div_part {divent} | R Documentation |
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
)
abundances |
An object of class abundances. |
q |
The order of diversity. |
estimator |
An estimator of diversity. |
level |
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 |
probability_estimator |
A string containing one of the possible estimators of the probability distribution (see probabilities). Used only for extrapolation. |
unveiling |
A string containing one of the possible unveiling methods to estimate the probabilities of the unobserved species (see probabilities). Used only for extrapolation. |
richness_estimator |
An estimator of richness to evaluate the total number of species, see div_richness. Used for interpolation and extrapolation. |
jack_alpha |
The risk level, 5% by default, used to optimize the jackknife order. |
jack_max |
The highest jackknife order allowed. Default is 10. |
coverage_estimator |
An estimator of sample coverage used by coverage. |
check_arguments |
If |
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
.
A tibble with diversity values at each scale.
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)