BioGeoBEARS-package	BioGeoBEARS-package
addslash	addslash
add_corners	add_corners
add_to_downpass_labels	add_to_downpass_labels
adf	adf
adf2	adf2
AICstats_2models	AICstats_2models
AkaikeWeights_and_Ratios_pairwise_on_summary_table_compared_to_ref	AkaikeWeights_and_Ratios_pairwise_on_summary_table_compared_to_ref
AkaikeWeights_on_summary_table	AkaikeWeights_on_summary_table
areas_list_to_states_list_new	areas_list_to_states_list_new
average_tr_tips	average_tr_tips
axisPhylo2	axisPhylo2
bears_2param_DIVA_fast	bears_2param_DIVA_fast
bears_2param_standard_fast	bears_2param_standard_fast
bears_2param_standard_fast_fixnode	bears_2param_standard_fast_fixnode
bears_2param_standard_fast_fortest	bears_2param_standard_fast_fortest
bears_2param_standard_fast_symOnly	bears_2param_standard_fast_symOnly
bears_2param_standard_fast_symOnly_simp	bears_2param_standard_fast_symOnly_simp
bears_2param_standard_slowQ_slowSP	bears_2param_standard_slowQ_slowSP
bears_3param_standard_fast	bears_3param_standard_fast
bears_3param_standard_fast_fixnode	bears_3param_standard_fast_fixnode
bears_3param_standard_fast_noJ	bears_3param_standard_fast_noJ
bears_4param_standard_fast	bears_4param_standard_fast
bears_5param_standard_fast	bears_5param_standard_fast
bears_5param_standard_fast_diffstart	bears_5param_standard_fast_diffstart
bears_5param_standard_fast_v	bears_5param_standard_fast_v
bears_6param_standard_fast_ys_v	bears_6param_standard_fast_ys_v
bears_9param_standard_fast_ys_v_cb	bears_9param_standard_fast_ys_v_cb
bears_optim_run	bears_optim_run
binary_ranges_to_letter_codes	binary_ranges_to_letter_codes
binary_range_to_letter_code_list	binary_range_to_letter_code_list
binary_range_to_letter_code_txt	binary_range_to_letter_code_txt
BioGeoBEARS	BioGeoBEARS-package
BioGeoBEARS_model	BioGeoBEARS_model-class
BioGeoBEARS_model_defaults	BioGeoBEARS_model_defaults
BioGeoBEARS_model_object_to_est_params	BioGeoBEARS_model_object_to_est_params
BioGeoBEARS_model_object_to_init_params	BioGeoBEARS_model_object_to_init_params
BioGeoBEARS_model_object_to_params_lower	BioGeoBEARS_model_object_to_params_lower
BioGeoBEARS_model_object_to_params_upper	BioGeoBEARS_model_object_to_params_upper
BioGeoBEARS_run	BioGeoBEARS_run-class
calcP_n	calcP_n
calcZ_part	calcZ_part
calc_AICc_column	calc_AICc_column
calc_AICc_vals	calc_AICc_vals
calc_AIC_column	calc_AIC_column
calc_AIC_vals	calc_AIC_vals
calc_linked_params_BioGeoBEARS_model_object	calc_linked_params_BioGeoBEARS_model_object
calc_loglike_for_optim	calc_loglike_for_optim
calc_loglike_for_optim_stratified	calc_loglike_for_optim_stratified
calc_loglike_sp	calc_loglike_sp
calc_loglike_sp_prebyte	calc_loglike_sp_prebyte
calc_loglike_sp_stratified	calc_loglike_sp_stratified
calc_obs_like	calc_obs_like
calc_post_prob_presence	calc_post_prob_presence
calc_prob_forward_onebranch_dense	calc_prob_forward_onebranch_dense
calc_prob_forward_onebranch_sparse	calc_prob_forward_onebranch_sparse
chainsaw2	chainsaw2
check_BioGeoBEARS_run	check_BioGeoBEARS_run
check_if_state_is_allowed	check_if_state_is_allowed
cls.df	cls.df
colors_legend	colors_legend
conditional_format_cell	conditional_format_cell
conditional_format_table	conditional_format_table
cornerlabels	cornerlabels
cornerpies	cornerpies
corner_coords	corner_coords
default_states_list	default_states_list
define_BioGeoBEARS_model_object	define_BioGeoBEARS_model_object
define_BioGeoBEARS_run	define_BioGeoBEARS_run
define_tipranges_object	define_tipranges_object
dfnums_to_numeric	dfnums_to_numeric
divide_probs_by_number_of_options_nums	divide_probs_by_number_of_options_nums
divide_probs_by_number_of_options_txt	divide_probs_by_number_of_options_txt
expand.grid.alt	expand.grid.alt
expand.grid.jc	expand.grid.jc
expokit_dgpadm_Qmat2	expokit_dgpadm_Qmat2
expokit_dgpadm_Qmat2_prebyte	expokit_dgpadm_Qmat2_prebyte
extend_tips_to_ultrametricize	extend_tips_to_ultrametricize
extract_numbers	extract_numbers
findall	findall
getAIC	getAIC
getAICc	getAICc
getAIC_weight_for_model1	getAIC_weight_for_model1
getareas_from_tipranges_object	getareas_from_tipranges_object
getname	getname
getranges_from_LagrangePHYLIP	getranges_from_LagrangePHYLIP
get_AICweight_ratio_model1_over_model2	get_AICweight_ratio_model1_over_model2
get_Akaike_weights_from_rel_likes	get_Akaike_weights_from_rel_likes
get_Akaike_weights_from_rel_likes_pairwise	get_Akaike_weights_from_rel_likes_pairwise
get_Akaike_weight_ratio_from_Akaike_pairwise_weights	get_Akaike_weight_ratio_from_Akaike_pairwise_weights
get_all_daughter_tips_of_a_node	get_all_daughter_tips_of_a_node
get_all_node_ages	get_all_node_ages
get_APE_nodenums	get_APE_nodenums
get_colors_for_numareas	get_colors_for_numareas
get_daughters	get_daughters
get_deltaAIC	get_deltaAIC
get_deltaAIC_pairwise_w_ref_model	get_deltaAIC_pairwise_w_ref_model
get_edge_times_before_present	get_edge_times_before_present
get_fn_prefix	get_fn_prefix
get_indices_of_branches_under_tips	get_indices_of_branches_under_tips
get_indices_of_tip_nodes	get_indices_of_tip_nodes
get_indices_where_list1_occurs_in_list2	get_indices_where_list1_occurs_in_list2
get_indices_where_list1_occurs_in_list2_noNA	get_indices_where_list1_occurs_in_list2_noNA
get_infparams_optimx	get_infparams_optimx
get_infparams_optimx_nosim	get_infparams_optimx_nosim
get_infprobs_of_simstates	get_infprobs_of_simstates
get_inf_LgL_etc_optimx	get_inf_LgL_etc_optimx
get_lagrange_nodenums	get_lagrange_nodenums
get_leftright_nodes_matrix_from_results	get_leftright_nodes_matrix_from_results
get_level	get_level
get_max_height_tree	get_max_height_tree
get_MLsplitprobs_from_results	get_MLsplitprobs_from_results
get_ML_probs	get_ML_probs
get_ML_states	get_ML_states
get_ML_states_from_relprobs	get_ML_states_from_relprobs
get_ML_state_indices	get_ML_state_indices
get_nodenums	get_nodenums
get_nodenum_structural_root	get_nodenum_structural_root
get_node_ages_of_tips	get_node_ages_of_tips
get_parent	get_parent
get_path_first	get_path_first
get_path_last	get_path_last
get_perEvent_probs	get_perEvent_probs
get_probvals	get_probvals
get_pruningwise_nodenums	get_pruningwise_nodenums
get_relative_prob_model1old	get_relative_prob_model1old
get_relative_prob_model2old	get_relative_prob_model2old
get_rownum_ref_model	get_rownum_ref_model
get_simparams	get_simparams
get_simstates	get_simstates
get_sister_node	get_sister_node
get_statesColors_table	get_statesColors_table
get_TF_tips	get_TF_tips
get_tiplabel_ranges	get_tiplabel_ranges
given_a_starting_state_simulate_branch_end	given_a_starting_state_simulate_branch_end
given_a_starting_state_simulate_split	given_a_starting_state_simulate_split
infprobs_to_probs_of_each_area	infprobs_to_probs_of_each_area
infprobs_to_probs_of_each_area_from_relprobs	infprobs_to_probs_of_each_area_from_relprobs
is.not.na	is.not.na
label_nodes_postorder_phylo3	label_nodes_postorder_phylo3
letter_strings_to_tipranges_df	letter_strings_to_tipranges_df
letter_string_to_binary	letter_string_to_binary
LGcpp_MLstate_per_node	LGcpp_MLstate_per_node
LGcpp_splits_fn_to_table	LGcpp_splits_fn_to_table
LGcpp_splits_fn_to_table2	LGcpp_splits_fn_to_table2
LGcpp_states_fn_to_table	LGcpp_states_fn_to_table
LGpy_MLsplit_per_node	LGpy_MLsplit_per_node
LGpy_splits_fn_to_table	LGpy_splits_fn_to_table
list2str	list2str
lrttest	lrttest
lrttest_on_summary_table	lrttest_on_summary_table
make_dispersal_multiplier_matrix	make_dispersal_multiplier_matrix
make_relprob_matrix_bi	make_relprob_matrix_bi
make_relprob_matrix_de	make_relprob_matrix_de
make_relprob_nummatrix_sp1	make_relprob_nummatrix_sp1
make_relprob_txtmatrix_sp1	make_relprob_txtmatrix_sp1
make_spmat_row	make_spmat_row
mapply_calc_obs_like	mapply_calc_obs_like
mapply_calc_post_prob_presence	mapply_calc_post_prob_presence
mapply_likelihoods	mapply_likelihoods
mapply_likelihoods_prebyte	mapply_likelihoods_prebyte
map_LGpy_MLsplits_to_tree	map_LGpy_MLsplits_to_tree
map_LG_MLsplits_to_tree	map_LG_MLsplits_to_tree
map_LG_MLsplits_to_tree_corners	map_LG_MLsplits_to_tree_corners
map_LG_MLstates_to_tree	map_LG_MLstates_to_tree
match_list1_in_list2	match_list1_in_list2
maxsize	maxsize
merge_words_nonwords	merge_words_nonwords
meval	meval
mix_colors_for_states	mix_colors_for_states
moref	moref
nodenums_bottom_up	nodenums_bottom_up
normat	normat
np	np
nullsym_to_NA	nullsym_to_NA
order_LGnodes	order_LGnodes
order_tipranges_by_tr	order_tipranges_by_tr
order_tipranges_by_tree_tips	order_tipranges_by_tree_tips
params_into_BioGeoBEARS_model_object	params_into_BioGeoBEARS_model_object
parse_lagrange_output	parse_lagrange_output
parse_lagrange_output_old	parse_lagrange_output_old
parse_lagrange_python_output	parse_lagrange_python_output
parse_lagrange_python_output_old	parse_lagrange_python_output_old
paste_rows_without_zeros	paste_rows_without_zeros
Pdata_given_rangerow	Pdata_given_rangerow
Pdata_given_rangerow_dp	Pdata_given_rangerow_dp
pdfit	pdfit
pdftable	pdftable
plot_BioGeoBEARS_model	plot_BioGeoBEARS_model
plot_BioGeoBEARS_results	plot_BioGeoBEARS_results
plot_cladogenesis_size_probabilities	plot_cladogenesis_size_probabilities
postorder_nodes_phylo4_return_table	postorder_nodes_phylo4_return_table
post_prob_states	post_prob_states
post_prob_states_matrix	post_prob_states_matrix
prflag	prflag
printall	printall
prob_of_states_from_prior_prob_areas	prob_of_states_from_prior_prob_areas
process_optim	process_optim
prt	prt
prt_tree_to_phylo4	prt_tree_to_phylo4
prune_specimens_to_species	prune_specimens_to_species
prune_states_list	prune_states_list
rangestxt_to_colors	rangestxt_to_colors
readfiles_BioGeoBEARS_run	readfiles_BioGeoBEARS_run
read_areas_allowed_fn	read_areas_allowed_fn
read_area_of_areas_fn	read_area_of_areas_fn
read_controls	read_controls
read_detections	read_detections
read_dispersal_multipliers_fn	read_dispersal_multipliers_fn
read_distances_fn	read_distances_fn
read_PHYLIP_data	read_PHYLIP_data
read_times_fn	read_times_fn
relative_probabilities_of_subsets	relative_probabilities_of_subsets
relative_probabilities_of_vicariants	relative_probabilities_of_vicariants
rel_likes_from_deltaAICs	rel_likes_from_deltaAICs
rel_likes_from_deltaAICs_pairwise	rel_likes_from_deltaAICs_pairwise
remove_null_rowcols_from_mat	remove_null_rowcols_from_mat
return_items_not_NA	return_items_not_NA
save_tipranges_to_LagrangePHYLIP	save_tipranges_to_LagrangePHYLIP
section_the_tree	section_the_tree
sfunc	sfunc
simstates_to_probs_of_each_area	simstates_to_probs_of_each_area
simulated_indexes_to_tipranges_file	simulated_indexes_to_tipranges_file
simulated_indexes_to_tipranges_object	simulated_indexes_to_tipranges_object
simulate_biogeog_history	simulate_biogeog_history
size_species_matrix	size_species_matrix
slashslash	slashslash
sourceall	sourceall
states_list_indexes_to_areastxt	states_list_indexes_to_areastxt
strsplit2	strsplit2
strsplit_whitespace	strsplit_whitespace
symbolic_cell_to_relprob_cell	symbolic_cell_to_relprob_cell
symbolic_cell_to_relprob_cell_sp	symbolic_cell_to_relprob_cell_sp
symbolic_to_P_matrix	symbolic_to_P_matrix
symbolic_to_Q_matrix	symbolic_to_Q_matrix
symbolic_to_Q_matrix_exper	symbolic_to_Q_matrix_exper
symbolic_to_relprob_matrix_sp	symbolic_to_relprob_matrix_sp
tiplikes_wDetectionModel	tiplikes_wDetectionModel
tipranges	tipranges-class
tipranges_to_area_strings	tipranges_to_area_strings
tipranges_to_tip_condlikes_of_data_on_each_state	tipranges_to_tip_condlikes_of_data_on_each_state
traverse_up	traverse_up
unlist_df	unlist_df
unlist_df2	unlist_df2
unlist_df3	unlist_df3
unlist_df4	unlist_df4
unlist_dtf_cols	unlist_dtf_cols
vfunc	vfunc
yfunc	yfunc
