A list object of class "HAC" with 13 elements that can be passed to
HAC.simrep
as follows:
input.seqsShould a FASTA file of aligned/trimmed DNA sequences be
inputted? Default is TRUE
subset.seqsShould a subsample of DNA sequences be taken? Default is
FALSE (can be altered by user)
prop.seqsProportion of DNA sequences to subsample. Default is NA
(can be altered by user)
prop.hapsProportion of haplotype labels to subsample. Default is
NULL
subset.hapsShould a subsample of haplotype labels be taken? Default
is NULL
NNumber of individuals. NA by default (computed automatically by
algorithm)
HstarNumber of unique species' haplotypes. NA by default (computed automatically by algorithm)
probsHaplotype frequency distribution vector. NA by default (computed automatically by algorithm)
pProportion of haplotypes to recover. p
= 0.95 by default.
permsNumber of permutations (replications). perms
= 10000 by
default.
conf.levelDesired confidence level for graphical output and interval estimation. conf.level
= 0.95 by default.
ci.typeType of confidence interval for graphical output.
ci.type = "quantile"
by default
num.itersNumber of iterations to compute. num.iters = NULL
by
default (i.e., all iterations are computed; users can specify
num.iters
= 1 for the first iteration.)
progressShould iteration output be printed to the R console? Default
is TRUE
filenameName of file where simulation results are to be saved.