f0: Number of Unobserved Species
In EricArcher/sprex: Species Richness and Extrapolation

ACE	R Documentation

Number of Unobserved Species

Description

Calculate the number of unobserved species (f0).

Usage

ACE(f)

Chao1(f)

Clench(f, pct.n = 0.85, num.reps = 100)

Swor1(f, N)

iChao1(f)

jack1(f)

jack2(f)

Arguments

`f`	a vector of species frequencies where `f[i]` is the number of species represented by only `i` samples.
`pct.n`	percent of samples to use in bootstrap draws. Must be in range of `0:1`.
`num.reps`	number of random re-orderings of samples to fit curve to.
`N`	population size.

Value

All functions return a vector containing the estimated number of species (s.est), unobserved species (f0), observed species (s.obs), and the total number of samples (n). Swor1 also returns the standard deviation of s.est as sd.s.est.

Author(s)

Eric Archer eric.archer@noaa.gov

References

Chao1, ACE: Colwell, R.K., A. Chao, N.J. Gotelli, S.-Y. Lin, C.X. Mao, R.L. Chazdon, and J.T. Longino. 2012. Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages. Journal of Plant Ecology 5(1):3-21.
jack1, jack2: Burnham, KP and WS Overton. 1978. Estimation of the size of a closed population when capture probabilities vary among animals. Biometrika 65(3):625-633.
Swor1: Chao, A. and C.-W. Lin. 2012. Nonparametric lower bounds for species richness and shared species richness under sampling without replacement. Biometrics 68:912-921.
iChao1: Chiu, C-H, Wang, Y-T, Walther, BA, and A Chao. 2014. An impro.ved nonparametric lower bound of species richness via a modified Good-Turing frequency formula. Biometrics 70(3):671-682.
clench: Clench, H. 1979. How to make regional lists of butterflies: Some thoughts. Journal of the Lepidopterists' Society 33(4):216-231.

Examples

data(osa.second.growth)
f <- expand.freqs(osa.second.growth)

ace.est <- ACE(f)
chao1.est <- Chao1(f)
jack1.est <- jack1(f)
jack2.est <- jack2(f)
swor1.est <- Swor1(f, 20000)
ichao1.est <- iChao1(f)
clench.est <- Clench(f, num.reps = 50)

f0.est <- cbind(
  ACE = ace.est["f0"],
  Chao1 = chao1.est["f0"],
  jack1 = jack1.est["f0"],
  jack2 = jack2.est["f0"],
  Swor1 = swor1.est["f0"],
  iChao1 = ichao1.est["f0"],
  clench = clench.est["f0"]
)
f0.est

EricArcher/sprex documentation built on Sept. 4, 2023, 8:35 a.m.