evolqg: Tools for Evolutionary Quantitative Genetics

Provides functions for covariance matrix comparisons, estimation of repeatabilities in measurements and matrices, and general evolutionary quantitative genetics tools.

AuthorAna Paula Assis, Diogo Melo, Edgar Zanella, Fabio Machado, Guilherme Garcia
Date of publication2017-02-02 01:04:50
MaintainerDiogo Melo <diogro@usp.br>
LicenseMIT + file LICENSE
Version0.2-5

View on CRAN

Man pages

AlphaRep: Alpha Repetability

BayesianCalculateMatrix: Calculate Covariance Matrix from a linear model fitted with...

BootstrapR2: R2 confidence intervals by bootstrap resampling

BootstrapRep: Bootstrap analysis via resampling

BootstrapStat: Non-Parametric population samples and statistic comparison

CalcAVG: Calculates mean correlations within- and between-modules

CalcICV: Calculates the ICV of a covariance matrix.

CalcR2: Mean Squared Correlations

CalcR2CvCorrected: Corrected integration value

CalcRepeatability: Parametric per trait Repeatabilities

CalculateMatrix: Calculate Covariance Matrix from a linear model fitted with...

ComparisonMap: Generic Comparison Map functions for creating parallel list...

CreateHypotMatrix: Creates binary correlation matrices

dentus: Example multivariate data set

dentus.tree: Tree for dentus example species

DriftTest: Test drift hypothesis

EigenTensorDecomposition: Eigentensor Decomposition

evolqg: EvolQG

ExtendMatrix: Control Inverse matrix noise with Extension

KrzCor: Compare matrices via Krzanowski Correlation

KrzProjection: Compare matrices via Modified Krzanowski Correlation

KrzSubspace: Krzanowski common subspaces analysis

LModularity: L Modularity

MantelCor: Compare matrices via Mantel Correlation

MantelModTest: Test single modularity hypothesis using Mantel correlation

MatrixCompare: Matrix Compare

MatrixDistance: 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...

MonteCarloStat: Parametric population samples with covariance or correlation...

MultiMahalanobis: Calculate Mahalonabis distance for many vectors

MultivDriftTest: Multivariate genetic drift test for 2 populations

Normalize: Normalize and Norm

OverlapDist: Distribution overlap distance

PCAsimilarity: 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

PlotRarefaction: Plot Rarefaction analysis

PlotTreeDriftTest: Plot results from TreeDriftTest

PrintMatrix: Print Matrix to file

ProjectMatrix: Project Covariance Matrix

RandCorr: Random correlation matrix

RandomMatrix: Random matrices for tests

RandomSkewers: Compare matrices via RandomSkewers

Rarefaction: Rarefaction analysis via ressampling

RarefactionStat: Non-Parametric rarefacted population samples and statistic...

RemoveSize: Remove Size Variation

RevertMatrix: Revert Matrix

RiemannDist: Matrix Riemann distance

RSProjection: Random Skewers projection

SingleComparisonMap: Generic Single Comparison Map functions for creating parallel...

SRD: Compare matrices via Selection Response Decomposition

TestModularity: Test modularity hypothesis

TreeDriftTest: Drift test along phylogeny

Functions

AlphaRep Man page
Autonomy Man page
BayesianCalculateMatrix Man page
BootstrapR2 Man page
BootstrapRep Man page
BootstrapStat Man page
CalcAVG Man page
CalcICV Man page
CalcR2 Man page
CalcR2CvCorrected Man page
CalcR2CvCorrected.default Man page
CalcR2CvCorrected.lm Man page
CalcRepeatability Man page
CalculateMatrix Man page
ComparisonMap Man page
ConditionalEvolvability Man page
Constraints Man page
CreateHypotMatrix Man page
dentus Man page
dentus.tree Man page
DriftTest Man page
EigenTensorDecomposition Man page
EigenTensorDecomposition.default Man page
EigenTensorDecomposition.list Man page
evolqg Man page
evolqg-package Man page
Evolvability Man page
ExtendMatrix Man page
Flexibility Man page
JackKnifeMINT Man page
JackKnifeMINT Man page
KrzCor Man page
KrzCor.default Man page
KrzCor.list Man page
KrzCor.mcmc_sample Man page
KrzProjection Man page
KrzProjection.default Man page
KrzProjection.list Man page
KrzSubspace Man page
LModularity Man page
MantelCor Man page
MantelCor.default Man page
MantelCor.list Man page
MantelCor.mcmc_sample Man page
MantelModTest Man page
MantelModTest.default Man page
MantelModTest.list Man page
MatrixCompare Man page
MatrixCor Man page
MatrixCor.default Man page
MatrixCor.list Man page
MatrixCor.mcmc_sample Man page
MatrixDistance Man page
MatrixDistance.default Man page
MatrixDistance.list Man page
MeanMatrix Man page
MeanMatrixStatistics Man page
MINT Man page
MonteCarloR2 Man page
MonteCarloRep Man page
MonteCarloStat Man page
MultiMahalanobis Man page
MultivDriftTest Man page
Norm Man page
Norm Man page
Normalize Man page
OverlapDist Man page
Pc1Percent Man page
PCAsimilarity Man page
PCAsimilarity.default Man page
PCAsimilarity.list Man page
PCAsimilarity.mcmc_sample Man page
PCScoreCorrelation Man page
PhyloCompare Man page
PhyloMantel Man page
PhyloW Man page
PlotRarefaction Man page
PlotRSprojection Man page
plot.SRD Man page
PlotTreeDriftTest Man page
PrintMatrix Man page
PrintMatrix.default Man page
PrintMatrix.list Man page
ProjectMatrix Man page
RandCorr Man page
RandomMatrix Man page
RandomSkewers Man page
RandomSkewers.default Man page
RandomSkewers.list Man page
RandomSkewers.mcmc_sample Man page
Rarefaction Man page
RarefactionStat Man page
RemoveSize Man page
Respondability Man page
RevertMatrix Man page
RiemannDist Man page
RSProjection Man page
SingleComparisonMap Man page
SRD Man page
SRD.default Man page
SRD.list Man page
TestModularity Man page
TreeDriftTest Man page

Files

evolqg
evolqg/inst
evolqg/inst/CITATION
evolqg/tests
evolqg/tests/testthat.R
evolqg/tests/testthat
evolqg/tests/testthat/test.MatrixDistances.r
evolqg/tests/testthat/test.Rarefaction.r
evolqg/tests/testthat/test.TestModularity.r
evolqg/tests/testthat/test.MonteCarloStat.r
evolqg/tests/testthat/test.MultiMahalanobis.r
evolqg/tests/testthat/test.DriftTest.r
evolqg/tests/testthat/test.CalcR2.r
evolqg/tests/testthat/test.CalcR2CvCorrected.r
evolqg/tests/testthat/test.AlphaRep.r
evolqg/tests/testthat/test.PhyloW.r
evolqg/tests/testthat/test.SRD.r
evolqg/tests/testthat/test.CalcRepeatability.r
evolqg/tests/testthat/test.MatrixComparisons.r
evolqg/tests/testthat/load.func.r
evolqg/tests/testthat/test.LModularity.r
evolqg/tests/testthat/iris.stats
evolqg/tests/testthat/test.RemoveSize.r
evolqg/tests/testthat/test.RandomCorr.r
evolqg/tests/testthat/test.RSProjection.r
evolqg/tests/testthat/test.CalculateMatrix.r
evolqg/tests/testthat/test.CalcICV.r
evolqg/tests/testthat/test.MINT.r
evolqg/tests/testthat/test.PCScoreCorrelation.r
evolqg/tests/testthat/test.PhyloCompare.r
evolqg/tests/testthat/test.MeanMatrix.r
evolqg/tests/testthat/test.BootstrapRep.r
evolqg/tests/testthat/test.ExtendMatrix.r
evolqg/tests/testthat/test.KrzSubspace.r
evolqg/tests/testthat/test.Normalize.r
evolqg/tests/testthat/test.MatrixStatistics.r
evolqg/src
evolqg/src/Makevars
evolqg/src/fast_RS.cpp
evolqg/src/Makevars.win
evolqg/src/RcppExports.cpp
evolqg/NAMESPACE
evolqg/data
evolqg/data/dentus.rda
evolqg/data/dentus.tree.rda
evolqg/R
evolqg/R/MatrixStatistics.R evolqg/R/EigenTensorDecomposition.R evolqg/R/MeanMatrix.R evolqg/R/PhyloW.R evolqg/R/CalcR2.R evolqg/R/RandomSkewers.R evolqg/R/MultiMahalanobis.R evolqg/R/CalcRepeatability.R evolqg/R/MultivDriftTest.R evolqg/R/DriftTest.R evolqg/R/RevertMatrix.R evolqg/R/CalculateMatrix.R evolqg/R/Rarefaction.R evolqg/R/PhyloMantel.R evolqg/R/PCScoreCorrelation.R evolqg/R/MINT.R evolqg/R/CalcR2CvCorrected.R evolqg/R/MatrixDistance.R evolqg/R/EvolQG.R evolqg/R/SingleComparisonMap.R evolqg/R/PhyloCompare.R evolqg/R/ComparisonMap.R evolqg/R/KrzCor.R evolqg/R/RcppExports.R evolqg/R/CalcICV.R evolqg/R/KrzProjection.R evolqg/R/RemoveSize.R evolqg/R/PCAsimilarity.R evolqg/R/RandomMatrix.R evolqg/R/MonteCarloStat.R evolqg/R/CreateHypotMatrix.R evolqg/R/BootstrapRep.R evolqg/R/RSProjection.R evolqg/R/AlphaRep.R evolqg/R/MantelModTest.R evolqg/R/KrzSubspace.R evolqg/R/l_modularity.R evolqg/R/CalcAVG.R evolqg/R/RandomCorr.R evolqg/R/PrintMatrix.R evolqg/R/Normalize.R evolqg/R/MatrixCompare.R evolqg/R/ExtendMatrix.R evolqg/R/ProjectMatrix.R evolqg/R/TestModularity.R evolqg/R/SRD.R evolqg/R/MantelCor.R
evolqg/MD5
evolqg/DESCRIPTION
evolqg/man
evolqg/man/MonteCarloR2.Rd evolqg/man/dentus.Rd evolqg/man/MINT.Rd evolqg/man/RevertMatrix.Rd evolqg/man/ComparisonMap.Rd evolqg/man/ExtendMatrix.Rd evolqg/man/ProjectMatrix.Rd evolqg/man/RiemannDist.Rd evolqg/man/MantelModTest.Rd evolqg/man/MonteCarloRep.Rd evolqg/man/SingleComparisonMap.Rd evolqg/man/PCScoreCorrelation.Rd evolqg/man/PlotTreeDriftTest.Rd evolqg/man/BootstrapRep.Rd evolqg/man/CalcAVG.Rd evolqg/man/RandomMatrix.Rd evolqg/man/CreateHypotMatrix.Rd evolqg/man/MultivDriftTest.Rd evolqg/man/Normalize.Rd evolqg/man/RandCorr.Rd evolqg/man/SRD.Rd evolqg/man/CalcR2CvCorrected.Rd evolqg/man/KrzSubspace.Rd evolqg/man/CalcR2.Rd evolqg/man/EigenTensorDecomposition.Rd evolqg/man/Rarefaction.Rd evolqg/man/PrintMatrix.Rd evolqg/man/CalcICV.Rd evolqg/man/BootstrapStat.Rd evolqg/man/AlphaRep.Rd evolqg/man/PhyloMantel.Rd evolqg/man/RemoveSize.Rd evolqg/man/PhyloW.Rd evolqg/man/TreeDriftTest.Rd evolqg/man/MatrixCompare.Rd evolqg/man/MeanMatrix.Rd evolqg/man/MeanMatrixStatistics.Rd evolqg/man/PhyloCompare.Rd evolqg/man/dentus.tree.Rd evolqg/man/CalcRepeatability.Rd evolqg/man/BootstrapR2.Rd evolqg/man/MultiMahalanobis.Rd evolqg/man/KrzCor.Rd evolqg/man/BayesianCalculateMatrix.Rd evolqg/man/RSProjection.Rd evolqg/man/LModularity.Rd evolqg/man/RarefactionStat.Rd evolqg/man/OverlapDist.Rd evolqg/man/RandomSkewers.Rd evolqg/man/DriftTest.Rd evolqg/man/evolqg.Rd evolqg/man/CalculateMatrix.Rd evolqg/man/KrzProjection.Rd evolqg/man/MantelCor.Rd evolqg/man/PCAsimilarity.Rd evolqg/man/PlotRarefaction.Rd evolqg/man/TestModularity.Rd evolqg/man/MatrixDistance.Rd evolqg/man/MonteCarloStat.Rd
evolqg/LICENSE

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.