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thijsjanzen
nLTT:Calculate the NLTT Statistic
Provides functions to calculate the normalised Lineage-Through- Time (nLTT) statistic, given two phylogenetic trees. The nLTT statistic measures the difference between two Lineage-Through-Time curves, where each curve is normalised both in time and in number of lineages.
Maintained by Thijs Janzen. Last updated 2 years ago.
nlttnltt-statisticphylogenetic-treesphylogenetics
110.0 match 6 stars 6.93 score 59 scriptsthijsjanzen
treestats:Phylogenetic Tree Statistics
Collection of phylogenetic tree statistics, collected throughout the literature. All functions have been written to maximize computation speed. The package includes umbrella functions to calculate all statistics, all balance associated statistics, or all branching time related statistics. Furthermore, the 'treestats' package supports summary statistic calculations on Ltables, provides speed-improved coding of branching times, Ltable conversion and includes algorithms to create intermediately balanced trees. Full description can be found in Janzen (2024) <doi:10.1016/j.ympev.2024.108168>.
Maintained by Thijs Janzen. Last updated 6 months ago.
5.3 match 16 stars 5.43 score 16 scripts 1 dependentsthijsjanzen
nodeSub:Simulate DNA Alignments Using Node Substitutions
Simulate DNA sequences for the node substitution model. In the node substitution model, substitutions accumulate additionally during a speciation event, providing a potential mechanistic explanation for substitution rate variation. This package provides tools to simulate such a process, simulate a reference process with only substitutions along the branches, and provides tools to infer phylogenies from alignments. More information can be found in Janzen (2021) <doi:10.1093/sysbio/syab085>.
Maintained by Thijs Janzen. Last updated 1 years ago.
1.5 match 1 stars 2.70 score 3 scripts