BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts
Version 0.2.1

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
URL http://phylo.wikidot.com/biogeobears
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("BioGeoBEARS")

Getting started

Package overview

Popular man pages

AICstats_2models: Calculate all the AIC and LRT stats between two models
calc_loglike_sp_stratified: Calculate log-likelihood with a transition matrix and...
expand.grid.alt: A faster version of expand.grid
getAIC: Calculate AIC
get_ML_states_from_relprobs: Extract the ML states at each node, from a table of relative...
LGcpp_splits_fn_to_table: Get the ML splits per node, from C++ LAGRANGE output
plot_BioGeoBEARS_results: Plot the results of a BioGeoBEARS run
See all...

All man pages Function index File listing

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

Files

inst
inst/CITATION
inst/REFERENCES.bib
inst/extdata
inst/extdata/examples
inst/extdata/examples/Cyrtandra_M0
inst/extdata/examples/Cyrtandra_M0/LGcpp
inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra.newick.bgkey.tre
inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra.newick.bgstates.tre
inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra_M0.lg
inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra.newick
inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra.newick.bgsplits.tre
inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra_geog.data
inst/extdata/examples/Cyrtandra_M0/LGcpp/Cyrtandra_M0_lgcpp_out.txt
inst/extdata/examples/Cyrtandra_M0/BGB
inst/extdata/examples/Cyrtandra_M0/BGB/Psychotria_geog.data
inst/extdata/examples/Cyrtandra_M0/BGB/Psychotria_5.2.newick
inst/extdata/examples/Cyrtandra_M0/LGpy_2013
inst/extdata/examples/Cyrtandra_M0/LGpy_2013/Cyrtandra_M0.lagrange.py
inst/extdata/examples/Cyrtandra_M0/LGpy_2013/Cyrtandra.newick
inst/extdata/examples/Cyrtandra_M0/LGpy_2013/Cyrtandra_M0.results.txt
inst/extdata/examples/Cyrtandra_M0/LGpy_2013/Cyrtandra_M0.results-1.txt
inst/extdata/examples/Cyrtandra_M0/LGpy_2012
inst/extdata/examples/Cyrtandra_M0/LGpy_2012/Cyrtandra_M0.lagrange.py
inst/extdata/examples/Cyrtandra_M0/LGpy_2012/Cyrtandra.newick
inst/extdata/examples/Cyrtandra_M0/LGpy_2012/Cyrtandra_M0.results.txt
inst/extdata/examples/Cyrtandra_M0/LGpy_2012/Cyrtandra_M0.results-1.txt
inst/extdata/examples/Psychotria_M1strat
inst/extdata/examples/Psychotria_M1strat/LGcpp
inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_5.2.newick.bgsplits.tre
inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_5.2.newick.bgstates.tre
inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_geog.data
inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_M1strat_lgcpp_out.txt
inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_5.2.newick.bgkey.tre
inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_M1_stratified.txt
inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M1strat/LGcpp/Psychotria_M1strat.lg
inst/extdata/examples/Psychotria_M1strat/BGB
inst/extdata/examples/Psychotria_M1strat/BGB/timeperiods.txt
inst/extdata/examples/Psychotria_M1strat/BGB/Psychotria_geog.data
inst/extdata/examples/Psychotria_M1strat/BGB/dispersal_multipliers.txt
inst/extdata/examples/Psychotria_M1strat/BGB/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M1strat/LGpy_2013
inst/extdata/examples/Psychotria_M1strat/LGpy_2013/psychotria_M1_strat.lagrange.py
inst/extdata/examples/Psychotria_M1strat/LGpy_2013/psychotria_M1_strat.results.txt
inst/extdata/examples/Psychotria_M1strat/LGpy_2013/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M1strat/LGpy_2012
inst/extdata/examples/Psychotria_M1strat/LGpy_2012/psychotria_M1_strat.lagrange.py
inst/extdata/examples/Psychotria_M1strat/LGpy_2012/psychotria_M1_strat.results.txt
inst/extdata/examples/Psychotria_M1strat/LGpy_2012/Psychotria_5.2.newick
inst/extdata/examples/_run_LAGRANGE_examples_v1.txt
inst/extdata/examples/Psychotria_M1
inst/extdata/examples/Psychotria_M1/LGcpp
inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_5.2.newick.bgsplits.tre
inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_M1.lg
inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_5.2.newick.bgstates.tre
inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_geog.data
inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_5.2.newick.bgkey.tre
inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_M1_lgcpp_out.txt
inst/extdata/examples/Psychotria_M1/BGB
inst/extdata/examples/Psychotria_M1/BGB/Psychotria_geog.data
inst/extdata/examples/Psychotria_M1/BGB/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M1/LGpy_2013
inst/extdata/examples/Psychotria_M1/LGpy_2013/psychotria_M1.results.txt
inst/extdata/examples/Psychotria_M1/LGpy_2013/psychotria_M1.lagrange.py
inst/extdata/examples/Psychotria_M1/LGpy_2013/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M1/LGpy_2012
inst/extdata/examples/Psychotria_M1/LGpy_2012/psychotria_M1.results.txt
inst/extdata/examples/Psychotria_M1/LGpy_2012/psychotria_M1.lagrange.py
inst/extdata/examples/Psychotria_M1/LGpy_2012/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M2strat
inst/extdata/examples/Psychotria_M2strat/LGcpp
inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_5.2.newick.bgsplits.tre
inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_M2strat_lgcpp_out.txt
inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_5.2.newick.bgstates.tre
inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_geog.data
inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_2areas_M2_eastward_only.rm.txt
inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_M2_stratified.txt
inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_5.2.newick.bgkey.tre
inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_M2strat.lg
inst/extdata/examples/Psychotria_M2strat/BGB
inst/extdata/examples/Psychotria_M2strat/BGB/timeperiods.txt
inst/extdata/examples/Psychotria_M2strat/BGB/Psychotria_geog.data
inst/extdata/examples/Psychotria_M2strat/BGB/dispersal_multipliers.txt
inst/extdata/examples/Psychotria_M2strat/BGB/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M2strat/LGpy_2013
inst/extdata/examples/Psychotria_M2strat/LGpy_2013/psychotria_M2_strat.lagrange.py
inst/extdata/examples/Psychotria_M2strat/LGpy_2013/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M2strat/LGpy_2013/psychotria_M2_strat.results.txt
inst/extdata/examples/Psychotria_M2strat/LGpy_2012
inst/extdata/examples/Psychotria_M2strat/LGpy_2012/psychotria_M2_strat.lagrange.py
inst/extdata/examples/Psychotria_M2strat/LGpy_2012/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M2strat/LGpy_2012/psychotria_M2_strat.results.txt
inst/extdata/examples/Psychotria_M0
inst/extdata/examples/Psychotria_M0/LGcpp
inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_5.2.newick.bgsplits.tre
inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_5.2.newick.bgstates.tre
inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_geog.data
inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_5.2.newick.bgkey.tre
inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_M0_lgcpp_out.txt
inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_M0.lg
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inst/extdata/examples/Psychotria_M0/BGB/Psychotria_geog.data
inst/extdata/examples/Psychotria_M0/BGB/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M0/LGpy_2013
inst/extdata/examples/Psychotria_M0/LGpy_2013/psychotria_M0.lagrange.py
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inst/extdata/examples/Psychotria_M0/LGpy_2013/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M0/LGpy_2012
inst/extdata/examples/Psychotria_M0/LGpy_2012/psychotria_M0.lagrange.py
inst/extdata/examples/Psychotria_M0/LGpy_2012/psychotria_M0.results.txt
inst/extdata/examples/Psychotria_M0/LGpy_2012/Psychotria_5.2.newick
inst/extdata/examples/_generic_run
inst/extdata/examples/_generic_run/LGcpp
inst/extdata/examples/_generic_run/LGcpp/tree.newick
inst/extdata/examples/_generic_run/LGcpp/lg_controls.lg
inst/extdata/examples/_generic_run/LGcpp/geog.data
inst/extdata/examples/_generic_run/BGB
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inst/extdata/examples/_generic_run/BGB/geog.data
inst/extdata/examples/Psychotria_M0strat
inst/extdata/examples/Psychotria_M0strat/LGcpp
inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_5.2.newick.bgsplits.tre
inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_M0strat.lg
inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_5.2.newick.bgstates.tre
inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_geog.data
inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_M0strat_lgcpp_out.txt
inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_5.2.newick.bgkey.tre
inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_M0_stratified.txt
inst/extdata/examples/Psychotria_M0strat/BGB
inst/extdata/examples/Psychotria_M0strat/BGB/timeperiods.txt
inst/extdata/examples/Psychotria_M0strat/BGB/Psychotria_geog.data
inst/extdata/examples/Psychotria_M0strat/BGB/dispersal_multipliers.txt
inst/extdata/examples/Psychotria_M0strat/BGB/areas_allowed_all1s.txt
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inst/extdata/examples/Psychotria_M0strat/LGpy_2013
inst/extdata/examples/Psychotria_M0strat/LGpy_2013/psychotria_M0_strat.lagrange.py
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inst/extdata/examples/Psychotria_M0strat/LGpy_2013/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M0strat/LGpy_2012
inst/extdata/examples/Psychotria_M0strat/LGpy_2012/psychotria_M0_strat.lagrange.py
inst/extdata/examples/Psychotria_M0strat/LGpy_2012/psychotria_M0_strat.results.txt
inst/extdata/examples/Psychotria_M0strat/LGpy_2012/Psychotria_5.2.newick
inst/extdata/examples/LAGRANGE_example_param_LnL_results.txt
inst/extdata/examples/Lonicera_M0
inst/extdata/examples/Lonicera_M0/LGcpp
inst/extdata/examples/Lonicera_M0/LGcpp/Lonicera_M0.lg
inst/extdata/examples/Lonicera_M0/LGcpp/Lonicera_M0_lgcpp_out.txt
inst/extdata/examples/Lonicera_M0/LGcpp/Lonicera.newick
inst/extdata/examples/Lonicera_M0/LGcpp/Lonicera_M0_lgcpp_out_orig.txt
inst/extdata/examples/Lonicera_M0/BGB
inst/extdata/examples/Lonicera_M0/BGB/Psychotria_geog.data
inst/extdata/examples/Lonicera_M0/BGB/Psychotria_5.2.newick
inst/extdata/examples/Lonicera_M0/LGpy_2013
inst/extdata/examples/Lonicera_M0/LGpy_2013/Lonicera_M0.results-1.txt
inst/extdata/examples/Lonicera_M0/LGpy_2013/Lonicera.newick
inst/extdata/examples/Lonicera_M0/LGpy_2013/Lonicera_M0.lagrange.py
inst/extdata/examples/Lonicera_M0/LGpy_2013/Lonicera_M0.results.txt
inst/extdata/examples/Lonicera_M0/LGpy_2012
inst/extdata/examples/Lonicera_M0/LGpy_2012/Lonicera_M0.results-1.txt
inst/extdata/examples/Lonicera_M0/LGpy_2012/Lonicera.newick
inst/extdata/examples/Lonicera_M0/LGpy_2012/Lonicera_M0.lagrange.py
inst/extdata/examples/Lonicera_M0/LGpy_2012/Lonicera_M0.results_orig.txt
inst/extdata/examples/Lonicera_M0/LGpy_2012/Lonicera_M0.results.txt
inst/extdata/examples/Psychotria_M2
inst/extdata/examples/Psychotria_M2/LGcpp
inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_5.2.newick.bgsplits.tre
inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_5.2.newick.bgstates.tre
inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_M2.lg
inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_geog.data
inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_2areas_M2_eastward_only.rm.txt
inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_5.2.newick.bgkey.tre
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inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_M2_lgcpp_out.txt
inst/extdata/examples/Psychotria_M2/BGB
inst/extdata/examples/Psychotria_M2/BGB/Psychotria_geog.data
inst/extdata/examples/Psychotria_M2/BGB/dispersal_multipliers.txt
inst/extdata/examples/Psychotria_M2/BGB/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M2/LGpy_2013
inst/extdata/examples/Psychotria_M2/LGpy_2013/psychotria_M2.results.txt
inst/extdata/examples/Psychotria_M2/LGpy_2013/psychotria_M2.lagrange.py
inst/extdata/examples/Psychotria_M2/LGpy_2013/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M2/LGpy_2012
inst/extdata/examples/Psychotria_M2/LGpy_2012/psychotria_M2.results.txt
inst/extdata/examples/Psychotria_M2/LGpy_2012/psychotria_M2.lagrange.py
inst/extdata/examples/Psychotria_M2/LGpy_2012/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M3strat
inst/extdata/examples/Psychotria_M3strat/LGcpp
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_5.2.newick.bgsplits.tre
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_M3strat.lg
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_M3_stratified.txt
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inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_geog.data
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_M3strat_lgcpp_out.txt
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_5.2.newick.bgkey.tre
inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_5.2.newick.bgsplits.tre
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_M3strat.lg
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_M3_stratified.txt
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_5.2.newick.bgstates.tre
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_geog.data
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_M3strat_lgcpp_out.txt
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_5.2.newick.bgkey.tre
inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M3strat/BGB
inst/extdata/examples/Psychotria_M3strat/BGB/timeperiods.txt
inst/extdata/examples/Psychotria_M3strat/BGB/Psychotria_geog.data
inst/extdata/examples/Psychotria_M3strat/BGB/dispersal_multipliers.txt
inst/extdata/examples/Psychotria_M3strat/BGB/areas_allowed.txt
inst/extdata/examples/Psychotria_M3strat/BGB/areas_allowed_all1s.txt
inst/extdata/examples/Psychotria_M3strat/BGB/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M3strat/LGpy_2013
inst/extdata/examples/Psychotria_M3strat/LGpy_2013/psychotria_M3_strat.lagrange.py
inst/extdata/examples/Psychotria_M3strat/LGpy_2013/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M3strat/LGpy_2013/psychotria_M3_strat.results.txt
inst/extdata/examples/Psychotria_M3strat/LGpy_2012
inst/extdata/examples/Psychotria_M3strat/LGpy_2012/psychotria_M3_strat.lagrange.py
inst/extdata/examples/Psychotria_M3strat/LGpy_2012/Psychotria_5.2.newick
inst/extdata/examples/Psychotria_M3strat/LGpy_2012/psychotria_M3_strat.results.txt
inst/extdata/examples/_process_Lagrange_outputs_v1.R
inst/extdata/Psychotria_detections_v1.txt
inst/extdata/Psychotria_geog_noAreaNames.data
inst/extdata/Psychotria_geog.data
inst/extdata/Psychotria_controls_v1.txt
inst/extdata/a_scripts
inst/extdata/a_scripts/BioGeoBEARS_LaplacesDemon_v1.R
inst/extdata/a_scripts/compare_LAGRANGE_w_BEARS_2param_v01.R
inst/extdata/a_scripts/plot_phylo3_nodecoords.R
inst/extdata/a_scripts/testrun.R
inst/extdata/Psychotria_5.2.newick
NAMESPACE
NEWS
R
R/BioGeoBEARS_simulate_v1.R
R/calc_loglike_sp_v01.R
R/BioGeoBEARS_models_v1.R
R/BioGeoBEARS_classes_v1.R
R/BioGeoBEARS_readwrite_v1.R
R/BioGeoBEARS_basics_v1.R
R/BioGeoBEARS_plots_v1.R
R/BioGeoBEARS_detection_v1.R
R/BioGeoBEARS_univ_model_v1.R
R/BioGeoBEARS-package.R
R/BioGeoBEARS_generics_v1.R
R/BioGeoBEARS_stratified_v1.R
MD5
DESCRIPTION
man
man/calc_loglike_for_optim_stratified.Rd
man/make_spmat_row.Rd
man/traverse_up.Rd
man/make_relprob_txtmatrix_sp1.Rd
man/expokit_dgpadm_Qmat2.Rd
man/axisPhylo2.Rd
man/bears_2param_standard_fast_symOnly_simp.Rd
man/get_infparams_optimx_nosim.Rd
man/parse_lagrange_python_output_old.Rd
man/binary_range_to_letter_code_list.Rd
man/get_ML_probs.Rd
man/get_all_daughter_tips_of_a_node.Rd
man/get_ML_states.Rd
man/binary_range_to_letter_code_txt.Rd
man/post_prob_states.Rd
man/bears_3param_standard_fast.Rd
man/unlist_df3.Rd
man/get_ML_state_indices.Rd
man/return_items_not_NA.Rd
man/BioGeoBEARS_model_defaults.Rd
man/BioGeoBEARS_model_object_to_params_upper.Rd
man/bears_3param_standard_fast_noJ.Rd
man/order_tipranges_by_tr.Rd
man/unlist_df.Rd
man/calc_loglike_sp.Rd
man/calc_AICc_vals.Rd
man/read_area_of_areas_fn.Rd
man/get_deltaAIC.Rd
man/plot_BioGeoBEARS_model.Rd
man/relative_probabilities_of_subsets.Rd
man/read_PHYLIP_data.Rd
man/calc_AICc_column.Rd
man/nodenums_bottom_up.Rd
man/define_BioGeoBEARS_run.Rd
man/bears_4param_standard_fast.Rd
man/states_list_indexes_to_areastxt.Rd
man/lrttest.Rd
man/calcP_n.Rd
man/get_nodenums.Rd
man/size_species_matrix.Rd
man/merge_words_nonwords.Rd
man/get_deltaAIC_pairwise_w_ref_model.Rd
man/bears_5param_standard_fast_diffstart.Rd
man/get_daughters.Rd
man/remove_null_rowcols_from_mat.Rd
man/parse_lagrange_python_output.Rd
man/get_nodenum_structural_root.Rd
man/simulated_indexes_to_tipranges_object.Rd
man/order_tipranges_by_tree_tips.Rd
man/prflag.Rd
man/maxsize.Rd
man/BioGeoBEARS_model_object_to_est_params.Rd
man/lrttest_on_summary_table.Rd
man/printall.Rd
man/section_the_tree.Rd
man/get_parent.Rd
man/get_TF_tips.Rd
man/simulated_indexes_to_tipranges_file.Rd
man/symbolic_to_P_matrix.Rd
man/moref.Rd
man/post_prob_states_matrix.Rd
man/get_APE_nodenums.Rd
man/symbolic_to_relprob_matrix_sp.Rd
man/AICstats_2models.Rd
man/get_level.Rd
man/readfiles_BioGeoBEARS_run.Rd
man/rangestxt_to_colors.Rd
man/bears_2param_standard_fast.Rd
man/colors_legend.Rd
man/tipranges_to_area_strings.Rd
man/symbolic_cell_to_relprob_cell.Rd
man/read_distances_fn.Rd
man/mapply_likelihoods.Rd
man/get_Akaike_weights_from_rel_likes_pairwise.Rd
man/bears_2param_DIVA_fast.Rd
man/prob_of_states_from_prior_prob_areas.Rd
man/relative_probabilities_of_vicariants.Rd
man/match_list1_in_list2.Rd
man/get_relative_prob_model2old.Rd
man/get_indices_of_tip_nodes.Rd
man/map_LG_MLsplits_to_tree_corners.Rd
man/getAICc.Rd
man/process_optim.Rd
man/BioGeoBEARS-package.Rd
man/get_inf_LgL_etc_optimx.Rd
man/extend_tips_to_ultrametricize.Rd
man/mapply_likelihoods_prebyte.Rd
man/get_perEvent_probs.Rd
man/calc_prob_forward_onebranch_dense.Rd
man/read_times_fn.Rd
man/calc_prob_forward_onebranch_sparse.Rd
man/AkaikeWeights_and_Ratios_pairwise_on_summary_table_compared_to_ref.Rd
man/LGpy_MLsplit_per_node.Rd
man/get_simstates.Rd
man/get_indices_where_list1_occurs_in_list2_noNA.Rd
man/get_edge_times_before_present.Rd
man/read_detections.Rd
man/conditional_format_cell.Rd
man/LGpy_splits_fn_to_table.Rd
man/add_to_downpass_labels.Rd
man/get_indices_where_list1_occurs_in_list2.Rd
man/adf2.Rd
man/adf.Rd
man/order_LGnodes.Rd
man/mapply_calc_post_prob_presence.Rd
man/define_BioGeoBEARS_model_object.Rd
man/prt_tree_to_phylo4.Rd
man/read_areas_allowed_fn.Rd
man/getAIC_weight_for_model1.Rd
man/BioGeoBEARS_model_object_to_params_lower.Rd
man/LGcpp_MLstate_per_node.Rd
man/read_controls.Rd
man/postorder_nodes_phylo4_return_table.Rd
man/get_pruningwise_nodenums.Rd
man/Pdata_given_rangerow_dp.Rd
man/cornerlabels.Rd
man/AkaikeWeights_on_summary_table.Rd
man/get_Akaike_weight_ratio_from_Akaike_pairwise_weights.Rd
man/check_if_state_is_allowed.Rd
man/calcZ_part.Rd
man/get_all_node_ages.Rd
man/prt.Rd
man/sourceall.Rd
man/make_relprob_matrix_de.Rd
man/calc_AIC_column.Rd
man/read_dispersal_multipliers_fn.Rd
man/is.not.na.Rd
man/unlist_dtf_cols.Rd
man/slashslash.Rd
man/get_AICweight_ratio_model1_over_model2.Rd
man/plot_BioGeoBEARS_results.Rd
man/expokit_dgpadm_Qmat2_prebyte.Rd
man/tipranges_to_tip_condlikes_of_data_on_each_state.Rd
man/get_indices_of_branches_under_tips.Rd
man/get_node_ages_of_tips.Rd
man/pdfit.Rd
man/get_lagrange_nodenums.Rd
man/tiplikes_wDetectionModel.Rd
man/make_relprob_nummatrix_sp1.Rd
man/getranges_from_LagrangePHYLIP.Rd
man/findall.Rd
man/get_max_height_tree.Rd
man/LGcpp_splits_fn_to_table.Rd
man/get_fn_prefix.Rd
man/calc_loglike_for_optim.Rd
man/unlist_df2.Rd
man/prune_specimens_to_species.Rd
man/LGcpp_states_fn_to_table.Rd
man/rel_likes_from_deltaAICs.Rd
man/get_tiplabel_ranges.Rd
man/parse_lagrange_output_old.Rd
man/LGcpp_splits_fn_to_table2.Rd
man/unlist_df4.Rd
man/map_LGpy_MLsplits_to_tree.Rd
man/calc_post_prob_presence.Rd
man/cornerpies.Rd
man/parse_lagrange_output.Rd
man/expand.grid.alt.Rd
man/make_dispersal_multiplier_matrix.Rd
man/get_infprobs_of_simstates.Rd
man/getAIC.Rd
man/addslash.Rd
man/average_tr_tips.Rd
man/dfnums_to_numeric.Rd
man/infprobs_to_probs_of_each_area.Rd
man/mix_colors_for_states.Rd
man/get_ML_states_from_relprobs.Rd
man/meval.Rd
man/check_BioGeoBEARS_run.Rd
man/binary_ranges_to_letter_codes.Rd
man/symbolic_cell_to_relprob_cell_sp.Rd
man/expand.grid.jc.Rd
man/calc_AIC_vals.Rd
man/symbolic_to_Q_matrix_exper.Rd
man/given_a_starting_state_simulate_branch_end.Rd
man/nullsym_to_NA.Rd
man/get_probvals.Rd
man/get_statesColors_table.Rd
man/calc_loglike_sp_stratified.Rd
man/paste_rows_without_zeros.Rd
man/calc_linked_params_BioGeoBEARS_model_object.Rd
man/strsplit2.Rd
man/get_leftright_nodes_matrix_from_results.Rd
man/bears_3param_standard_fast_fixnode.Rd
man/letter_string_to_binary.Rd
man/prune_states_list.Rd
man/simstates_to_probs_of_each_area.Rd
man/tipranges-class.Rd
man/mapply_calc_obs_like.Rd
man/divide_probs_by_number_of_options_txt.Rd
man/bears_2param_standard_fast_fortest.Rd
man/BioGeoBEARS_run-class.Rd
man/get_sister_node.Rd
man/Pdata_given_rangerow.Rd
man/divide_probs_by_number_of_options_nums.Rd
man/calc_loglike_sp_prebyte.Rd
man/corner_coords.Rd
man/vfunc.Rd
man/rel_likes_from_deltaAICs_pairwise.Rd
man/bears_2param_standard_slowQ_slowSP.Rd
man/get_relative_prob_model1old.Rd
man/extract_numbers.Rd
man/bears_9param_standard_fast_ys_v_cb.Rd
man/get_path_last.Rd
man/get_path_first.Rd
man/bears_5param_standard_fast_v.Rd
man/get_Akaike_weights_from_rel_likes.Rd
man/bears_5param_standard_fast.Rd
man/list2str.Rd
man/letter_strings_to_tipranges_df.Rd
man/bears_2param_standard_fast_fixnode.Rd
man/chainsaw2.Rd
man/plot_cladogenesis_size_probabilities.Rd
man/normat.Rd
man/get_rownum_ref_model.Rd
man/infprobs_to_probs_of_each_area_from_relprobs.Rd
man/make_relprob_matrix_bi.Rd
man/sfunc.Rd
man/params_into_BioGeoBEARS_model_object.Rd
man/BioGeoBEARS_model-class.Rd
man/BioGeoBEARS_model_object_to_init_params.Rd
man/areas_list_to_states_list_new.Rd
man/yfunc.Rd
man/get_simparams.Rd
man/save_tipranges_to_LagrangePHYLIP.Rd
man/cls.df.Rd
man/symbolic_to_Q_matrix.Rd
man/get_MLsplitprobs_from_results.Rd
man/default_states_list.Rd
man/map_LG_MLsplits_to_tree.Rd
man/simulate_biogeog_history.Rd
man/label_nodes_postorder_phylo3.Rd
man/add_corners.Rd
man/get_infparams_optimx.Rd
man/define_tipranges_object.Rd
man/conditional_format_table.Rd
man/given_a_starting_state_simulate_split.Rd
man/get_colors_for_numareas.Rd
man/bears_2param_standard_fast_symOnly.Rd
man/bears_optim_run.Rd
man/calc_obs_like.Rd
man/np.Rd
man/bears_6param_standard_fast_ys_v.Rd
man/strsplit_whitespace.Rd
man/getareas_from_tipranges_object.Rd
man/getname.Rd
man/pdftable.Rd
man/map_LG_MLstates_to_tree.Rd
BioGeoBEARS documentation built on May 19, 2017, 6:50 p.m.

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