Generic function for calculating metacommunity-level diversity.
metadiv(data, qs)
# S4 method for powermean
metadiv(data, qs)
# S4 method for relativeentropy
metadiv(data, qs)
# S4 method for metacommunity
metadiv(data, qs)matrix of mode numeric; containing diversity
components
vector of mode numeric containing q values
metadiv() returns a standard output of class rdiv
data may be input as one of three different classes:
powermean: raw or normalised metacommunity alpha, rho or gamma
diversity components; will calculate metacommunity-level raw or normalised
metacommunity alpha, rho or gamma diversity
relativeentropy: raw or normalised metacommunity beta
diversity components; will calculate metacommunity-level raw or normalised
metacommunity beta diversity
metacommunity: will calculate all metacommunity measures of
diversity
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.
# Define metacommunity
pop <- data.frame(a = c(1,3), b = c(1,1))
pop <- pop / sum(pop)
meta <- metacommunity(pop)
# Calculate metacommunity gamma diversity (takes the power mean)
g <- raw_gamma(meta)
metadiv(g, 0:2)
#> measure q type_level type_name partition_level partition_name diversity
#> 1 gamma 0 types metacommunity 2.000000
#> 2 gamma 1 types metacommunity 1.889882
#> 3 gamma 2 types metacommunity 1.800000
#> 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
# Calculate metacommunity beta diversity (takes the relative entropy)
b <- raw_beta(meta)
metadiv(b, 0:2)
#> measure q type_level type_name partition_level partition_name diversity
#> 1 raw beta 0 types metacommunity 0.5555556
#> 2 raw beta 1 types metacommunity 0.5455618
#> 3 raw beta 2 types metacommunity 0.5380435
#> 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
# Calculate all measures of metacommunity diversity
metadiv(meta, 0:2)
#> measure q type_level type_name partition_level partition_name
#> 1 raw alpha 0 types metacommunity
#> 2 raw alpha 1 types metacommunity
#> 3 raw alpha 2 types metacommunity
#> 4 normalised alpha 0 types metacommunity
#> 5 normalised alpha 1 types metacommunity
#> 6 normalised alpha 2 types metacommunity
#> 7 raw beta 0 types metacommunity
#> 8 raw beta 1 types metacommunity
#> 9 raw beta 2 types metacommunity
#> 10 normalised beta 0 types metacommunity
#> 11 normalised beta 1 types metacommunity
#> 12 normalised beta 2 types metacommunity
#> 13 raw rho 0 types metacommunity
#> 14 raw rho 1 types metacommunity
#> 15 raw rho 2 types metacommunity
#> 16 normalised rho 0 types metacommunity
#> 17 normalised rho 1 types metacommunity
#> 18 normalised rho 2 types metacommunity
#> 19 gamma 0 types metacommunity
#> 20 gamma 1 types metacommunity
#> 21 gamma 2 types metacommunity
#> diversity dat_id transformation normalised k max_d
#> 1 4.0000000 naive NA NA NA NA
#> 2 3.4641016 naive NA NA NA NA
#> 3 3.0000000 naive NA NA NA NA
#> 4 2.0000000 naive NA NA NA NA
#> 5 1.8329728 naive NA NA NA NA
#> 6 1.7142857 naive NA NA NA NA
#> 7 0.5555556 naive NA NA NA NA
#> 8 0.5455618 naive NA NA NA NA
#> 9 0.5380435 naive NA NA NA NA
#> 10 1.0000000 naive NA NA NA NA
#> 11 1.0310472 naive NA NA NA NA
#> 12 1.0607143 naive NA NA NA NA
#> 13 2.0000000 naive NA NA NA NA
#> 14 1.8329728 naive NA NA NA NA
#> 15 1.7142857 naive NA NA NA NA
#> 16 1.0000000 naive NA NA NA NA
#> 17 0.9698877 naive NA NA NA NA
#> 18 0.9411765 naive NA NA NA NA
#> 19 2.0000000 naive NA NA NA NA
#> 20 1.8898816 naive NA NA NA NA
#> 21 1.8000000 naive NA NA NA NA