GeoMAPI_assign_edges: Assign edges for GeoMAPI analysis
In mrc-ide/genescaper: Allele frequency mapping and outlier detection

GeoMAPI_assign_edges

R Documentation

Assign edges for GeoMAPI analysis

Description

Given an GeneScapeR project with a grid already loaded (see ?create_hex_grid), determine which pairwise edges in the data intersect each grid cell. Assumes an elliptical projection along each edge with the start- and end-points becoming the two foci of the ellipse, and with the eccentricity defined by the user. See Details for suggestions on how to choose this parameter.

Usage

GeoMAPI_assign_edges(
  project,
  eccentricity = 0.9,
  max_dist = Inf,
  silent = FALSE,
  pb_markdown = FALSE
)

Arguments

`project`	a genescaper project, as produced by the `genescaper_project()` function.
`eccentricity`	eccentricity of ellipses, defined as half the distance between foci divided by the semi-major axis. e = sqrt{1 - b^2/a^2}, where e is the eccentricity, a is the length of the semi-major axis, and b is the length of the semi-minor axis. Eccentricity ranges between 0 (perfect circle) and 1 (straight line between foci). An eccentricity of 0 is not allowed in this case because it would result in an infinitely large circle.
`max_dist`	edges shorter than this length are discarded prior to assignment. Can be used to focus on short distance signals.
`silent`	if `TRUE` then no output is produced during function evaluation.
`pb_markdown`	whether to run progress bars in markdown mode, in which case they are updated once at the end to avoid large amounts of output.