Forward Genetic Simulation of Cancer Progression with Epistasis

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Documentation for package ‘OncoSimulR’ version 4.0.2

• 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.