Utilities for community abundances (objects of class "abundances").
Usage
abd_species(abundances, check_arguments = TRUE)
abd_sum(abundances, as_numeric = FALSE, check_arguments = TRUE)
prob_species(species_distribution, check_arguments = TRUE)Arguments
- abundances
an object of class abundances.
- check_arguments
if
TRUE, the function arguments are verified. Should be set toFALSEto save time when the arguments have been checked elsewhere.- as_numeric
if
TRUE, a number or a numeric vector is returned rather than a tibble.- species_distribution
an object of class species_distribution.
Value
abd_species() returns a tibble containing the species abundance columns only,
to simplify numeric operations.
prob_species() returns the same tibble but values are probabilities.
abd_sum() returns the sample sizes of the communities in a numeric vector.
Examples
abd_species(paracou_6_abd)
#> # A tibble: 4 × 335
#> Abarema_jupunba Abarema_mataybifolia Amaioua_guianensis Amanoa_congesta
#> <int> <int> <int> <int>
#> 1 2 2 1 1
#> 2 2 0 1 0
#> 3 2 2 0 0
#> 4 4 0 0 0
#> # ℹ 331 more variables: Amanoa_guianensis <int>, Ambelania_acida <int>,
#> # Amphirrhox_longifolia <int>, Andira_coriacea <int>, Apeiba_glabra <int>,
#> # Aspidosperma_album <int>, Aspidosperma_cruentum <int>,
#> # Aspidosperma_excelsum <int>, Bocoa_prouacensis <int>,
#> # Brosimum_guianense <int>, Brosimum_rubescens <int>, Brosimum_utile <int>,
#> # Carapa_surinamensis <int>, Caryocar_glabrum <int>, Casearia_decandra <int>,
#> # Casearia_javitensis <int>, Catostemma_fragrans <int>, …
prob_species(paracou_6_abd)
#> # A tibble: 4 × 335
#> Abarema_jupunba Abarema_mataybifolia Amaioua_guianensis Amanoa_congesta
#> <dbl> <dbl> <dbl> <dbl>
#> 1 0.00212 0.00212 0.00106 0.00106
#> 2 0.00229 0 0.00115 0
#> 3 0.00215 0.00215 0 0
#> 4 0.00501 0 0 0
#> # ℹ 331 more variables: 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>, …
abd_sum(paracou_6_abd)
#> # A tibble: 4 × 3
#> site weight abundance
#> <chr> <dbl> <dbl>
#> 1 subplot_1 1.56 942
#> 2 subplot_2 1.56 872
#> 3 subplot_3 1.56 929
#> 4 subplot_4 1.56 798