Package: evolved 1.0.0

Matheus Januario

evolved: Open Software for Teaching Evolutionary Biology at Multiple Scales Through Virtual Inquiries

"Evolutionary Virtual Education" - 'evolved' - provides multiple tools to help educators (especially at the graduate level or in advanced undergraduate level courses) apply inquiry-based learning in general evolution classes. In particular, the tools provided include functions that simulate evolutionary processes (e.g., genetic drift, natural selection within a single locus) or concepts (e.g. Hardy-Weinberg equilibrium, phylogenetic distribution of traits). More than only simulating, the package also provides tools for students to analyze (e.g., measuring, testing, visualizing) datasets with characteristics that are common to many fields related to evolutionary biology. Importantly, the package is heavily oriented towards providing tools for inquiry-based learning - where students follow scientific practices to actively construct knowledge. For additional details, see package's vignettes.

Authors:Matheus Januario [aut, cph, cre], Jennifer Auler [aut], Andressa Viol [aut], Daniel Rabosky [aut]

evolved_1.0.0.tar.gz
evolved_1.0.0.zip(r-4.5)evolved_1.0.0.zip(r-4.4)evolved_1.0.0.zip(r-4.3)
evolved_1.0.0.tgz(r-4.4-any)evolved_1.0.0.tgz(r-4.3-any)
evolved_1.0.0.tar.gz(r-4.5-noble)evolved_1.0.0.tar.gz(r-4.4-noble)
evolved_1.0.0.tgz(r-4.4-emscripten)evolved_1.0.0.tgz(r-4.3-emscripten)
evolved.pdf |evolved.html
evolved/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/auler-j/evolved/issues

Datasets:

On CRAN:

6.88 score 3 stars 23 scripts 366 downloads 17 exports 38 dependencies

Last updated 3 days agofrom:41dc0d76d1. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 20 2024
R-4.5-winOKDec 20 2024
R-4.5-linuxOKDec 20 2024
R-4.4-winOKDec 20 2024
R-4.4-macOKDec 20 2024
R-4.3-winOKDec 20 2024
R-4.3-macOKDec 20 2024

Exports:calcFossilDivTTcheckAndFixUltrametriccountSeqDiffsestimateSpeciationfitCRBDis.ProteinSeqlttPlotNatSelSimOneGenHWSimplotNatSelplotPaintedWhalesplotProteinSeqplotRawFossilOccsplotWFDriftsimulateBirthDeathRichsimulateTreeWFDriftSim

Dependencies:apecliclusterGenerationcodacodetoolscombinatcpp11DEoptimdeSolvedigestdiversitreedoParallelexpmfastmatchforeachgenericsglueigraphiteratorslatticelifecyclemagrittrmapsMASSMatrixmnormtnlmenumDerivoptimParallelphangornphytoolspkgconfigquadprogRcpprlangscatterplot3dsubplexvctrs

Birth-death models and deep time

Rendered frombirthdeath_deeptime.Rmdusingknitr::rmarkdownon Dec 20 2024.

Last update: 2024-05-17
Started: 2024-04-20

Birth-death models and molecular phylogenies

Rendered frombirthdeath_phylogenies.Rmdusingknitr::rmarkdownon Dec 20 2024.

Last update: 2024-11-28
Started: 2024-05-09

Clocks and Rocks

Rendered fromrocks_and_clocks.Rmdusingknitr::rmarkdownon Dec 20 2024.

Last update: 2024-11-28
Started: 2023-12-24

Allele frequency change and selection

Rendered fromdeeptime_clocks.Rmdusingknitr::rmarkdownon Dec 20 2024.

Last update: 2024-05-17
Started: 2024-03-26

Introduction to the fossil record

Rendered fromdeeptime_rocks.Rmdusingknitr::rmarkdownon Dec 20 2024.

Last update: 2024-11-28
Started: 2024-03-26

Introduction to R

Rendered fromintro_R.Rmdusingknitr::rmarkdownon Dec 20 2024.

Last update: 2024-11-28
Started: 2024-03-26

Phylogenies and diversification

Rendered fromphylogenies_and_diversification.Rmdusingknitr::rmarkdownon Dec 20 2024.

Last update: 2024-05-17
Started: 2024-01-08

Sampling alleles, genetic drift and effective population size

Rendered frompopgen_drift.Rmdusingknitr::rmarkdownon Dec 20 2024.

Last update: 2024-11-28
Started: 2024-03-26

Introduction to evolutionary genetics

Rendered frompopgen_intro.Rmdusingknitr::rmarkdownon Dec 20 2024.

Last update: 2024-05-17
Started: 2024-03-26

Tools for population genetics

Rendered frompopulation_genetics.Rmdusingknitr::rmarkdownon Dec 20 2024.

Last update: 2024-03-26
Started: 2023-05-18

Allele frequency change and selection

Rendered frompopgen_selection.Rmdusingknitr::rmarkdownon Dec 20 2024.

Last update: 2024-11-28
Started: 2024-03-26

Readme and manuals

Help Manual

Help pageTopics
Occurrences of ammonoid fossilsammonoidea_fossil
Birds species listbirds_spp
Calculate paleo diversity curves through different methodscalcFossilDivTT
Find and fix small rounding errors in ultrametric treescheckAndFixUltrametric
Counting protein sequence differencescountSeqDiffs
Cytochrome Oxidase sequencescytOxidase
Whale body size and speciation ratesdata_whales
Occurrence of dinosaur fossilsdinos_fossil
Estimate speciation assuming a pure-birth processestimateSpeciation
Fit a constant-rate birth-death process to a phylogenyfitCRBD
Make a lineage through time (LTT) plotlttPlot
Occurrences of mammal fossilsmammals_fossil
Mammals species listmammals_spp
Simulating natural selection through time in a bi-allelic geneNatSelSim
Simulating one generation of genotypes under Hardy-Weinberg equilibriumOneGenHWSim
Plot NatSelSim outputplotNatSel
Plotting the whale phylogeny and coloring its cladesplotPaintedWhales
Plot protein sequence(s)plotProteinSeq
Plot a literal interpretation of a fossil recordplotRawFossilOccs
Plot WFDriftSim outputplotWFDrift
Details, generics, and methods for the 'ProteinSeq' classhead.ProteinSeq is.ProteinSeq print.ProteinSeq ProteinSeq summary.ProteinSeq tail.ProteinSeq
Simulating richness through birth-death processessimulateBirthDeathRich
Simulating a phylogenetic trees through the birth-death processsimulateTree
Fossil Time seriestimeseries_fossil
Occurrence of trilobite fossilstrilob_fossil
Simulating generations of genetic drift in a Wright–Fisher (WF) populationWFDriftSim
Whale Phylogenywhale_phylo