# Evolutionary Quantitative Genetics

## Documentation for package ‘evolqg’ version 0.3-2

- DESCRIPTION file.

## Help Pages

A B C D E F J K L M N O P R S T

## -- 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 --

Flexibility | 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 --

OverlapDist | 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 --

TestModularity | Test modularity hypothesis
TPS | TPS transform
TreeDriftTest | Drift test along phylogeny