## Set parameters for hypothetical species ##

> N<-100

> Hstar<-10

> probs<-c(rep(0.30, 3), rep(0.10/7, 7)) # three dominant haplotypes each with 30% frequency

### Run simulations ###

> HACSObj<-HACHypothetical(N = N, Hstar = Hstar, probs = probs)

> HAC.simrep(HACSObj)

Simulating haplotype accumulation...

—=========================================================— 100%

—Measures of Sampling Closeness —

Mean number of haplotypes sampled: 8.3291

Mean number of haplotypes not sampled: 1.6709

Proportion of haplotypes sampled: 0.83291

Proportion of haplotypes not sampled: 0.16709

Mean value of N*: 120.061

Mean number of specimens not sampled: 20.06099

Desired level of haplotype recovery has not yet been reached

—====================================================— 100%

—Measures of Sampling Closeness —

Mean number of haplotypes sampled: 9.2999

Mean number of haplotypes not sampled: 0.7001

Proportion of haplotypes sampled: 0.92999

Proportion of haplotypes not sampled: 0.07001

Mean value of N*: 179.5718

Mean number of specimens not sampled: 12.57182

Desired level of haplotype recovery has not yet been reached

—======================================================— 100%

—Measures of Sampling Closeness —

Mean number of haplotypes sampled: 9.5358

Mean number of haplotypes not sampled: 0.4642

Proportion of haplotypes sampled: 0.95358

Proportion of haplotypes not sampled: 0.04642

Mean value of N*: 188.7623

Mean number of specimens not sampled: 8.762348

Desired level of haplotype recovery has been reached

———- Finished. ———-

The initial guess for sampling sufficiency was N = 100 individuals

The algorithm converged after 6 iterations and took 33.215 s

The estimate of sampling sufficiency for p = 95% haplotype recovery is N∗ = 180 individuals

( 95% CI [178.278–181.722])

The number of additional specimens required to be sampled for p = 95% haplotype recovery is

N* - N = 80 individuals