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
BioGeoBEARS-package     BioGeography with Bayesian (and likelihood)
                        Evolutionary Analysis of RangeS
BioGeoBEARS_model       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 model object
BioGeoBEARS_model_object_to_params_upper
                        Produce the upper limit on the parameters from
                        a BioGeoBEARS model object
BioGeoBEARS_run         An object of class BioGeoBEARS_run holding the
                        model inputs
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
Pdata_given_rangerow    Calculate probability of detection data given a
                        true geographic range and a detection
                        probability
Pdata_given_rangerow_dp
                        Calculate probability of detection data given a
                        true geographic range and a detection
                        probability
add_corners             Iterate up through a plotted tree, getting the
                        coordinates of the corners
add_to_downpass_labels
                        Iterate up and down a tree in C++ LAGRANGE
                        downpass order
addslash                Add a slash to a directory name if needed
adf                     Convert to data.frame, without factors
adf2                    Convert to data.frame, without factors
areas_list_to_states_list_new
                        Convert a list of areas to a list of geographic
                        ranges (states); R version
average_tr_tips         Average the heights of (non-fossil) tips to
                        make ultrametric-ish.
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) - older test version
bears_2param_standard_fast_symOnly
                        2-parameter model, no cladogenesis model (as in
                        BayArea or other purely continuous-time model)
bears_2param_standard_fast_symOnly_simp
                        2-parameter model, no cladogenesis model (as in
                        BayArea or other purely continuous-time model)
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 (founder-event
                        speciation)
bears_4param_standard_fast
                        4-parameter model, adding j (founder-event
                        speciation) and v (vicariance proportion)
bears_5param_standard_fast
                        5-parameter model, adding j (founder-event
                        speciation), v (vicariance proportion), and
                        maxent_constraint_01 (weighting for size of
                        smaller-ranged descendant lineage)
bears_5param_standard_fast_diffstart
                        5-parameter model, with different starting
                        points for optimization
bears_5param_standard_fast_v
                        5-parameter model, adding j (founder-event
                        speciation), v (vicariance proportion), and
                        maxent_constraint_01v (vicariance daughter
                        sizes)
bears_6param_standard_fast_ys_v
                        6-parameter model, adding j (founder-event
                        speciation), v (vicariance proportion), and
                        both maxent_constraint_01 and
                        maxent_constraint_01v
bears_9param_standard_fast_ys_v_cb
                        6-parameter model, adding j (founder-event
                        speciation), v (vicariance proportion), and
                        both maxent_constraint_01 and
                        maxent_constraint_01v
bears_optim_run         Run ML search from 'BioGeoBEARS_run' object
binary_range_to_letter_code_list
                        Convert binary presence/absence codes (1/0) to
                        a list of text area names
binary_range_to_letter_code_txt
                        Convert binary presence/absence codes (1/0) to
                        text area names
binary_ranges_to_letter_codes
                        Convert binary presence/absence codes (1/0) to
                        a list of text area names
calcP_n                 Calculate Z (part of equation 6.4 of Harte
                        2011)
calcZ_part              Calculate Z (equation 6.3 of Harte 2011)
calc_AIC_column         Calculate AICs to make a column in a table
calc_AIC_vals           Calculate AICs for a list of models
calc_AICc_column        Calculate AICc values for a list of models
calc_AICc_vals          Calculate AICc values for a list of models
calc_linked_params_BioGeoBEARS_model_object
                        Update parameters that are deterministic
                        functions of free parameters
calc_loglike_for_optim
                        Take model parameters and the data and
                        calculate the log-likelihood
calc_loglike_for_optim_stratified
                        Take model parameters and the data and
                        calculate the log-likelihood - stratified
                        version
calc_loglike_sp         Calculate log-likelihood with a transition
                        matrix and speciation events - byte-compiled
calc_loglike_sp_prebyte
                        Calculate log-likelihood with a transition
                        matrix and speciation events -
                        pre-byte-compiled
calc_loglike_sp_stratified
                        Calculate log-likelihood with a transition
                        matrix and speciation events, and with
                        stratification
calc_obs_like           Calculate likelihood of count data given true
                        presence/absence and parameters
calc_post_prob_presence
                        Calculate posterior probability of presence,
                        given count data and parameters
calc_prob_forward_onebranch_dense
                        Dense matrix exponentiation forward on a
                        branch, with rexpokit
calc_prob_forward_onebranch_sparse
                        Sparse matrix exponentiation forward on a
                        branch, with rexpokit
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 areas-allowed matrix.
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 probabilities
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 before present
extract_numbers         Extract just the numbers from a string,
                        including decimal points
findall                 Get indices of all matches to a list
getAIC                  Calculate AIC
getAIC_weight_for_model1
                        Calculate Akaike Weight
getAICc                 Calculate AICc
get_AICweight_ratio_model1_over_model2
                        Calculate ratio of Akaike Weights
get_APE_nodenums        Get R internal node numbers
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 of the models
get_Akaike_weights_from_rel_likes_pairwise
                        Calculate the Akaike Weights, from the relative
                        likelihoods of the models
get_ML_probs            Get the probability of the ML state for each
                        node, from a BioGeoBEARS model results list
get_ML_state_indices    Extract the indices for the ML states at each
                        node, given a row of relative probabilities
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 probabilities - old version
get_MLsplitprobs_from_results
                        Extract the ML probs for the base of each
                        branch above a split
get_TF_tips             Get TRUE/FALSE for nodes being tips
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_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) below each tip
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 list
get_indices_where_list1_occurs_in_list2_noNA
                        Return (first!) indices in second list matching
                        the first list, excluding NAs
get_inf_LgL_etc_optimx
                        Get the inferred parameters from a results
                        object (utility function)
get_infparams_optimx    Get the inferred parameters from an ML
                        optimization
get_infparams_optimx_nosim
                        Get the inferred parameters from an ML
                        optimization (different filenames)
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 node
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_node_ages_of_tips   Get the ages of each tip above the root
get_nodenum_structural_root
                        Gets the root node
get_nodenums            Get the unique node numbers in a tree
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 maxent distribution (equations
                        6.3-6.4 of Harte 2011)
get_pruningwise_nodenums
                        Get internal node numbers in pruningwise order
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 text string.
get_sister_node         Get the node sister to two nodes
get_statesColors_table
                        Make a color table for each area and their
                        combinations
get_tiplabel_ranges     For each tip, get a text string of the areas in
                        a tipranges object.
getareas_from_tipranges_object
                        Get the names of the areas in a tipranges
                        object
getname                 Collapse range abbreviations to strings
getranges_from_LagrangePHYLIP
                        Read a LAGRANGE PHYLIP-style file containing
                        geographic ranges into a 'tipranges' object
given_a_starting_state_simulate_branch_end
                        Given the state at the start of a branch,
                        simulate the state at the end of the branch
given_a_starting_state_simulate_split
                        Given the state just below a node, simulate the
                        states after speciation
infprobs_to_probs_of_each_area
                        Convert probabilities of each state, to the
                        probabilities of presence in each area
infprobs_to_probs_of_each_area_from_relprobs
                        Convert relative probabilities matrix to the
                        probabilities of presence in each area
is.not.na               Check for not NA
label_nodes_postorder_phylo3
                        Add postorder node number labels to a phylo3
                        tree object.
letter_string_to_binary
                        Convert ranges in the form of letters (A, AB,
                        BFG, etc.) to binary state number codes
letter_strings_to_tipranges_df
                        Convert ranges in the form of letters (A, AB,
                        BFG, etc.) to a 'tipranges' object
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 table
make_dispersal_multiplier_matrix
                        Make a default matrix of relative dispersal
                        probabilities between areas
make_relprob_matrix_bi
                        Make a relative probability matrix for a single
                        speciation (bifurcation) event
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 unobserved-speciation transition matrix
                        (numeric version)
make_relprob_txtmatrix_sp1
                        Convert a observed-speciation transition matrix
                        to an unobserved-speciation transition matrix
                        (text version)
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 (C++ LAGRANGE version)
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 (Python version)
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 different length
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 e.g. r8s)
normat                  Utility functions to help deal with matrices
                        Normalize a transition matrix
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 R
order_tipranges_by_tr   Order the tipranges in a tipranges object so
                        they match the order of tips in a tree
order_tipranges_by_tree_tips
                        Reorder the rows in a 'tipranges' object, to
                        correspond to tree tips
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 matrix, excluding zeros
pdfit                   Print a table to LaTeX format
pdftable                Print a table to LaTeX format
plot_BioGeoBEARS_model
                        Graphical display of your anagenetic and
                        cladogenetic biogeography models
plot_BioGeoBEARS_results
                        Plot the results of a BioGeoBEARS run
plot_cladogenesis_size_probabilities
                        Graphical display of P(daughter rangesize) for
                        your input or inferred speciation model
post_prob_states        Calculate posterior probability of each
                        states/geographic ranges, given prior
                        probabilities and data likelihoods
post_prob_states_matrix
                        Calculate posterior probability of each
                        states/geographic ranges, given prior
                        probabilities and data likelihoods
postorder_nodes_phylo4_return_table
                        Get a table of node numbers, including DIVA
                        node numbers
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 range in a list of
                        states/geographic ranges
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 pruned tree and tipranges object
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_PHYLIP_data        Read a PHYLIP-format file
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 taphonomic control
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
read_times_fn           Read in the stratification time breakpoints
readfiles_BioGeoBEARS_run
                        Read in the extra input files, if any
rel_likes_from_deltaAICs
                        Calculate the relative likelihoods of the
                        models, from the deltaAIC
rel_likes_from_deltaAICs_pairwise
                        Calculate the relative likelihoods of the
                        models, from the deltaAICs, pairwise
relative_probabilities_of_subsets
                        Calculate probability of different descendant
                        rangesizes, for the smaller descendant, in
                        subset speciation
relative_probabilities_of_vicariants
                        Calculate probability of different descendant
                        rangesizes, for the smaller descendant, in
                        vicariant speciation
remove_null_rowcols_from_mat
                        Remove rows or columns representing a null
                        geographic range from a matrix
return_items_not_NA     Remove NAs from a vector/list
save_tipranges_to_LagrangePHYLIP
                        Save a tipranges object to a LAGRANGE
                        PHYLIP-style file containing binary-encoded
                        geographic ranges
section_the_tree        Section a tree for stratified analysis
sfunc                   Extract the appropriate probability for a
                        subset speciation event, given text code for
                        rangesize of smaller descendant, and ancestor
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 and cladogenesis model
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 matrix
slashslash              Remove double slash (slash a slash)
sourceall               Source all .R files in a directory, except
                        "compile" and "package" files
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 numeric value).
symbolic_cell_to_relprob_cell_sp
                        Convert symbolic cell (a text equation) to
                        relprob cell (a numeric value) - speciation
                        matrix version
symbolic_to_P_matrix    Convert symbolic matrix to relprob matrix
symbolic_to_Q_matrix    Convert symbolic matrix to an instantaneous
                        rate matrix (Q matrix)
symbolic_to_Q_matrix_exper
                        Experimental version of
                        'symbolic_to_Q_matrix_exper', including base
                        frequencies
symbolic_to_relprob_matrix_sp
                        Convert symbolic matrix (with text equations)
                        to relprob matrix (numeric values) - speciation
                        matrix version
tiplikes_wDetectionModel
                        Calculate probability of detection data for
                        each OTU at each range in a list of
                        states/geographic ranges
tipranges               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, and dfnums_to_numeric
unlist_dtf_cols         Unlist the columns in a data.frame
vfunc                   Extract the appropriate probability for a
                        vicariant speciation event, given text code for
                        rangesize of smaller descendant, and ancestor
yfunc                   Extract the appropriate probability for a
                        sympatric/range-copying speciation event, given
                        text code for rangesize of smaller descendant,
                        and ancestor
