abc_smc_nltt            A function to perform Approximate Bayesian
                        Computation within a Sequential Markov Chain
                        (ABC-SMC), for diversification analysis of
                        phylogenetic trees.
check_input_event_times
                        Checks that event times are correct
check_phylogenies       Check if the input is a valid collection of one
                        or more phylogenies
check_step_type         Check if the step type is valid
check_time_unit         Check if the time unit is valid
default_params_doc      This function does nothing. It is intended to
                        inherit is parameters' documentation.
exampleTrees            example trees to test the functionality of the
                        package
get_average_nltt_matrix
                        Get the average nLTT from a collection of
                        phylogenies
get_branching_times     Collect the branching times from the stem age
get_n_lineages          Collect the number of lineages from the stem
                        age
get_nltt_values         Get the nLTT values in time
get_norm_brts           Collect the normalized branching times from the
                        stem age
get_norm_n              Collect the normalized number of lineages from
                        the stem age
get_phylogeny_nltt_matrix
                        Extract the nLTT matrix from a phylogeny
mcmc_nltt               function, using a Monte Carlo Markov Chain
nLTT-package            Package providing functions to visualize the
                        normalized Lineage-Through-Time statistic, and
                        calculate the difference between two nLTT
                        curves
nLTTstat                Calculate the difference between two normalized
                        Lineage-Through-Time curves, given two
                        phylogenetic trees.
nLTTstat_exact          Calculate the exact difference between two
                        normalized Lineage-Through-Time curves, given
                        two phylogenetic trees.
nltt_diff               Calculates the exact difference between the
                        lineage through time curves of tree1 & tree2
                        (normalized in time and for the number of
                        lineages)
nltt_diff_exact         Calculates the exact, difference between the
                        lineage through time curves of tree1 & tree2
                        (normalized in time and for the number of
                        lineages)
nltt_diff_exact_brts    Calculates the exact difference between the
                        nLTT curves of the branching times
nltt_diff_exact_calc_extinct
                        Calculates the exact difference between the
                        nLTT curves of the event times. This includes
                        extinction events.
nltt_diff_exact_extinct
                        Calculates the exact difference between the
                        nLTT curves of the event times. This includes
                        extinction events.
nltt_diff_exact_norm_brts
                        Calculates the exact difference between the
                        nLTT curves of the branching times
nltt_lines              Normalized version of the ape function
                        ltt.lines.
nltt_plot               Normalized version of the ape function ltt.plot
nltts_diff              Calculates the nLTT statistic between each
                        phylogeny in a collection compared to a same
                        focal/reference tree
nltts_plot              Get the average nLTT from a collection of
                        phylogenies
stretch_nltt_matrix     Stretch matrix 'm' with a timestep resolution
                        of 'dt'.
