API for nmatzke/BioGeoBEARS
BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

Global functions
AICstats_2models Source code
AkaikeWeights_and_Ratios_pairwise_on_summary_table_compared_to_r Source code
AkaikeWeights_on_summary_table Source code
BioGeoBEARS_model_defaults Source code
BioGeoBEARS_model_object_to_est_params Source code
BioGeoBEARS_model_object_to_init_params Source code
BioGeoBEARS_model_object_to_params_lower Source code
BioGeoBEARS_model_object_to_params_upper Source code
DIVA_NEXUS_MacClade_block Source code
DIVA_NEXUS_header Source code
LGcpp_MLstate_per_node Source code
LGcpp_splits_fn_to_table Source code
LGcpp_splits_fn_to_table2 Source code
LGcpp_states_fn_to_table Source code
LGpy_MLsplit_per_node Source code
LGpy_splits_fn_to_table Source code
Pdata_given_rangerow Source code
Pdata_given_rangerow_dp Source code
Pmat_to_Qmat Source code
Qmat_to_Rmat Source code
Qmat_to_Rmat_COO Source code
Rmat_perfect_to_Qmat Source code
Rmat_to_Qmat Source code
Rmat_to_Qmat_noScaling Source code
Rmat_to_Qmat_noScaling_COO Source code
SSEsim_results_processed_into_res Source code
SSEsim_results_processed_to_anagenetic_events_table Source code
SSEsim_results_processed_to_cladogenetic_events_table Source code
SSEsim_run Source code
SSEsim_setup_inputs Source code
SSEsim_to_files Source code
add_cladogenetic_events_to_trtable Source code
add_fossil_randomly Source code
add_fossils_from_xls_randomly Source code
add_fossils_to_many_trees Source code
add_hook Source code
add_hooks Source code
add_jts_to_BioGeoBEARS_run_object Source code
add_list_of_fossil_tips_to_tipranges Source code
add_random_direct_ancestor_hook Source code
add_random_side_branch Source code
add_statum_boundaries_to_phylo_plot Source code
add_to_downpass_labels Source code
add_trait_to_BioGeoBEARS_run_object Source code
addslash Source code
adf Source code
adf2 Source code
allQs Source code
areas_list_to_states_list_new Source code
assign_rates_asym Source code
assign_rates_sym Source code
average_tr_tips Source code
basefreqs_to_basefreqs_mat Source code
bears_optim_run Source code
binary_range_to_letter_code_list Source code
binary_range_to_letter_code_txt Source code
binary_ranges_to_letter_codes Source code
calcP_n Source code
calcZ_part Source code
calc_AIC_column Source code
calc_AIC_vals Source code
calc_AICc_column Source code
calc_AICc_vals Source code
calc_BSM_mean_node_states Source code
calc_independent_likelihoods_on_each_branch_prebyte Source code
calc_linked_params_BioGeoBEARS_model_object Source code
calc_loglike_for_optim Source code
calc_loglike_for_optim_neg Source code
calc_loglike_for_optim_stratified Source code
calc_loglike_for_optim_stratified_neg Source code
calc_loglike_sp_prebyte Source code
calc_loglike_sp_stratified Source code
calc_obs_like Source code
calc_post_prob_presence Source code
calc_prob_forward_onebranch_dense Source code
calc_prob_forward_onebranch_sparse Source code
calc_uppass_probs_new2 Source code
calc_uppass_scenario_probs_new2 Source code
catdf Source code
cft Source code
chainsaw2 Source code
check_BioGeoBEARS_run Source code
check_ML_vs_BSM Source code
check_if_state_is_allowed Source code
check_if_state_is_allowed_by_adjacency Source code
check_tipranges_for_allQs Source code
check_trfn Source code
cls.df Source code
combine_3matrices Source code Source code
combine_3matrices2 Source code Source code
combine_matrices_into_supermatrix Source code
combine_matrices_into_supermatrix_w_names Source code
compare_two_name_lists Source code
conditional_format_cell Source code
conditional_format_table Source code
convert_SSEsim_to_stochastic_mapping_results_format Source code
convert_clado_1desc_to_anagenetic Source code
convert_full_simtree_nodenums_to_observed_simtree_nodenums Source code
convert_simtr_observed_events_to_prelim_stochastic_mapping_forma Source code
coo2crs Source code
correct_de_events_on_observed_tree Source code
count_ana_clado_events Source code
count_ana_dispersal_events Source code
count_clado_dispersal_events Source code
count_clado_events_nonjump Source code
count_events_huge_tables Source code
counts_of_each_rate Source code
counts_of_each_rate_minus_rowcol Source code
define_BioGeoBEARS_model_object Source code
define_BioGeoBEARS_run Source code
define_tipranges_object Source code
dfn2n Source code
dfnums_to_numeric Source code
diri_probs Source code
dispersal_multipliers_matrix_from_BioGeoBEARS_run_object Source code
dist_between_direct_ancestors Source code
divide_probs_by_number_of_options_nums Source code
divide_probs_by_number_of_options_txt Source code
edges_existing_at_correct_time_bp_TF Source code
edges_table_to_tipranges_object Source code
empcdf Source code
error_checks_for_fossils_xls Source code
event_txt_into_events_row Source code
events_table_into_txt Source code
events_table_row_into_txt Source code
events_txt_into_events_table Source code
events_txt_list_into_events_table Source code
exp_SparseM Source code
exp_cmdstr Source code
exp_cmdstr_list Source code
expand.grid.alt Source code
expand.grid.jc Source code
expokit_dgpadm_Qmat2_prebyte Source code
exponentiate_sparse_matrix_w_lots_of_zeros Source code
extend_tips_to_ultrametricize Source code
extract_numbers Source code
extract_param_inference Source code
extract_params_from_BioGeoBEARS_results_object Source code
figure_out_step_val Source code Source code
find_instring Source code
find_str_inlist Source code
findall Source code
fix_BioGeoBEARS_params_minmax Source code
geog_ancstates_from_both Source code
getAIC Source code
getAIC_weight_for_model1 Source code
getAICc Source code
get_AICweight_ratio_model1_over_model2 Source code
get_APE_nodenums Source code
get_Akaike_weight_ratio_from_Akaike_pairwise_weights Source code
get_Akaike_weights_from_rel_likes Source code
get_Akaike_weights_from_rel_likes_pairwise Source code
get_LnL_from_BioGeoBEARS_results_object Source code
get_LnL_from_GenSA Source code
get_LnL_from_optim Source code
get_LnL_from_optim_result Source code
get_LnL_from_optimx2012 Source code
get_LnL_from_optimx2013 Source code
get_ML_probs Source code
get_ML_state_indices Source code
get_ML_states Source code
get_ML_states_from_relprobs Source code
get_MLsplitprobs_from_results Source code
get_Qmat_COOmat_from_BioGeoBEARS_run_object Source code
get_Qmat_COOmat_from_res Source code
get_TF_tips Source code
get_all_daughter_tips_of_a_node Source code
get_all_node_ages Source code
get_bigmatrix_dim Source code
get_clado_perEvent_weights Source code
get_daughter_nodes Source code
get_daughter_tipnames Source code
get_daughter_tipnums Source code
get_daughters Source code
get_dej_params_row_from_SSEsim_results_processed Source code
get_deltaAIC Source code
get_deltaAIC_pairwise_w_ref_model Source code
get_distribution_of_range_sizes_in_states_list Source code
get_distribution_of_range_sizes_in_tipranges Source code
get_dmat_times_from_BioGeoBEARS_run_object Source code
get_dmat_times_from_res Source code
get_edge_times_before_present Source code
get_fn_prefix Source code
get_huge_events_tables_from_BSM_Rdata Source code
get_indices_of_branches_under_tips Source code
get_indices_of_tip_nodes Source code
get_indices_where_list1_occurs_in_list2 Source code
get_indices_where_list1_occurs_in_list2_noNA Source code
get_inf_LgL_etc_optimx Source code
get_inf_ML_stateprobs Source code
get_infparams_optimx Source code
get_infparams_optimx_nosim Source code
get_infprobs_of_simstates Source code
get_inputs_for_stochastic_mapping Source code
get_inputs_for_stochastic_mapping_from_results_object Source code
get_inputs_for_stochastic_mapping_stratified Source code
get_lagrange_nodenums Source code
get_leftright_nodes_matrix_from_results Source code
get_level Source code
get_max_height_tree Source code
get_node_ages_of_tips Source code
get_nodenum_structural_root Source code
get_nodenums Source code
get_params_from_GenSA Source code
get_params_from_optim Source code
get_params_from_optim_or_optimx_result Source code
get_params_from_optimx2012 Source code
get_params_from_optimx2013 Source code
get_parent Source code
get_parent_for_trace_parents_up Source code
get_path_first Source code
get_path_last Source code
get_possible_branches_to_add_fossils_to Source code
get_probvals Source code
get_pruningwise_nodenums Source code
get_rangesize_prior_by_observed_rangesize Source code
get_rownum_ref_model Source code
get_simparams Source code
get_simstates Source code
get_simtr_full_to_observed_node_translation Source code
get_sister_node Source code
get_spPmat_inputs_from_BGB Source code
get_tip_likelihoods_of_subbranch_from_resCondlikes_given_master_ Source code
get_tiplabel_ranges Source code
get_tipranges_from_detects_df Source code
getareanames_from_tipranges_object Source code
getareas_from_tipranges_object Source code
getname Source code
getranges_from_LagrangePHYLIP Source code
given_a_starting_state_get_prob_of_each_split_scenario Source code
given_a_starting_state_simulate_branch_end Source code
given_a_starting_state_simulate_split Source code
hist_event_counts Source code
hist_sim_v_inf_vals Source code
impose_min_brlen Source code
infprobs_to_probs_of_each_area Source code
infprobs_to_probs_of_each_area_from_relprobs Source code
infprobs_to_probs_of_each_rangesize Source code
is.not.na Source code
is_list_not_dataframe Source code
isblank_TF Source code
label_nodes_postorder_phylo3 Source code
label_table_of_anagenetic_events Source code
label_table_of_cladogenetic_events Source code
letter_string_to_binary Source code
letter_strings_to_tipranges_df Source code
level_tree_tips Source code
linear_regression_plot Source code
list2str Source code
lrttest Source code
lrttest_on_summary_table Source code
make_BSMs Source code
make_BioGeoBEARS_manytrees_results_object Source code
make_dispersal_multiplier_matrix Source code
make_list_of_indices_from_2_lists Source code Source code
make_lotsa_sparse_matrices Source code
make_relprob_matrix_bi Source code
make_relprob_matrix_de Source code
make_relprob_nummatrix_sp1 Source code
make_relprob_txtmatrix_sp1 Source code
make_sparse_matrix Source code
make_sparse_matrix_by_i Source code
make_spmat_row Source code
mapply_calc_obs_like Source code
mapply_calc_post_prob_presence Source code
mapply_likelihoods_prebyte Source code
mat2q Source code
mat_to_Qmat_as_list Source code
match_list1_in_list2 Source code
matpow Source code
matpow2 Source code
matpowfast Source code
matpowfast2 Source code
matrix_to_spam Source code
merge_words_nonwords Source code
meval Source code
minmax_pretty Source code
modify_Qmat_with_trait Source code
modify_a_rate Source code
modify_rate_matrix_categories Source code
moref Source code
nesting_mats Source code
nesting_mats_w_names Source code
nodenums_DIVA Source code
nodenums_bottom_up Source code
normat Source code Source code
np Source code
nparams_from_optimx2013 Source code
nullsym_to_NA Source code
ones Source code
opd Source code
openwd Source code
order_tipranges_by_tr Source code
order_tipranges_by_tree_tips Source code
params_into_BioGeoBEARS_model_object Source code
parse_lagrange_output Source code
parse_lagrange_output_old Source code
parse_lagrange_python_output Source code
parse_lagrange_python_output_old Source code
paste_rows_without_zeros Source code
plot_BSM_fns Source code
plot_BioGeoBEARS_results Source code
plot_inf_accuracy_vs_SSEsims_v2 Source code
plot_params_from_multiple_trees Source code
plot_simDEC_DECJ_inferences Source code
post_prob_states Source code
post_prob_states_matrix Source code
postorder_nodes_phylo4_return_table Source code
prflag Source code
printall Source code
prob_each_split_scenario_to_uppass_probs Source code
prob_of_states_from_prior_prob_areas Source code
process_DIVA_output Source code
process_optim Source code
prt Source code
prt_tree_to_phylo4 Source code
prune_specimens_to_species Source code
prune_states_list Source code
prune_states_list_by_adjacency Source code
put_jcol_after_ecol Source code
put_params_into_optim_or_optimx_result Source code
read_PHYLIP_data Source code
read_area_of_areas_fn Source code
read_areas_adjacency_fn Source code
read_areas_allowed_fn Source code
read_controls Source code
read_detections Source code
read_dispersal_multipliers_fn Source code
read_distances_fn Source code
read_envdistances_fn Source code
read_times_fn Source code
readfiles_BioGeoBEARS_run Source code
rel_likes_from_deltaAICs Source code
rel_likes_from_deltaAICs_pairwise Source code
relative_probabilities_of_subsets Source code
relative_probabilities_of_vicariants Source code
remove_multiple_commas_from_strings_in_list Source code
remove_null_rowcols_from_mat Source code
rerun_optimization_w_HiLow Source code
return_items_not_NA Source code
runBSM Source code
run_all_exponentiation_methods Source code
run_bears_optim_on_multiple_trees Source code
run_exp_timetests Source code
run_lotsa_exp_functions Source code
run_lotsa_exponentiations Source code
sample_split_scenario Source code
sample_split_scenario2 Source code
sample_uppass_split_scenario_given_probs_ancstate Source code
save_tipranges_to_LagrangePHYLIP Source code
scale_BGB_params Source code
section_the_tree Source code
sfunc Source code
simstates_to_probs_of_each_area Source code
simulate_biogeog_history Source code
simulate_source_area_ana Source code
simulate_source_area_clado Source code
simulate_source_areas_ana_clado Source code
simulated_indexes_to_tipranges_file Source code
simulated_indexes_to_tipranges_object Source code
size_half_tri_nodiag Source code
size_species_matrix Source code
slashslash Source code
sort_list_of_lists_of_numbers Source code
sourceall Source code
sourceall_git Source code
spPmat_inputs_from_BioGeoBEARS_model_object Source code
spPmat_inputs_to_COO_weights_columnar Source code
split_key_item Source code
states_list_0based_to_ranges_txt_list Source code
states_list_indexes_to_areastxt Source code
stochastic_map_branch Source code
stochastic_map_given_inputs Source code
stochastic_mapping_on_stratified Source code
strsplit2 Source code
strsplit_whitespace Source code
sumdiag Source code
summarize_Qmats Source code
summarize_stateprobs_on_master_tree Source code
sumoffdiag Source code
symbolic_cell_to_relprob_cell Source code
symbolic_cell_to_relprob_cell_sp Source code
symbolic_to_P_matrix Source code
symbolic_to_Q_matrix Source code
symbolic_to_Q_matrix_exper Source code
symbolic_to_relprob_matrix_sp Source code
table2 Source code
testexp Source code
testexp2 Source code
testexp_sub Source code
tiplikes_wDetectionModel Source code
tipranges_from_BGB_run_object Source code
tipranges_from_detects_fn Source code
tipranges_to_DIVA_DATAblock_format Source code
tipranges_to_area_strings Source code
tipranges_to_tip_condlikes_of_data_on_each_state Source code
trace_parents_up Source code
trait_ancstates_from_both Source code
traits_results_to_geogOnly_traitsOnly Source code
traverse_up Source code
tree_to_DIVA_TREE_block Source code
trim2 Source code
uniq_rates Source code
uniqs_of_each_rate_minus_rowcol Source code
uniquify_clado_events Source code
unlist_df Source code
unlist_df2 Source code
unlist_df3 Source code
unlist_df4 Source code
unlist_dtf_cols Source code
unscale_BGB_params Source code
update_BioGeoBEARS_model_object_w_optimx_result Source code
vfunc Source code
write_DIVA_cmds Source code
yfunc Source code
zeros_diag_ones_offdiag Source code
zerosmat Source code
nmatzke/BioGeoBEARS documentation built on July 12, 2019, 12:27 p.m.