Man pages for NickWilliamsSanger/rsimpop
Simulates Cellular Evolution using a Continous Time Birth Death Model
| addCellCompartment | Adds a new cell compartment to a simpop configuration |
| add_descendent_counts_to_tree | Adds a vector "dcount" to a phylo object giving the number of... |
| addDifferentiationEvents | Adds a differentiation events to a simpop. Can either specify... |
| addDriverEvent | Adds a driver event to a current simpop |
| combine_simpops | Concatenates simpops (maintains population size trajectory... |
| continue_driver_process_sim | Restarts a multiple driver scenario |
| convert_annualS_to_s | Converts annual growth selection coefficient to per division... |
| C_subsample_pop | Wrapper function for sub-sampling a simpop object |
| get_all_node_children | Gets all descendents of the specified node. |
| getDefaultConfig | Gets a simple default configuration with one compartment |
| get_edge_info | Gets summary edge information specified by child node of an... |
| get_elapsed_time_tree | Gets elapsed time tree with optional mutational aquisition... |
| get_node_children | Gets node id of immediate descendents of the specified nodes. |
| get_samples_in_clade | Gets tip labels of tips that descend from the specified node |
| get_subsampled_tree | Gets subsampled tree - retaining events information... |
| get_tree_from_simpop | Converts simpop into an augmented APE phylo object of extant... |
| initSimPop | Initialises rsimpop |
| node_labels | Adds node labels to an existing tree plot |
| plot.simpop | Plot simpop population trajectory |
| plot_tree | Plots an ape phylo tree |
| plot_tree_events | Plots simpop events on a the tree |
| run_driver_process_sim | Runs a multiple driver scenario |
| run_neutral_sim | Runs a simple neutral simulation |
| run_neutral_trajectory | Runs a simple single compartment neutral simulation with a... |
| run_selection_sim | Runs a single compartment/single driver scenario |
| run_transient_selection | Runs a single compartment/single driver scenario with... |
| sim_pop | Simulates Evolution of Cell Population using a Continuous... |
