Evolutionary Quantitative Genetics

Documentation for package ‘evolqg’ version 0.3-4

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EvolQG

-- A --

AlphaRep	Alpha repeatability
Autonomy	Calculate mean values for various matrix statistics

-- B --

BayesianCalculateMatrix	Calculate Covariance Matrix from a linear model fitted with lm() using different estimators
BootstrapR2	R2 confidence intervals by bootstrap resampling
BootstrapRep	Bootstrap analysis via resampling
BootstrapStat	Non-Parametric population samples and statistic comparison

-- C --

CalcAVG	Calculates mean correlations within- and between-modules
CalcEigenVar	Integration measure based on eigenvalue dispersion
CalcICV	Calculates the ICV of a covariance matrix.
CalcR2	Mean Squared Correlations
CalcR2CvCorrected	Corrected integration value
CalcR2CvCorrected.default	Corrected integration value
CalcR2CvCorrected.lm	Corrected integration value
CalcRepeatability	Parametric per trait repeatabilities
CalculateMatrix	Calculate Covariance Matrix from a linear model fitted with lm()
Center2MeanJacobianFast	Centered jacobian residuals
ComparisonMap	Generic Comparison Map functions for creating parallel list methods Internal functions for making eficient comparisons.
ConditionalEvolvability	Calculate mean values for various matrix statistics
Constraints	Calculate mean values for various matrix statistics
CreateHypotMatrix	Creates binary correlation matrices

-- D --

DeltaZCorr	Compare matrices via the correlation between response vectors
DeltaZCorr.default	Compare matrices via the correlation between response vectors
DeltaZCorr.list	Compare matrices via the correlation between response vectors
dentus	Example multivariate data set
dentus.tree	Tree for dentus example species
DriftTest	Test drift hypothesis

-- E --

EigenTensorDecomposition	Eigentensor Decomposition
EigenTensorDecomposition.default	Eigentensor Decomposition
EigenTensorDecomposition.list	Eigentensor Decomposition
evolqg	EvolQG
Evolvability	Calculate mean values for various matrix statistics
ExtendMatrix	Control Inverse matrix noise with Extension

-- F --

Calculate mean values for various matrix statistics

-- J --

JackKnifeMINT	Modularity and integration analysis tool
JacobianArray	Local Jacobian calculation

-- K --

KrzCor	Compare matrices via Krzanowski Correlation
KrzCor.default	Compare matrices via Krzanowski Correlation
KrzCor.list	Compare matrices via Krzanowski Correlation
KrzCor.mcmc_sample	Compare matrices via Krzanowski Correlation
KrzProjection	Compare matrices via Modified Krzanowski Correlation
KrzProjection.default	Compare matrices via Modified Krzanowski Correlation
KrzProjection.list	Compare matrices via Modified Krzanowski Correlation
KrzSubspace	Krzanowski common subspaces analysis
KrzSubspaceBootstrap	Quasi-Bayesian Krzanowski subspace comparison
KrzSubspaceDataFrame	Extract confidence intervals from KrzSubspaceBootstrap

-- L --

LModularity	L Modularity
LocalShapeVariables	Local Shape Variables

-- M --

MantelCor	Compare matrices via Mantel Correlation
MantelCor.default	Compare matrices via Mantel Correlation
MantelCor.list	Compare matrices via Mantel Correlation
MantelCor.mcmc_sample	Compare matrices via Mantel Correlation
MantelModTest	Test single modularity hypothesis using Mantel correlation
MantelModTest.default	Test single modularity hypothesis using Mantel correlation
MantelModTest.list	Test single modularity hypothesis using Mantel correlation
MatrixCompare	Matrix Compare
MatrixCor	Compare matrices via Mantel Correlation
MatrixCor.default	Compare matrices via Mantel Correlation
MatrixCor.list	Compare matrices via Mantel Correlation
MatrixCor.mcmc_sample	Compare matrices via Mantel Correlation
MatrixDistance	Matrix distance
MatrixDistance.default	Matrix distance
MatrixDistance.list	Matrix distance
MeanMatrix	Mean Covariance Matrix
MeanMatrixStatistics	Calculate mean values for various matrix statistics
MINT	Modularity and integration analysis tool
MonteCarloR2	R2 confidence intervals by parametric sampling
MonteCarloRep	Parametric repeatabilities with covariance or correlation matrices
MonteCarloStat	Parametric population samples with covariance or correlation matrices
MultiMahalanobis	Calculate Mahalonabis distance for many vectors
MultivDriftTest	Multivariate genetic drift test for 2 populations

-- N --

Norm	Normalize and Norm
Normalize	Normalize and Norm

-- O --

Distribution overlap distance

-- P --

Partition2HypotMatrix	Create binary hypothesis
Pc1Percent	Calculate mean values for various matrix statistics
PCAsimilarity	Compare matrices using PCA similarity factor
PCAsimilarity.default	Compare matrices using PCA similarity factor
PCAsimilarity.list	Compare matrices using PCA similarity factor
PCAsimilarity.mcmc_sample	Compare matrices using PCA similarity factor
PCScoreCorrelation	PC Score Correlation Test
PhyloCompare	Compares sister groups
PhyloMantel	Mantel test with phylogenetic permutations
PhyloW	Calculates ancestral states of some statistic
plot.SRD	Compare matrices via Selection Response Decomposition
PlotKrzSubspace	Plot KrzSubspace boostrap comparison
PlotRarefaction	Plot Rarefaction analysis
PlotRSprojection	Random Skewers projection
PlotTreeDriftTest	Plot results from TreeDriftTest
PrintMatrix	Print Matrix to file
PrintMatrix.default	Print Matrix to file
PrintMatrix.list	Print Matrix to file
ProjectMatrix	Project Covariance Matrix

-- R --

RandCorr	Random correlation matrix
RandomMatrix	Random matrices for tests
RandomSkewers	Compare matrices via RandomSkewers
RandomSkewers.default	Compare matrices via RandomSkewers
RandomSkewers.list	Compare matrices via RandomSkewers
RandomSkewers.mcmc_sample	Compare matrices via RandomSkewers
Rarefaction	Rarefaction analysis via resampling
RarefactionStat	Non-Parametric rarefacted population samples and statistic comparison
ratones	Linear distances for five mouse lines
RelativeEigenanalysis	Relative Eigenanalysis
RemoveSize	Remove Size Variation
Respondability	Calculate mean values for various matrix statistics
RevertMatrix	Revert Matrix
RiemannDist	Matrix Riemann distance
Rotate2MidlineMatrix	Midline rotate
RSProjection	Random Skewers projection

-- S --

SingleComparisonMap	Generic Single Comparison Map functions for creating parallel list methods Internal functions for making efficient comparisons.
SRD	Compare matrices via Selection Response Decomposition
SRD.default	Compare matrices via Selection Response Decomposition
SRD.list	Compare matrices via Selection Response Decomposition

-- T --