Generic function for calculating individual-level diversity.
inddiv(data, qs)
# S4 method for powermean
inddiv(data, qs)
# S4 method for relativeentropy
inddiv(data, qs)
# S4 method for metacommunity
inddiv(data, qs)matrix of mode numeric; containing diversity
components
vector of mode numeric containing q values
inddiv() returns a standard output of class rdiv
data may be input as three different classes:
power_mean: calculates raw and normalised subcommunity alpha, rho
or gamma diversity by taking the powermean of diversity components
relativeentropy: calculates raw or normalised subcommunity beta
diversity by taking the relative entropy of diversity components
metacommunity: calculates all subcommunity 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 <- cbind.data.frame(A = c(1,1), B = c(2,0), C = c(3,1))
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)
inddiv(g, 0:2)
#> measure q type_level type_name partition_level partition_name diversity
#> 1 gamma 0 type sp1 subcommunity A 1.333333
#> 2 gamma 0 type sp2 subcommunity A 4.000000
#> 3 gamma 0 type sp1 subcommunity B 1.333333
#> 4 gamma 0 type sp2 subcommunity B 0.000000
#> 5 gamma 0 type sp1 subcommunity C 1.333333
#> 6 gamma 0 type sp2 subcommunity C 4.000000
#> 7 gamma 1 type sp1 subcommunity A 1.333333
#> 8 gamma 1 type sp2 subcommunity A 4.000000
#> 9 gamma 1 type sp1 subcommunity B 1.333333
#> 10 gamma 1 type sp2 subcommunity B 0.000000
#> 11 gamma 1 type sp1 subcommunity C 1.333333
#> 12 gamma 1 type sp2 subcommunity C 4.000000
#> 13 gamma 2 type sp1 subcommunity A 1.333333
#> 14 gamma 2 type sp2 subcommunity A 4.000000
#> 15 gamma 2 type sp1 subcommunity B 1.333333
#> 16 gamma 2 type sp2 subcommunity B 0.000000
#> 17 gamma 2 type sp1 subcommunity C 1.333333
#> 18 gamma 2 type sp2 subcommunity C 4.000000
#> 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
#> 7 naive NA NA NA NA
#> 8 naive NA NA NA NA
#> 9 naive NA NA NA NA
#> 10 naive NA NA NA NA
#> 11 naive NA NA NA NA
#> 12 naive NA NA NA NA
#> 13 naive NA NA NA NA
#> 14 naive NA NA NA NA
#> 15 naive NA NA NA NA
#> 16 naive NA NA NA NA
#> 17 naive NA NA NA NA
#> 18 naive NA NA NA NA
# Calculate subcommunity beta diversity (takes the relative entropy)
b <- raw_beta(meta)
inddiv(b, 0:2)
#> measure q type_level type_name partition_level partition_name diversity
#> 1 raw beta 0 type sp1 subcommunity A 0.1666667
#> 2 raw beta 0 type sp2 subcommunity A 0.5000000
#> 3 raw beta 0 type sp1 subcommunity B 0.3333333
#> 4 raw beta 0 type sp2 subcommunity B NaN
#> 5 raw beta 0 type sp1 subcommunity C 0.5000000
#> 6 raw beta 0 type sp2 subcommunity C 0.5000000
#> 7 raw beta 1 type sp1 subcommunity A 0.1666667
#> 8 raw beta 1 type sp2 subcommunity A 0.5000000
#> 9 raw beta 1 type sp1 subcommunity B 0.3333333
#> 10 raw beta 1 type sp2 subcommunity B NaN
#> 11 raw beta 1 type sp1 subcommunity C 0.5000000
#> 12 raw beta 1 type sp2 subcommunity C 0.5000000
#> 13 raw beta 2 type sp1 subcommunity A 0.1666667
#> 14 raw beta 2 type sp2 subcommunity A 0.5000000
#> 15 raw beta 2 type sp1 subcommunity B 0.3333333
#> 16 raw beta 2 type sp2 subcommunity B NaN
#> 17 raw beta 2 type sp1 subcommunity C 0.5000000
#> 18 raw beta 2 type sp2 subcommunity C 0.5000000
#> 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
#> 7 naive NA NA NA NA
#> 8 naive NA NA NA NA
#> 9 naive NA NA NA NA
#> 10 naive NA NA NA NA
#> 11 naive NA NA NA NA
#> 12 naive NA NA NA NA
#> 13 naive NA NA NA NA
#> 14 naive NA NA NA NA
#> 15 naive NA NA NA NA
#> 16 naive NA NA NA NA
#> 17 naive NA NA NA NA
#> 18 naive NA NA NA NA
# Calculate all measures of individual diversity
inddiv(meta, 0:2)
#> measure q type_level type_name partition_level partition_name
#> 1 raw alpha 0 type sp1 subcommunity A
#> 2 raw alpha 0 type sp2 subcommunity A
#> 3 raw alpha 0 type sp1 subcommunity B
#> 4 raw alpha 0 type sp2 subcommunity B
#> 5 raw alpha 0 type sp1 subcommunity C
#> 6 raw alpha 0 type sp2 subcommunity C
#> 7 raw alpha 1 type sp1 subcommunity A
#> 8 raw alpha 1 type sp2 subcommunity A
#> 9 raw alpha 1 type sp1 subcommunity B
#> 10 raw alpha 1 type sp2 subcommunity B
#> 11 raw alpha 1 type sp1 subcommunity C
#> 12 raw alpha 1 type sp2 subcommunity C
#> 13 raw alpha 2 type sp1 subcommunity A
#> 14 raw alpha 2 type sp2 subcommunity A
#> 15 raw alpha 2 type sp1 subcommunity B
#> 16 raw alpha 2 type sp2 subcommunity B
#> 17 raw alpha 2 type sp1 subcommunity C
#> 18 raw alpha 2 type sp2 subcommunity C
#> 19 normalised alpha 0 type sp1 subcommunity A
#> 20 normalised alpha 0 type sp2 subcommunity A
#> 21 normalised alpha 0 type sp1 subcommunity B
#> 22 normalised alpha 0 type sp2 subcommunity B
#> 23 normalised alpha 0 type sp1 subcommunity C
#> 24 normalised alpha 0 type sp2 subcommunity C
#> 25 normalised alpha 1 type sp1 subcommunity A
#> 26 normalised alpha 1 type sp2 subcommunity A
#> 27 normalised alpha 1 type sp1 subcommunity B
#> 28 normalised alpha 1 type sp2 subcommunity B
#> 29 normalised alpha 1 type sp1 subcommunity C
#> 30 normalised alpha 1 type sp2 subcommunity C
#> 31 normalised alpha 2 type sp1 subcommunity A
#> 32 normalised alpha 2 type sp2 subcommunity A
#> 33 normalised alpha 2 type sp1 subcommunity B
#> 34 normalised alpha 2 type sp2 subcommunity B
#> 35 normalised alpha 2 type sp1 subcommunity C
#> 36 normalised alpha 2 type sp2 subcommunity C
#> 37 raw beta 0 type sp1 subcommunity A
#> 38 raw beta 0 type sp2 subcommunity A
#> 39 raw beta 0 type sp1 subcommunity B
#> 40 raw beta 0 type sp2 subcommunity B
#> 41 raw beta 0 type sp1 subcommunity C
#> 42 raw beta 0 type sp2 subcommunity C
#> 43 raw beta 1 type sp1 subcommunity A
#> 44 raw beta 1 type sp2 subcommunity A
#> 45 raw beta 1 type sp1 subcommunity B
#> 46 raw beta 1 type sp2 subcommunity B
#> 47 raw beta 1 type sp1 subcommunity C
#> 48 raw beta 1 type sp2 subcommunity C
#> 49 raw beta 2 type sp1 subcommunity A
#> 50 raw beta 2 type sp2 subcommunity A
#> 51 raw beta 2 type sp1 subcommunity B
#> 52 raw beta 2 type sp2 subcommunity B
#> 53 raw beta 2 type sp1 subcommunity C
#> 54 raw beta 2 type sp2 subcommunity C
#> 55 normalised beta 0 type sp1 subcommunity A
#> 56 normalised beta 0 type sp2 subcommunity A
#> 57 normalised beta 0 type sp1 subcommunity B
#> 58 normalised beta 0 type sp2 subcommunity B
#> 59 normalised beta 0 type sp1 subcommunity C
#> 60 normalised beta 0 type sp2 subcommunity C
#> 61 normalised beta 1 type sp1 subcommunity A
#> 62 normalised beta 1 type sp2 subcommunity A
#> 63 normalised beta 1 type sp1 subcommunity B
#> 64 normalised beta 1 type sp2 subcommunity B
#> 65 normalised beta 1 type sp1 subcommunity C
#> 66 normalised beta 1 type sp2 subcommunity C
#> 67 normalised beta 2 type sp1 subcommunity A
#> 68 normalised beta 2 type sp2 subcommunity A
#> 69 normalised beta 2 type sp1 subcommunity B
#> 70 normalised beta 2 type sp2 subcommunity B
#> 71 normalised beta 2 type sp1 subcommunity C
#> 72 normalised beta 2 type sp2 subcommunity C
#> 73 raw rho 0 type sp1 subcommunity A
#> 74 raw rho 0 type sp2 subcommunity A
#> 75 raw rho 0 type sp1 subcommunity B
#> 76 raw rho 0 type sp2 subcommunity B
#> 77 raw rho 0 type sp1 subcommunity C
#> 78 raw rho 0 type sp2 subcommunity C
#> 79 raw rho 1 type sp1 subcommunity A
#> 80 raw rho 1 type sp2 subcommunity A
#> 81 raw rho 1 type sp1 subcommunity B
#> 82 raw rho 1 type sp2 subcommunity B
#> 83 raw rho 1 type sp1 subcommunity C
#> 84 raw rho 1 type sp2 subcommunity C
#> 85 raw rho 2 type sp1 subcommunity A
#> 86 raw rho 2 type sp2 subcommunity A
#> 87 raw rho 2 type sp1 subcommunity B
#> 88 raw rho 2 type sp2 subcommunity B
#> 89 raw rho 2 type sp1 subcommunity C
#> 90 raw rho 2 type sp2 subcommunity C
#> 91 normalised rho 0 type sp1 subcommunity A
#> 92 normalised rho 0 type sp2 subcommunity A
#> 93 normalised rho 0 type sp1 subcommunity B
#> 94 normalised rho 0 type sp2 subcommunity B
#> 95 normalised rho 0 type sp1 subcommunity C
#> 96 normalised rho 0 type sp2 subcommunity C
#> 97 normalised rho 1 type sp1 subcommunity A
#> 98 normalised rho 1 type sp2 subcommunity A
#> 99 normalised rho 1 type sp1 subcommunity B
#> 100 normalised rho 1 type sp2 subcommunity B
#> 101 normalised rho 1 type sp1 subcommunity C
#> 102 normalised rho 1 type sp2 subcommunity C
#> 103 normalised rho 2 type sp1 subcommunity A
#> 104 normalised rho 2 type sp2 subcommunity A
#> 105 normalised rho 2 type sp1 subcommunity B
#> 106 normalised rho 2 type sp2 subcommunity B
#> 107 normalised rho 2 type sp1 subcommunity C
#> 108 normalised rho 2 type sp2 subcommunity C
#> 109 gamma 0 type sp1 subcommunity A
#> 110 gamma 0 type sp2 subcommunity A
#> 111 gamma 0 type sp1 subcommunity B
#> 112 gamma 0 type sp2 subcommunity B
#> 113 gamma 0 type sp1 subcommunity C
#> 114 gamma 0 type sp2 subcommunity C
#> 115 gamma 1 type sp1 subcommunity A
#> 116 gamma 1 type sp2 subcommunity A
#> 117 gamma 1 type sp1 subcommunity B
#> 118 gamma 1 type sp2 subcommunity B
#> 119 gamma 1 type sp1 subcommunity C
#> 120 gamma 1 type sp2 subcommunity C
#> 121 gamma 2 type sp1 subcommunity A
#> 122 gamma 2 type sp2 subcommunity A
#> 123 gamma 2 type sp1 subcommunity B
#> 124 gamma 2 type sp2 subcommunity B
#> 125 gamma 2 type sp1 subcommunity C
#> 126 gamma 2 type sp2 subcommunity C
#> diversity dat_id transformation normalised k max_d
#> 1 8.0000000 naive NA NA NA NA
#> 2 8.0000000 naive NA NA NA NA
#> 3 4.0000000 naive NA NA NA NA
#> 4 NaN naive NA NA NA NA
#> 5 2.6666667 naive NA NA NA NA
#> 6 8.0000000 naive NA NA NA NA
#> 7 8.0000000 naive NA NA NA NA
#> 8 8.0000000 naive NA NA NA NA
#> 9 4.0000000 naive NA NA NA NA
#> 10 NaN naive NA NA NA NA
#> 11 2.6666667 naive NA NA NA NA
#> 12 8.0000000 naive NA NA NA NA
#> 13 8.0000000 naive NA NA NA NA
#> 14 8.0000000 naive NA NA NA NA
#> 15 4.0000000 naive NA NA NA NA
#> 16 NaN naive NA NA NA NA
#> 17 2.6666667 naive NA NA NA NA
#> 18 8.0000000 naive NA NA NA NA
#> 19 2.0000000 naive NA NA NA NA
#> 20 2.0000000 naive NA NA NA NA
#> 21 1.0000000 naive NA NA NA NA
#> 22 NaN naive NA NA NA NA
#> 23 1.3333333 naive NA NA NA NA
#> 24 4.0000000 naive NA NA NA NA
#> 25 2.0000000 naive NA NA NA NA
#> 26 2.0000000 naive NA NA NA NA
#> 27 1.0000000 naive NA NA NA NA
#> 28 NaN naive NA NA NA NA
#> 29 1.3333333 naive NA NA NA NA
#> 30 4.0000000 naive NA NA NA NA
#> 31 2.0000000 naive NA NA NA NA
#> 32 2.0000000 naive NA NA NA NA
#> 33 1.0000000 naive NA NA NA NA
#> 34 NaN naive NA NA NA NA
#> 35 1.3333333 naive NA NA NA NA
#> 36 4.0000000 naive NA NA NA NA
#> 37 0.1666667 naive NA NA NA NA
#> 38 0.5000000 naive NA NA NA NA
#> 39 0.3333333 naive NA NA NA NA
#> 40 NaN naive NA NA NA NA
#> 41 0.5000000 naive NA NA NA NA
#> 42 0.5000000 naive NA NA NA NA
#> 43 0.1666667 naive NA NA NA NA
#> 44 0.5000000 naive NA NA NA NA
#> 45 0.3333333 naive NA NA NA NA
#> 46 NaN naive NA NA NA NA
#> 47 0.5000000 naive NA NA NA NA
#> 48 0.5000000 naive NA NA NA NA
#> 49 0.1666667 naive NA NA NA NA
#> 50 0.5000000 naive NA NA NA NA
#> 51 0.3333333 naive NA NA NA NA
#> 52 NaN naive NA NA NA NA
#> 53 0.5000000 naive NA NA NA NA
#> 54 0.5000000 naive NA NA NA NA
#> 55 0.6666667 naive NA NA NA NA
#> 56 2.0000000 naive NA NA NA NA
#> 57 1.3333333 naive NA NA NA NA
#> 58 NaN naive NA NA NA NA
#> 59 1.0000000 naive NA NA NA NA
#> 60 1.0000000 naive NA NA NA NA
#> 61 0.6666667 naive NA NA NA NA
#> 62 2.0000000 naive NA NA NA NA
#> 63 1.3333333 naive NA NA NA NA
#> 64 NaN naive NA NA NA NA
#> 65 1.0000000 naive NA NA NA NA
#> 66 1.0000000 naive NA NA NA NA
#> 67 0.6666667 naive NA NA NA NA
#> 68 2.0000000 naive NA NA NA NA
#> 69 1.3333333 naive NA NA NA NA
#> 70 NaN naive NA NA NA NA
#> 71 1.0000000 naive NA NA NA NA
#> 72 1.0000000 naive NA NA NA NA
#> 73 6.0000000 naive NA NA NA NA
#> 74 2.0000000 naive NA NA NA NA
#> 75 3.0000000 naive NA NA NA NA
#> 76 NaN naive NA NA NA NA
#> 77 2.0000000 naive NA NA NA NA
#> 78 2.0000000 naive NA NA NA NA
#> 79 6.0000000 naive NA NA NA NA
#> 80 2.0000000 naive NA NA NA NA
#> 81 3.0000000 naive NA NA NA NA
#> 82 NaN naive NA NA NA NA
#> 83 2.0000000 naive NA NA NA NA
#> 84 2.0000000 naive NA NA NA NA
#> 85 6.0000000 naive NA NA NA NA
#> 86 2.0000000 naive NA NA NA NA
#> 87 3.0000000 naive NA NA NA NA
#> 88 NaN naive NA NA NA NA
#> 89 2.0000000 naive NA NA NA NA
#> 90 2.0000000 naive NA NA NA NA
#> 91 1.5000000 naive NA NA NA NA
#> 92 0.5000000 naive NA NA NA NA
#> 93 0.7500000 naive NA NA NA NA
#> 94 NaN naive NA NA NA NA
#> 95 1.0000000 naive NA NA NA NA
#> 96 1.0000000 naive NA NA NA NA
#> 97 1.5000000 naive NA NA NA NA
#> 98 0.5000000 naive NA NA NA NA
#> 99 0.7500000 naive NA NA NA NA
#> 100 NaN naive NA NA NA NA
#> 101 1.0000000 naive NA NA NA NA
#> 102 1.0000000 naive NA NA NA NA
#> 103 1.5000000 naive NA NA NA NA
#> 104 0.5000000 naive NA NA NA NA
#> 105 0.7500000 naive NA NA NA NA
#> 106 NaN naive NA NA NA NA
#> 107 1.0000000 naive NA NA NA NA
#> 108 1.0000000 naive NA NA NA NA
#> 109 1.3333333 naive NA NA NA NA
#> 110 4.0000000 naive NA NA NA NA
#> 111 1.3333333 naive NA NA NA NA
#> 112 0.0000000 naive NA NA NA NA
#> 113 1.3333333 naive NA NA NA NA
#> 114 4.0000000 naive NA NA NA NA
#> 115 1.3333333 naive NA NA NA NA
#> 116 4.0000000 naive NA NA NA NA
#> 117 1.3333333 naive NA NA NA NA
#> 118 0.0000000 naive NA NA NA NA
#> 119 1.3333333 naive NA NA NA NA
#> 120 4.0000000 naive NA NA NA NA
#> 121 1.3333333 naive NA NA NA NA
#> 122 4.0000000 naive NA NA NA NA
#> 123 1.3333333 naive NA NA NA NA
#> 124 0.0000000 naive NA NA NA NA
#> 125 1.3333333 naive NA NA NA NA
#> 126 4.0000000 naive NA NA NA NA