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>.

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openblascpp

7.48 score 21 stars 1 dependents 30 scripts 571 downloads

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.

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nlttnltt-statisticphylogenetic-treesphylogenetics

6.94 score 6 stars 61 scripts 686 downloads

GenomeAdmixR - Simulate Admixture of Genomes

Individual-based simulations forward in time, simulating how patterns in ancestry along the genome change after admixture. Full description can be found in Janzen (2021) <doi:10.1111/2041-210X.13612>.

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cpp

6.07 score 5 stars 19 scripts 230 downloads

GUILDS - Implementation of Sampling Formulas for the Unified Neutral Model of Biodiversity and Biogeography, with or without Guild Structure

A collection of sampling formulas for the unified neutral model of biogeography and biodiversity. Alongside the sampling formulas, it includes methods to perform maximum likelihood optimization of the sampling formulas, methods to generate data given the neutral model, and methods to estimate the expected species abundance distribution. Sampling formulas included in the GUILDS package are the Etienne Sampling Formula (Etienne 2005), the guild sampling formula, where guilds are assumed to differ in dispersal ability (Janzen et al. 2015), and the guilds sampling formula conditioned on guild size (Janzen et al. 2015).

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cpp

5.97 score 3 stars 12 dependents 16 scripts 1.1k downloads

junctions - The Breakdown of Genomic Ancestry Blocks in Hybrid Lineages

Individual based simulations of hybridizing populations, where the accumulation of junctions is tracked. Furthermore, mathematical equations are provided to verify simulation outcomes. Both simulations and mathematical equations are based on Janzen (2018, <doi:10.1101/058107>) and Janzen (2022, <doi:10.1111/1755-0998.13519>).

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cpp

4.98 score 2 stars 16 scripts 627 downloads

STEPCAM - ABC-SMC Inference of STEPCAM

Collection of model estimation, and model plotting functions related to the STEPCAM family of community assembly models. STEPCAM is a STEPwise Community Assembly Model that infers the relative contribution of Dispersal Assembly, Habitat Filtering and Limiting Similarity from a dataset consisting of the combination of trait and abundance data. See also <doi:10.1890/14-0454.1> for more information.

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4.86 score 6 stars 12 scripts 536 downloads

simRestore - Simulate the Effect of Management Policies on Restoration Efforts

Simulation methods to study the effect of management policies on efforts to restore populations back to their original genetic composition. Allows for single-scenario simulation and for optimization of specific chosen scenarios. Further information can be found in Hernandez, Janzen and Lavretsky (2023) <doi:10.1111/1755-0998.13892>.

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cpp

3.18 score 4 scripts 147 downloads

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>.

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cppopenjdk

2.70 score 1 stars 3 scripts 598 downloads