beta_dis {hilldiv}

Beta dissimilarity

Description

Compute dissimilarity or similarity values based on beta diversities (neutral or phylogenetic) and sample size.

Usage

beta_dis(beta, qvalue, N, metric, type)

Arguments

beta

A numeric beta diversity value or an object outputted by function div_part() (which contains all the information to compute (dis)similarities).

qvalue

A positive number, usually between 0 and 5, but most commonly 0, 1 or 2. It can be an integer or contain decimals.

N

An integer indicating sample size, the number of sampling units to be used to compute the (dis)similarity measures. The argument is ovewritten if a 'div_part' object is used.

metric

A vector containing "C", "U", "V" or "S". C: Sørensen-type overlap or complement. U: Jaccard-type overlap or complement. V: Sørensen-type turnover or complement. S: Jaccard-type turnover or complement. See hilldiv wiki for further information.

type

A character object containing either "similarity" or "dissimilarity". If 'similarity' is used, similarity metrics (0: completely different composition - 1: identical composition) are returned. If 'dissimilarity' is used, dissimilarity metrics (0: identical composition - 1:completely different composition) are returned.

Details

(Dis)similarity computation from beta diversities based on Hill numbers

Author(s)

Antton Alberdi, [e-mail]

References

Alberdi, A., Gilbert, M.T.P. (2019). A guide to the application of Hill numbers to DNA-based diversity analyses. Molecular Ecology Resources, 19, 804-817.

Chao, A., Chiu, C.H., & Hsieh, T. C. (2012). Proposing a resolution to debates on diversity partitioning. Ecology, 93, 2037-2051.

Jost, L. (2007). Partitioning diversity into independent alpha and beta components. Ecology, 88, 2427-2439.

See Also

div_part, gamma_div, pair_dis

Examples

data(bat.diet.otutable)
data(bat.diet.tree)
#Manually indicating beta diversity, order of diversity and sample size
beta_dis(beta=4.5,qvalue=1,N=8)
beta_dis(beta=4.5,qvalue=1,N=8,metric="C",type="similarity")
#Using an object created with the function div_part()
divpartobject <- div_part(bat.diet.otutable,qvalue=0,tree=bat.diet.tree)
beta_dis(divpartobject)
beta_dis(divpartobject,metric="S",type="similarity")