Calculate \(\gamma\), \(\beta\) and \(\alpha\) diversities of a metacommunity.
div_part(
abundances,
q = 1,
estimator = c("UnveilJ", "ChaoJost", "ChaoShen", "GenCov", "Grassberger", "Holste",
"Marcon", "UnveilC", "UnveiliC", "ZhangGrabchak"),
level = NULL,
probability_estimator = c("Chao2015", "Chao2013", "ChaoShen", "naive"),
unveiling = c("geometric", "uniform", "none"),
richness_estimator = c("jackknife", "iChao1", "Chao1", "naive"),
jack_alpha = 0.05,
jack_max = 10,
coverage_estimator = c("ZhangHuang", "Chao", "Turing", "Good"),
check_arguments = TRUE
)An object of class abundances.
The order of diversity.
An estimator of diversity.
The level of interpolation or extrapolation.
It may be a sample size (an integer) or a sample coverage
(a number between 0 and 1).
If not NULL, the asymptotic estimator is ignored.
A string containing one of the possible estimators of the probability distribution (see probabilities). Used only for extrapolation.
A string containing one of the possible unveiling methods to estimate the probabilities of the unobserved species (see probabilities). Used only for extrapolation.
An estimator of richness to evaluate the total number of species, see div_richness. Used for interpolation and extrapolation.
The risk level, 5% by default, used to optimize the jackknife order.
The highest jackknife order allowed. Default is 10.
An estimator of sample coverage used by coverage.
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 diversity values at each scale.
The function computes \(\gamma\) diversity after building a metacommunity from local communities according to their weight (Marcon et al. 2014) . \(\alpha\) entropy is the weighted mean local entropy, converted into Hill numbers to obtain \(\alpha\) diversity. \(\beta\) diversity is obtained as the ratio of \(\gamma\) to \(\alpha\).
Marcon E, Scotti I, Hérault B, Rossi V, Lang G (2014). “Generalization of the Partitioning of Shannon Diversity.” Plos One, 9(3), e90289. doi:10.1371/journal.pone.0090289 .
div_part(paracou_6_abd)
#> # A tibble: 7 × 6
#> site scale estimator order diversity weight
#> <chr> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 Metacommunity gamma "UnveilJ" 1 111. 6.25
#> 2 Metacommunity beta "" 1 1.09 NA
#> 3 Metacommunity alpha "" 1 102. NA
#> 4 subplot_1 community "UnveilJ" 1 96.3 1.56
#> 5 subplot_2 community "UnveilJ" 1 113. 1.56
#> 6 subplot_3 community "UnveilJ" 1 105. 1.56
#> 7 subplot_4 community "UnveilJ" 1 94.6 1.56