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

## Documentation for package ‘evolved’ version 1.0.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

birds_spp | Birds species list
calcFossilDivTT | Calculate paleo diversity curves through different methods
checkAndFixUltrametric | Find and fix small rounding errors in ultrametric trees
countSeqDiffs | Counting protein sequence differences
cytOxidase | Cytochrome Oxidase sequences
data_whales | Whale body size and speciation rates
dinos_fossil | Occurrence of dinosaur fossils
estimateSpeciation | Estimate speciation assuming a pure-birth process
fitCRBD | Fit a constant-rate birth-death process to a phylogeny
head.ProteinSeq | Details, generics, and methods for the 'ProteinSeq' class
is.ProteinSeq | Details, generics, and methods for the 'ProteinSeq' class
lttPlot | Make a lineage through time (LTT) plot
NatSelSim | Simulating natural selection through time in a bi-allelic gene
OneGenHWSim | Simulating one generation of genotypes under Hardy-Weinberg equilibrium
plotNatSel | Plot NatSelSim output
plotPaintedWhales | Plotting the whale phylogeny and coloring its clades
plotProteinSeq | Plot protein sequence(s)
plotRawFossilOccs | Plot a literal interpretation of a fossil record
plotWFDrift | Plot WFDriftSim output
print.ProteinSeq | Details, generics, and methods for the 'ProteinSeq' class
ProteinSeq | Details, generics, and methods for the 'ProteinSeq' class
simulateBirthDeathRich | Simulating richness through birth-death processes
simulateTree | Simulating a phylogenetic trees through the birth-death process
summary.ProteinSeq | Details, generics, and methods for the 'ProteinSeq' class
tail.ProteinSeq | Details, generics, and methods for the 'ProteinSeq' class
timeseries_fossil | Fossil Time series
WFDriftSim | Simulating generations of genetic drift in a Wright–Fisher (WF) population
whale_phylo | Whale Phylogeny