signatselect: signatselect: Identifying signatures of selection

Description Usage Arguments Details Value

tsinfer computes the selection coefficient, population size and initial frequency for the logistic using a Gaussian approximation of the Kimura expression for time-series variant-frequency data.

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tsinfer(tvec, bvec, nvec, maxiter = 200, prec = 1e-06, iffreq = FALSE,
  ifneut = FALSE, iffixedf0 = FALSE, verbose = FALSE, mins = -2,
  maxs = 2, minalpha = 10, maxalpha = 1e+08, minf0 = -10, maxf0 = 10)

`tvec`	Time coordinates for the time-series (start with 0)
`bvec`	Number of new form per time point
`nvec`	Total number of samples per time point
`maxiter`	Maximum number of iterations
`prec`	Precision for optimisation
`iffreq`	whether to assume that the sample frequencies are the population frequencies (default=FALSE)
`ifneut`	whether to compute only the neutral model (default=FALSE)
`iffixedf0`	whether to use the initial sample frequency as the initial frequency of the logistic component of the model (default=FALSE)
`verbose`	whether to print intermediate output (detault=FALSE)
`mins`	minimum s value to consider (default=-2)
`maxs`	maximum s value to consider (default=2)
`minalpha`	minimum alpha value to consider (default=10)
`maxalpha`	maximum alpha value to consider (default=1e8)
`minf0`	minimum f0 value to consider in log-odds (default=-10)
`maxf0`	maximum f0 value to consider in log-odds (default=10)

Essential arguments are tvec (time point labels for time series starting at 0), bvec (number of new variants at each time point), and nvec (total number of samples at each time point).

A list with the neutral and non-neutral parameter values and associated log-likelihoods The output of the execution is the following list: s = selection coefficient for non-neutral model alpha = population size for non-neutral model f0 = initial frequency for the logistic in non-neutral model LL = log-likelihood of non-neutral model s.0 = 0 (selection coefficient for the neutral model) alpha.0 = population size for the neutral model f0.0 = initial frequency for the logistic in neutral model LL.0 = log-likelihood of neutral model

benmarwick/signatselect documentation built on Dec. 4, 2019, 4:22 p.m.