evolqg: Tools for Evolutionary Quantitative Genetics
Version 0.2-5

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

Browse man pages Browse package API and functions Browse package files

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("evolqg")

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 Source code
Autonomy Man page Source code
BayesianCalculateMatrix Man page Source code
BinToDec Source code
BootstrapR2 Man page Source code
BootstrapRep Man page Source code
BootstrapStat Man page Source code
CalcAVG Man page Source code
CalcICV Man page Source code
CalcR2 Man page Source code
CalcR2CvCorrected Man page Source code
CalcR2CvCorrected.default Man page Source code
CalcR2CvCorrected.lm Man page Source code
CalcRepeatability Man page Source code
CalculateMatrix Man page Source code
CombineHypot Source code
ComparisonMap Man page Source code
ConditionalEvolvability Man page Source code
Constraints Man page Source code
CreateHypotMatrix Man page Source code
CreateWithinLandMat Source code
DecToBin Source code
DriftTest Man page Source code
EigenTensorDecomposition Man page Source code
EigenTensorDecomposition.default Man page Source code
EigenTensorDecomposition.list Man page Source code
Evolvability Man page Source code
ExtendMatrix Man page Source code
Flexibility Man page Source code
JackKnifeMINT Man page Man page Source code
KrzCor Man page Source code
KrzCor.default Man page Source code
KrzCor.list Man page Source code
KrzCor.mcmc_sample Man page Source code
KrzProjection Man page Source code
KrzProjection.default Man page Source code
KrzProjection.list Man page Source code
KrzSubspace Man page Source code
LModularity Man page Source code
MINT Man page Source code
MantelCor Man page Source code
MantelCor.default Man page Source code
MantelCor.list Man page Source code
MantelCor.mcmc_sample Man page Source code
MantelModTest Man page Source code
MantelModTest.default Man page Source code
MantelModTest.list Man page Source code
MatrixCompare Man page Source code
MatrixCor Man page Source code
MatrixCor.default Man page Source code
MatrixCor.list Man page Source code
MatrixCor.mcmc_sample Man page Source code
MatrixDistance Man page Source code
MatrixDistance.default Man page Source code
MatrixDistance.list Man page Source code
MeanMatrix Man page Source code
MeanMatrixStatistics Man page Source code
MonteCarloR2 Man page Source code
MonteCarloRep Man page Source code
MonteCarloStat Man page Source code
MultiMahalanobis Man page Source code
MultivDriftTest Man page Source code
Norm Man page Man page Source code
Normalize Man page Source code
OverlapDist Man page Source code
PCAsimilarity Man page Source code
PCAsimilarity.default Man page Source code
PCAsimilarity.list Man page Source code
PCAsimilarity.mcmc_sample Man page Source code
PCScoreCorrelation Man page Source code
Pc1Percent Man page Source code
PhyloCompare Man page Source code
PhyloMantel Man page Source code
PhyloW Man page Source code
PlotRSprojection Man page Source code
PlotRarefaction Man page Source code
PlotTreeDriftTest Man page Source code
PrintMatrix Man page Source code
PrintMatrix.default Man page Source code
PrintMatrix.list Man page Source code
ProjectMatrix Man page Source code
RS Source code
RSProjection Man page Source code
RandCorr Man page Source code
RandomMatrix Man page Source code
RandomSkewers Man page Source code
RandomSkewers.default Man page Source code
RandomSkewers.list Man page Source code
RandomSkewers.mcmc_sample Man page Source code
Rarefaction Man page Source code
RarefactionStat Man page Source code
RemoveSize Man page Source code
Respondability Man page Source code
RevertMatrix Man page Source code
RiemannDist Man page Source code
SRD Man page Source code
SRD.default Man page Source code
SRD.list Man page Source code
SingleComparisonMap Man page Source code
SingleMINT Source code
TestModularity Man page Source code
TreeDriftTest Man page Source code
dentus Man page
dentus.tree Man page
doComparisonBS Source code
doComparisonMC Source code
evolqg Man page
evolqg-package Man page
gamma Source code
getDescendants Source code
getMeans Source code
lower.tri.land Source code
permPhylo Source code
phyloPermute Source code
phyloProb Source code
plot.SRD Man page Source code
print.mcmc_sample Source code

Files

inst
inst/CITATION
tests
tests/testthat.R
tests/testthat
tests/testthat/test.MatrixDistances.r
tests/testthat/test.Rarefaction.r
tests/testthat/test.TestModularity.r
tests/testthat/test.MonteCarloStat.r
tests/testthat/test.MultiMahalanobis.r
tests/testthat/test.DriftTest.r
tests/testthat/test.CalcR2.r
tests/testthat/test.CalcR2CvCorrected.r
tests/testthat/test.AlphaRep.r
tests/testthat/test.PhyloW.r
tests/testthat/test.SRD.r
tests/testthat/test.CalcRepeatability.r
tests/testthat/test.MatrixComparisons.r
tests/testthat/load.func.r
tests/testthat/test.LModularity.r
tests/testthat/iris.stats
tests/testthat/test.RemoveSize.r
tests/testthat/test.RandomCorr.r
tests/testthat/test.RSProjection.r
tests/testthat/test.CalculateMatrix.r
tests/testthat/test.CalcICV.r
tests/testthat/test.MINT.r
tests/testthat/test.PCScoreCorrelation.r
tests/testthat/test.PhyloCompare.r
tests/testthat/test.MeanMatrix.r
tests/testthat/test.BootstrapRep.r
tests/testthat/test.ExtendMatrix.r
tests/testthat/test.KrzSubspace.r
tests/testthat/test.Normalize.r
tests/testthat/test.MatrixStatistics.r
src
src/Makevars
src/fast_RS.cpp
src/Makevars.win
src/RcppExports.cpp
NAMESPACE
data
data/dentus.rda
data/dentus.tree.rda
R
R/MatrixStatistics.R
R/EigenTensorDecomposition.R
R/MeanMatrix.R
R/PhyloW.R
R/CalcR2.R
R/RandomSkewers.R
R/MultiMahalanobis.R
R/CalcRepeatability.R
R/MultivDriftTest.R
R/DriftTest.R
R/RevertMatrix.R
R/CalculateMatrix.R
R/Rarefaction.R
R/PhyloMantel.R
R/PCScoreCorrelation.R
R/MINT.R
R/CalcR2CvCorrected.R
R/MatrixDistance.R
R/EvolQG.R
R/SingleComparisonMap.R
R/PhyloCompare.R
R/ComparisonMap.R
R/KrzCor.R
R/RcppExports.R
R/CalcICV.R
R/KrzProjection.R
R/RemoveSize.R
R/PCAsimilarity.R
R/RandomMatrix.R
R/MonteCarloStat.R
R/CreateHypotMatrix.R
R/BootstrapRep.R
R/RSProjection.R
R/AlphaRep.R
R/MantelModTest.R
R/KrzSubspace.R
R/l_modularity.R
R/CalcAVG.R
R/RandomCorr.R
R/PrintMatrix.R
R/Normalize.R
R/MatrixCompare.R
R/ExtendMatrix.R
R/ProjectMatrix.R
R/TestModularity.R
R/SRD.R
R/MantelCor.R
MD5
DESCRIPTION
man
man/MonteCarloR2.Rd
man/dentus.Rd
man/MINT.Rd
man/RevertMatrix.Rd
man/ComparisonMap.Rd
man/ExtendMatrix.Rd
man/ProjectMatrix.Rd
man/RiemannDist.Rd
man/MantelModTest.Rd
man/MonteCarloRep.Rd
man/SingleComparisonMap.Rd
man/PCScoreCorrelation.Rd
man/PlotTreeDriftTest.Rd
man/BootstrapRep.Rd
man/CalcAVG.Rd
man/RandomMatrix.Rd
man/CreateHypotMatrix.Rd
man/MultivDriftTest.Rd
man/Normalize.Rd
man/RandCorr.Rd
man/SRD.Rd
man/CalcR2CvCorrected.Rd
man/KrzSubspace.Rd
man/CalcR2.Rd
man/EigenTensorDecomposition.Rd
man/Rarefaction.Rd
man/PrintMatrix.Rd
man/CalcICV.Rd
man/BootstrapStat.Rd
man/AlphaRep.Rd
man/PhyloMantel.Rd
man/RemoveSize.Rd
man/PhyloW.Rd
man/TreeDriftTest.Rd
man/MatrixCompare.Rd
man/MeanMatrix.Rd
man/MeanMatrixStatistics.Rd
man/PhyloCompare.Rd
man/dentus.tree.Rd
man/CalcRepeatability.Rd
man/BootstrapR2.Rd
man/MultiMahalanobis.Rd
man/KrzCor.Rd
man/BayesianCalculateMatrix.Rd
man/RSProjection.Rd
man/LModularity.Rd
man/RarefactionStat.Rd
man/OverlapDist.Rd
man/RandomSkewers.Rd
man/DriftTest.Rd
man/evolqg.Rd
man/CalculateMatrix.Rd
man/KrzProjection.Rd
man/MantelCor.Rd
man/PCAsimilarity.Rd
man/PlotRarefaction.Rd
man/TestModularity.Rd
man/MatrixDistance.Rd
man/MonteCarloStat.Rd
LICENSE
evolqg documentation built on May 19, 2017, 11:52 p.m.