Estimation of species richness in a community

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Description

ChaoSpecies: Estimation of species richness in a single community based on five types of data: Type (1) abundance data (datatype="abundance"), Type (1A) abundance-frequency counts
(datatype="abundance_freq_count"), Type (2) incidence-frequency data (datatype = "incidence_freq"), Type (2A) incidence-frequency counts (datatype="incidence_freq_count"), and Type (2B) incidence-raw data (datatype="incidence_raw"); see SpadeR-package details for data input formats.

Usage

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ChaoSpecies(data, datatype = c("abundance", "abundance_freq_count",
  "incidence_freq", "incidence_freq_count", "incidence_raw"), k = 10,
  conf = 0.95)

Arguments

data

a matrix/data.frame of species abundances/incidences.

datatype

type of input data, "abundance", "abundance_freq_count", "incidence_freq", "incidence_freq_count" or "incidence_raw".

k

the cut-off point (default = 10), which separates species into "abundant" and "rare" groups for abundance data for the estimator ACE; it separates species into "frequent" and "infrequent" groups for incidence data for the estimator ICE.

conf

a positive number 1 specifying the level of confidence interval.

Value

a list of three objects:

$Basic_data_information and $Rare_species_group/$Infreq_species_group for summarizing data information.

$Species_table for showing a table of various species richness estimates, standard errors, and the associated confidence intervals.

References

Chao, A., and Chiu, C. H. (2012). Estimation of species richness and shared species richness. In N. Balakrishnan (ed). Methods and Applications of Statistics in the Atmospheric and Earth Sciences. p.76-111, Wiley, New York.

Chao, A., and Chiu, C. H. (2016). Nonparametric estimation and comparison of species richness. Wiley Online Reference in the Life Science. In: eLS. John Wiley and Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0026329.

Chao, A., and Chiu, C. H. (2016). Species richness: estimation and comparison. Wiley StatsRef: Statistics Reference Online. 1-26.

Chiu, C. H., Wang Y. T., Walther B. A. and Chao A. (2014). An improved non-parametric lower bound of species richness via the Good-Turing frequency formulas. Biometrics, 70, 671-682.

Gotelli, N. G. and Chao, A. (2013). Measuring and estimating species richness, species diver- sity, and biotic similarity from sampling data. Encyclopedia of Biodiversity, 2nd Edition, Vol. 5, 195-211, Waltham, MA.

Examples

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data(ChaoSpeciesData)
# Type (1) abundance data
ChaoSpecies(ChaoSpeciesData$Abu,"abundance",k=10,conf=0.95)
# Type (1A) abundance-frequency counts data
ChaoSpecies(ChaoSpeciesData$Abu_count,"abundance_freq_count",k=10,conf=0.95)
# Type (2) incidence-frequency data
ChaoSpecies(ChaoSpeciesData$Inci,"incidence_freq",k=10,conf=0.95)
# Type (2A) incidence-frequency counts data
ChaoSpecies(ChaoSpeciesData$Inci_count,"incidence_freq_count",k=10,conf=0.95)
# Type (2B) incidence-raw data 
ChaoSpecies(ChaoSpeciesData$Inci_raw,"incidence_raw",k=10,conf=0.95)