nLTT-package |
Package providing functions to visualize the normalized Lineage-Through-Time statistic, and calculate the difference between two nLTT curves |
abc_smc_nltt |
A function to perform Approximate Bayesian Computation within a Sequential Markov Chain (ABC-SMC), for diversification analysis of phylogenetic trees. |
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_nltt_values |
Collects the nLTT values of all phylogenies in the melted/uncast/long form |
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_n_lineages |
Collect the number of lineages from the stem age |
get_phylogeny_nltt_matrix |
Extract the nLTT matrix from a phylogeny |
mcmc_nltt |
Code to perform Metropolis-Hastings MCMC for a diversification model, given a phylogenetic tree. This function was used in the MEE paper to calculate the likelihood reference estimates. |
nLTT |
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. |
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 |
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_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 |
stretch_nltt_matrix |
Stretch matrix 'm' with a timestep resolution of 'dt'. |