API for DAISIE
Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Global functions
Bats_GreaterAntilles Man page
Biwa_datalist Man page
DAISIE Man page
DAISIE-package Man page
DAISIE_CS_max_steps Man page Source code
DAISIE_ExpEIN Man page Source code
DAISIE_IC Man page Source code
DAISIE_IW_num_threads Man page Source code
DAISIE_IW_pars Source code
DAISIE_KLdist Source code
DAISIE_ML Man page Source code
DAISIE_ML1 Man page Source code
DAISIE_ML2 Man page Source code
DAISIE_ML4 Man page Source code
DAISIE_ML_CS Man page
DAISIE_ML_IW Man page Source code
DAISIE_MW_ML Man page Source code
DAISIE_MW_loglik_choosepar Source code
DAISIE_ONEcolonist Man page Source code
DAISIE_SR_ML Man page Source code
DAISIE_SR_ML_CS Man page
DAISIE_SR_loglik Source code
DAISIE_SR_loglik_CS Man page
DAISIE_SR_loglik_all Man page Source code
DAISIE_SR_loglik_all_choosepar Source code
DAISIE_SR_sim Man page Source code
DAISIE_SR_sim_core Man page Source code
DAISIE_abm_factor Man page Source code
DAISIE_calc_sumstats_pcrates Man page Source code
DAISIE_convert_to_classic_plot Man page Source code
DAISIE_convertprobdist Man page Source code
DAISIE_create_island Man page Source code
DAISIE_create_island_trait Source code
DAISIE_dataprep Man page Source code
DAISIE_eq Source code
DAISIE_extract_stt_median Man page Source code
DAISIE_format_CS Man page Source code
DAISIE_format_CS_full_stt Man page Source code
DAISIE_format_CS_sampled_stt Man page Source code
DAISIE_format_CS_trait Source code
DAISIE_format_GW Man page Source code
DAISIE_format_IW Man page Source code
DAISIE_format_IW_full_stt Man page Source code
DAISIE_format_IW_sampled_stt Man page Source code
DAISIE_format_IW_trait Source code
DAISIE_integrate Source code
DAISIE_integrate_const Source code
DAISIE_integrate_time Source code
DAISIE_loglik Source code
DAISIE_loglik_CS Man page
DAISIE_loglik_CS_choice Source code
DAISIE_loglik_IW Man page Source code
DAISIE_loglik_IW_M1 Source code
DAISIE_loglik_IW_choosepar Source code
DAISIE_loglik_all Man page Source code
DAISIE_loglik_all_choosepar Source code
DAISIE_loglik_all_choosepar2 Source code
DAISIE_loglik_all_choosepar4 Source code
DAISIE_loglik_high_lambda Source code
DAISIE_loglik_integrand Man page Source code
DAISIE_loglik_integrate Man page Source code
DAISIE_loglik_rhs Source code
DAISIE_loglik_rhs1 Source code
DAISIE_loglik_rhs2 Source code
DAISIE_loglik_rhs_IW Source code
DAISIE_loglik_rhs_precomp Source code
DAISIE_loglik_rhs_time Source code
DAISIE_loglik_rhs_time1 Source code
DAISIE_loglik_rhs_time2 Source code
DAISIE_make_archipelago Man page Source code
DAISIE_make_global Man page Source code
DAISIE_margprobdist Man page Source code
DAISIE_nonoceanic_spec Man page Source code
DAISIE_numcol Man page Source code
DAISIE_numcol_dist Source code
DAISIE_ode_cs Source code
DAISIE_plot_age_diversity Man page Source code
DAISIE_plot_area Man page Source code
DAISIE_plot_cladogenesis Man page Source code
DAISIE_plot_comparison_stts Man page Source code
DAISIE_plot_extinction Man page Source code
DAISIE_plot_immigration Man page Source code
DAISIE_plot_input Man page Source code
DAISIE_plot_island Man page
DAISIE_plot_pc_rates Man page Source code
DAISIE_plot_sims Man page Source code
DAISIE_plot_stt Man page Source code
DAISIE_probdist Man page Source code
DAISIE_probdist_rhs Source code
DAISIE_sample_event_cr Man page Source code
DAISIE_sample_event_time_dep Man page Source code
DAISIE_sample_event_trait_dep Man page Source code
DAISIE_sim Man page Source code
DAISIE_sim_MW Man page
DAISIE_sim_core_cr Man page Source code
DAISIE_sim_core_cr_shift Man page Source code
DAISIE_sim_core_time_dep Man page Source code
DAISIE_sim_core_trait_dep Man page Source code
DAISIE_sim_cr Man page
DAISIE_sim_cr_cs Man page Source code
DAISIE_sim_cr_gw Man page Source code
DAISIE_sim_cr_iw Man page Source code
DAISIE_sim_cr_shift Man page Source code
DAISIE_sim_global Source code
DAISIE_sim_min_type2 Man page Source code
DAISIE_sim_relaxed_rate Man page Source code
DAISIE_sim_time_dep Man page Source code
DAISIE_sim_time_dep_cs Man page Source code
DAISIE_sim_time_dep_gw Man page Source code
DAISIE_sim_time_dep_iw Man page Source code
DAISIE_sim_trait_dep Man page Source code
DAISIE_sim_update_state_cr Man page Source code
DAISIE_sim_update_state_time_dep Man page Source code
DAISIE_sim_update_state_trait_dep Man page Source code
DAISIE_spec_tables Source code
Galapagos_datalist Man page
Galapagos_datalist_2types Man page
Galapagos_datatable Man page
Macaronesia_datalist Man page
NewZealand_birds_datalist Man page
add_brt_table Source code
add_column_to_dataframe Man page Source code
antidiagSums Source code
approximate_logp0 Source code
archipelago_data Man page
archipelagos41 Man page
are_area_pars Man page Source code
are_hyper_pars Man page Source code
are_max_rates Man page Source code
are_max_rates_gt_rates Man page Source code
are_rates Man page Source code
are_trait_pars Man page Source code
bin2dec Source code
calcMN Source code
calc_Abeta Man page Source code
calc_next_timeval Man page Source code
calc_next_timeval_shift Man page Source code
calc_peak Man page Source code
checkprobs Source code
checkprobs2 Source code
convert_parameters_MW Source code
countimmi Source code
countspecies Man page Source code
countspeciestype1 Source code
countstac Source code
counttype1 Source code
create_CS_version Man page Source code
create_area_pars Man page Source code
create_full_CS_stt Man page Source code
create_full_CS_stt_trait Source code
create_hyper_pars Man page Source code
create_l0ki Source code
create_pars Man page Source code
create_trait_pars Man page Source code
daisie_odeint_cs Man page
daisie_odeint_iw Man page
dec2bin Source code
dec2binmat Source code
default_params_doc Man page Source code
distance_dep_options1_fun Source code
divdepvec Source code
divdepvec1 Source code
divdepvecproc Source code
f_sigmoidal_neg Source code
f_sigmoidal_pos Source code
fconstr13 Source code
fconstr15 Source code
frogs_datalist Man page
frogs_datatable Man page
get_ana_rate Man page Source code
get_clado_rate Man page Source code
get_clado_rate_per_capita Man page Source code
get_ext_rate Man page Source code
get_ext_rate_per_capita Man page Source code
get_global_max_area Man page Source code
get_global_min_area Man page Source code
get_immig_rate Man page Source code
get_immig_rate_per_capita Man page Source code
get_trans_rate Man page Source code
integral_peak Man page Source code
is_island_ontogeny_input Man page Source code
is_sea_level_input Man page Source code
is_simulation_outputs Man page Source code
island_area Man page Source code
island_area_vector Man page Source code
islands_10reps_RAW Man page
islands_1type_1000reps Man page
islands_2types_1000reps Man page
kimat Source code
nndivdep Source code
odeproc Source code
order_pars1 Source code
par_shift Source code
print_parameters_and_loglik Source code
quantiles Source code
remove_empty_elements Man page Source code
rho Man page Source code
sample_relaxed_rate Man page Source code
selectrows Source code
shift_before_certain_brts Source code
stac_table Man page
transform_gamma_pars Man page Source code
translate_island_ontogeny Man page Source code
translate_sea_level Man page Source code
update_max_rates Man page Source code
update_rates Man page Source code
update_rates_trait Source code
DAISIE documentation built on June 2, 2022, 5:07 p.m.