RSE-package: Number of Newly Discovered Rare Species Estimation

In RSE: Number of Newly Discovered Rare Species Estimation

Description

RSE: an R package for predicting numbers of rare species newly discoverd in additional ecological samples

Details

RSE is an R package for estimating the number of new rare species in additional ecological samples. The methods used here include a Bayesian-weighted estimator and two unweighted estimators.

Author(s)

Youhua Chen (Chengdu Institute of Biology, Chinese Academy of Sciences);
Tsung-Jen Shen (Institute of Statistics & Department of Applied Mathematics, National Chung Hsing University)
Maintainer:
Youhua Chen <[e-mail]>

References

Shen TJ, Chen YH (2018) Predicting the number of newly discovered rare species: a Bayesian weight approach. Conservation Biology, In press.

Examples

###########################
#for abundance-based data type
data(HerpetologicalData)
## two columns represent two samples of species abundance data
X.merge = HerpetologicalData
## the first column is treated as the original sample
X.col1 = X.merge[,1]
## the second column is treated as the additional sample
X.col2 = X.merge[,2]
Xi = X.col1
## the number of individuals of the additional sample 
m = sum(X.col2)
print(Pred.abundance.rare(boot.rep = 100, f=NULL, xi=Xi, m = m, k.show = 3))

###########################
#for incidence-based data type
data(CanadaMite)
## two columns represent two samples of incidence counts
X.merge = CanadaMite
## the first column is treated as the original sample
X.col1 = X.merge[,1]
## the number of quadrats in the first sample
nT = 16
## the number of quadrats in the additional sample (i.e., the second column)
u = 16
print(Pred.incidence.rare(boot.rep = 100, Q=NULL, xi=X.col1, nT=nT, u=u, k.show = 3))

RSE documentation built on May 2, 2019, 5:58 a.m.