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

Share:

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.

Author
Nicholas J. Matzke [aut, cre, cph]
Date of publication
2014-01-02 15:15:11
Maintainer
Nicholas J. Matzke <matzke@berkeley.edu>
License
GPL (>= 2)
Version
0.2.1
URLs

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...

Files in this package

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
BioGeoBEARS/inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_5.2.newick.bgsplits.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_M1.lg
BioGeoBEARS/inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_5.2.newick.bgstates.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_geog.data
BioGeoBEARS/inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_5.2.newick.bgkey.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M1/LGcpp/Psychotria_5.2.newick
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
BioGeoBEARS/inst/extdata/examples/Psychotria_M2strat/LGcpp/Psychotria_5.2.newick
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
BioGeoBEARS/inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M0/LGcpp/Psychotria_M0.lg
BioGeoBEARS/inst/extdata/examples/Psychotria_M0/BGB
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
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_5.2.newick.bgstates.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_geog.data
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_M0strat_lgcpp_out.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_5.2.newick.bgkey.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/LGcpp/Psychotria_M0_stratified.txt
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
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/BGB/Psychotria_5.2.newick
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
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/LGpy_2013/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M0strat/LGpy_2012
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
BioGeoBEARS/inst/extdata/examples/Lonicera_M0/LGcpp
BioGeoBEARS/inst/extdata/examples/Lonicera_M0/LGcpp/Lonicera_M0.lg
BioGeoBEARS/inst/extdata/examples/Lonicera_M0/LGcpp/Lonicera_M0_lgcpp_out.txt
BioGeoBEARS/inst/extdata/examples/Lonicera_M0/LGcpp/Lonicera.newick
BioGeoBEARS/inst/extdata/examples/Lonicera_M0/LGcpp/Lonicera_M0_lgcpp_out_orig.txt
BioGeoBEARS/inst/extdata/examples/Lonicera_M0/BGB
BioGeoBEARS/inst/extdata/examples/Lonicera_M0/BGB/Psychotria_geog.data
BioGeoBEARS/inst/extdata/examples/Lonicera_M0/BGB/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Lonicera_M0/LGpy_2013
BioGeoBEARS/inst/extdata/examples/Lonicera_M0/LGpy_2013/Lonicera_M0.results-1.txt
BioGeoBEARS/inst/extdata/examples/Lonicera_M0/LGpy_2013/Lonicera.newick
BioGeoBEARS/inst/extdata/examples/Lonicera_M0/LGpy_2013/Lonicera_M0.lagrange.py
BioGeoBEARS/inst/extdata/examples/Lonicera_M0/LGpy_2013/Lonicera_M0.results.txt
BioGeoBEARS/inst/extdata/examples/Lonicera_M0/LGpy_2012
BioGeoBEARS/inst/extdata/examples/Lonicera_M0/LGpy_2012/Lonicera_M0.results-1.txt
BioGeoBEARS/inst/extdata/examples/Lonicera_M0/LGpy_2012/Lonicera.newick
BioGeoBEARS/inst/extdata/examples/Lonicera_M0/LGpy_2012/Lonicera_M0.lagrange.py
BioGeoBEARS/inst/extdata/examples/Lonicera_M0/LGpy_2012/Lonicera_M0.results_orig.txt
BioGeoBEARS/inst/extdata/examples/Lonicera_M0/LGpy_2012/Lonicera_M0.results.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M2
BioGeoBEARS/inst/extdata/examples/Psychotria_M2/LGcpp
BioGeoBEARS/inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_5.2.newick.bgsplits.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_5.2.newick.bgstates.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_M2.lg
BioGeoBEARS/inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_geog.data
BioGeoBEARS/inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_2areas_M2_eastward_only.rm.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_5.2.newick.bgkey.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M2/LGcpp/Psychotria_M2_lgcpp_out.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M2/BGB
BioGeoBEARS/inst/extdata/examples/Psychotria_M2/BGB/Psychotria_geog.data
BioGeoBEARS/inst/extdata/examples/Psychotria_M2/BGB/dispersal_multipliers.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M2/BGB/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M2/LGpy_2013
BioGeoBEARS/inst/extdata/examples/Psychotria_M2/LGpy_2013/psychotria_M2.results.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M2/LGpy_2013/psychotria_M2.lagrange.py
BioGeoBEARS/inst/extdata/examples/Psychotria_M2/LGpy_2013/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M2/LGpy_2012
BioGeoBEARS/inst/extdata/examples/Psychotria_M2/LGpy_2012/psychotria_M2.results.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M2/LGpy_2012/psychotria_M2.lagrange.py
BioGeoBEARS/inst/extdata/examples/Psychotria_M2/LGpy_2012/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGcpp
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_5.2.newick.bgsplits.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_M3strat.lg
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_M3_stratified.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_5.2.newick.bgstates.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_geog.data
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_M3strat_lgcpp_out.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_5.2.newick.bgkey.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGcpp/Psychotria_5.2.newick
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGcpp_v2
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_5.2.newick.bgsplits.tre
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_M3strat.lg
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_M3_stratified.txt
BioGeoBEARS/inst/extdata/examples/Psychotria_M3strat/LGcpp_v2/Psychotria_5.2.newick.bgstates.tre
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