BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

BioGeoBEARS allows probabilistic inference of both historical biogeography (ancestral geographic ranges on a phylogeny) as well as comparison of different models of range evolution. It reproduces the model available in LAGRANGE (Ree and Smith 2008), as well as making available numerous additional models. For example, LAGRANGE as typically run has two free parameters, d (dispersal rate, i.e. the rate of range addition along a phylogenetic branch) and e (extinction rate, really the rate of local range loss along a phylogenetic branch). LAGRANGE also has a fixed cladogenic model which gives equal probability to a number of allowed range inheritance events, e.g.: (1) vicariance, (2) a new species starts in a subset of the ancestral range, (3) the ancestral range is copied to both species; in all cases, at least one species must have a starting range of size 1. LAGRANGE assigns equal probability to each of these events, and zero probability to other events. BioGeoBEARS adds an additional cladogenic event: founder-event speciation (the new species jumps to a range outside of the ancestral range), and also allows the relative weighting of the different sorts of events to be made into free parameters, allowing optimization and standard model choice procedures to pick the best model. The relative probability of different descendent range sizes is also parameterized and thus can also be specified or estimated. The flexibility available in BioGeoBEARS also enables the natural incorporation of (1) imperfect detection of geographic ranges in the tips, and (2) inclusion of fossil geographic range data, when the fossils are tips on the phylogeny. Bayesian analysis has been implemented through use of the "LaplacesDemon" package, however this package is now maintained off of CRAN, so its usage is not formally included in BioGeoBEARS at the current time. CITATION INFO: This package is the result of my Ph.D. research, please cite the package if you use it! Type: citation(package="BioGeoBEARS") to get the citation information.

AuthorNicholas J. Matzke [aut, cre, cph]
Date of publication2014-01-02 15:15:11
MaintainerNicholas J. Matzke <matzke@berkeley.edu>
LicenseGPL (>= 2)
Version0.2.1
http://phylo.wikidot.com/biogeobears

View on CRAN

Man pages

add_corners: Iterate up through a plotted tree, getting the coordinates of...

addslash: Add a slash to a directory name if needed

add_to_downpass_labels: Iterate up and down a tree in C++ LAGRANGE downpass order

adf: Convert to data.frame, without factors

adf2: Convert to data.frame, without factors

AICstats_2models: Calculate all the AIC and LRT stats between two models

AkaikeWeights_and_Ratios_pairwise_on_summary_table_compared_to_ref: Get the ratio between the pairwise Akaike Weights

AkaikeWeights_on_summary_table: Calculate Akaike Weights, and add to table

areas_list_to_states_list_new: Convert a list of areas to a list of geographic ranges...

average_tr_tips: Average the heights of (non-fossil) tips to make...

axisPhylo2: axisPhylo with more flexibility in labeling

bears_2param_DIVA_fast: 2-parameter model, fixed cladogenesis model (as in LAGRANGE)

bears_2param_standard_fast: 2-parameter model, fixed cladogenesis model (as in LAGRANGE)

bears_2param_standard_fast_fixnode: 2-parameter model, fixed cladogenesis model (as in LAGRANGE)

bears_2param_standard_fast_fortest: 2-parameter model, fixed cladogenesis model (as in LAGRANGE)...

bears_2param_standard_fast_symOnly: 2-parameter model, no cladogenesis model (as in BayArea or...

bears_2param_standard_fast_symOnly_simp: 2-parameter model, no cladogenesis model (as in BayArea or...

bears_2param_standard_slowQ_slowSP: 2-parameter model, fixed cladogenesis model - slow version

bears_3param_standard_fast: 3-parameter model, adding j (founder-event speciation)

bears_3param_standard_fast_fixnode: 3-parameter model, adding j (founder-event speciation)

bears_3param_standard_fast_noJ: 3-parameter model, adding v (vicariance proportion), but no j...

bears_4param_standard_fast: 4-parameter model, adding j (founder-event speciation) and v...

bears_5param_standard_fast: 5-parameter model, adding j (founder-event speciation), v...

bears_5param_standard_fast_diffstart: 5-parameter model, with different starting points for...

bears_5param_standard_fast_v: 5-parameter model, adding j (founder-event speciation), v...

bears_6param_standard_fast_ys_v: 6-parameter model, adding j (founder-event speciation), v...

bears_9param_standard_fast_ys_v_cb: 6-parameter model, adding j (founder-event speciation), v...

bears_optim_run: Run ML search from 'BioGeoBEARS_run' object

binary_ranges_to_letter_codes: Convert binary presence/absence codes (1/0) to a list of text...

binary_range_to_letter_code_list: Convert binary presence/absence codes (1/0) to a list of text...

binary_range_to_letter_code_txt: Convert binary presence/absence codes (1/0) to text area...

BioGeoBEARS_model-class: An object of class BioGeoBEARS_model holding the model inputs

BioGeoBEARS_model_defaults: Set up a default BioGeoBEARS model object

BioGeoBEARS_model_object_to_est_params: Extract estimated parameters from a BioGeoBEARS model object

BioGeoBEARS_model_object_to_init_params: Produce initial parameters from a BioGeoBEARS model object

BioGeoBEARS_model_object_to_params_lower: Produce the lower limit on the parameters from a BioGeoBEARS...

BioGeoBEARS_model_object_to_params_upper: Produce the upper limit on the parameters from a BioGeoBEARS...

BioGeoBEARS-package: BioGeography with Bayesian (and likelihood) Evolutionary...

BioGeoBEARS_run-class: An object of class BioGeoBEARS_run holding the model inputs

calc_AICc_column: Calculate AICc values for a list of models

calc_AIC_column: Calculate AICs to make a column in a table

calc_AICc_vals: Calculate AICc values for a list of models

calc_AIC_vals: Calculate AICs for a list of models

calc_linked_params_BioGeoBEARS_model_object: Update parameters that are deterministic functions of free...

calc_loglike_for_optim: Take model parameters and the data and calculate the...

calc_loglike_for_optim_stratified: Take model parameters and the data and calculate the...

calc_loglike_sp: Calculate log-likelihood with a transition matrix and...

calc_loglike_sp_prebyte: Calculate log-likelihood with a transition matrix and...

calc_loglike_sp_stratified: Calculate log-likelihood with a transition matrix and...

calc_obs_like: Calculate likelihood of count data given true...

calcP_n: Calculate Z (part of equation 6.4 of Harte 2011)

calc_post_prob_presence: Calculate posterior probability of presence, given count data...

calc_prob_forward_onebranch_dense: Dense matrix exponentiation forward on a branch, with...

calc_prob_forward_onebranch_sparse: Sparse matrix exponentiation forward on a branch, with...

calcZ_part: Calculate Z (equation 6.3 of Harte 2011)

chainsaw2: Saw a tree off at a particular time before present

check_BioGeoBEARS_run: Check the inputs for various problems

check_if_state_is_allowed: Check if a geographic range/state is allowed, given an...

cls.df: Get the class for each column in a list

colors_legend: Plot a colors legend for geographic ranges

conditional_format_cell: Conditionally format a number (mostly)

conditional_format_table: Conditionally format the numbers (mostly) in a table

corner_coords: Get the corner coordinates

cornerlabels: Make labels for plotting ranges on corners

cornerpies: Make pie charts for plotting ranges on corners

default_states_list: Default input for a states_list

define_BioGeoBEARS_model_object: Define a BioGeoBEARS_model class and object

define_BioGeoBEARS_run: Define a maximum likelihood search, perhaps stratified

define_tipranges_object: Define a tipranges class and object

dfnums_to_numeric: Get the class for each column in a list

divide_probs_by_number_of_options_nums: Divide each type of event by its frequency, return calculated...

divide_probs_by_number_of_options_txt: Divide each type of event by its frequency

expand.grid.alt: A faster version of expand.grid

expand.grid.jc: An even faster version of expand.grid

expokit_dgpadm_Qmat2: A byte-compiled version of expokit_dgpadm_Qmat2_prebyte

expokit_dgpadm_Qmat2_prebyte: A version of expokit_dgpadm_Qmat to byte-compile

extend_tips_to_ultrametricize: Take a tree, extend all tips (including fossils) up to 0.0 my...

extract_numbers: Extract just the numbers from a string, including decimal...

findall: Get indices of all matches to a list

getAIC: Calculate AIC

getAICc: Calculate AICc

getAIC_weight_for_model1: Calculate Akaike Weight

get_AICweight_ratio_model1_over_model2: Calculate ratio of Akaike Weights

get_Akaike_weight_ratio_from_Akaike_pairwise_weights: Get the ratio between the pairwise Akaike Weights

get_Akaike_weights_from_rel_likes: Calculate the Akaike Weights, from the relative likelihoods...

get_Akaike_weights_from_rel_likes_pairwise: Calculate the Akaike Weights, from the relative likelihoods...

get_all_daughter_tips_of_a_node: Get all the daughter tips of a node

get_all_node_ages: Get the ages of all the nodes in the tree (above the root)

get_APE_nodenums: Get R internal node numbers

getareas_from_tipranges_object: Get the names of the areas in a tipranges object

get_colors_for_numareas: Get colors for a certain number of single areas

get_daughters: Get all the direct daughters nodes of a node

get_deltaAIC: Calculate deltaAIC

get_deltaAIC_pairwise_w_ref_model: Calculate deltaAIC

get_edge_times_before_present: Get the times of the top and bottom of each edge

get_fn_prefix: Get everything BEFORE the last suffix (.nex or whatever)

get_indices_of_branches_under_tips: Get the indices of the branches (row number in edge matrix)...

get_indices_of_tip_nodes: Get TRUE/FALSE for nodes being tips

get_indices_where_list1_occurs_in_list2: Return (first!) indices in second list matching the first...

get_indices_where_list1_occurs_in_list2_noNA: Return (first!) indices in second list matching the first...

get_inf_LgL_etc_optimx: Get the inferred parameters from a results object (utility...

get_infparams_optimx: Get the inferred parameters from an ML optimization

get_infparams_optimx_nosim: Get the inferred parameters from an ML optimization...

get_infprobs_of_simstates: Get the probabilities of the true (simulated) states

get_lagrange_nodenums: Get internal node numbers in LAGRANGE's downpass order

get_leftright_nodes_matrix_from_results: Make a table of the Right and Left nodes descending from each...

get_level: Get a node's level in the tree

get_max_height_tree: Get the maximum age of all the nodes (above the root)

get_ML_probs: Get the probability of the ML state for each node, from a...

get_MLsplitprobs_from_results: Extract the ML probs for the base of each branch above a...

get_ML_state_indices: Extract the indices for the ML states at each node, given a...

get_ML_states: Get ML states from a BioGeoBEARS model results list

get_ML_states_from_relprobs: Extract the ML states at each node, from a table of relative...

getname: Collapse range abbreviations to strings

get_node_ages_of_tips: Get the ages of each tip above the root

get_nodenums: Get the unique node numbers in a tree

get_nodenum_structural_root: Gets the root node

get_parent: Get the direct parent node of a node

get_path_first: Get the text that comes before the last slash

get_path_last: Get the text that comes after the last slash

get_perEvent_probs: Get the per-event probabilities at cladogenesis

get_probvals: Calculate probability of ordered discrete states using a...

get_pruningwise_nodenums: Get internal node numbers in pruningwise order

getranges_from_LagrangePHYLIP: Read a LAGRANGE PHYLIP-style file containing geographic...

get_relative_prob_model1old: Calculate relative probability of model 1 (=Akaike Weight)

get_relative_prob_model2old: Calculate relative probability of model 1 (Akaike Weight)

get_rownum_ref_model: Get rownum of named model

get_simparams: Get the simulated model parameters from the row of a table

get_simstates: Load the simulation information from an underscore delimited...

get_sister_node: Get the node sister to two nodes

get_statesColors_table: Make a color table for each area and their combinations

get_TF_tips: Get TRUE/FALSE for nodes being tips

get_tiplabel_ranges: For each tip, get a text string of the areas in a tipranges...

given_a_starting_state_simulate_branch_end: Given the state at the start of a branch, simulate the state...

given_a_starting_state_simulate_split: Given the state just below a node, simulate the states after...

infprobs_to_probs_of_each_area: Convert probabilities of each state, to the probabilities of...

infprobs_to_probs_of_each_area_from_relprobs: Convert relative probabilities matrix to the probabilities of...

is.not.na: Check for not NA

label_nodes_postorder_phylo3: Add postorder node number labels to a phylo3 tree object.

letter_strings_to_tipranges_df: Convert ranges in the form of letters (A, AB, BFG, etc.) to a...

letter_string_to_binary: Convert ranges in the form of letters (A, AB, BFG, etc.) to...

LGcpp_MLstate_per_node: Get the ML states per node, from a states table

LGcpp_splits_fn_to_table: Get the ML splits per node, from C++ LAGRANGE output

LGcpp_splits_fn_to_table2: Get the ML splits per node, from Python LAGRANGE output

LGcpp_states_fn_to_table: Get the ML states per node, from C++ LAGRANGE output

LGpy_MLsplit_per_node: Get the ML splits per node, from a splits table

LGpy_splits_fn_to_table: Get the ML splits per node, from Python LAGRANGE output

list2str: Convert a list of items to a string

lrttest: Calculate Likelihood Ratio Test (LRT)

lrttest_on_summary_table: Calculate Likelihood Ratio Test (LRT) results, and add to...

make_dispersal_multiplier_matrix: Make a default matrix of relative dispersal probabilities...

make_relprob_matrix_bi: Make a relative probability matrix for a single speciation...

make_relprob_matrix_de: Make a relative dispersal probability matrix (in text form)

make_relprob_nummatrix_sp1: Convert a observed-speciation transition matrix to an...

make_relprob_txtmatrix_sp1: Convert a observed-speciation transition matrix to an...

make_spmat_row: Construct a (text) cell of the cladogenesis/speciation matrix

map_LG_MLsplits_to_tree: Take the table of ML splits and node number and map on tree...

map_LG_MLsplits_to_tree_corners: Map splits to the corners on a phylogeny

map_LG_MLstates_to_tree: Map states to the nodes on a phylogeny

map_LGpy_MLsplits_to_tree: Take the table of ML splits and node number and map on tree...

mapply_calc_obs_like: Mapply version of calc_obs_like()

mapply_calc_post_prob_presence: Mapply version of calc_post_prob_presence()

mapply_likelihoods: Use mapply on matrix exponentiations - post-byte-compiling

mapply_likelihoods_prebyte: Use mapply on matrix exponentiations - pre-byte-compiling

match_list1_in_list2: Return TRUE for list1 items when they occur in list2

maxsize: Get the maximum rangesize for a given ancestral rangesize

merge_words_nonwords: Merge lists of words and nonwords (numbers) that may be of...

meval: 'eval()' function for use in 'sapply'

mix_colors_for_states: Mix colors logically to produce colors for multi-area ranges

moref: print to screen the header of a file

nodenums_bottom_up: Assign node labels in bottom-up, left-first format (as in...

normat: Utility functions to help deal with matrices Normalize a...

np: normalizePath shortcut

nullsym_to_NA: Convert a specified null range code to NA

order_LGnodes: Order LAGRANGE-numbered nodes so that they can be plotted in...

order_tipranges_by_tr: Order the tipranges in a tipranges object so they match the...

order_tipranges_by_tree_tips: Reorder the rows in a 'tipranges' object, to correspond to...

params_into_BioGeoBEARS_model_object: Feed modified parameters back into a BioGeoBEARS model object

parse_lagrange_output: Parse the output file from python 'LAGRANGE'

parse_lagrange_output_old: Parse the output file from python 'LAGRANGE' - older version

parse_lagrange_python_output: Parse the output file from python 'LAGRANGE'

parse_lagrange_python_output_old: Parse the output file from python 'LAGRANGE' - old version

paste_rows_without_zeros: Concatenate cells in each row of a text-based transition...

Pdata_given_rangerow: Calculate probability of detection data given a true...

Pdata_given_rangerow_dp: Calculate probability of detection data given a true...

pdfit: Print a table to LaTeX format

pdftable: Print a table to LaTeX format

plot_BioGeoBEARS_model: Graphical display of your anagenetic and cladogenetic...

plot_BioGeoBEARS_results: Plot the results of a BioGeoBEARS run

plot_cladogenesis_size_probabilities: Graphical display of P(daughter rangesize) for your input or...

postorder_nodes_phylo4_return_table: Get a table of node numbers, including DIVA node numbers

post_prob_states: Calculate posterior probability of each states/geographic...

post_prob_states_matrix: Calculate posterior probability of each states/geographic...

prflag: Utility function to conditionally print intermediate results

printall: Print an entire table to screen

prob_of_states_from_prior_prob_areas: Calculate probability of detection data for each OTU at each...

process_optim: Extract 'optim' results to a row

prt: Print tree in table format

prt_tree_to_phylo4: prt_tree_to_phylo4

prune_specimens_to_species: Take a tree and species names/geography table and produce a...

prune_states_list: Cut down the states list according to areas_allowed_mat

rangestxt_to_colors: Convert a list of ranges text (KOM, MH, KOMIH, etc.)

read_area_of_areas_fn: Read in the area areas by time

read_areas_allowed_fn: Read in the area areas by time

read_controls: Read a file with the total number of detections in a...

read_detections: Read a file with detection counts per area

read_dispersal_multipliers_fn: Read in the hard-coded dispersal multipliers from file

read_distances_fn: Read in the distances by time

readfiles_BioGeoBEARS_run: Read in the extra input files, if any

read_PHYLIP_data: Read a PHYLIP-format file

read_times_fn: Read in the stratification time breakpoints

relative_probabilities_of_subsets: Calculate probability of different descendant rangesizes, for...

relative_probabilities_of_vicariants: Calculate probability of different descendant rangesizes, for...

rel_likes_from_deltaAICs: Calculate the relative likelihoods of the models, from the...

rel_likes_from_deltaAICs_pairwise: Calculate the relative likelihoods of the models, from the...

remove_null_rowcols_from_mat: Remove rows or columns representing a null geographic range...

return_items_not_NA: Remove NAs from a vector/list

save_tipranges_to_LagrangePHYLIP: Save a tipranges object to a LAGRANGE PHYLIP-style file...

section_the_tree: Section a tree for stratified analysis

sfunc: Extract the appropriate probability for a subset speciation...

simstates_to_probs_of_each_area: Convert simulated states to probabilities of each area

simulate_biogeog_history: Simulate a biogeographical history, given a transition matrix...

simulated_indexes_to_tipranges_file: Convert simulated Qmat 0-based indexes to a tipranges file

simulated_indexes_to_tipranges_object: Convert simulated Qmat 0-based indexes to a tipranges object

size_species_matrix: Calculate the dimensions of the cladogenesis/speciation...

slashslash: Remove double slash (slash a slash)

sourceall: Source all .R files in a directory, except "compile" and...

states_list_indexes_to_areastxt: States (ranges) lists to txt string of the areas

strsplit2: String splitting shortcut

strsplit_whitespace: Split strings on whitespace

symbolic_cell_to_relprob_cell: Convert symbolic cell (a text equation) to relprob matrix (a...

symbolic_cell_to_relprob_cell_sp: Convert symbolic cell (a text equation) to relprob cell (a...

symbolic_to_P_matrix: Convert symbolic matrix to relprob matrix

symbolic_to_Q_matrix: Convert symbolic matrix to an instantaneous rate matrix (Q...

symbolic_to_Q_matrix_exper: Experimental version of 'symbolic_to_Q_matrix_exper',...

symbolic_to_relprob_matrix_sp: Convert symbolic matrix (with text equations) to relprob...

tiplikes_wDetectionModel: Calculate probability of detection data for each OTU at each...

tipranges-class: The tipranges class

tipranges_to_area_strings: Convert tipranges binary coding to range strings

tipranges_to_tip_condlikes_of_data_on_each_state: Convert a tipranges object to the tip likelihoods

traverse_up: Traverse the tree from node up to the tips

unlist_df: Unlist the columns in a data.frame

unlist_df2: Unlist the columns in a data.frame, with more checks

unlist_df3: Unlist the columns in a data.frame, with more checks and adf

unlist_df4: Unlist the columns in a data.frame, with more checks, adf,...

unlist_dtf_cols: Unlist the columns in a data.frame

vfunc: Extract the appropriate probability for a vicariant...

yfunc: Extract the appropriate probability for a...

Functions

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

Files

BioGeoBEARS
BioGeoBEARS/inst
BioGeoBEARS/inst/CITATION
BioGeoBEARS/inst/REFERENCES.bib
BioGeoBEARS/inst/extdata
BioGeoBEARS/inst/extdata/examples
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0/LGcpp
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra.newick.bgkey.tre
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra.newick.bgstates.tre
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra_M0.lg
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra.newick
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra.newick.bgsplits.tre
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra_geog.data
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra_M0_lgcpp_out.txt
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0/BGB
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0/BGB/Psychotria_geog.data
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0/BGB/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0/LGpy_2013
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0/LGpy_2013/Cyrtandra_M0.lagrange.py
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0/LGpy_2013/Cyrtandra.newick
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0/LGpy_2013/Cyrtandra_M0.results.txt
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0/LGpy_2013/Cyrtandra_M0.results-1.txt
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0/LGpy_2012
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0/LGpy_2012/Cyrtandra_M0.lagrange.py
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0/LGpy_2012/Cyrtandra.newick
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0/LGpy_2012/Cyrtandra_M0.results.txt
BioGeoBEARS/inst/extdata/examples/Cyrtandra_M0/LGpy_2012/Cyrtandra_M0.results-1.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/LGcpp
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_5.2.newick.bgsplits.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_5.2.newick.bgstates.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_geog.data
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_M1strat_lgcpp_out.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_5.2.newick.bgkey.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_M1_stratified.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_M1strat.lg
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/BGB
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/BGB/timeperiods.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/BGB/Psychotria_geog.data
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/BGB/dispersal_multipliers.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/BGB/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/LGpy_2013
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/LGpy_2013/psychotria_M1_strat.lagrange.py
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/LGpy_2013/psychotria_M1_strat.results.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/LGpy_2013/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/LGpy_2012
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/LGpy_2012/psychotria_M1_strat.lagrange.py
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/LGpy_2012/psychotria_M1_strat.results.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M1strat/LGpy_2012/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/_run_LAGRANGE_examples_v1.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M1
BioGeoBEARS/inst/extdata/examples/Psychotria_M1/LGcpp
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BioGeoBEARS/inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_M1.lg
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BioGeoBEARS/inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_geog.data
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BioGeoBEARS/inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_M1_lgcpp_out.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M1/BGB
BioGeoBEARS/inst/extdata/examples/Psychotria_M1/BGB/Psychotria_geog.data
BioGeoBEARS/inst/extdata/examples/Psychotria_M1/BGB/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M1/LGpy_2013
BioGeoBEARS/inst/extdata/examples/Psychotria_M1/LGpy_2013/psychotria_M1.results.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M1/LGpy_2013/psychotria_M1.lagrange.py
BioGeoBEARS/inst/extdata/examples/Psychotria_M1/LGpy_2013/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M1/LGpy_2012
BioGeoBEARS/inst/extdata/examples/Psychotria_M1/LGpy_2012/psychotria_M1.results.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M1/LGpy_2012/psychotria_M1.lagrange.py
BioGeoBEARS/inst/extdata/examples/Psychotria_M1/LGpy_2012/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/LGcpp
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_5.2.newick.bgsplits.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_M2strat_lgcpp_out.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_5.2.newick.bgstates.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_geog.data
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_2areas_M2_eastward_only.rm.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_M2_stratified.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_5.2.newick.bgkey.tre
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BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_M2strat.lg
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/BGB
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/BGB/timeperiods.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/BGB/Psychotria_geog.data
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/BGB/dispersal_multipliers.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/BGB/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/LGpy_2013
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/LGpy_2013/psychotria_M2_strat.lagrange.py
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/LGpy_2013/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/LGpy_2013/psychotria_M2_strat.results.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/LGpy_2012
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/LGpy_2012/psychotria_M2_strat.lagrange.py
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/LGpy_2012/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/LGpy_2012/psychotria_M2_strat.results.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M0
BioGeoBEARS/inst/extdata/examples/Psychotria_M0/LGcpp
BioGeoBEARS/inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_5.2.newick.bgsplits.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_5.2.newick.bgstates.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_geog.data
BioGeoBEARS/inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_5.2.newick.bgkey.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_M0_lgcpp_out.txt
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BioGeoBEARS/inst/extdata/examples/Psychotria_M0/BGB/Psychotria_geog.data
BioGeoBEARS/inst/extdata/examples/Psychotria_M0/BGB/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M0/LGpy_2013
BioGeoBEARS/inst/extdata/examples/Psychotria_M0/LGpy_2013/psychotria_M0.lagrange.py
BioGeoBEARS/inst/extdata/examples/Psychotria_M0/LGpy_2013/psychotria_M0.results.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M0/LGpy_2013/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M0/LGpy_2012
BioGeoBEARS/inst/extdata/examples/Psychotria_M0/LGpy_2012/psychotria_M0.lagrange.py
BioGeoBEARS/inst/extdata/examples/Psychotria_M0/LGpy_2012/psychotria_M0.results.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M0/LGpy_2012/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/_generic_run
BioGeoBEARS/inst/extdata/examples/_generic_run/LGcpp
BioGeoBEARS/inst/extdata/examples/_generic_run/LGcpp/tree.newick
BioGeoBEARS/inst/extdata/examples/_generic_run/LGcpp/lg_controls.lg
BioGeoBEARS/inst/extdata/examples/_generic_run/LGcpp/geog.data
BioGeoBEARS/inst/extdata/examples/_generic_run/BGB
BioGeoBEARS/inst/extdata/examples/_generic_run/BGB/tree.newick
BioGeoBEARS/inst/extdata/examples/_generic_run/BGB/geog.data
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/LGcpp
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_5.2.newick.bgsplits.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_M0strat.lg
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BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_geog.data
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_M0strat_lgcpp_out.txt
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BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_5.2.newick
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BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/BGB
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/BGB/timeperiods.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/BGB/Psychotria_geog.data
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/BGB/dispersal_multipliers.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/BGB/areas_allowed_all1s.txt
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BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/LGpy_2013
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/LGpy_2013/psychotria_M0_strat.lagrange.py
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/LGpy_2013/psychotria_M0_strat.results.txt
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BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/LGpy_2012/psychotria_M0_strat.lagrange.py
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/LGpy_2012/psychotria_M0_strat.results.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/LGpy_2012/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/LAGRANGE_example_param_LnL_results.txt
BioGeoBEARS/inst/extdata/examples/Lonicera_M0
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BioGeoBEARS/inst/extdata/examples/Lonicera_M0/LGcpp/Lonicera_M0_lgcpp_out.txt
BioGeoBEARS/inst/extdata/examples/Lonicera_M0/LGcpp/Lonicera.newick
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BioGeoBEARS/inst/extdata/examples/Lonicera_M0/BGB
BioGeoBEARS/inst/extdata/examples/Lonicera_M0/BGB/Psychotria_geog.data
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BioGeoBEARS/inst/extdata/examples/Lonicera_M0/LGpy_2012/Lonicera_M0.results.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M2
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BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_geog.data
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_M3strat_lgcpp_out.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_5.2.newick.bgkey.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/BGB
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/BGB/timeperiods.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/BGB/Psychotria_geog.data
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/BGB/dispersal_multipliers.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/BGB/areas_allowed.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/BGB/areas_allowed_all1s.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/BGB/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGpy_2013
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGpy_2013/psychotria_M3_strat.lagrange.py
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGpy_2013/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGpy_2013/psychotria_M3_strat.results.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGpy_2012
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGpy_2012/psychotria_M3_strat.lagrange.py
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGpy_2012/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGpy_2012/psychotria_M3_strat.results.txt
BioGeoBEARS/inst/extdata/examples/_process_Lagrange_outputs_v1.R
BioGeoBEARS/inst/extdata/Psychotria_detections_v1.txt
BioGeoBEARS/inst/extdata/Psychotria_geog_noAreaNames.data
BioGeoBEARS/inst/extdata/Psychotria_geog.data
BioGeoBEARS/inst/extdata/Psychotria_controls_v1.txt
BioGeoBEARS/inst/extdata/a_scripts
BioGeoBEARS/inst/extdata/a_scripts/BioGeoBEARS_LaplacesDemon_v1.R
BioGeoBEARS/inst/extdata/a_scripts/compare_LAGRANGE_w_BEARS_2param_v01.R
BioGeoBEARS/inst/extdata/a_scripts/plot_phylo3_nodecoords.R
BioGeoBEARS/inst/extdata/a_scripts/testrun.R
BioGeoBEARS/inst/extdata/Psychotria_5.2.newick
BioGeoBEARS/NAMESPACE
BioGeoBEARS/NEWS
BioGeoBEARS/R
BioGeoBEARS/R/BioGeoBEARS_simulate_v1.R BioGeoBEARS/R/calc_loglike_sp_v01.R BioGeoBEARS/R/BioGeoBEARS_models_v1.R BioGeoBEARS/R/BioGeoBEARS_classes_v1.R BioGeoBEARS/R/BioGeoBEARS_readwrite_v1.R BioGeoBEARS/R/BioGeoBEARS_basics_v1.R BioGeoBEARS/R/BioGeoBEARS_plots_v1.R BioGeoBEARS/R/BioGeoBEARS_detection_v1.R BioGeoBEARS/R/BioGeoBEARS_univ_model_v1.R BioGeoBEARS/R/BioGeoBEARS-package.R BioGeoBEARS/R/BioGeoBEARS_generics_v1.R BioGeoBEARS/R/BioGeoBEARS_stratified_v1.R
BioGeoBEARS/MD5
BioGeoBEARS/DESCRIPTION
BioGeoBEARS/man
BioGeoBEARS/man/calc_loglike_for_optim_stratified.Rd BioGeoBEARS/man/make_spmat_row.Rd BioGeoBEARS/man/traverse_up.Rd BioGeoBEARS/man/make_relprob_txtmatrix_sp1.Rd BioGeoBEARS/man/expokit_dgpadm_Qmat2.Rd BioGeoBEARS/man/axisPhylo2.Rd BioGeoBEARS/man/bears_2param_standard_fast_symOnly_simp.Rd BioGeoBEARS/man/get_infparams_optimx_nosim.Rd BioGeoBEARS/man/parse_lagrange_python_output_old.Rd BioGeoBEARS/man/binary_range_to_letter_code_list.Rd BioGeoBEARS/man/get_ML_probs.Rd BioGeoBEARS/man/get_all_daughter_tips_of_a_node.Rd BioGeoBEARS/man/get_ML_states.Rd BioGeoBEARS/man/binary_range_to_letter_code_txt.Rd BioGeoBEARS/man/post_prob_states.Rd BioGeoBEARS/man/bears_3param_standard_fast.Rd BioGeoBEARS/man/unlist_df3.Rd BioGeoBEARS/man/get_ML_state_indices.Rd BioGeoBEARS/man/return_items_not_NA.Rd BioGeoBEARS/man/BioGeoBEARS_model_defaults.Rd BioGeoBEARS/man/BioGeoBEARS_model_object_to_params_upper.Rd BioGeoBEARS/man/bears_3param_standard_fast_noJ.Rd BioGeoBEARS/man/order_tipranges_by_tr.Rd BioGeoBEARS/man/unlist_df.Rd BioGeoBEARS/man/calc_loglike_sp.Rd BioGeoBEARS/man/calc_AICc_vals.Rd BioGeoBEARS/man/read_area_of_areas_fn.Rd BioGeoBEARS/man/get_deltaAIC.Rd BioGeoBEARS/man/plot_BioGeoBEARS_model.Rd BioGeoBEARS/man/relative_probabilities_of_subsets.Rd BioGeoBEARS/man/read_PHYLIP_data.Rd BioGeoBEARS/man/calc_AICc_column.Rd BioGeoBEARS/man/nodenums_bottom_up.Rd BioGeoBEARS/man/define_BioGeoBEARS_run.Rd BioGeoBEARS/man/bears_4param_standard_fast.Rd BioGeoBEARS/man/states_list_indexes_to_areastxt.Rd BioGeoBEARS/man/lrttest.Rd BioGeoBEARS/man/calcP_n.Rd BioGeoBEARS/man/get_nodenums.Rd BioGeoBEARS/man/size_species_matrix.Rd BioGeoBEARS/man/merge_words_nonwords.Rd BioGeoBEARS/man/get_deltaAIC_pairwise_w_ref_model.Rd BioGeoBEARS/man/bears_5param_standard_fast_diffstart.Rd BioGeoBEARS/man/get_daughters.Rd BioGeoBEARS/man/remove_null_rowcols_from_mat.Rd BioGeoBEARS/man/parse_lagrange_python_output.Rd BioGeoBEARS/man/get_nodenum_structural_root.Rd BioGeoBEARS/man/simulated_indexes_to_tipranges_object.Rd BioGeoBEARS/man/order_tipranges_by_tree_tips.Rd BioGeoBEARS/man/prflag.Rd BioGeoBEARS/man/maxsize.Rd BioGeoBEARS/man/BioGeoBEARS_model_object_to_est_params.Rd BioGeoBEARS/man/lrttest_on_summary_table.Rd BioGeoBEARS/man/printall.Rd BioGeoBEARS/man/section_the_tree.Rd BioGeoBEARS/man/get_parent.Rd BioGeoBEARS/man/get_TF_tips.Rd BioGeoBEARS/man/simulated_indexes_to_tipranges_file.Rd BioGeoBEARS/man/symbolic_to_P_matrix.Rd BioGeoBEARS/man/moref.Rd BioGeoBEARS/man/post_prob_states_matrix.Rd BioGeoBEARS/man/get_APE_nodenums.Rd BioGeoBEARS/man/symbolic_to_relprob_matrix_sp.Rd BioGeoBEARS/man/AICstats_2models.Rd BioGeoBEARS/man/get_level.Rd BioGeoBEARS/man/readfiles_BioGeoBEARS_run.Rd BioGeoBEARS/man/rangestxt_to_colors.Rd BioGeoBEARS/man/bears_2param_standard_fast.Rd BioGeoBEARS/man/colors_legend.Rd BioGeoBEARS/man/tipranges_to_area_strings.Rd BioGeoBEARS/man/symbolic_cell_to_relprob_cell.Rd BioGeoBEARS/man/read_distances_fn.Rd BioGeoBEARS/man/mapply_likelihoods.Rd BioGeoBEARS/man/get_Akaike_weights_from_rel_likes_pairwise.Rd BioGeoBEARS/man/bears_2param_DIVA_fast.Rd BioGeoBEARS/man/prob_of_states_from_prior_prob_areas.Rd BioGeoBEARS/man/relative_probabilities_of_vicariants.Rd BioGeoBEARS/man/match_list1_in_list2.Rd BioGeoBEARS/man/get_relative_prob_model2old.Rd BioGeoBEARS/man/get_indices_of_tip_nodes.Rd BioGeoBEARS/man/map_LG_MLsplits_to_tree_corners.Rd BioGeoBEARS/man/getAICc.Rd BioGeoBEARS/man/process_optim.Rd BioGeoBEARS/man/BioGeoBEARS-package.Rd BioGeoBEARS/man/get_inf_LgL_etc_optimx.Rd BioGeoBEARS/man/extend_tips_to_ultrametricize.Rd BioGeoBEARS/man/mapply_likelihoods_prebyte.Rd BioGeoBEARS/man/get_perEvent_probs.Rd BioGeoBEARS/man/calc_prob_forward_onebranch_dense.Rd BioGeoBEARS/man/read_times_fn.Rd BioGeoBEARS/man/calc_prob_forward_onebranch_sparse.Rd BioGeoBEARS/man/AkaikeWeights_and_Ratios_pairwise_on_summary_table_compared_to_ref.Rd BioGeoBEARS/man/LGpy_MLsplit_per_node.Rd BioGeoBEARS/man/get_simstates.Rd BioGeoBEARS/man/get_indices_where_list1_occurs_in_list2_noNA.Rd BioGeoBEARS/man/get_edge_times_before_present.Rd BioGeoBEARS/man/read_detections.Rd BioGeoBEARS/man/conditional_format_cell.Rd BioGeoBEARS/man/LGpy_splits_fn_to_table.Rd BioGeoBEARS/man/add_to_downpass_labels.Rd BioGeoBEARS/man/get_indices_where_list1_occurs_in_list2.Rd BioGeoBEARS/man/adf2.Rd BioGeoBEARS/man/adf.Rd BioGeoBEARS/man/order_LGnodes.Rd BioGeoBEARS/man/mapply_calc_post_prob_presence.Rd BioGeoBEARS/man/define_BioGeoBEARS_model_object.Rd BioGeoBEARS/man/prt_tree_to_phylo4.Rd BioGeoBEARS/man/read_areas_allowed_fn.Rd BioGeoBEARS/man/getAIC_weight_for_model1.Rd BioGeoBEARS/man/BioGeoBEARS_model_object_to_params_lower.Rd BioGeoBEARS/man/LGcpp_MLstate_per_node.Rd BioGeoBEARS/man/read_controls.Rd BioGeoBEARS/man/postorder_nodes_phylo4_return_table.Rd BioGeoBEARS/man/get_pruningwise_nodenums.Rd BioGeoBEARS/man/Pdata_given_rangerow_dp.Rd BioGeoBEARS/man/cornerlabels.Rd BioGeoBEARS/man/AkaikeWeights_on_summary_table.Rd BioGeoBEARS/man/get_Akaike_weight_ratio_from_Akaike_pairwise_weights.Rd BioGeoBEARS/man/check_if_state_is_allowed.Rd BioGeoBEARS/man/calcZ_part.Rd BioGeoBEARS/man/get_all_node_ages.Rd BioGeoBEARS/man/prt.Rd BioGeoBEARS/man/sourceall.Rd BioGeoBEARS/man/make_relprob_matrix_de.Rd BioGeoBEARS/man/calc_AIC_column.Rd BioGeoBEARS/man/read_dispersal_multipliers_fn.Rd BioGeoBEARS/man/is.not.na.Rd BioGeoBEARS/man/unlist_dtf_cols.Rd BioGeoBEARS/man/slashslash.Rd BioGeoBEARS/man/get_AICweight_ratio_model1_over_model2.Rd BioGeoBEARS/man/plot_BioGeoBEARS_results.Rd BioGeoBEARS/man/expokit_dgpadm_Qmat2_prebyte.Rd BioGeoBEARS/man/tipranges_to_tip_condlikes_of_data_on_each_state.Rd BioGeoBEARS/man/get_indices_of_branches_under_tips.Rd BioGeoBEARS/man/get_node_ages_of_tips.Rd BioGeoBEARS/man/pdfit.Rd BioGeoBEARS/man/get_lagrange_nodenums.Rd BioGeoBEARS/man/tiplikes_wDetectionModel.Rd BioGeoBEARS/man/make_relprob_nummatrix_sp1.Rd BioGeoBEARS/man/getranges_from_LagrangePHYLIP.Rd BioGeoBEARS/man/findall.Rd BioGeoBEARS/man/get_max_height_tree.Rd BioGeoBEARS/man/LGcpp_splits_fn_to_table.Rd BioGeoBEARS/man/get_fn_prefix.Rd BioGeoBEARS/man/calc_loglike_for_optim.Rd BioGeoBEARS/man/unlist_df2.Rd BioGeoBEARS/man/prune_specimens_to_species.Rd BioGeoBEARS/man/LGcpp_states_fn_to_table.Rd BioGeoBEARS/man/rel_likes_from_deltaAICs.Rd BioGeoBEARS/man/get_tiplabel_ranges.Rd BioGeoBEARS/man/parse_lagrange_output_old.Rd BioGeoBEARS/man/LGcpp_splits_fn_to_table2.Rd BioGeoBEARS/man/unlist_df4.Rd BioGeoBEARS/man/map_LGpy_MLsplits_to_tree.Rd BioGeoBEARS/man/calc_post_prob_presence.Rd BioGeoBEARS/man/cornerpies.Rd BioGeoBEARS/man/parse_lagrange_output.Rd BioGeoBEARS/man/expand.grid.alt.Rd BioGeoBEARS/man/make_dispersal_multiplier_matrix.Rd BioGeoBEARS/man/get_infprobs_of_simstates.Rd BioGeoBEARS/man/getAIC.Rd BioGeoBEARS/man/addslash.Rd BioGeoBEARS/man/average_tr_tips.Rd BioGeoBEARS/man/dfnums_to_numeric.Rd BioGeoBEARS/man/infprobs_to_probs_of_each_area.Rd BioGeoBEARS/man/mix_colors_for_states.Rd BioGeoBEARS/man/get_ML_states_from_relprobs.Rd BioGeoBEARS/man/meval.Rd BioGeoBEARS/man/check_BioGeoBEARS_run.Rd BioGeoBEARS/man/binary_ranges_to_letter_codes.Rd BioGeoBEARS/man/symbolic_cell_to_relprob_cell_sp.Rd BioGeoBEARS/man/expand.grid.jc.Rd BioGeoBEARS/man/calc_AIC_vals.Rd BioGeoBEARS/man/symbolic_to_Q_matrix_exper.Rd BioGeoBEARS/man/given_a_starting_state_simulate_branch_end.Rd BioGeoBEARS/man/nullsym_to_NA.Rd BioGeoBEARS/man/get_probvals.Rd BioGeoBEARS/man/get_statesColors_table.Rd BioGeoBEARS/man/calc_loglike_sp_stratified.Rd BioGeoBEARS/man/paste_rows_without_zeros.Rd BioGeoBEARS/man/calc_linked_params_BioGeoBEARS_model_object.Rd BioGeoBEARS/man/strsplit2.Rd BioGeoBEARS/man/get_leftright_nodes_matrix_from_results.Rd BioGeoBEARS/man/bears_3param_standard_fast_fixnode.Rd BioGeoBEARS/man/letter_string_to_binary.Rd BioGeoBEARS/man/prune_states_list.Rd BioGeoBEARS/man/simstates_to_probs_of_each_area.Rd BioGeoBEARS/man/tipranges-class.Rd BioGeoBEARS/man/mapply_calc_obs_like.Rd BioGeoBEARS/man/divide_probs_by_number_of_options_txt.Rd BioGeoBEARS/man/bears_2param_standard_fast_fortest.Rd BioGeoBEARS/man/BioGeoBEARS_run-class.Rd BioGeoBEARS/man/get_sister_node.Rd BioGeoBEARS/man/Pdata_given_rangerow.Rd BioGeoBEARS/man/divide_probs_by_number_of_options_nums.Rd BioGeoBEARS/man/calc_loglike_sp_prebyte.Rd BioGeoBEARS/man/corner_coords.Rd BioGeoBEARS/man/vfunc.Rd BioGeoBEARS/man/rel_likes_from_deltaAICs_pairwise.Rd BioGeoBEARS/man/bears_2param_standard_slowQ_slowSP.Rd BioGeoBEARS/man/get_relative_prob_model1old.Rd BioGeoBEARS/man/extract_numbers.Rd BioGeoBEARS/man/bears_9param_standard_fast_ys_v_cb.Rd BioGeoBEARS/man/get_path_last.Rd BioGeoBEARS/man/get_path_first.Rd BioGeoBEARS/man/bears_5param_standard_fast_v.Rd BioGeoBEARS/man/get_Akaike_weights_from_rel_likes.Rd BioGeoBEARS/man/bears_5param_standard_fast.Rd BioGeoBEARS/man/list2str.Rd BioGeoBEARS/man/letter_strings_to_tipranges_df.Rd BioGeoBEARS/man/bears_2param_standard_fast_fixnode.Rd BioGeoBEARS/man/chainsaw2.Rd BioGeoBEARS/man/plot_cladogenesis_size_probabilities.Rd BioGeoBEARS/man/normat.Rd BioGeoBEARS/man/get_rownum_ref_model.Rd BioGeoBEARS/man/infprobs_to_probs_of_each_area_from_relprobs.Rd BioGeoBEARS/man/make_relprob_matrix_bi.Rd BioGeoBEARS/man/sfunc.Rd BioGeoBEARS/man/params_into_BioGeoBEARS_model_object.Rd BioGeoBEARS/man/BioGeoBEARS_model-class.Rd BioGeoBEARS/man/BioGeoBEARS_model_object_to_init_params.Rd BioGeoBEARS/man/areas_list_to_states_list_new.Rd BioGeoBEARS/man/yfunc.Rd BioGeoBEARS/man/get_simparams.Rd BioGeoBEARS/man/save_tipranges_to_LagrangePHYLIP.Rd BioGeoBEARS/man/cls.df.Rd BioGeoBEARS/man/symbolic_to_Q_matrix.Rd BioGeoBEARS/man/get_MLsplitprobs_from_results.Rd BioGeoBEARS/man/default_states_list.Rd BioGeoBEARS/man/map_LG_MLsplits_to_tree.Rd BioGeoBEARS/man/simulate_biogeog_history.Rd BioGeoBEARS/man/label_nodes_postorder_phylo3.Rd BioGeoBEARS/man/add_corners.Rd BioGeoBEARS/man/get_infparams_optimx.Rd BioGeoBEARS/man/define_tipranges_object.Rd BioGeoBEARS/man/conditional_format_table.Rd BioGeoBEARS/man/given_a_starting_state_simulate_split.Rd BioGeoBEARS/man/get_colors_for_numareas.Rd BioGeoBEARS/man/bears_2param_standard_fast_symOnly.Rd BioGeoBEARS/man/bears_optim_run.Rd BioGeoBEARS/man/calc_obs_like.Rd BioGeoBEARS/man/np.Rd BioGeoBEARS/man/bears_6param_standard_fast_ys_v.Rd BioGeoBEARS/man/strsplit_whitespace.Rd BioGeoBEARS/man/getareas_from_tipranges_object.Rd BioGeoBEARS/man/getname.Rd BioGeoBEARS/man/pdftable.Rd BioGeoBEARS/man/map_LG_MLstates_to_tree.Rd

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