Package: evoTS 1.0.3

Kjetil Lysne Voje

evoTS: Analyses of Evolutionary Time-Series

Facilitates univariate and multivariate analysis of evolutionary sequences of phenotypic change. The package extends the modeling framework available in the 'paleoTS' package. Please see <https://klvoje.github.io/evoTS/index.html> for information about the package and the implemented models.

Authors:Kjetil Lysne Voje [aut, cre]

evoTS_1.0.3.tar.gz
evoTS_1.0.3.zip(r-4.5)evoTS_1.0.3.zip(r-4.4)evoTS_1.0.3.zip(r-4.3)
evoTS_1.0.3.tgz(r-4.4-any)evoTS_1.0.3.tgz(r-4.3-any)
evoTS_1.0.3.tar.gz(r-4.5-noble)evoTS_1.0.3.tar.gz(r-4.4-noble)
evoTS_1.0.3.tgz(r-4.4-emscripten)evoTS_1.0.3.tgz(r-4.3-emscripten)
evoTS.pdf |evoTS.html✨
evoTS/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/klvoje/evots/issues

Datasets:
  • diameter_S.yellowstonensis - Evolutionary sequence (time-series) of phenotypic change in diameter in the lineage Stephanodiscus yellowstonensis
  • ribs_S.yellowstonensis - Evolutionary sequence (time-series) of phenotypic change in the number of ribs in the lineage Stephanodiscus yellowstonensis

On CRAN:

4.26 score 184 scripts 215 downloads 29 exports 78 dependencies

Last updated 5 months agofrom:651458ccd4. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 26 2024
R-4.5-winWARNINGOct 26 2024
R-4.5-linuxWARNINGOct 26 2024
R-4.4-winWARNINGOct 26 2024
R-4.4-macWARNINGOct 26 2024
R-4.3-winWARNINGOct 26 2024
R-4.3-macWARNINGOct 26 2024

Exports:fit.all.univariatefit.mode.shiftfit.multivariate.OUfit.multivariate.OU.user.definedfit.multivariate.URWfit.multivariate.URW.shiftloglik.surface.accelloglik.surface.decelloglik.surface.GRWloglik.surface.OUloglik.surface.OUBMloglik.surface.stasisloglik.surface.URWmake.multivar.evoTSopt.accel.single.Ropt.accel.single.R.zero.corropt.decel.single.Ropt.decel.single.R.zero.corropt.joint.accelopt.joint.decelopt.joint.OUBMopt.single.Ropt.single.R.zero.corrplotevoTSplotevoTS.multivariatesim.accel.decelsim.multi.OUsim.multi.URWsim.OUBM

Dependencies:askpassbase64encbslibcachemclicodetoolscolorspacecpp11crosstalkcurldata.tabledigestdoParalleldplyrevaluatefansifarverfastmapfontawesomeforeachfsgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttrisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemnormtmunsellmvtnormnlmeopensslpaleoTSpillarpkgconfigplotlypracmapromisespurrrR6rappdirsRColorBrewerRcpprlangrmarkdownsassscalesstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Class for fit to evolutionary sequence (time-series) modelsas.evoTS.multi.BW.acceldecel.fit
Class for fit to evolutionary sequence (time-series) modelsas.evoTS.multi.BW.fit
Class for fit to evolutionary sequence (time-series) modelsas.evoTS.multi.OU.fit
Class for fit to evolutionary sequence (time-series) modelsas.evoTS.multi.URW.fit
Class for fit to evolutionary sequence (time-series) modelsas.evoTS.multi.URW.shift.fit
Class for fit to evolutionary sequence (time-series) modelsas.evoTSfit.OUBM
Evolutionary sequence (time-series) of phenotypic change in diameter in the lineage Stephanodiscus yellowstonensisdiameter_S.yellowstonensis
Fit all univariate models to an evolutionary sequence (time-series).fit.all.univariate
Fit two models to two separate segments to an evolutionary sequence (time-series).fit.mode.shift
Fit predefined multivariate Ornstein-Uhlenbeck models to multivariate evolutionary sequence (time-series) data.fit.multivariate.OU
Fit user-defined multivariate Ornstein-Uhlenbeck models to multivariate evolutionary sequence (time-series) data.fit.multivariate.OU.user.defined
Fit multivariate Unbiased Random Walk models to multivariate evolutionary sequence (time-series) data.fit.multivariate.URW
Fit separate multivariate Unbiased Random Walk models to two different segments of a multivariate evolutionary sequence (time-series).fit.multivariate.URW.shift
Log-likelihoods for evolutionary modelslogL.joint.accel_decel
Log-likelihoods for evolutionary modelslogL.joint.accel.decel.single.R
Log-likelihoods for evolutionary modelslogL.joint.accel.decel.single.R.zero.corr
Log-likelihoods for evolutionary modelslogL.joint.multi.OUOU
Log-likelihoods for evolutionary modelslogL.joint.multi.OUOU.user
Log-likelihoods for evolutionary modelslogL.joint.multi.R
Log-likelihoods for evolutionary modelslogL.joint.OU.BM
Log-likelihoods for evolutionary modelslogL.joint.single.R
Log-likelihoods for evolutionary modelslogL.joint.single.R.zero.corr
Log-likelihoods for evolutionary modelslogL.joint.Stasis.OU
Log-likelihoods for evolutionary modelslogL.joint.URW.URW
Calculate the log-likelihood surface for a part of parameter spaceloglik.surface.accel
Calculate the log-likelihood surface for a part of parameter spaceloglik.surface.decel
Calculate the log-likelihood surface for a part of parameter spaceloglik.surface.GRW
Calculate the log-likelihood surface for a part of parameter spaceloglik.surface.OU
Calculate the log-likelihood surface for a part of parameter spaceloglik.surface.OUBM
Calculate the log-likelihood surface for a part of parameter spaceloglik.surface.stasis
Calculate the log-likelihood surface for a part of parameter spaceloglik.surface.URW
Makes a multivariate data set ofmake.multivar.evoTS
Fit multivariate Unbiased Random Walk with increasing (exponential accelerating) rate of change through time.opt.accel.single.R
Fit multivariate Unbiased Random Walk model with uncorrelated trait changes and with increasing (exponential accelerating) rate of change through time.opt.accel.single.R.zero.corr
Fit multivariate Unbiased Random Walk with decreasing (exponential decaying) rate of change through time.opt.decel.single.R
Fit multivariate Unbiased Random Walk model with uncorrelated trait changes and with decreasing (exponential decaying) rate of change through time.opt.decel.single.R.zero.corr
Fit an Unbiased Random Walk with an accelerating rate of change through time.opt.joint.accel
Fit an Unbiased Random Walk with an decelerating rate of change through time.opt.joint.decel
Fit an Ornstein-Uhlenbeck model with an optimum that evolves according to a Unbiased Random Walk.opt.joint.OUBM
Optimization and log-likelihoods for pairs of models.opt.joint.URW.Stasis
Fit multivariate Unbiased Random Walk model.opt.single.R
Fit multivariate Unbiased Random Walk model with uncorrelated trait changes.opt.single.R.zero.corr
Plot a paleoTS objectplotevoTS
Plots multivariate evolutionary sequence (time-series) data setplotevoTS.multivariate
Evolutionary sequence (time-series) of phenotypic change in the number of ribs in the lineage Stephanodiscus yellowstonensisribs_S.yellowstonensis
Simulate an Unbiased Random Walk with an accelerating or decelerating rate of change through time.sim.accel.decel
Simulate multivariate Ornstein-Uhlenbeck evolutionary sequence data setssim.multi.OU
Simulate multivariate evolutionary sequence data that evolve according to an Unbiased Random Walksim.multi.URW
Simulate an Ornstein-Uhlenbeck process with optimum changing according to an unbiased random walksim.OUBM