proximity: Make potentials object-spatial proximity

In stuartWagenius/mateable: Assess Mating Potential in Space and Time

Make potentials object–spatial proximity

Description

Calculate one of several measures of spatial proximity

Usage

proximity(
  scene,
  method,
  averageType = "mean",
  subject = "all",
  zeroPotDist = NULL,
  k = 6
)

Arguments

scene	a matingScene object
method	one of "maxProp", "maxPropSqrd", or 'knn.dist'; see details for further description
averageType	whether to calculate individual and population proximity using the mean or median
subject	whether you want pair, individual, population, or all. Specifying more than one is allowed.
zeroPotDist	the distance at which potential should be equal to zero
k	the number of the nearest neighbor to search, if method is "knn.dist". Defaults to 6, but must be less than population size.

Details

If method is "maxProp" then proximity between two individuals will be calculated as 1 - distance/max(distance). If method is "maxPropSqrd" then proximity between two individuals will be calculated as (1 - distance/max(distance))^2. If method is "knn.dist" then the function This uses FNN::knn.dist to return the Euclidian distance of the kth nearest neighbor.

Value

A potentials object containing one more more of the following, depending the input for subject:
If subject is "population" the return list will contain a numeric value that has a range depending on the method. If subject is "pair" the return list will contain a matrix with all pairwise proximity comparisons. If subject is "individual" the return list will contain a dataframe with a column containing IDs and a column containing proximity values. If subject is "all" the return list will contain all three of the items above.

Author(s)

Danny Hanson

Examples

pop <- simulateScene()
proximity(pop, "maxProp")

stuartWagenius/mateable documentation built on Feb. 9, 2023, 2:33 p.m.