When a simulation is run via HAC.simrep
, envr
will contain 20 elements as follows:
conf.levelThe desired confidence level. Default is conf.level = 0.95
.
dA dataframe with three columns: specimens (specs), accumulated haplotypes (means), and standard deviation (sd)
filenameThe name of the file where results are to be saved. Default is NULL.
highThe upper endpoint of the desired level confidence interval for the 'true' required sample size
HstarNumber of unique species' haplotypes
input.seqsShould DNA sequences be inputted? Default is FALSE.
itersThe number of iterations required to reach convergence
lowThe upper endpoint of the desired level confidence interval for the 'true' required sample size
NThe starting sample size used to initialize the algorithm
NstarThe final (extrapolated) sample size
pThe user-specified level of haplotype recovery. Default is p
= 0.95.
permsThe user-specified number of permutations (replications). Default is perms
= 10000.
probsHaplotype frequency distribution vector
progressShould iteration results be outputted to the console? Default is TRUE.
prop.hapsIf subset.haps
= TRUE, the user-specified proportion of haplotype labels to recover
prop.seqsIf subset.seqs
= TRUE, the user-specified proportion of DNA sequencess to recover
ptmA timer to track progress of the algorithm in seconds
RThe proportion of haplotypes recovered by the algorithm
subset.hapsShould a subsample of haplotype labels be taken? Default is FALSE.
subset.seqsShould a subsample of DNA sequences be taken? Default is FALSE.