Skip to contents

Univariate Pair Correlation Function

Source: R/pair_correlation.R
pair_correlation.Rd

The pair correlation function g(r) is the derivative of Ripley's K, so it measures clustering at a radius rather than cumulatively up to it. It is correspondingly slower to compute and noisier at small r.

xloc and yloc, if NULL, are taken as the midpoints of XMin/XMax and YMin/YMax.

Usage

pair_correlation(
  mif,
  mnames,
  r_range = NULL,
  num_permutations = 100,
  edge_correction = "translation",
  keep_permutation_distribution = FALSE,
  workers = 1,
  overwrite = FALSE,
  xloc = NULL,
  yloc = NULL,
  ...
)

Arguments

mif

object of class mif

mnames

character vector of marker names

r_range

numeric vector including 0. If NULL, spatstat chooses the range.

num_permutations

integer number of permutations used to estimate CSR

edge_correction

edge correction passed to spatstat.explore::pcf()

keep_permutation_distribution

boolean; keep each permutation's result or average them to one row per marker and radius

workers

integer number of CPU cores used to process samples in parallel

overwrite

boolean; replace an existing univariate_pair_correlation slot rather than appending it as a new Run

xloc, yloc

the x and y columns giving cell centres. If left NULL, XMin, XMax, YMin and YMax must be present.

...

other parameters passed to spatstat.explore::pcf(), plus support for deprecated argument names (see Details).

Value

mif object with the univariate_pair_correlation derived slot filled or appended to

Details

keep_perm_dis is accepted as a deprecated alias for keep_permutation_distribution.

Output columns

As of 2.0.0 this function returns the same columns as ripleys_k(), with Observed g in place of Observed K. Theoretical g and Permuted g are now Theoretical CSR and Permuted CSR, Degree of Correlation * is now Degree of Clustering *, and Permuted_larger_than_Observed is now Permutations Larger than Observed. Exact CSR is present but always NA: the closed-form CSR shortcut available to ripleys_k() has not been implemented for the pair correlation function yet.