Learning objectives | Introduction | Genetic drift: qualitative expectation | Genetic drift: building intuition | Dissecting the variability in outcomes | Genetic drift and heterozygosity decay | Effective population size | Some food for thought: | Historical note | References:
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:
evolved_1.0.0.tar.gz
evolved_1.0.0.zip(r-4.7-any)evolved_1.0.0.zip(r-4.6-any)evolved_1.0.0.zip(r-4.5-any)
evolved_1.0.0.tgz(r-4.6-any)evolved_1.0.0.tgz(r-4.5-any)
evolved_1.0.0.tar.gz(r-4.7-any)evolved_1.0.0.tar.gz(r-4.6-any)
evolved_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
evolved/json (API)
| # Install 'evolved' in R: |
| install.packages('evolved', repos = c('https://mjanuario.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mjanuario/evolved/issues
Pkgdown/docs site:https://mjanuario.github.io
Datasets:
- ammonoidea_fossil - Occurrences of ammonoid fossils
- birds_spp - Birds species list
- cytOxidase - Cytochrome Oxidase sequences
- data_whales - Whale body size and speciation rates
- dinos_fossil - Occurrence of dinosaur fossils
- mammals_fossil - Occurrences of mammal fossils
- mammals_spp - Mammals species list
- timeseries_fossil - Fossil Time series
- trilob_fossil - Occurrence of trilobite fossils
- whale_phylo - Whale Phylogeny
biodiversity-sciencecomparative-methodsdata-driven-educationevolutionary-biologyinquiry-based-learningmacroevolutionpaleobiologyphylogeneticspopulation-geneticsscience-educationsimulation-based-learning
Last updated from:300aa21549. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | NOTE | 143 | ||
| source / vignettes | OK | 230 | ||
| linux-release | NOTE | 159 | ||
| macos-release | NOTE | 150 | ||
| macos-oldrel | NOTE | 219 | ||
| windows-devel | NOTE | 117 | ||
| windows-release | NOTE | 94 | ||
| windows-oldrel | NOTE | 94 | ||
| wasm-release | OK | 140 |
Exports:calcFossilDivTTcheckAndFixUltrametriccountSeqDiffsestimateSpeciationfitCRBDis.ProteinSeqlttPlotNatSelSimOneGenHWSimplotNatSelplotPaintedWhalesplotProteinSeqplotRawFossilOccsplotWFDriftsimulateBirthDeathRichsimulateTreeWFDriftSim
Dependencies:apecliclusterGenerationcodacodetoolscombinatcpp11DEoptimdeSolvedigestdiversitreedoParallelexpmfastmatchforeachgenericsglueigraphiteratorslatticelifecyclemagrittrmapsMASSMatrixmnormtnlmenumDerivoptimParallelphangornphytoolspkgconfigquadprogRcpprlangscatterplot3dsubplexvctrs
Sampling alleles, genetic drift and effective population size
Last update: 2025-12-17
Started: 2024-03-26
Introduction to R
Learning objectives | Introduction | R basics | R as a vector calculator | Objects in R | Appending elements | Indexing | Time for a pause and ponder | Matrices | Logical tests | Data frames | Functions | Installing and running packages | Scripts | File paths and directories | Getting help | Generation of random numbers | Plotting (and plot annotation) | Loops | Last remarks | References
Last update: 2025-12-17
Started: 2025-12-17
DNA sequence evolution
Learning objectives | Introduction | Exploring sequence data | A simple measure of genetic distance | The Poisson correction | Some food for thought: | Building a molecular clock | Molecular clocks and inferences about deep-time | The Jukes-Cantor correction | The uncertainty of your molecular clock | Brief introduction to intervals derived from log-likelihood | References
Last update: 2025-12-01
Started: 2024-03-26
If you never used R before...
What is R and how can I install it? | What is RStudio and how can I install it? | Starting R and RStudio: | Working Routine in R | Step 1: Setting work directory | Step 2: Checking working directory | Step 3: Saving files | Step 4: Compiling/knitting your RMarkdown | Step 5: Sourcing R scripts | Step 6: Loading external data | Step 7: Debbuging one specific strange behavior some students found | What is RMarkdown and how can I install it (optional)? | More on RMarkdown | RMarkdown advantages | An example of why RMarkdown is so neat: | RMarkdown practice (part I) | RMarkdown practice (part II)
Last update: 2025-11-28
Started: 2025-11-28
Birth-death models and molecular phylogenies
Learning objectives | Introduction | Simulating phylogenetic trees | What affects speciation and extinction? | Shifts in diversification rates | References:
Last update: 2024-11-28
Started: 2024-05-09
Clocks and Rocks
The fossil record: | Comparing molecular patterns
Last update: 2024-11-28
Started: 2023-12-24
Introduction to the fossil record
Learning objectives | Introduction | Exploring fossil occurrences | A brief introduction to temporal ranges | The K-Pg mass extinction | Something to think about: | The pull of the recent | Diversity patterns in deep time | The spatial distribution of the record | Drawing conclusions from the fossil record | Technical note: Dating fossils in absolute time | References:
Last update: 2024-11-28
Started: 2024-03-26
Allele frequency change and selection
Learning objectives | Introduction | Breeding effective population size | Mutation-drift equilibrium | Selection | The case of the peppered moths | References
Last update: 2024-11-28
Started: 2024-03-26
Birth-death models and deep time
Learning objectives | Introduction | The birth-death (BD) model | Glossary: | Deterministic expectations of the BD model | Estimation under the simplest BD | Effects of variation on the net diversification rate | The birth-death model is a stochastic process | Adding in extinction | Age-richness models and empirical richness through time | Some food for thought: | References:
Last update: 2024-05-17
Started: 2024-04-20
Phylogenies and diversification
Molecular phylogenies: | Diversification
Last update: 2024-05-17
Started: 2024-01-08
Introduction to evolutionary genetics
Learning objectives | Introduction | Simple math notation | Probability of independent events | Random number generators and density/mass probability functions | Malthusian growth | Calculating and visualizing exponential growth in R | Mendelian genetics and Hardy-Weinberg Equilibrium (HWE) at a single locus | Kermode bear from British Columbia | Calculating allele frequencies from genotypes | A statistical approach to test for HWE and a given allele frequency | Heterozygosity | HWE, deleterious alleles, and mutation | Mendelian genetics at multiple loci | Describing genetic variation in DNA segments | References:
Last update: 2024-05-17
Started: 2024-03-26
Tools for population genetics
Hardy-Weinberg equilibrium | Genetic drift | Natural selection | References:
Last update: 2024-03-26
Started: 2023-05-18
