.

. by Margherita Bruno

1. getInstance

2. RandomNumberGenerator

3. createInstance

4. sample

5. getExponential

6. getUniform

7. removeChild

8. getSibling

9. PhyloNode

10. addChild

11. addEvent

12. clear

13. CellCompartment

14. addNode

15. getSub

16. getNodes

17. setNumNonEmptyIndices

18. getSubCounts

19. printInfo

20. checkPop

21. getTotalRate

22. setRates

23. getTotalDivisionRate

24. CellSimulation

25. getNewPhyloNode

26. setCompartmentInfo

27. resetNtips

28. run

29. doEvent

30. update_edge_matrix

31. setCompartmentInfoRecursively

32. die

33. recycle

34. divide

35. initSimPop

36. sim_pop

37. standardiseTree

38. get_tree_from_simpop

39. plot_simpop

40. get_subsampled_tree

41. checkValidPhylo

42. assign_celltype

43. get_elapsed_time_tree

44. combine_simpops

45. getDefaultConfig

46. addCellCompartment

47. addDifferentiationEvents

48. make_star_tree

49. addDriverEvent

50. recalculateFitnessV2

51. setSimData

52. initRSimPop

53. sim_pop2

54. populate_edge_info

55. populateEvents

56. populateCompartmentsInfo

57. sub_sample

58. deleteTips

59. snap

60. getPopulationTrace