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evolqg (version 0.3-4)

Evolutionary Quantitative Genetics

Description

Provides functions for covariance matrix comparisons, estimation of repeatabilities in measurements and matrices, and general evolutionary quantitative genetics tools. Melo D, Garcia G, Hubbe A, Assis A P, Marroig G. (2016) .

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Version

Install

install.packages('evolqg')

Monthly Downloads

386

Version

0.3-4

License

MIT + file LICENSE

Maintainer

Last Published

December 5th, 2023

Functions in evolqg (0.3-4)

LocalShapeVariables

Local Shape Variables

Control Inverse matrix noise with Extension

Compare matrices via Mantel Correlation

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

Center2MeanJacobianFast

Centered jacobian residuals

Local Jacobian calculation

CalcRepeatability

Parametric per trait repeatabilities

Integration measure based on eigenvalue dispersion

Calculates the ICV of a covariance matrix.

Compare matrices via the correlation between response vectors

Bootstrap analysis via resampling

CalculateMatrix

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

Test drift hypothesis

R2 confidence intervals by parametric sampling

Modularity and integration analysis tool

Parametric repeatabilities with covariance or correlation matrices

PlotTreeDriftTest

Plot results from TreeDriftTest

PlotRarefaction

Plot Rarefaction analysis

Random Skewers projection

Random correlation matrix

KrzSubspaceDataFrame

Extract confidence intervals from KrzSubspaceBootstrap

Rarefaction analysis via resampling

EigenTensorDecomposition

Eigentensor Decomposition

Compare matrices via Krzanowski Correlation

Parametric population samples with covariance or correlation matrices

Test single modularity hypothesis using Mantel correlation

Krzanowski common subspaces analysis

SingleComparisonMap

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

MultiMahalanobis

Calculate Mahalonabis distance for many vectors

KrzSubspaceBootstrap

Quasi-Bayesian Krzanowski subspace comparison

PCScoreCorrelation

PC Score Correlation Test

RarefactionStat

Non-Parametric rarefacted population samples and statistic comparison

Partition2HypotMatrix

Create binary hypothesis

Rotate2MidlineMatrix

Compare matrices via Selection Response Decomposition

Mean Covariance Matrix

Matrix distance

Mantel test with phylogenetic permutations

PlotKrzSubspace

Plot KrzSubspace boostrap comparison

Compares sister groups

Calculates ancestral states of some statistic

Compare matrices via Modified Krzanowski Correlation

MeanMatrixStatistics

Calculate mean values for various matrix statistics

RelativeEigenanalysis

Relative Eigenanalysis

MultivDriftTest

Multivariate genetic drift test for 2 populations

Normalize and Norm

Print Matrix to file

Remove Size Variation

Project Covariance Matrix

Matrix Riemann distance

Distribution overlap distance

Example multivariate data set

Tree for dentus example species

Compare matrices using PCA similarity factor

Random matrices for tests

Compare matrices via RandomSkewers

Linear distances for five mouse lines

Test modularity hypothesis

Drift test along phylogeny

Alpha repeatability

BayesianCalculateMatrix

Calculate Covariance Matrix from a linear model fitted with lm() using different estimators

Non-Parametric population samples and statistic comparison

Calculates mean correlations within- and between-modules

CreateHypotMatrix

Creates binary correlation matrices

R2 confidence intervals by bootstrap resampling

Mean Squared Correlations

CalcR2CvCorrected

Corrected integration value