Man pages for TheoPannetier/DDvTDtools
Compare diversity-dependent (DD) and time-dependent (TD) diversification models

arg_init_kAccepted values of argument init_k
arg_optimPossible values of argument optim
arg_paraGet possible values of argument para
arg_simPossible values of argument sim
assert_DDvTD_wdAssert that DDvTD is the working directory
assert_init_kAsserts input init parameter is supported
assert_optimAssert the value of 'optim' is a valid model name for...
assert_paraAssert the value of 'para' is a valid parameter combination...
assert_simAssert the value of 'sim' is a valid model name for...
check_convergence_optimCheck optimisation results for completeness
check_duplicated_rowsCheck a results data frame does not have duplicated rows
check_incomplete_rowsCheck a results data frame for NAs in rows
check_init_parsCheck initial parameter values for run_optim
check_loglikelihood_existsCheck a results data frame for log-likelihood
check_missing_mcsCheck a results data frame for missing rows
count_errors_logCount errors in a log file
default_pars2_dd1Default DD pars2 argument passed to DDD
default_pars2_td4Default TD pars2 argument passed to DDD
fill_missing_rowsFill missing results row with default values
fix_indexingFix indexing of results data frame
format_optim_results_rowAssemble a row of results for run_optim output
get_brtsExtract a set of branching times from a dataset of simulated...
get_default_initparsGet default initial parameter values for run_optim...
get_delta_aicComputes the AIC difference between DD and TD
get_init_kGet values for argument init_k
get_KprimeCompute K' from la0, mu0, K
get_ltt_tblsGet LTT tables and average LTT for a set of trees
get_multi_brtsExtract multiple sets of branching times from a dataset of...
get_p_tblCompute threshold values and proportions of correct model...
get_summary_ltt_tblGet lineage-through-time summaries for a set of phylogenetic...
join_optim_tblsRead a pair of 'optim' tables and join them together
params_docDocumentation for main parameters of the model
para_to_parsTranslate 'para' argument into parameter values
pipePipe operator
plot_avg_lttPlot average lineage-through-time plots
plot_lrPlot log-LR distribution for DD & TD trees
plot_ltt_nestedPlot n distribution inside a ltt plot
plot_n_distribPlot the distribution of N for DD & TD trees as violin plots
read_optim_resultsRead results of the model optimisation
read_simLoad a simulated trees dataset
read_sim_multiPhyloLoad a simulated dataset as a multiPhylo object
results_optim_structStructure of the optimisation results data frames
run_optimRun maximum likelihood optimisation of a model on simulated...
run_optim_empirical_simsRun optimisation on trees simulated from empirical...
run_optim_from_nRun maximum likelihood esimation starting from the number of...
run_simSimulate a set of phylogenetic trees under a time-dependent...
set_DDvTD_dir_structSet the structure of the DDvTD directory and enter it
TheoPannetier/DDvTDtools documentation built on Oct. 22, 2020, 2:31 p.m.