TestModularity {evolqg}

Test modularity hypothesis

Description

Tests modularity hypothesis using cor.matrix matrix and trait groupings

Usage

TestModularity(
  cor.matrix,
  modularity.hypot,
  permutations = 1000,
  MHI = FALSE,
  ...,
  landmark.dim = NULL,
  withinLandmark = FALSE
)

Arguments

cor.matrix

Correlation matrix

modularity.hypot

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

permutations

Number of permutations, to be passed to MantelModTest

MHI

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

...

additional arguments passed to MantelModTest

landmark.dim

Used if permutations should be performed maintaining landmark structure in geometric morphometric data. Either 2 for 2d data or 3 for 3d data. Default is NULL for non geometric morphometric data.

withinLandmark

Logical. If TRUE within-landmark correlations are used in the calculation of matrix correlation. Only used if landmark.dim is passed, default is FALSE.

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 hypothesis 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

MantelModTest

Examples

cor.matrix <- RandomMatrix(10)
rand.hypots <- matrix(sample(c(1, 0), 30, replace=TRUE), 10, 3)
mod.test <- TestModularity(cor.matrix, rand.hypots)

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