Test modularity hypothesis

Share:

Description

Tests modularity hypothesis using cor.matrix matrix and trait groupings

Usage

1
2
3
4
TestModularity(cor.matrix, modularity.hipot, permutations = 100,
  MHI = FALSE)

CreateHipotMatrix(modularity.hipot)

Arguments

cor.matrix

Correlation matrix

modularity.hipot

Matrix of hypothesis. Each line represents a trait and each column a module. if modularity.hipot[i,j] == 1, trait i is in module j.

permutations

Number of permutations, to be passed to MantelCor

MHI

Indicates if test should use Modularity Hypothesis Index instead of AVG Ratio

Value

Returns mantel correlation and associated probability for each modularity hypothesis, along with AVG+, AVG-, AVG Ratio for each module. A total hypothesis combining all hypotesis is also tested.

Author(s)

Diogo Melo, Guilherme Garcia

References

Porto, Arthur, Felipe B. Oliveira, Leila T. Shirai, Valderes Conto, and Gabriel Marroig. 2009. "The Evolution of Modularity in the Mammalian Skull I: Morphological Integration Patterns and Magnitudes." Evolutionary Biology 36 (1): 118-35. doi:10.1007/s11692-008-9038-3.

See Also

MantelCor

Examples

1
2
3
4
5
6
7
cor.matrix <- RandomMatrix(10)
rand.hipots <- matrix(sample(c(1, 0), 30, replace=TRUE), 10, 3)
mod.test <- TestModularity(cor.matrix, rand.hipots)

cov.matrix <- RandomMatrix(10, 1, 1, 10)
cov.mod.test <- TestModularity(cov.matrix, rand.hipots, MHI = TRUE)
nosize.cov.mod.test <- TestModularity(RemoveSize(cov.matrix), rand.hipots, MHI = TRUE)

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.