| 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. |