single_sensitivity: Single sensitivity analysis
In bailey-lab/coiaf: Complexity of Infection Estimation with Allele Frequencies

single_sensitivity

R Documentation

Single sensitivity analysis

Description

Runs a single full COI sensitivity analysis.

Usage

single_sensitivity(
  disc_or_cont,
  coi = 3,
  max_coi = 25,
  plmaf = runif(1000, 0, 0.5),
  coverage = 200,
  alpha = 1,
  overdispersion = 0,
  relatedness = 0,
  epsilon = 0,
  seq_error = 0.01,
  bin_size = 20,
  comparison = "overall",
  distance = "squared",
  coi_method = "variant",
  use_bins = FALSE
)

Arguments

`disc_or_cont`	Whether to run a discrete or continuous COI estimation.
`coi`	Complexity of infection.
`max_coi`	A number indicating the maximum COI to compare the simulated data to.
`plmaf`	Vector of population-level minor allele frequencies at each locus.
`coverage`	Coverage at each locus. If a single value is supplied then the same coverage is applied over all loci.
`alpha`	Shape parameter of the symmetric Dirichlet prior on strain proportions.
`overdispersion`	The extent to which counts are over-dispersed relative to the binomial distribution. Counts are Beta-Binomially distributed, with the beta distribution having shape parameters \mjseqn\fracpoverdispersion and \mjseqn\frac1-poverdispersion.
`relatedness`	The probability that a strain in mixed infections is related to another. The implementation is similar to relatedness as defined in THE REAL McCOIL simulations (\Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.1371/journal.pcbi.1005348")}): "... simulated relatedness (r) among lineages within the same host by sampling alleles either from an existing lineage within the same host (with probability r) or from the population (with probability (1-r))."
`epsilon`	The probability of a single read being miscalled as the other allele. This error is applied in both directions.
`seq_error`	The level of sequencing error that is assumed. If no value is inputted, then we infer the level of sequence error.
`bin_size`	This argument is no longer supported; to estimate the COI, all data points are used. Data points are not grouped in bins of changing `plaf`.
`comparison`	This argument is no longer supported; this function will compare the theoretical curve and sample curve for all PLMAFs.
`distance`	This argument is no longer supported; this function will solve a weighted least squares minimization problem.
`coi_method`	The method we will use to generate the theoretical relationship. The method is either "variant" or "frequency". The default value is "variant".
`use_bins`	This argument is no longer supported; to estimate the COI, all data points are used. Data points are not grouped in bins of changing `plaf`.