AbdFreqCount {entropart} | R Documentation |
Counts the number of species observed the same number of times.
AbdFreqCount(Ns, Level = NULL, PCorrection="Chao2015", Unveiling="geom",
RCorrection="Rarefy", CheckArguments = TRUE)
Ns |
A numeric vector containing species abundances. |
Level |
The level of interpolation or extrapolation. It may be an an arbitrary sample size (an integer) or a sample coverage (a number between 0 and 1). |
PCorrection |
A string containing one of the possible corrections to estimate a probability distribution in |
Unveiling |
A string containing one of the possible unveiling methods to estimate the probabilities of the unobserved species in |
RCorrection |
A string containing a correction recognized by |
CheckArguments |
Logical; if |
The Abundance Frequency Count (Chao et al., 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 as.ProbaVector
and eq. (5) of Chao et al. (2014).
A two-column matrix. The first column contains the number of observations, the second one the number of species observed this number of times.
Chao, A., Gotelli, N. J., Hsieh, T. C., Sander, E. L., Ma, K. H., Colwell, R. K., Ellison, A. M (2014). Rarefaction and extrapolation with Hill numbers: A framework for sampling and estimation in species diversity studies. Ecological Monographs, 84(1): 45-67.
Chao, A., Hsieh, T. C., Chazdon, R. L., Colwell, R. K., Gotelli, N. J. (2015) Unveiling the Species-Rank Abundance Distribution by Generalizing Good-Turing Sample Coverage Theory. Ecology 96(5): 1189-1201.
# Load Paracou data (number of trees per species in two 1-ha plot of a tropical forest
# and their taxonomy)
data(Paracou618)
# Ns is the vector of abundances of the first plot
Ns <- Paracou618.MC$Nsi[, 1]
# Return the abundance frequency count
(AbdFreqCount(Ns) -> afc)
plot(afc, xlab="Number of observations", ylab="Number of species")
lines(afc)