abc_smc_nltt | A function to perform Approximate Bayesian Computation within... |
check_input_event_times | Checks that event times are correct |
check_phylogenies | Check if the input is a valid collection of one or more... |
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... |
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_diff | Calculates the exact difference between the lineage through... |
nltt_diff_exact | Calculates the exact, difference between the lineage through... |
nltt_diff_exact_brts | Calculates the exact difference between the nLTT curves of... |
nltt_diff_exact_calc_extinct | Calculates the exact difference between the nLTT curves of... |
nltt_diff_exact_extinct | Calculates the exact difference between the nLTT curves of... |
nltt_diff_exact_norm_brts | Calculates the exact difference between the nLTT curves of... |
nLTT-internal | Internal nLTT functions |
nltt_lines | Normalized version of the ape function ltt.lines. |
nLTT-package | Package providing functions to visualize the normalized... |
nltt_plot | Normalized version of the ape function ltt.plot |
nltts_diff | Calculates the nLTT statistic between each phylogeny in a... |
nltts_plot | Get the average nLTT from a collection of phylogenies |
nLTTstat | Calculate the difference between two normalized... |
nLTTstat_exact | Calculate the exact difference between two normalized... |
stretch_nltt_matrix | Stretch matrix 'm' with a timestep resolution of 'dt'. |
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