The ordinariness of a species is the average similarity of its individuals with others (Leinster and Cobbold 2012) .
An object of class species_distribution.
A similarity matrix, that can be obtained by fun_similarity. Its default value is the identity matrix.
If TRUE, a number or a numeric vector is returned rather than a tibble.
If TRUE, the function arguments are verified.
Should be set to FALSE to save time when the arguments have been checked elsewhere.
A tibble with the ordinariness of each species, or a matrix if
argument as_numeric is TRUE.
All species of the species_distribution must be found in the matrix of
similarities if it is named.
If it is not, its size must equal the number of species.
Then, the order of species is assumed to be the same as that of the
species_distribution.
Leinster T, Cobbold C (2012). “Measuring Diversity: The Importance of Species Similarity.” Ecology, 93(3), 477--489. doi:10.1890/10-2402.1 .
fun_ordinariness(paracou_6_abd, fun_similarity(paracou_6_fundist))
#> # A tibble: 4 × 337
#> site weight Abarema_jupunba Abarema_mataybifolia Amaioua_guianensis
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 subplot_1 1.56 0.794 0.801 0.702
#> 2 subplot_2 1.56 0.790 0.785 0.694
#> 3 subplot_3 1.56 0.790 0.793 0.701
#> 4 subplot_4 1.56 0.797 0.797 0.695
#> # ℹ 332 more variables: Amanoa_congesta <dbl>, Amanoa_guianensis <dbl>,
#> # Ambelania_acida <dbl>, Amphirrhox_longifolia <dbl>, Andira_coriacea <dbl>,
#> # Apeiba_glabra <dbl>, Aspidosperma_album <dbl>, Aspidosperma_cruentum <dbl>,
#> # Aspidosperma_excelsum <dbl>, Bocoa_prouacensis <dbl>,
#> # Brosimum_guianense <dbl>, Brosimum_rubescens <dbl>, Brosimum_utile <dbl>,
#> # Carapa_surinamensis <dbl>, Caryocar_glabrum <dbl>, Casearia_decandra <dbl>,
#> # Casearia_javitensis <dbl>, Catostemma_fragrans <dbl>, …
# Compare with probabilities
probabilities(paracou_6_abd)
#> # A tibble: 4 × 337
#> site weight Abarema_jupunba Abarema_mataybifolia Amaioua_guianensis
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 subplot_1 1 0.00212 0.00212 0.00106
#> 2 subplot_2 1 0.00229 0 0.00115
#> 3 subplot_3 1 0.00215 0.00215 0
#> 4 subplot_4 1 0.00501 0 0
#> # ℹ 332 more variables: Amanoa_congesta <dbl>, Amanoa_guianensis <dbl>,
#> # Ambelania_acida <dbl>, Amphirrhox_longifolia <dbl>, Andira_coriacea <dbl>,
#> # Apeiba_glabra <dbl>, Aspidosperma_album <dbl>, Aspidosperma_cruentum <dbl>,
#> # Aspidosperma_excelsum <dbl>, Bocoa_prouacensis <dbl>,
#> # Brosimum_guianense <dbl>, Brosimum_rubescens <dbl>, Brosimum_utile <dbl>,
#> # Carapa_surinamensis <dbl>, Caryocar_glabrum <dbl>, Casearia_decandra <dbl>,
#> # Casearia_javitensis <dbl>, Catostemma_fragrans <dbl>, …
# Decrease similarities so that ordinariness is close to probability
fun_ordinariness(paracou_6_abd, fun_similarity(paracou_6_fundist, rate = 100))
#> # A tibble: 4 × 337
#> site weight Abarema_jupunba Abarema_mataybifolia Amaioua_guianensis
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 subplot_1 1.56 0.00217 0.00221 0.00110
#> 2 subplot_2 1.56 0.00233 0.0000526 0.00116
#> 3 subplot_3 1.56 0.00220 0.00225 0.00000939
#> 4 subplot_4 1.56 0.00508 0.0000470 0.000000101
#> # ℹ 332 more variables: Amanoa_congesta <dbl>, Amanoa_guianensis <dbl>,
#> # Ambelania_acida <dbl>, Amphirrhox_longifolia <dbl>, Andira_coriacea <dbl>,
#> # Apeiba_glabra <dbl>, Aspidosperma_album <dbl>, Aspidosperma_cruentum <dbl>,
#> # Aspidosperma_excelsum <dbl>, Bocoa_prouacensis <dbl>,
#> # Brosimum_guianense <dbl>, Brosimum_rubescens <dbl>, Brosimum_utile <dbl>,
#> # Carapa_surinamensis <dbl>, Caryocar_glabrum <dbl>, Casearia_decandra <dbl>,
#> # Casearia_javitensis <dbl>, Catostemma_fragrans <dbl>, …