compute_coi_regression: Compute COI based on residuals of all loci against...

In bailey-lab/coiaf: Complexity of Infection Estimation with Allele Frequencies

Compute COI based on residuals of all loci against theoretical curves

Description

Compute COI based on residuals of all loci against theoretical curves

Usage

compute_coi_regression(
  data,
  data_type,
  max_coi = 25,
  seq_error = 0.01,
  distance = "squared",
  coi_method = "variant",
  seq_error_bin_size = 20
)

Arguments

data	The data for which the COI will be computed.
data_type	The type of the data to be analyzed. One of "sim" or "real".
max_coi	A number indicating the maximum COI to compare the simulated data to.
seq_error	The level of sequencing error that is assumed. If no value is inputted, then we infer the level of sequence error.
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".
seq_error_bin_size	Number of loci in smallest bin for estimating sequence error

Value

A list of the following:

• coi: The predicted COI of the sample.

• probability: A probability density function representing the probability of each COI.

bailey-lab/coiaf documentation built on April 26, 2023, 6:32 p.m.