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.
a matrix/data.frame of species abundances/incidences.
type of input data, "abundance", "abundance_freq_count", "incidence_freq", "incidence_freq_count" or "incidence_raw".
a vector of nonnegative numbers specifying the diversity orders for which Hill numbers will be estimated. If
a list of seven objects:
$Basic_data for summarizing data information.
$Species_richness for showing various species richness estimates along with related statistics.
$Shannon_diversity for showing various Shannon index/diversity estimates.
$Simpson_diversity for showing two Simpson index/diversity estimates.
$Hill_numbers for showing Hill number (diversity) estimates of diversity orders specified in the argument
Chao, A., and Chiu, C. H. (2012). Estimation of species richness and shared species richness. In N. Balakrishnan (ed). Methods and Applications of Statistics in the Atmospheric and Earth Sciences. p.76-111, Wiley, New York.
Chao, A. and Jost, L. (2015). Estimating diversity and entropy profiles via discovery rates of new species. Methods in Ecology and Evolution, 6, 873-882.
Chao, A., Wang, Y. T. and Jost, L. (2013). Entropy and the species accumulation curve: a novel estimator of entropy via discovery rates of new species. Methods in Ecology and Evolution 4, 1091-1110.
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## Not run: data(DiversityData) # Type (1) abundance data Diversity(DiversityData$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)
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