Diversity {SpadeR}

Estimation of species diversity (Hill numbers)

Description

Diversity: Estimating a continuous diversity profile in one community including species rich- ness, Shannon diversity and Simpson diversity). This function also supplies plots of empirical and estimated continuous diversity profiles. Various estimates for Shannon entropy and the Gini- Simpson index are also computed. All five types of data are supported: 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

Diversity(data, datatype = c("abundance", "abundance_freq_count",
  "incidence_freq", "incidence_freq_count", "incidence_raw"), q = NULL)

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".

q

a vector of nonnegative numbers specifying the diversity orders for which Hill numbers will be estimated. If NULL, then Hill numbers will be estimated at order q from 0 to 3 with increments of 0.25.

Value

a list of seven objects:

$Basic_data for summarizing data information.

$Species_richness for showing various species richness estimates along with related statistics.

$Shannon_index and $Shannon_diversity for showing various Shannon index/diversity estimates.

$Simpson_index and $Simpson_diversity for showing two Simpson index/diversity estimates.

$Hill_numbers for showing Hill number (diversity) estimates of diversity orders specified in the argument q.

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 Jost, L. (2015). Estimating diversity and entropy profiles via discovery rates of new species. Methods in Ecology and Evolution, 6, 873-882.

Chao, A., Wang, Y. T. and Jost, L. (2013). Entropy and the species accumulation curve: a novel estimator of entropy via discovery rates of new species. Methods in Ecology and Evolution 4, 1091-1110.

Examples

## Not run: 
data(DiversityData)
# Type (1) abundance data 
Diversity(DiversityData$Abu,"abundance",q=c(0,0.5,1,1.5,2))
# Type (1A) abundance-frequency counts data 
Diversity(DiversityData$Abu_count,"abundance_freq_count",q=seq(0,3,by=0.5))
# Type (2) incidence-frequency data 
Diversity(DiversityData$Inci,"incidence_freq",q=NULL)
# Type (2A) incidence-frequency counts data 
Diversity(DiversityData$Inci_freq_count,"incidence_freq_count",q=NULL)
# Type (2B) incidence-raw data 
Diversity(DiversityData$Inci_raw,"incidence_raw",q=NULL)

## End(Not run)