SiPhyNetwork

A simulator for reticulate evolution under a birth-death-hybridization process. Here the birth-death process is extended to consider reticulate Evolution by allowing hybridization events to occur. The general purpose simulator allows the modeling of three different reticulate patterns: lineage generative hybridization, lineage neutral hybridization, and lineage degenerative hybridization. Users can also specify hybridization events to be dependent on a trait value or genetic distance. We also extend some phylogenetic tree utility and plotting functions for networks. We allow two different stopping conditions: simulated to a fixed time or number of taxa. When simulating to a fixed number of taxa, the user can simulate under the Generalized Sampling Approach that properly simulates phylogenies when assuming a uniform prior on the root age.

Last 30 days

This package has been downloaded 612 times in the last 30 days. This could be a paper that people cite without reading. Reaching the medium popularity echelon is no small feat! The following heatmap shows the distribution of downloads per day. Yesterday, it was downloaded 8 times.

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Last 365 days

This package has been downloaded 8,268 times in the last 365 days. A solid achievement! Enough downloads to get noticed at department meetings. The day with the most downloads was Sep 11, 2024 with 74 downloads.

The following line graph shows the downloads per day. You can hover over the graph to see the exact number of downloads per day.