OncoSimulWide2Long      Convert the 'pops.by.time' component of an
                        'oncosimul' object into "long" format.
POM                     Obtain Lines of Descent and Paths of the
                        Maximum and their diversity from simulations.
allFitnessEffects       Create fitness and mutation effects
                        specification from restrictions, epistasis, and
                        order effects.
benchmark_1             Summary results from some benchmarks reported
                        in the vignette.
evalAllGenotypes        Evaluate fitness/mutator effects of one or all
                        possible genotypes.
ex_missing_drivers_b11
                        An example where there are intermediate missing
                        drivers.
examplePosets           Example posets
examplesFitnessEffects
                        Examples of fitness effects
mcfLs                   mcfLs simulation from the vignette
oncoSimulIndiv          Simulate tumor progression for one or more
                        individuals, optionally returning just a sample
                        in time.
plot.fitnessEffects     Plot fitnessEffects objects.
plot.oncosimul          Plot simulated tumor progression data.
plotClonePhylog         Plot a parent-child relationship of the clones.
plotFitnessLandscape    Plot a fitness landscape.
plotPoset               Plot a poset.
poset                   Poset
rfitness                Generate random fitness.
samplePop               Obtain a sample from a population of
                        simulations.
simOGraph               Simulate oncogenetic/CBN/XMPN DAGs.
to_Magellan             Create output for MAGELLAN and obtain MAGELLAN
                        statistics.
