gdistPair1: Genetic distance for data with genotyping errors
In innager/unfazeD: Genetic Distance for Malaria Transmission and Relatedness

Description Usage Arguments Value

View source: R/unfazeD.R

Distance when estimated COI is less than |Ux|: COI increased to |Ux| for a given locus only. ***Handling of the situation where alleles with estimated allele frequency of 0 are present: probUxUy crashes only if present in both Ux and Uy; however, if present in either one, the likelihood is 0, so no need to calculate.

gdistPair1(
  pair,
  afreq,
  coi,
  nr = 100,
  nm = min(coi),
  rval = NULL,
  reval = NULL,
  equalr = FALSE,
  out = "mle",
  alpha = 0.05
)

`pair`	a list of length two containing two samples.
`afreq`	a list of allele frequencies. Each element of the list corresponds to a locus.
`coi`	a vector indicating complexity of infection for each sample.
`nr`	an integer value for the resolution of the grid (nr - 1 values between 0 and 1), over which the likelihood will be calculated. Ignored if non-null `reval` is provided.
`nm`	the number of related pairs of strains for evaluation.
`rval`	{r} values for the grid or for evaluation when `equalr` is `TRUE`. If `NULL`, will be evenly spaced between 0 and 1 and interval 1/nr.
`reval`	the grid of {r} combinations, over which the likelihood will be calculated. A matrix where each column represents a single combination.
`equalr`	a logical value. If `TRUE`, only equal values of r for different pairs of strains are evaluated.
`out`	a character string for the type of results to be returned. If `"mle"`, an estimate is returned, if `"llik"` - a vector of log-likelihood for each combination.
`alpha`	significance level.

If out = "mle": a vector of length 1 if equalr = TRUE or of length nm otherwise, containing estimated {r} (or vector /matrix if not just first).
If out = "llike", a vector of log-likelihood values for each evaluated combination.
If out = "all", a list containing an estimate, log-likelihood, maximum log-likelihood, {r} values corresponding to the acceptance region determined by the significance level, and the size of that region (as a proportion of all evaluated).