Tools for Evolutionary Quantitative Genetics


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Documentation for package ‘evolqg’ version 0.2-9

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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()
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

-- 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

-- L --

LModularity L Modularity

-- 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
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
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
TreeDriftTest Drift test along phylogeny