subdiv | R Documentation |
Generic function for calculating subcommunity-level diversity.
subdiv(data, qs) ## S4 method for signature 'powermean' subdiv(data, qs) ## S4 method for signature 'relativeentropy' subdiv(data, qs) ## S4 method for signature 'metacommunity' subdiv(data, qs)
data |
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qs |
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data
may be input as one of three different classes:
powermean
: raw or normalised metacommunity alpha, rho or gamma
diversity components; will calculate subcommunity-level raw or normalised
metacommunity alpha, rho or gamma diversity
relativeentropy
: raw or normalised metacommunity beta
diversity components; will calculate subcommunity-level raw or normalised
metacommunity beta diversity
metacommunity
: will calculate all subcommunity measures of
diversity
subdiv()
returns a standard output of class rdiv
Reeve, R., T. Leinster, C. Cobbold, J. Thompson, N. Brummitt, S. Mitchell, and L. Matthews. 2016. How to partition diversity. arXiv 1404.6520v3:1–9.
inddiv
for type-level diversity and
metadiv
for metacommunity-level diversity.
# Define metacommunity pop <- data.frame(a = c(1,3), b = c(1,1)) row.names(pop) <- paste0("sp", 1:2) pop <- pop/sum(pop) meta <- metacommunity(pop) # Calculate subcommunity gamma diversity (takes the power mean) g <- raw_gamma(meta) subdiv(g, 0:2) # Calculate subcommunity beta diversity (takes the relative entropy) b <- raw_beta(meta) subdiv(b, 0:2) # Calculate all measures of subcommunity diversity subdiv(meta, 0:2)
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