Table 1. Parameters inputted (first 7) and outputted (last six) by HAC.sim() and HAC.simrep(), along with their definitions.

Range refers to plausible values that each parameter can assume within the haplotype accumulation curve simulation algorithm. [ and ] indicate that a given value is included in the range interval; whereas, ( and ) indicate that a given value is excluded from the range interval. Simulation progress can be tracked through setting progress = TRUE within HACHypothetical() or HACReal(). Users can optionally specify that a file be created containing all information outputted to the R console (via the argument filename, which can be named as the user wishes).

Parameter	Definition	Range
N	total number of specimens/DNA sequences	(1, ∞)
H*	total number of unique haplotypes	(1, N]
probs	haplotype probability distribution vector	(0, 1)
p	proportion of haplotypes to recover	(0, 1]
perms	total number of permutations	(1, ∞)
input.seqs	analyze FASTA file of species DNA sequences	TRUE, FALSE
conf.level	desired confidence level for confidence interval calculation	(0, 1)
H	cumulative mean number of haplotypes sampled	[1, H∗]
H∗ − H	cumulative mean number of haplotypes not sampled	[0, H∗)
$R=\frac{H}{H^{\ast }}$	cumulative mean fraction of haplotypes sampled	(0, 1]
$\frac{H^{\ast }-H}{H^{\ast }}$	cumulative mean fraction of haplotypes not sampled	[0, 1)
N∗	mean specimen sample size corresponding to H∗	[ N, ∞)
N∗ − N	mean number of individuals not sampled	[0, N]