{ "_id": "6a1e8a5d1d7bb097a0a684e8", "Package": "SiPhyNetwork", "Title": "A Phylogenetic Simulator for Reticulate Evolution", "Version": "1.1.0", "Authors@R": "c(person(\"Joshua\", \"Justison\", email = \"justisnojo@gmail.com\", role = c(\"aut\", \"cre\",\"cph\")),\nperson(c(\"Claudia\",\"Solis-Lemus\"), role=c(\"aut\",\"cph\")),\nperson(c(\"Tracy\",\"A.\"), \"Heath\", role=c(\"aut\",\"cph\")),\nperson(\"Klaus\", \"Schliep\", role = c(\"cph\"), comment = c(\"modified code from ape in 'write.net.R' and 'read.net.R'. Crediting original copyright holder\")),\nperson(\"Emmanuel\", \"Paradis\", role = c(\"cph\"), comment = c(\"modified code from ape in 'write.net.R' and 'read.net.R'. Crediting original copyright holder\")),\nperson(\"Daniel\", \"Lawson\", role = c(\"cph\"), comment = c(\"modified code from ape in 'write.net.R' and 'read.net.R'. Crediting original copyright holder\"))\n)", "Description": "A simulator for reticulate evolution under a\nbirth-death-hybridization process. Here the birth-death process\nis extended to consider reticulate Evolution by allowing\nhybridization events to occur. The general purpose simulator\nallows the modeling of three different reticulate patterns:\nlineage generative hybridization, lineage neutral\nhybridization, and lineage degenerative hybridization. Users\ncan also specify hybridization events to be dependent on a\ntrait value or genetic distance. We also extend some\nphylogenetic tree utility and plotting functions for networks.\nWe allow two different stopping conditions: simulated to a\nfixed time or number of taxa. When simulating to a fixed number\nof taxa, the user can simulate under the Generalized Sampling\nApproach that properly simulates phylogenies when assuming a\nuniform prior on the root age.", "License": "GPL-3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr", "Repository": "https://jjustison.r-universe.dev", "Date/Publication": "2024-09-06 17:46:59 UTC", "RemoteUrl": "https://github.com/jjustison/siphynetwork", "RemoteRef": "HEAD", "RemoteSha": "7e2c4153bb3f3530120f7916ddbc771f5f3d39b3", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-02 07:37:37 UTC", "User": "root" }, "Author": "Joshua Justison [aut, cre, cph],\nClaudia Solis-Lemus [aut, cph],\nTracy A. Heath [aut, cph],\nKlaus Schliep [cph] (modified code from ape in 'write.net.R' and\n'read.net.R'. Crediting original copyright holder),\nEmmanuel Paradis [cph] (modified code from ape in 'write.net.R' and\n'read.net.R'. Crediting original copyright holder),\nDaniel Lawson [cph] (modified code from ape in 'write.net.R' and\n'read.net.R'. Crediting original copyright holder)", "Maintainer": "Joshua Justison ", "MD5sum": "b8091b24fd5100161c93c4c2e26d8bee", "_user": "jjustison", "_type": "src", "_file": "SiPhyNetwork_1.1.0.tar.gz", "_fileid": "0ba7c6e695825a40a01af5378bfd3ebd9a5c666358e0b6eac445451148a5920f", "_filesize": 1692717, "_sha256": "0ba7c6e695825a40a01af5378bfd3ebd9a5c666358e0b6eac445451148a5920f", "_created": "2026-06-02T07:37:37.000Z", "_published": "2026-06-02T07:46:37.181Z", "_distro": "noble", "_jobs": [ { "job": 79022166861, "time": 133, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7351720946" }, { "job": 79022166798, "time": 140, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7351721972" }, { "job": 79022166782, "time": 134, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7351722167" }, { "job": 79022166799, "time": 135, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7351720100" }, { 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"time": 110, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7351712095" } ], "_buildurl": "https://github.com/r-universe/jjustison/actions/runs/26805450562", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/jjustison/siphynetwork", "_commit": { "id": "7e2c4153bb3f3530120f7916ddbc771f5f3d39b3", "author": "Justison ", "committer": "Justison ", "message": "bug fix for bug fix on issue #10\n", "time": 1725644819 }, "_maintainer": { "name": "Joshua Justison", "email": "justisnojo@gmail.com", "login": "jjustison", "description": "", "uuid": 19258474 }, "_registered": true, "_dependencies": [ { "package": "Rcpp", "role": "LinkingTo" }, { "package": "stats", "role": "Imports" }, { "package": "ape", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "rstackdeque", "role": "Imports" }, { "package": "lifecycle", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "markdown", "role": "Suggests" } ], "_owner": "jjustison", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 11, "_contributors": [ { "user": "jjustison", "count": 95, "uuid": 19258474 } ], "_userbio": { "uuid": 19258474, "type": "user", "name": "Joshua Justison" }, "_downloads": { "count": 690, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SiPhyNetwork" }, "_devurl": "https://github.com/jjustison/siphynetwork", "_searchresults": 33, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/SiPhyNetwork.html", "manual.pdf" ], "_homeurl": "https://github.com/jjustison/siphynetwork", "_realowner": "jjustison", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2022-09-20" }, { "version": "1.0.1", "date": "2022-09-29" }, { "version": "1.1.0", "date": "2023-04-14" } ], "_exports": [ "biconnectedComponents", "deleteTips", "getNetworkLevel", "incompleteSampling", "isFUstable", "isNormal", "isTreeBased", "isTreeChild", "ltt.network", "make.beta.draw", "make.categorical.draw", "make.exp.decay", "make.linear.decay", "make.polynomial.decay", "make.stepwise", "make.trait.model", "make.uniform.draw", "network.gsa", "plottable.net", "read.net", "reconstructedNetwork", "sim.bdh.age", "sim.bdh.taxa.gsa", "sim.bdh.taxa.ssa", "write.net" ], "_help": [ { "page": "biconnectedComponents", "title": "Biconnected Components", "topics": [ "biconnectedComponents" ] }, { "page": "deleteTips", "title": "Remove tips from a phylogenetic Network", "topics": [ "deleteTips" ] }, { "page": "getNetworkLevel", "title": "Get the level of a Network", "topics": [ "getNetworkLevel" ] }, { "page": "incompleteSampling", "title": "Sample Tips on a Phylogenetic Network", "topics": [ "incompleteSampling" ] }, { "page": "isFUStable", "title": "Determine whether a phylogeny is FU-stable", "topics": [ "isFUstable" ] }, { "page": "isNormal", "title": "#' Determine whether a phylogeny is Normal", "topics": [ "isNormal" ] }, { "page": "isTreeBased", "title": "Determine whether a network is tree-based", "topics": [ "isTreeBased" ] }, { "page": "isTreeChild", "title": "Determine whether a network is tree-child", "topics": [ "isTreeChild" ] }, { "page": "ltt.network", "title": "Lineages thru time on a network", "topics": [ "ltt.network" ] }, { "page": "make.beta.draw", "title": "Function that makes a draw from a beta distribution", "topics": [ "make.beta.draw" ] }, { "page": "make.categorical.draw", "title": "Function that makes a draw from a categorical distribution", "topics": [ "make.categorical.draw" ] }, { "page": "make.exp.decay", "title": "Make an exponential decay function", "topics": [ "make.exp.decay" ] }, { "page": "make.linear.decay", "title": "Make a linear decay function", "topics": [ "make.linear.decay" ] }, { "page": "make.polynomial.decay", "title": "Make a polynomial decay function", "topics": [ "make.polynomial.decay" ] }, { "page": "make.stepwise", "title": "Make a stepwise decay function", "topics": [ "make.stepwise" ] }, { "page": "make.trait.model", "title": "Model for trait evolution across the phylogeny", "topics": [ "make.trait.model" ] }, { "page": "make.uniform.draw", "title": "Function that makes a draw from a uniform distribution", "topics": [ "make.uniform.draw" ] }, { "page": "network.gsa", "title": "Sample under the Generalized Sampling Approach", "topics": [ "network.gsa" ] }, { "page": "plottable.net", "title": "Create a more Plotting-Friendly phylogenetic Network", "topics": [ "plottable.net" ] }, { "page": "read.net", "title": "Read a Network from Parenthetic Format", "topics": [ "read.net" ] }, { "page": "reconstructedNetwork", "title": "Remove Extinct Lineages from a Phylogenetic Network", "topics": [ "reconstructedNetwork" ] }, { "page": "sim.bdh.age", "title": "Simulate a Phylogenetic Network to a Specified Number of Taxa", "topics": [ "sim.bdh.age" ] }, { "page": "sim.bdh.taxa.gsa", "title": "Simulate a Phylogenetic Network to a Specified Number of Taxa", "topics": [ "sim.bdh.taxa.gsa" ] }, { "page": "sim.bdh.taxa.ssa", "title": "Simulate a Phylogenetic Network to a Specified Number of Taxa", "topics": [ "sim.bdh.taxa.ssa" ] }, { "page": "write.net", "title": "Write a Network in Parenthetic Format", "topics": [ "write.net" ] } ], "_readme": "https://github.com/jjustison/siphynetwork/raw/HEAD/README.md", "_rundeps": [ "ape", "cli", "digest", "lattice", "lifecycle", "nlme", "Rcpp", "rlang", "rstackdeque" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "introduction.Rmd", "filename": "introduction.html", "title": "Introduction", "author": "Josh Justison", "engine": "knitr::knitr", "headings": [ "Overview", "Introduction", "The SiPhyNetwork Package", "Simulating Networks", "Example 1: Simulating Networks Under A Simple Hybridization Model", "Types of Hybridization", "Example 2 Types of Hybridization in SiPhyNetwork", "Characterizing And Using Phylogenetic Networks", "Example 3 Plotting Networks", "Example 4 Network Classification", "Example 5 Network Input And Output", "Reconstructed Phylogenies & Incomplete Sampling", "Example 6: Post-hoc Incomplete Sampling an Reconstructed Networks", "More Complex Hybridization Models", "Example 7A: Hybridizations Dependent On Genetic Distance", "Example 7B: Trait Dependent Hybridization", "Works Cited" ], "created": "2021-02-27 22:26:31", "modified": "2023-04-13 18:39:43", "commits": 19 } ], "_score": 5.258876629372131, "_indexed": true, "_nocasepkg": "siphynetwork", "_universes": [ "jjustison" ], "_binaries": [ { "r": "4.7.0", 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