proximity: 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
)

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.

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.

Author

Danny Hanson

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.

Examples

Run this code

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

Run the code above in your browser using DataLab