transitivity {Perc}

calculate transitivity measurements for a matrix

Description

transitivity calculate transitivity measurements for a matrix

Usage

transitivity(conf, strict = FALSE)

Arguments

conf

an N-by-N conflict matrix whose (i,j)th element is the number of times i defeated j

strict

a logical vector of length 1 (TRUE or FALSE). It is used in transitivity definition for alpha estimation. It should be set to TRUE when a transitive triangle is defined as all pathways in the triangle go to the same direction; it should be set to FALSE when a transitive triangle is defined as PRIMARY pathways in the triangle go to the same direction. Strict = FALSE by default.

Details

transitivity is calculated as the proportion transitive triangles in the total of transitive and intransitive triangles. transitivity is used to estimate alpha, which is used in turn in imputing information from indirect pathways as to what degree we can trust information from indirect pathways. Greater transitivity is associated with assigning higher weight to information from indirect pathways.

Value

A list of four elements.

transitive

The number of transitive triangles.

intransitive

The number of intransitive triangles.

transitivity

transitivity, the proportion of transitive triangles.

alpha

The value of alpha corresponding to this value of transitivity.

See Also

countPaths, findIDpaths, conductance

Examples

# convert an edgelist to conflict matrix
confmatrix <- as.conflictmat(sampleEdgelist)
# transitivity calculation
conftrans <- transitivity(confmatrix, strict = FALSE)
conftrans$transitive
conftrans$intransitive
conftrans$transitivity
conftrans$alpha