# Forward Genetic Simulation of Cancer Progression with Epistasis

## Documentation for package ‘OncoSimulR’ version 4.4.0

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

## Help Pages

adapt_interventions_to_cpp | Function that checks and creates an specification for interventions.
adapt_rules_to_cpp | Functions that check and create specifications for user variables and rules.
allFitnessEffects | Create fitness and mutation effects specification from restrictions, epistasis, and order effects.
allMutatorEffects | Create fitness and mutation effects specification from restrictions, epistasis, and order effects.
atex2b | Runs from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
atex4 | Runs from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
atex5 | Runs from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
benchmark_1 | Summary results from some benchmarks reported in the vignette.
benchmark_1_0.05 | Summary results from some benchmarks reported in the vignette.
benchmark_2 | Summary results from some benchmarks reported in the vignette.
benchmark_3 | Summary results from some benchmarks reported in the vignette.
check_acttion | Functions that check and create specifications for user variables and rules.
check_double_id | Function that checks and creates an specification for interventions.
check_double_rule_id | Functions that check and create specifications for user variables and rules.
check_same_name | Functions that check and create specifications for user variables and rules.
check_what_happens | Function that checks and creates an specification for interventions.
createInterventions | Function that checks and creates an specification for interventions.
createRules | Functions that check and create specifications for user variables and rules.
createUserVars | Functions that check and create specifications for user variables and rules.
diversityLOD | Obtain Lines of Descent and Paths of the Maximum and their diversity from simulations.
diversityPOM | Obtain Lines of Descent and Paths of the Maximum and their diversity from simulations.
evalAllGenotypes | Evaluate fitness/mutator effects of one or all possible genotypes.
evalAllGenotypesFitAndMut | Evaluate fitness/mutator effects of one or all possible genotypes.
evalAllGenotypesMut | Evaluate fitness/mutator effects of one or all possible genotypes.
evalGenotype | Evaluate fitness/mutator effects of one or all possible genotypes.
evalGenotypeFitAndMut | Evaluate fitness/mutator effects of one or all possible genotypes.
evalGenotypeMut | Evaluate fitness/mutator effects of one or all possible genotypes.
examplePosets | Example posets
examplesFitnessEffects | Examples of fitness effects
ex_missing_drivers_b11 | An example where there are intermediate missing drivers.
ex_missing_drivers_b12 | An example where there are intermediate missing drivers.
LOD | Obtain Lines of Descent and Paths of the Maximum and their diversity from simulations.
LOD.oncosimul2 | Obtain Lines of Descent and Paths of the Maximum and their diversity from simulations.
LOD.oncosimulpop | Obtain Lines of Descent and Paths of the Maximum and their diversity from simulations.
Magellan_stats | Create output for MAGELLAN and obtain MAGELLAN statistics.
mcfLs | mcfLs simulation from the vignette
oncoSimulIndiv | Simulate tumor progression for one or more individuals, optionally returning just a sample in time.
oncoSimulPop | Simulate tumor progression for one or more individuals, optionally returning just a sample in time.
oncoSimulSample | Simulate tumor progression for one or more individuals, optionally returning just a sample in time.
OncoSimulWide2Long | Convert the 'pops.by.time' component of an 'oncosimul' object into "long" format.
osi | Runs from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
osi_with_ints | Runs from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
plot.evalAllGenotypes | Plot a fitness landscape.
plot.evalAllGenotypesMut | Plot a fitness landscape.
plot.fitnessEffects | Plot fitnessEffects objects.
plot.genotype_fitness_matrix | Plot a fitness landscape.
plot.oncosimul | Plot simulated tumor progression data.
plot.oncosimulpop | Plot simulated tumor progression data.
plotClonePhylog | Plot a parent-child relationship of the clones.
plotFitnessLandscape | Plot a fitness landscape.
plotPoset | Plot a poset.
POM | Obtain Lines of Descent and Paths of the Maximum and their diversity from simulations.
POM.oncosimul2 | Obtain Lines of Descent and Paths of the Maximum and their diversity from simulations.
POM.oncosimulpop | Obtain Lines of Descent and Paths of the Maximum and their diversity from simulations.
poset | Poset
print.oncosimul | Simulate tumor progression for one or more individuals, optionally returning just a sample in time.
print.oncosimulpop | Simulate tumor progression for one or more individuals, optionally returning just a sample in time.
print.sampledGenotypes | Obtain a sample from a population of simulations.
rfitness | Generate random fitness.
sampledGenotypes | Obtain a sample from a population of simulations.
samplePop | Obtain a sample from a population of simulations.
simOGraph | Simulate oncogenetic/CBN/XMPN DAGs.
simT2 | Runs from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
simT3 | Runs from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
simul_period_1 | Runs from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
smyelo3v57 | Runs from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
summary.oncosimul | Simulate tumor progression for one or more individuals, optionally returning just a sample in time.
summary.oncosimulpop | Simulate tumor progression for one or more individuals, optionally returning just a sample in time.
s_3_a | Runs from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
s_3_b | Runs from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
to_Magellan | Create output for MAGELLAN and obtain MAGELLAN statistics.
transform_intervention | Function that checks and creates an specification for interventions.
transform_rule | Functions that check and create specifications for user variables and rules.
uvex2 | Runs from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
uvex3 | Runs from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
verify_interventions | Function that checks and creates an specification for interventions.
verify_rules | Functions that check and create specifications for user variables and rules.
verify_user_vars | Functions that check and create specifications for user variables and rules.
woAntibS | Runs from simulations of frequency-dependent examples shown in the vignette.