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Bivariate Pair Correlation Function

Source: R/bi_pair_correlation.R
bi_pair_correlation.Rd

The cross-type pair correlation function: clustering of counted cells at distance r from anchor cells, as a density rather than a cumulative count. Cells positive for both markers of a pair are excluded from that pair.

Usage

bi_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, or a two-column data frame of anchor/counted marker combinations to run

r_range

numeric vector of radii. If NULL, spatstat chooses the range.

num_permutations

integer number of permutations used to estimate CSR

edge_correction

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

keep_permutation_distribution

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

workers

integer number of CPU cores used to process samples in parallel

overwrite

boolean; replace an existing bivariate_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::pcfcross(), plus support for deprecated argument names (see Details).

Value

mif object with the bivariate_pair_correlation slot filled

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 bi_ripleys_k(), with Observed g in place of Observed K. From/To are now Anchor/Counted, Theoretical g/Permuted g are now Theoretical CSR/Permuted CSR, Degree of Correlation * is now Degree of Clustering *, and Permuted_larger_than_Observed is now Permutations Larger than Observed.