Package: evolqg 0.3-5

Diogo Melo

evolqg: Evolutionary Quantitative Genetics

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) <doi:10.12688/f1000research.7082.3>.

Authors:Diogo Melo [aut, cre], Ana Paula Assis [aut], Edgar Zanella [ctb], Fabio Andrade Machado [aut], Guilherme Garcia [aut], Alex Hubbe [rev], Gabriel Marroig [ths]

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evolqg.pdf |evolqg.html✨
evolqg/json (API)

# Install 'evolqg' in R:
install.packages('evolqg', repos = c('https://lem-usp.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/lem-usp/evolqg/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • dentus - Example multivariate data set
  • dentus.tree - Tree for dentus example species
  • ratones - Linear distances for five mouse lines

On CRAN:

76 exports 10 stars 2.37 score 92 dependencies 4 mentions 102 scripts 511 downloads

Last updated 5 months agofrom:1c3a698a5f. Checks:OK: 7 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 13 2024
R-4.5-win-x86_64NOTESep 13 2024
R-4.5-linux-x86_64NOTESep 13 2024
R-4.4-win-x86_64OKSep 13 2024
R-4.4-mac-x86_64OKSep 13 2024
R-4.4-mac-aarch64OKSep 13 2024
R-4.3-win-x86_64OKSep 13 2024
R-4.3-mac-x86_64OKSep 13 2024
R-4.3-mac-aarch64OKSep 13 2024

Exports:AlphaRepAutonomyBayesianCalculateMatrixBootstrapR2BootstrapRepBootstrapStatCalcAVGCalcEigenVarCalcICVCalcR2CalcR2CvCorrectedCalcRepeatabilityCalculateMatrixCenter2MeanJacobianFastConditionalEvolvabilityConstraintsCreateHypotMatrixDeltaZCorrDriftTestEigenTensorDecompositionEvolvabilityExtendMatrixFlexibilityJackKnifeMINTJacobianArrayKrzCorKrzProjectionKrzSubspaceKrzSubspaceBootstrapKrzSubspaceDataFrameLModularityLocalShapeVariablesMantelCorMantelModTestMatrixCompareMatrixCorMatrixDistanceMeanMatrixMeanMatrixStatisticsMINTMonteCarloR2MonteCarloRepMonteCarloStatMultiMahalanobisMultivDriftTestNormNormalizeOverlapDistPartition2HypotMatrixPc1PercentPCAsimilarityPCScoreCorrelationPhyloComparePhyloMantelPhyloWPlotKrzSubspacePlotRarefactionPlotRSprojectionPlotTreeDriftTestPrintMatrixProjectMatrixRandomMatrixRandomSkewersRarefactionRarefactionStatRelativeEigenanalysisRemoveSizeRespondabilityRevertMatrixRiemannDistRotate2MidlineMatrixRSProjectionSRDTestModularityTPSTreeDriftTest

Dependencies:apebase64encbezierbslibcachemclassclassIntcliclustercodacodetoolscolorRampscolorspacecpp11DBIdigestdoParallele1071evaluateexpmfansifarverfastmapfontawesomeforeachfsggplot2gluegtablehighrhtmltoolshtmlwidgetsigraphisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglatticelifecyclemagrittrMASSMatrixMatrixModelsmcmcMCMCpackmemoisemgcvmimeMorphomunsellmvtnormnlmenumDerivpermutepillarpkgconfigplyrproxyquantregR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenreshape2rglrlangrmarkdownRvcgs2sassscalessfSparseMstringistringrsurvivaltibbletinytexunitsutf8vctrsveganviridisLitewithrwkxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Alpha repeatabilityAlphaRep
Calculate Covariance Matrix from a linear model fitted with lm() using different estimatorsBayesianCalculateMatrix
R2 confidence intervals by bootstrap resamplingBootstrapR2
Bootstrap analysis via resamplingBootstrapRep
Non-Parametric population samples and statistic comparisonBootstrapStat
Calculates mean correlations within- and between-modulesCalcAVG
Integration measure based on eigenvalue dispersionCalcEigenVar
Calculates the ICV of a covariance matrix.CalcICV
Mean Squared CorrelationsCalcR2
Corrected integration valueCalcR2CvCorrected CalcR2CvCorrected.default CalcR2CvCorrected.lm
Parametric per trait repeatabilitiesCalcRepeatability
Calculate Covariance Matrix from a linear model fitted with lm()CalculateMatrix
Centered jacobian residualsCenter2MeanJacobianFast
Generic Comparison Map functions for creating parallel list methods Internal functions for making eficient comparisons.ComparisonMap
Creates binary correlation matricesCreateHypotMatrix
Compare matrices via the correlation between response vectorsDeltaZCorr DeltaZCorr.default DeltaZCorr.list
Example multivariate data setdentus
Tree for dentus example speciesdentus.tree
Test drift hypothesisDriftTest
Eigentensor DecompositionEigenTensorDecomposition EigenTensorDecomposition.default EigenTensorDecomposition.list
EvolQGevolqg-package evolqg
Control Inverse matrix noise with ExtensionExtendMatrix
Local Jacobian calculationJacobianArray
Compare matrices via Krzanowski CorrelationKrzCor KrzCor.default KrzCor.list KrzCor.mcmc_sample
Compare matrices via Modified Krzanowski CorrelationKrzProjection KrzProjection.default KrzProjection.list
Krzanowski common subspaces analysisKrzSubspace
Quasi-Bayesian Krzanowski subspace comparisonKrzSubspaceBootstrap
Extract confidence intervals from KrzSubspaceBootstrapKrzSubspaceDataFrame
L ModularityLModularity
Local Shape VariablesLocalShapeVariables
Compare matrices via Mantel CorrelationMantelCor MantelCor.default MantelCor.list MantelCor.mcmc_sample MatrixCor MatrixCor.default MatrixCor.list MatrixCor.mcmc_sample
Test single modularity hypothesis using Mantel correlationMantelModTest MantelModTest.default MantelModTest.list
Matrix CompareMatrixCompare
Matrix distanceMatrixDistance MatrixDistance.default MatrixDistance.list
Mean Covariance MatrixMeanMatrix
Calculate mean values for various matrix statisticsAutonomy ConditionalEvolvability Constraints Evolvability Flexibility MeanMatrixStatistics Pc1Percent Respondability
Modularity and integration analysis toolJackKnifeMINT MINT
R2 confidence intervals by parametric samplingMonteCarloR2
Parametric repeatabilities with covariance or correlation matricesMonteCarloRep
Parametric population samples with covariance or correlation matricesMonteCarloStat
Calculate Mahalonabis distance for many vectorsMultiMahalanobis
Multivariate genetic drift test for 2 populationsMultivDriftTest
Normalize and NormNorm Normalize
Distribution overlap distanceOverlapDist
Create binary hypothesisPartition2HypotMatrix
Compare matrices using PCA similarity factorPCAsimilarity PCAsimilarity.default PCAsimilarity.list PCAsimilarity.mcmc_sample
PC Score Correlation TestPCScoreCorrelation
Compares sister groupsPhyloCompare
Mantel test with phylogenetic permutationsPhyloMantel
Calculates ancestral states of some statisticPhyloW
Plot KrzSubspace boostrap comparisonPlotKrzSubspace
Plot Rarefaction analysisPlotRarefaction
Plot results from TreeDriftTestPlotTreeDriftTest
Print Matrix to filePrintMatrix PrintMatrix.default PrintMatrix.list
Project Covariance MatrixProjectMatrix
Random correlation matrixRandCorr
Random matrices for testsRandomMatrix
Compare matrices via RandomSkewersRandomSkewers RandomSkewers.default RandomSkewers.list RandomSkewers.mcmc_sample
Rarefaction analysis via resamplingRarefaction
Non-Parametric rarefacted population samples and statistic comparisonRarefactionStat
Linear distances for five mouse linesratones
Relative EigenanalysisRelativeEigenanalysis
Remove Size VariationRemoveSize
Revert MatrixRevertMatrix
Matrix Riemann distanceRiemannDist
Midline rotateRotate2MidlineMatrix
Random Skewers projectionPlotRSprojection RSProjection
Generic Single Comparison Map functions for creating parallel list methods Internal functions for making efficient comparisons.SingleComparisonMap
Compare matrices via Selection Response Decompositionplot.SRD SRD SRD.default SRD.list
Test modularity hypothesisTestModularity
TPS transformTPS
Drift test along phylogenyTreeDriftTest