecology 85, 2717-2727.

Gotelli, N J; R K Colwell. 2011. Estimating species richness. 39-54 in Magurran, A E, and B J McGill, editors. Biological diversity: frontiers in measurement and assessment. Oxford University Press, Oxford, New York NY.

Rennolls, K; Y Laumonier. 2006. A new local estimator of regional species diversity, in terms of 'shadow species', with a case study from Sumatra. J Tropical Ecology 22:321-329.

Smith, E.P. & van Belle, G. 1984. Nonparametric estimation of species richness. Biometrics 40, 119-129.

See Also

richRarefy for rarefaction curves, and richCurve for a function to give richness estimates for sub-sets of samples.

Examples

data(seedbank)

richACE(seedbank)