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

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Documentation for package ‘evolved’ version 1.0.0

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