Package: TreEvo 0.22.1
TreEvo: Using ABC to Understand Trait Evolution
Various functions for estimating parameters of trait evolution in comparative analyses using Approximate Bayesian Computation.
Authors:
TreEvo_0.22.1.tar.gz
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TreEvo_0.22.1.tgz(r-4.4-any)TreEvo_0.22.1.tgz(r-4.3-any)
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TreEvo.pdf |TreEvo.html✨
TreEvo/json (API)
# Install 'TreEvo' in R: |
install.packages('TreEvo', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bomeara/treevo/issues
- ancStateExample - Example Analysis Output of a Simulated Dataset
- genRateExample - Example Analysis Output of a Simulated Dataset
- resultsBMExample - Example Analysis Output of a Simulated Dataset
- resultsBoundExample - Example Analysis Output of a Simulated Dataset
- simCharExample - Example Analysis Output of a Simulated Dataset
- simPhyExample - Example Analysis Output of a Simulated Dataset
Last updated 1 years agofrom:f0e13d5bb4. Checks:OK: 1 WARNING: 6. Indexed: no.
Target | Result | Date |
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Doc / Vignettes | OK | Aug 23 2024 |
R-4.5-win | WARNING | Aug 23 2024 |
R-4.5-linux | WARNING | Aug 23 2024 |
R-4.4-win | WARNING | Aug 23 2024 |
R-4.4-mac | WARNING | Aug 23 2024 |
R-4.3-win | WARNING | Aug 23 2024 |
R-4.3-mac | WARNING | Aug 23 2024 |
Exports:autoregressiveIntrinsicautoregressiveIntrinsicTimeSlicesautoregressiveIntrinsicTimeSlicesConstantMeanautoregressiveIntrinsicTimeSlicesConstantSigmaboundaryIntrinsicboundaryMaxIntrinsicboundaryMinIntrinsicboxcoxTransformationboxcoxTransformationMatrixbrownianIntrinsiccompareListIPDdoRun_prcdoRun_rejdoSimulationeveryoneDisplacementExtrinsicExponentiallyDecayingPushExtrinsicgetBMRatePriorgetTraitBoundsFPKgetUnivariatePosteriorCurvegetUnivariatePriorCurvehighestDensityIntervallandscapeFPK_IntrinsicmaxBoundaryAutoregressiveIntrinsicminBoundaryAutoregressiveIntrinsicmultiOptimaIntrinsicnearestNeighborDisplacementExtrinsicnullExtrinsicnullIntrinsicpairwiseESSpairwiseKSparallelSimulateWithPriorsparentOffspringPlotsplot_landscapeFPK_modelplotABC_3DplotPosteriorsplotPriorplotUnivariatePosteriorVsPriorPLSTransformreturnPLSModelsimulateWithPriorssummarizePosteriortestMultivarOutlierHDR
Dependencies:apeaskpassbase64encbslibcachemcliclusterGenerationcodacodetoolscolorspacecombinatcorpcorcovrcpp11crayoncurlDEoptimdigestdoParallelevaluateexpmfansifarverfastmapfastmatchfontawesomeforeachfsfuturefuture.applygenericsggplot2ggseqlogoglobalsgluegmpgtablehighrhtmltoolshtmlwidgetshttrigraphisobanditeratorsjquerylibjsonliteknitrlabelinglatticelazyevallifecyclelistenvmagrittrmapsMASSmathjaxrMatrixmemoisemgcvmimemnormtmunsellmvtnormnlmenumDerivopenssloptimParallelparallellypartitionsphangornphylolmphytoolspillarpkgconfigplspolynomquadprogR6rappdirsrbibutilsRColorBrewerRcppRcppGSLRcppZigguratRdpackrexrglrlangrmarkdownsassscalesscatterplot3dsetssystibbletinytexutf8vctrsviridisLitewithrxfunyaml
Readme and manuals
Help Manual
Help page | Topics |
---|---|
TreEvo-abc for comparative methods | TreEvo-package TreEvo Treevo treevo |
Box-Cox Transformation for Simulation Summary Values | boxcoxTransformation boxcoxTransformationMatrix |
Plot Interparticle Distance between Runs | compareListIPD |
Run Approximate Bayesian Computation for Phylogenetic Comparative Methods | doRun doRun_prc doRun_rej |
Discrete-Time Character Simulation | doSimulation |
Extrinsic Character Evolution Models | abcmodels.extrinsic everyoneDisplacementExtrinsic ExponentiallyDecayingPushExtrinsic extrinsicModels nearestNeighborDisplacementExtrinsic nullExtrinsic |
Get Brownian Motion Rate Prior | getBMRatePrior |
Highest Density Interval | highestDensityInterval |
Intrinsic Character Evolution Models | abcmodels.intrinsic autoregressiveIntrinsic autoregressiveIntrinsicTimeSlices autoregressiveIntrinsicTimeSlicesConstantMean autoregressiveIntrinsicTimeSlicesConstantSigma boundaryIntrinsic boundaryMaxIntrinsic boundaryMinIntrinsic brownianIntrinsic intrinsicModels maxBoundaryAutoregressiveIntrinsic minBoundaryAutoregressiveIntrinsic nullIntrinsic |
Intrinsic Trait Evolution Model for a Macroevolutionary Landscape on a Fokker-Planck-Kolmogorov Potential Surface (Boucher et al., 2018) | getTraitBoundsFPK landscapeFPK_Intrinsic plot_landscapeFPK_model |
Fitting Univariate Partial Least Squares Models to Free Parameters in ABC | methodsPLS PLSTransform returnPLSModel |
Single Evolutionary Regime Model with Multiple Optima | multiOptimaIntrinsic |
Pairwise Effective Sample Size | pairwiseESS |
Pairwise Kolmogorov-Smirnov test | pairwiseKS |
Plotting Parent-Offspring Particles | parentOffspringPlots |
3D ABCplots | plotABC_3D |
Plot posterior distributions | plotPosteriors |
Plotting, Summarizing and Comparing the Prior and Posterior Distributions | getUnivariatePosteriorCurve getUnivariatePriorCurve plotPrior plotPriorPost plotUnivariatePosteriorVsPrior |
Example Analysis Output of a Simulated Dataset | ancStateExample genRateExample resultsBMExample resultsBoundExample simCharExample simPhyExample simRunExample |
Simulate data for initial TreEvo analysis | parallelSimulateWithPriors simulateWithPriors |
Summarize Posterior Distribution for a Free Parameter | summarizePosterior |
Test If an Outlier Is Within a Highest Density Region of a Multivariate Cloud of Data Points | testMultivarOutlierHDR |