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.

Author
Ana Paula Assis, Diogo Melo, Edgar Zanella, Fabio Machado, Guilherme Garcia
Date of publication
2016-06-04 19:35:00
Maintainer
Diogo Melo <diogro@usp.br>
License
MIT + file LICENSE
Version
0.2-4

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
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...
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
MatrixCompare
Matrix Compare
MatrixDistance
Matrix distance
MeanMatrix
Mean Covariance Matrix
MeanMatrixStatistics
Calculate mean values for various matrix statistics
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

Files in this package

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/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.PCScoreCorrelation.r
evolqg/tests/testthat/test.PhyloCompare.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/l-modularity.cpp
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/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/BootstrapRep.R
evolqg/R/RSProjection.R
evolqg/R/AlphaRep.R
evolqg/R/KrzSubspace.R
evolqg/R/l_modularity.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/RevertMatrix.Rd
evolqg/man/ComparisonMap.Rd
evolqg/man/ExtendMatrix.Rd
evolqg/man/ProjectMatrix.Rd
evolqg/man/RiemannDist.Rd
evolqg/man/MonteCarloRep.Rd
evolqg/man/SingleComparisonMap.Rd
evolqg/man/PCScoreCorrelation.Rd
evolqg/man/PlotTreeDriftTest.Rd
evolqg/man/BootstrapRep.Rd
evolqg/man/RandomMatrix.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