div_phylo {divent} | R Documentation |
Phylogenetic Diversity of a Community
Description
Estimate the diversity of species from abundance or probability data and a phylogenetic tree. Several estimators are available to deal with incomplete sampling.
Usage
div_phylo(x, tree, q = 1, ...)
## S3 method for class 'numeric'
div_phylo(
x,
tree,
q = 1,
normalize = TRUE,
estimator = c("UnveilJ", "ChaoJost", "ChaoShen", "GenCov", "Grassberger", "Marcon",
"UnveilC", "UnveiliC", "ZhangGrabchak", "naive", "Bonachela", "Holste"),
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"),
as_numeric = FALSE,
...,
check_arguments = TRUE
)
## S3 method for class 'species_distribution'
div_phylo(
x,
tree,
q = 1,
normalize = TRUE,
estimator = c("UnveilJ", "ChaoJost", "ChaoShen", "GenCov", "Grassberger", "Marcon",
"UnveilC", "UnveiliC", "ZhangGrabchak", "naive", "Bonachela", "Holste"),
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"),
gamma = FALSE,
as_numeric = FALSE,
...,
check_arguments = TRUE
)
Arguments
x |
An object, that may be a named numeric vector (names are species names) containing abundances or probabilities, or an object of class abundances or probabilities. |
tree |
an ultrametric, phylogenetic tree. May be an object of class phylo_divent, ape::phylo, ade4::phylog or stats::hclust. |
q |
a number: the order of diversity. |
... |
Unused. |
normalize |
if |
estimator |
An estimator of asymptotic 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. |
as_numeric |
if |
check_arguments |
if |
gamma |
if |
Details
Bias correction requires the number of individuals. See div_hill for estimators.
Entropy can be estimated at a specified level of interpolation or extrapolation, either a chosen sample size or sample coverage (Chao et al. 2014), rather than its asymptotic value. See accum_tsallis for details.
Value
A tibble with the site names, the estimators used and the estimated diversity
References
Chao A, Gotelli NJ, Hsieh TC, Sander EL, Ma KH, Colwell RK, Ellison AM (2014). “Rarefaction and Extrapolation with Hill Numbers: A Framework for Sampling and Estimation in Species Diversity Studies.” Ecological Monographs, 84(1), 45–67. doi:10.1890/13-0133.1.
Examples
div_phylo(paracou_6_abd, tree = paracou_6_taxo, q = 2)
# At 80% coverage
div_phylo(paracou_6_abd, tree = paracou_6_taxo, q = 2, level = 0.8)
# Gamma entropy
div_phylo(paracou_6_abd, tree = paracou_6_taxo, q = 2, gamma = TRUE)