Calculates similarity sensitive raw subcommunity alpha diversity (an
estimate of naive-community metacommunity diversity). This measure may be
calculated for a series of orders, represented as a vector of qs.
raw_sub_alpha(meta, qs)object of class metacommunity
vector of mode numeric containing q values
raw_sub_alpha returns a standard output of class rdiv
R. Reeve, T. Leinster, C. Cobbold, J. Thompson, N. Brummitt, S. Mitchell, and L. Matthews. 2016. How to partition diversity. arXiv 1404.6520v3:1–9.
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 raw subcommunity alpha diversity
raw_sub_alpha(meta, 0:2)
#> measure q type_level type_name partition_level partition_name diversity
#> 1 raw alpha 0 types subcommunity a 3.000000
#> 2 raw alpha 0 types subcommunity b 6.000000
#> 3 raw alpha 1 types subcommunity a 2.632148
#> 4 raw alpha 1 types subcommunity b 6.000000
#> 5 raw alpha 2 types subcommunity a 2.400000
#> 6 raw alpha 2 types subcommunity b 6.000000
#> dat_id transformation normalised k max_d
#> 1 naive NA NA NA NA
#> 2 naive NA NA NA NA
#> 3 naive NA NA NA NA
#> 4 naive NA NA NA NA
#> 5 naive NA NA NA NA
#> 6 naive NA NA NA NA