spatialsegregation-segregationFun {spatialsegregation}R Documentation

Spatial Segregation Function

Description

Compute the spatial exposure (segregation vs. mingling) features from a given multitype point pattern. Usage of shortcuts minglingF, isarF, shannonF and simpsonF highly recommended.

Usage

     segregationFun(pp, fpar = NULL, graph_parvec = 1:20, graph_type = "knn",
    toroidal = FALSE, dbg = FALSE, funtype = 1, doDists = FALSE,
    prepR = 0, prepGraph = NULL, included = NULL, minusR = NULL,
    relative = FALSE)

Arguments

pp Multitype point pattern (see package 'spatstat')
fpar Default NULL. Parameter(s) for the measure. Mingling: c(i,j), where i= only for type i (0 for all), j=1 -> ratio version. ISAR: i, i=type (integer). Others: NULL.
graph_parvec Default 1:20 (parvec in shortcuts). Vector for the neighbourhood defining graph, e.g. "geometric" graph with different "r".
graph_type Default "knn". Type of the neighbourhood graph. Accepts: "knn", "geometric", "delauney", "gabriel".
toroidal Default FALSE. If TRUE, use a toroidal correction in distance calculation. Works only for rectangular windows and "geometric" or "knn" graph.
dbg Default FALSE. Print additional runtime texts.
funtype Default 1. 1=Mingling index, 2=Shannon, 3=Simpson, 4=ISAR.
doDists Default TRUE. Precalculate distances for speed. Be aware of memory requirements, O(n*n)!
prepR Default 0. If >0, shrink the search space for connections in the graph by searching only points within distance R (precalculates geometric graph).
prepGraph Precalculated graph for the point pattern. If not NULL, The graph_par, graph_parvec, toroidal and prepR are ignored and calculations are carried using only prepGraph. Useful for huge datasets.
included boolean-vector of length |pp|. included[i]==TRUE => pp[i] included in calculations. See the next parameter for quick minus-sampling.
minusR If given included-vector is created with points with distance atleast minusR from the border.
relative Default FALSE. If TRUE, scale the parvec to a unit distance using intensity. Only for "geometric" graph. Useful for comparison of different scale pp's.

Details

General function for computing the spatial exposure (segregation/mingling) features. Used by minglingF, shannonF, simpsonF and isarF, which should be preferred for better (and nicer) outcome.

Possible neighbourhood relations for the spatial version include geometric, k-nearest neighbours, Delauney, and Gabriel. Delauney and Gabriel are parameter free, so given parvec has no meaning. In geometric graph, parvec is a vector of distances (sizes of the surrounding 'disc') and for k-nn parvec is the vector of neighbourhood abundances for each point to consider in the calculation of the spatial exposure measures.

The basic type of spatial summary uses range 'r', or 'geometric' graph with varying neighbourhood parameter 'r'. We default to 'k-nn' graph as the exposure effect should be free of spatial scattering.

For geometric and knn, the calculations are done by shrinking the graph given by the largest value of parvec. If dealing with large datasets, it is advisable to give preprocessing range, prepR. The algorithm first calculates a geometric graph with parameter prepR, and uses this as basis for finding the needed neighbourhoods. Speeds up calculations. prepGraph, if given, functions like the preprocess geometric graph. But make sure prepR is large enough (e.g. in geometric, prepR>max(parvec)).

The doDists option speeds up calculations by precomputing the pairwise distances but takes O(n^2) memory!

For border correction, use minusR for reduced border correction (for rectangular windows only). If using geometric or knn neighbourhoods, the option toroidal for toroidal correction is also available. The vector included can be given for more specific minus-correction, only those points with TRUE (1) value are used in calculation. However, the neighbourhoods are calculated with all points.

Date: 2009-03-09
License: GPL v2 or later

Author(s)

Tuomas Rajala University of Jyvaskyla, Finland tarajala@maths.jyu.fi


[Package spatialsegregation version 1.93 Index]