HACReal: Set up an object to simulate haplotype accumulation curves...

In jphill01/HACSim.R: Iterative Extrapolation of Species' Haplotype Accumulation Curves for Genetic Diversity Assessment

Set up an object to simulate haplotype accumulation curves for a real species

Description

Helper function which creates an object containing necessary information to run a simulation of haplotype accumulation for a real species of interest

Usage

HACReal(perms = 10000, p = 0.95, conf.level = 0.95, 
ci.type = "quantile", subsample = FALSE, prop = NULL, 
progress = TRUE, num.iters = NULL, filename = NULL)

Arguments

perms	Number of permutations (replications)
p	Proportion of haplotypes to recover
conf.level	Desired confidence level for graphical output and interval estimation
ci.type	Type of confidence interval for graphical output. Choose from "quantile" or "asymptotic"
subsample	Is a subsample of DNA sequences desired?
prop	If subsample = TRUE, the proportion of DNA sequences to subsample
num.iters	Number of iterations to compute
progress	Should iteration output be printed to the R console?
filename	Name of file where simulation results are to be saved

Value

A list object of class "HAC" with 13 elements that can be passed to HAC.simrep as follows:

input.seqs	Should a FASTA file of aligned/trimmed DNA sequences be inputted? Default is TRUE
subset.seqs	Should a subsample of DNA sequences be taken? Default is FALSE (can be altered by user)
prop.seqs	Proportion of DNA sequences to subsample. Default is NA (can be altered by user)
prop.haps	Proportion of haplotype labels to subsample. Default is NULL
subset.haps	Should a subsample of haplotype labels be taken? Default is NULL
N	Number of individuals. NA by default (computed automatically by algorithm)
Hstar	Number of unique species' haplotypes. NA by default (computed automatically by algorithm)
probs	Haplotype frequency distribution vector. NA by default (computed automatically by algorithm)
p	Proportion of haplotypes to recover. p = 0.95 by default.
perms	Number of permutations (replications). perms = 10000 by default.
conf.level	Desired confidence level for graphical output and interval estimation. conf.level = 0.95 by default.
ci.type	Type of confidence interval for graphical output. ci.type = "quantile" by default
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.)
progress	Should iteration output be printed to the R console? Default is TRUE
filename	Name of file where simulation results are to be saved.

Examples

    ## Simulate real species ##
    # outputs file called "output.csv"
    HACSObj <- HACReal(filename = "output") 
    
    ## Simulate real species - subsampling ##
    # subsamples 25% of DNA sequences
    HACSObj <- HACReal(subsample = TRUE, prop = 0.25, conf.level = 0.95, 
    filename = "output") 
    
    ## Simulate real species and all parameters changed - subsampling ##
    HACSObj <- HACReal(perms = 10000, p = 0.90, subsample = TRUE, 
    prop = 0.15, conf.level = 0.99, num.iters = 1, filename = "output")

jphill01/HACSim.R documentation built on March 4, 2024, 2:49 p.m.