abd_freq_count {divent} | R Documentation |
Abundance Frequency Count of a Community
Description
Count the number of species observed the same number of times.
Usage
abd_freq_count(
abd,
level = NULL,
probability_estimator = c("Chao2015", "Chao2013", "ChaoShen", "naive"),
unveiling = c("geometric", "uniform", "none"),
richness_estimator = c("jackknife", "iChao1", "Chao1", "rarefy", "naive"),
jack_alpha = 0.05,
jack_max = 10,
coverage_estimator = c("ZhangHuang", "Chao", "Turing", "Good"),
check_arguments = TRUE
)
Arguments
abd |
A numeric vector containing species abundances. |
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 |
A string containing an estimator recognized by div_richness to evaluate the total number of species in probabilities. Used only for 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 |
Details
The Abundance Frequency Count (Chao and Jost 2015) is the number of species observed each number of times. It is a way to summarize the species distribution.
It can be estimated at a specified level of interpolation or extrapolation. Extrapolation relies on the estimation of the estimation of the asymptotic distribution of the community by probabilities and eq. (5) of (Chao et al. 2014).
Value
A two-column tibble. The first column contains the number of observations, the second one the number of species observed this number of times.
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.
Chao A, Jost L (2015).
“Estimating Diversity and Entropy Profiles via Discovery Rates of New Species.”
Methods in Ecology and Evolution, 6(8), 873–882.
doi:10.1111/2041-210X.12349.
Examples
abd_freq_count(as.numeric(paracou_6_abd[1, ]))