HACHypothetical: 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 hypothetical species

Description

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

Usage

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

Arguments

N	Number of individuals
Hstar	Number of unique species' haplotypes
probs	Haplotype frequency distribution vector
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 haplotype labels desired?
prop	If subsample = TRUE, the proportion of haplotype labels 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 FALSE
subset.seqs	Should a subsample of DNA sequences be taken? Default is FALSE
prop.seqs	Proportion of DNA sequences to subsample. Default is NULL
prop.haps	Proportion of haplotype labels to subsample. Default is NULL (can be altered by user)
subset.haps	Should a subsample of haplotype labels be taken? Default is NULL (can be altered by user)
N	Number of individuals. NA by default (provided by user)
Hstar	Number of unique species' haplotypes. NA by default (provided by user)
probs	Haplotype frequency distribution vector. NA by default (provided by user)
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.

Note

N must be greater than 1 and greater than or equal to Hstar.

Hstar must be greater than 1.

probs must have a length equal to Hstar and its elements must sum to 1.

Examples

  ## Simulate hypothetical species ##
  
  N <- 100 # total number of sampled individuals
  Hstar <- 10 # total number of haplotypes
  probs <- rep(1/Hstar, Hstar) # equal haplotype frequency distribution
  
  # outputs a CSV file called "output.csv"
  HACSObj <- HACHypothetical(N = N, Hstar = Hstar, probs = probs, 
  filename = "output") 
  
  ## Simulate hypothetical species - subsampling ##
  # subsamples 25% of haplotype labels
  HACSObj <- HACHypothetical(N = N, Hstar = Hstar, probs = probs, 
  perms = 1000, p = 0.95, subsample = TRUE, prop = 0.25, 
  conf.level = 0.95, filename = "output") 
  
  ## Simulate hypothetical species and all paramaters changed - subsampling ##
  HACSObj <- HACHypothetical(N = N, Hstar = Hstar, probs = probs, 
  perms = 10000, p = 0.90, subsample = TRUE, prop = 0.15, conf.level = 0.95, 
  num.iters = 1, filename = "output")
  

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