enve.recplot2.findPeaks.em {enveomics.R}

Enveomics: Recruitment Plot (2) Em Peak Finder

Description

Identifies peaks in the population histogram using a Gaussian Mixture Model Expectation Maximization (GMM-EM) method.

Usage

enve.recplot2.findPeaks.em(
  x,
  max.iter = 1000,
  ll.diff.res = 1e-08,
  components = 2,
  rm.top = 0.05,
  verbose = FALSE,
  init,
  log = TRUE
)

Arguments

x

An enve.RecPlot2 object.

max.iter

Maximum number of EM iterations.

ll.diff.res

Maximum Log-Likelihood difference to be considered as convergent.

components

Number of distributions assumed in the mixture.

rm.top

Top-values to remove before finding peaks, as a quantile probability. This step is useful to remove highly conserved regions, but can be turned off by setting rm.top=0. The quantile is determined after removing zero-coverage windows.

verbose

Display (mostly debugging) information.

init

Initialization parameters. By default, these are derived from k-means clustering. A named list with vectors for mu, sd, and alpha, each of length components.

log

Logical value indicating if the estimations should be performed in natural logarithm units. Do not change unless you know what you're doing.

Value

Returns a list of enve.RecPlot2.Peak objects.

Author(s)

Luis M. Rodriguez-R [aut, cre]