HACHypothetical {HACSim}

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")