envr: Simulation variable storage environment

In HACSim: Iterative Extrapolation of Species' Haplotype Accumulation Curves for Genetic Diversity Assessment

Simulation variable storage environment

Description

envr is a new (initially empty) environment that is created when HACSim is loaded.

Value

When a simulation is run via HAC.simrep, envr will contain 26 elements as follows:

ci.type	Type of confidence interval to compute and plot. Default is conf.type = "quantile".
conf.level	The desired confidence level. Default is conf.level = 0.95.
d	A dataframe with Nstar - X rows and five columns: specimens (specs), accumulated haplotypes (means), standard deviations (sds) and quantiles (both lower and upper)
df.out	A dataframe with iters rows and six columns displaying "Measures of Sampling Closeness".
filename	The name of the file where results are to be saved. Default is NULL.
Hstar	Number of unique species' haplotypes
input.seqs	Should DNA sequences be inputted? Default is FALSE.
iters	The number of iterations required to reach convergence
N	The starting sample size used to initialize the algorithm
Nstar	The final (extrapolated) sample size
Nstar.high	The upper endpoint of the desired level confidence interval for the 'true' required sample size
Nstar.low	The lower endpoint of the desired level confidence interval for the 'true' required sample size
num.iters	Number 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.)
p	The user-specified level of haplotype recovery. Default is p = 0.95.
perms	The user-specified number of permutations (replications). Default is perms = 10000.
probs	Haplotype frequency distribution vector
progress	Should iteration results be outputted to the console? Default is TRUE.
prop.haps	If subset.haps = TRUE, the user-specified proportion of haplotype labels to recover
prop.seqs	If subset.seqs = TRUE, the user-specified proportion of DNA sequences to recover
ptm	A timer to track progress of the algorithm in seconds
R	The proportion of haplotypes recovered by the algorithm
R.low	The lower endpoint of the desired level confidence interval for the 'true' fraction of haplotypes captured
R.up	The upper endpoint of the desired level confidence interval for the 'true' fraction of haplotypes captured
subset.haps	Should a subsample of haplotype labels be taken? Default is FALSE.
subset.seqs	Should a subsample of DNA sequences be taken? Default is FALSE.
X	Mean number of specimens not sampled

Examples

# Returns the frequencies of each haplotype in the extrapolated sample 
max(envr$d$specs) * envr$probs

# Returns the extrapolated sample size corresponding to the dotted line 
# in the last iteration plot
envr$d[which(envr$d$means >= envr$p * envr$Hstar), ][1, 1]

HACSim documentation built on June 13, 2022, 9:05 a.m.