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

assemble_landscape_dataAssemble log-likelihood landscape data for plotting
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_initparsCheck initial parameter values for run_ML
compare_method_bdPeform a comparison of integration methods for DDD::bd_ML
compare_method_ddPeform a comparison of integration methods for DDD::dd_ML
count_errorsCount errors in a log file
cure_error_rowsCure format for erroneous results
default_pars2_dd1Predefined pars2 argument for dd_loglik as used in DDvTD
default_pars2_td4Predefined pars2 argument for bd_loglik as used in DDvTD
fill_missing_rowsFill missing results row with default values
fit_td_setophagaFit the time-dependent model on Setophaga phylogeny
fix_indexingFix indexing of results data frame
get_avg_ltt_tableReturn the average number of lineage over time for a dataset
get_brtsExtract a set of branching times from a dataset of simulated...
get_dAIC_DDvTDCompute AIC_DD - AIC_TD for a set of trees
get_default_initparsGet default initial parameter values for run_ML optimisation
get_empty_optim_dfGet an empty skeleton for run_ML output data frame.
get_KprimeCompute K' from la0, mu0, K
get_likelihood_along_KCompute the likelihood landscape along the K-axis
get_LR_DDvTDCompute logL_DD - logL_TD for a set of trees
get_multi_brtsExtract multiple sets of branching times from a dataset of...
get_optim_df_rowFormat run_ML optimisation results in a data frame row
get_optim_namesGet possible values of optim argument
get_para_valuesGet possible values of para argument
get_possible_init_kAccepted values of argument init_k
get_sim_multiPhyloLoad a simulated dataset as a multiPhylo object
get_sim_namesGet possible values of sim argument
para_to_parsTranslate 'para' argument into parameter values
plot_avg_lttPlot the average LTTs of paired DD and TD trees
plot_dAIC_DDvTDPlot dAIC distribution for DD & TD trees
plot_dAIC_paraPlot dAIC distribution for a set of parameter sets
plot_loglik_landscape_KPlot likelihood landscapes along K
plot_LR_DDvTDPlot logLR distribution for DD & TD trees
plot_LR_paraPlot logLR distribution for a set of parameter sets
plot_ltt_nestedPlot n distribution inside a ltt plot
plot_n_distribPlot the distribution of N for DD & TD trees
plot_quantilesAdd quantile bars to logLR distribution plot
plot_tree_infoPlot main features of a simulated tree
read_optim_tableAccess a table with model fitting results
read_treesLoad a simulated trees dataset
run_from_nRun maximum likelihood esimation starting from the number of...
run_liklandscapesCompute likelihood landscape along K for a range of trees
run_MLRun maximum likelihood esimation of a diversification model...
simulate_treesSimulate a set of phylogenetic trees under a time-dependent...
TheoPannetier/DDvTDtools documentation built on July 19, 2019, 8:11 a.m.