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evolqg (version 0.2-2)

Tools for Evolutionary Quantitative Genetics

Description

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

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Version

Install

install.packages('evolqg')

Monthly Downloads

658

Version

0.2-2

License

MIT + file LICENSE

Maintainer

Diogo Melo

Last Published

December 17th, 2015

Functions in evolqg (0.2-2)

CalculateMatrix

Calculate Covariance Matrix from a linear model fitted with lm()
MeanMatrixStatistics

Calculate mean values for various matrix statistics
MultiMahalanobis

Calculate Mahalonabis distance for many vectors
ExtendMatrix

Control Inverse matrix noise with Extension
MonteCarloR2

R2 confidence intervals by parametric sampling
MultivDriftTest

Multivariate genetic drift test for 2 populations
BootstrapRep

Bootstrap analysis via resampling
PCScoreCorrelation

PC Score Correlation Test
MatrixDistance

Matrix distance
CalcR2CvCorrected

Corrected integration value
SRD

Compare matrices via Selection Response Decomposition
ComparisonMap

Generic Comparison Map functions for creating parallel list methods Internal functions for making eficient comparisons.
PhyloW

Calculates ancestral states of some statistic
SingleComparisonMap

Generic Single Comparison Map functions for creating parallel list methods Internal functions for making eficient comparisons.
RandomMatrix

Random matrices for tests
DriftTest

Test drift hypothesis
Normalize

Normalize and Norm
MantelCor

Compare matrices via Mantel Correlation
BootstrapR2

R2 confidence intervals by bootstrap resampling
CalcR2

Mean Squared Correlations
evolqg

EvolQG
RandCorr

Random correlation matrix
OverlapDist

Distribution overlap distance
Rarefaction

Rarefaction analysis via ressampling
PCAsimilarity

Compare matrices using PCA similarity factor
RandomSkewers

Compare matrices via RandomSkewers
PrintMatrix

Print Matrix to file
KrzCor

Compare matrices via Krzanowski Correlation
MonteCarloRep

Parametric repeatabilities with covariance or correlation matrices
dentus.tree

Tree for dentus example species
PlotTreeDriftTest

Plot results from TreeDriftTest
AncestralStates

Fast estimation of ML ancestral stated for multivariate continous traits
BootstrapStat

Non-Parametric population samples and statistic comparison
dentus

Example multivariate data set
CalcICV

Calculates the ICV of a covariance matrix.
LModularity

L Modularity
PlotRarefaction

Plot Rarefaction analysis
CalcRepeatability

Parametric per trait Repeatabilities
TreeDriftTest

Drift test along phylogeny
RiemannDist

Matrix Riemann distance
AlphaRep

Alpha Repetability
KrzProjection

Compare matrices via Modified Krzanowski Correlation
PhyloCompare

Compares sister groups
MatrixCompare

Matrix Compare
MonteCarloStat

Parametric population samples with covariance or correlation matrices
RSProjection

Random Skewers projection
RarefactionStat

Non-Parametric rarefacted population samples and statistic comparison
LinearParsimony

Estimation of Linear Parcimony ancestral stated for multivariate continous traits
RemoveSize

Remove Size Variation
TestModularity

Test modularity hypothesis