When a simulation is run via HAC.simrep
, envr
will contain
26 elements as follows:
ci.typeType of confidence interval to compute and plot. Default is
conf.type = "quantile"
.
conf.levelThe desired confidence level. Default is
conf.level = 0.95
.
dA dataframe with Nstar - X
rows and five columns: specimens
(specs), accumulated haplotypes (means), standard deviations (sds) and
quantiles (both lower and upper)
df.outA dataframe with iters
rows and six columns displaying
"Measures of Sampling Closeness".
filenameThe name of the file where results are to be saved. Default
is NULL.
HstarNumber of unique species' haplotypes
input.seqsShould DNA sequences be inputted? Default is FALSE.
itersThe number of iterations required to reach convergence
NThe starting sample size used to initialize the algorithm
NstarThe final (extrapolated) sample size
Nstar.highThe upper endpoint of the desired level confidence interval
for the 'true' required sample size
Nstar.lowThe lower endpoint of the desired level confidence interval
for the 'true' required sample size
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.)
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 sequences to recover
ptmA timer to track progress of the algorithm in seconds
RThe proportion of haplotypes recovered by the algorithm
R.lowThe lower endpoint of the desired level confidence interval for
the 'true' fraction of haplotypes captured
R.upThe upper endpoint of the desired level confidence interval for the
'true' fraction of haplotypes captured
subset.hapsShould a subsample of haplotype labels be taken? Default is
FALSE.
subset.seqsShould a subsample of DNA sequences be taken? Default is
FALSE.
XMean number of specimens not sampled