SimilarityPair: Estimation of two-assemblage similarity measures
In AnneChao/SpadeR: Species-Richness Prediction and Diversity Estimation with R

Description Usage Arguments Value References Examples

SimilarityPair: Estimation various similarity indices for two assemblages. The richness-based indices include the classic two-community Jaccard and Sorensen indices; the abundance-based indices include the Horn, Morisita-Horn, regional species-overlap, two-community Bray-Curtis and the abundance-based Jaccard and Sorensen indices. Three types of data are supported: Type (1) abundance data (datatype="abundance"), Type (2) incidence-frequency data (datatype="incidence_freq"), and Type (2B) incidence-raw data (datatype="incidence_raw"); see SpadeR-package details for data input formats.

1 2	SimilarityPair(X, datatype = c("abundance", "incidence_freq", "incidence_raw"), units, nboot = 200)

`X`	a matrix/data.frame of species abundances/incidences.
`datatype`	type of input data, "abundance", "incidence_freq" or "incidence_raw".
`units`	number of sampling units in each community. For `datatype = "incidence_raw"`, users must specify the number of sampling units taken from each community. This argument is not needed for "abundance" and "incidence_freq" data.
`nboot`	an integer specifying the number of replications.

a list of ten objects:

$datatype for showing the specified data types (abundance or incidence).

$info for summarizing data information.

$Empirical_richness for showing the observed values of the richness-based similarity indices include the classic two-community Jaccard and Sorensen indices.

$Empirical_relative for showing the observed values of the equal-weighted similarity indices for comparing species relative abundances including Horn, Morisita-Horn, regional overlap, Chao-Jaccard and Chao-Sorensen abundance (or incidence) measures based on species relative abundances.

$Empirical_WtRelative for showing the observed value of the Horn similarity index for comparing size-weighted species relative abundances based on Shannon entropy under equal-effort sampling.

$Empirical_absolute for showing the observed values of the similarity indices for comparing absolute abundances. These measures include the Shannon-entropy-based measure, Morisita-Horn and the regional overlap measures based on species absolute abundances, as well as the Bray-Curtis index. All measures are valid only under equal-effort sampling.

The corresponding four objects for showing the estimated similarity indices are: $estimated_richness, $estimated_relative, $estimated_WtRelative and $estimated_Absolute.

Chao, A., Chazdon, R. L., Colwell, R. K. and Shen, T.-J. (2005). A new statistical approach for assessing similarity of species composition with incidence and abundance data. Ecology Letters, 8, 148-159.

Chao, A., and Chiu, C. H. (2016). Bridging the variance and diversity decomposition approaches to beta diversity via similarity and differentiation measures. Methods in Ecology and Evolution, 7, 919-928.

Chao, A., Jost, L., Hsieh, T. C., Ma, K. H., Sherwin, W. B. and Rollins, L. A. (2015). Expected Shannon entropy and Shannon differentiation between subpopulations for neutral genes under the finite island model. Plos One, 10:e0125471.

Chiu, C. H., Jost, L. and Chao, A. (2014). Phylogenetic beta diversity, similarity, and differentiation measures based on Hill numbers. Ecological Monographs, 84, 21-44.

## Not run: 
data(SimilarityPairData)
# Type (1) abundance data 
SimilarityPair(SimilarityPairData$Abu,"abundance",nboot=200)
# Type (2) incidence-frequency data 
SimilarityPair(SimilarityPairData$Inci,"incidence_freq",nboot=200)
# Type (2B) incidence-raw data 
SimilarityPair(SimilarityPairData$Inci_raw,"incidence_raw",units=c(19,17),nboot=200)

## End(Not run)