evolqg (version 0.3-4)

MantelModTest: Test single modularity hypothesis using Mantel correlation

Description

Calculates the correlation and Mantel significance test between a hypothetical binary modularity matrix and a correlation matrix. Also gives mean correlation within- and between-modules. This function is usually only called by TestModularity.

Usage

MantelModTest(cor.hypothesis, cor.matrix, ...)
# S3 method for default
MantelModTest(
  cor.hypothesis,
  cor.matrix,
  permutations = 1000,
  MHI = FALSE,
  ...,
  landmark.dim = NULL,
  withinLandmark = FALSE
)
# S3 method for list
MantelModTest(
  cor.hypothesis,
  cor.matrix,
  permutations = 1000,
  MHI = FALSE,
  landmark.dim = NULL,
  withinLandmark = FALSE,
  ...,
  parallel = FALSE
)

Value

Returns a vector with the matrix correlation, significance via Mantel, within- and between module correlation.

Arguments

cor.hypothesis

Hypothetical correlation matrix, with 1s within-modules and 0s between modules.

cor.matrix

Observed empirical correlation matrix.

...

additional arguments passed to MantelCor

permutations

Number of permutations used in significance calculation.

MHI

Indicates if Modularity Hypothesis Index should be calculated instead of AVG Ratio.

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 correlation are used in calculation of correlation. Only used if landmark.dim is passed, default is FALSE.

parallel

if TRUE computations are done in parallel. Some foreach back-end must be registered, like doParallel or doMC.

Author

Diogo Melo, Guilherme Garcia

Details

CalcAVG can be used when a significance test is not required.

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.

Modularity and Morphometrics: Error Rates in Hypothesis Testing Guilherme Garcia, Felipe Bandoni de Oliveira, Gabriel Marroig bioRxiv 030874; doi: http://dx.doi.org/10.1101/030874

See Also

mantel,MantelCor,CalcAVG,TestModularity

Examples

# Create a single modularity hypothesis:
hypot = rep(c(1, 0), each = 6)
cor.hypot = CreateHypotMatrix(hypot)

# First with an unstructured matrix:
un.cor = RandomMatrix(12)
MantelModTest(cor.hypot, un.cor)

# Now with a modular matrix:
hypot.mask = matrix(as.logical(cor.hypot), 12, 12)
mod.cor = matrix(NA, 12, 12)
mod.cor[ hypot.mask] = runif(length(mod.cor[ hypot.mask]), 0.8, 0.9) # within-modules
mod.cor[!hypot.mask] = runif(length(mod.cor[!hypot.mask]), 0.3, 0.4) # between-modules
diag(mod.cor) = 1
mod.cor = (mod.cor + t(mod.cor))/2 # correlation matrices should be symmetric

MantelModTest(cor.hypot, mod.cor)