Man pages for richelbilderbeek/splendid
Likelihood model for diversification processes with single lineage rate shifts

cat2cat2
check_inputCheck input
create_data_file_nameCreate data file name
create_results_file_nameCreate results file name
default_params_docThis function does nothing. It is intended to inherit is...
get_condsSim Conditionings
get_function_namesGet function names
get_logliksLoglik functions
get_model_nameCut word "loglik" from a name
get_model_namesCheck if provided models make sense
get_n_0sStarting species
get_param_namesGet the names of the parameters used in the model
get_pkg_nameGet package name
get_sim_condsConditioning functions
l_2_brtsConvert l_0 to brts
lik_cond_0Lik conditioning 0
lik_cond_1Lik conditioning 1
lik_cond_2Lik conditioning 2
lik_cond_3Lik conditioning 3
loglik_dummyDummy loglik function
main_save_filesSave data and results
mlsls Maximum Likelihood
pars_transform_backTransform parameters back
pars_transform_forwardTransform parameters
print_infoPrint information about simulated data
p_transition_matrixTransition matrix builder
simSimulate an sls process
sim_adapt_l_matrix_sizeIncrease the size of the l_0 table if needed
sim_check_survivalCheck if a clade survives untile final_time
sim_cond_0Sim conditioning 0
sim_cond_1Sim conditioning 1
sim_cond_2Sim conditioning 2
sim_cond_3Sim conditioning 3
sim_cond_checkCheck if inputs for conditioning make sense
sim_conditioningCheck if the conditioning is fulfilled
sim_cut_l_matrixCuts the l_0 table only to the useful rows
sim_decide_eventDetermines the event
sim_eventApply the event to the simulation
sim_eventsEvents
sim_get_brtsExtract the branching times from data
sim_get_mothercladeGet the motherclade of a given clade
sim_get_n_0Initialize n for a new clade
sim_get_parsGet parameters
sim_get_poolGet the pool from the l_0 table
sim_get_shifts_infoGet shifts' information
sim_get_standard_l_2Creates the standard l_2
sim_get_t_0Initialize t for a new clade
sim_initialize_data_new_cladeInitialize data for a new clade
sim_read_l_1Reads l_1
sim_sample_deltasSample deltas for Doob-Gillespie
sim_use_eventUpdate data and time given the event
sls_mainRun the full sls routine
richelbilderbeek/splendid documentation built on Jan. 14, 2019, 6:59 a.m.