{
"_id": "6ace278aa14063b82c3b07a9",
"Package": "jackalope",
"Type": "Package",
"Title": "A Swift, Versatile Phylogenomic and High-Throughput Sequencing\nSimulator",
"Version": "1.1.6",
"Authors@R": "person(c(\"Lucas\", \"A.\"), \"Nell\", email = \"lucnell@gmail.com\", \nrole = c(\"cph\", \"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-3209-0517\"))",
"Description": "Simply and efficiently simulates (i) variants from\nreference genomes and (ii) reads from both Illumina\n and Pacific Biosciences (PacBio)\n platforms. It can either read reference\ngenomes from FASTA files or simulate new ones. Genomic variants\ncan be simulated using summary statistics, phylogenies, Variant\nCall Format (VCF) files, and coalescent simulations—the latter\nof which can include selection, recombination, and demographic\nfluctuations. 'jackalope' can simulate single, paired-end, or\nmate-pair Illumina reads, as well as PacBio reads. These\nsimulations include sequencing errors, mapping qualities,\nmultiplexing, and optical/polymerase chain reaction (PCR)\nduplicates. Simulating Illumina sequencing is based on ART by\nHuang et al. (2012) . PacBio\nsequencing simulation is based on SimLoRD by Stöcker et al.\n(2016) . All outputs can be\nwritten to standard file formats.",
"License": "MIT + file LICENSE",
"Encoding": "UTF-8",
"LazyData": "true",
"biocViews": "",
"SystemRequirements": "GNU make",
"RoxygenNote": "7.3.3",
"Roxygen": "list(markdown = TRUE)",
"VignetteBuilder": "knitr",
"URL": "https://github.com/lucasnell/jackalope",
"BugReports": "https://github.com/lucasnell/jackalope/issues",
"Config/pak/sysreqs": "make libbz2-dev liblzma-dev xz-utils zlib1g-dev",
"Repository": "https://lucasnell.r-universe.dev",
"Date/Publication": "2025-09-29 20:30:24 UTC",
"RemoteUrl": "https://github.com/lucasnell/jackalope",
"RemoteRef": "HEAD",
"RemoteSha": "b119c7728dc909e12347dbb2165309756d7cf84f",
"NeedsCompilation": "yes",
"Packaged": {
"Date": "2026-10-13 12:15:33 UTC",
"User": "root"
},
"Author": "Lucas A. Nell [cph, aut, cre] (ORCID:\n)",
"Maintainer": "Lucas A. Nell ",
"_user": "lucasnell",
"_type": "src",
"_file": "jackalope_1.1.6.tar.gz",
"_fileid": "https://r2.ropensci.org/bef16554585b9d94c85c3f808a803a610424df1ba5ec58af11ff3ec55f8ade9a",
"_filesize": 1957860,
"_sha256": "bef16554585b9d94c85c3f808a803a610424df1ba5ec58af11ff3ec55f8ade9a",
"_expires": "2027-01-21T12:43:52.000Z",
"_created": "2026-10-13T12:15:33.000Z",
"_published": "2026-10-13T12:43:54.414Z",
"_buildurl": "https://github.com/r-universe/lucasnell/actions/runs/38395421687",
"_status": "success",
"_host": "GitHub-Actions",
"_jobs": [
{
"job": 115291839861,
"time": 207,
"config": "linux-devel-arm64",
"r": "4.7.0",
"check": "OK",
"artifact": "11812417033"
},
{
"job": 115291839561,
"time": 193,
"config": "linux-devel-x86_64",
"r": "4.7.0",
"check": "OK",
"artifact": "11812416987"
},
{
"job": 115291839691,
"time": 198,
"config": "linux-release-arm64",
"r": "4.6.1",
"check": "OK",
"artifact": "11812426998"
},
{
"job": 115291839570,
"time": 227,
"config": "linux-release-x86_64",
"r": "4.6.1",
"check": "OK",
"artifact": "11812452240"
},
{
"job": 115291839638,
"time": 280,
"config": "macos-oldrel-arm64",
"r": "4.5.3",
"check": "OK",
"artifact": "11812998350"
},
{
"job": 115291839572,
"time": 370,
"config": "macos-oldrel-x86_64",
"r": "4.5.3",
"check": "OK",
"artifact": "11813142750"
},
{
"job": 115291839577,
"time": 193,
"config": "macos-release-arm64",
"r": "4.6.1",
"check": "OK",
"artifact": "11814006722"
},
{
"job": 115291839603,
"time": 427,
"config": "macos-release-x86_64",
"r": "4.6.1",
"check": "OK",
"artifact": "11813113559"
},
{
"job": 115289561873,
"time": 320,
"config": "source",
"r": "4.6.1",
"check": "OK",
"artifact": "11811862057"
},
{
"job": 115291839427,
"time": 235,
"config": "wasm-release",
"r": "4.6.0",
"check": "FAIL",
"artifact": ""
},
{
"job": 115291839629,
"time": 491,
"config": "windows-devel-arm64",
"r": "4.7.0",
"check": "OK",
"artifact": "11812995329"
},
{
"job": 115291839764,
"time": 300,
"config": "windows-devel-x86_64",
"r": "4.7.0",
"check": "OK",
"artifact": "11811782957"
},
{
"job": 115291839643,
"time": 305,
"config": "windows-oldrel-x86_64",
"r": "4.5.3",
"check": "OK",
"artifact": "11812112597"
},
{
"job": 115291839735,
"time": 494,
"config": "windows-release-arm64",
"r": "4.6.1",
"check": "OK",
"artifact": "11812667682"
},
{
"job": 115291839699,
"time": 224,
"config": "windows-release-x86_64",
"r": "4.6.1",
"check": "OK",
"artifact": "11812252249"
}
],
"_upstream": "https://github.com/lucasnell/jackalope",
"_commit": {
"id": "b119c7728dc909e12347dbb2165309756d7cf84f",
"author": "Lucas Nell ",
"committer": "Lucas Nell ",
"message": "Updated cran-comments, NEWS, and CRAN-SUBMISSION\n",
"time": 1759177824
},
"_maintainer": {
"name": "Lucas A. Nell",
"email": "lucnell@gmail.com",
"login": "lucasnell",
"description": "",
"uuid": 15268280,
"orcid": "0000-0003-3209-0517"
},
"_distro": "resolute",
"_registered": true,
"_dependencies": [
{
"package": "R",
"version": ">= 2.10",
"role": "Depends"
},
{
"package": "Rcpp",
"role": "LinkingTo"
},
{
"package": "RcppArmadillo",
"role": "LinkingTo"
},
{
"package": "RcppProgress",
"role": "LinkingTo"
},
{
"package": "Rhtslib",
"role": "LinkingTo"
},
{
"package": "ape",
"role": "Imports"
},
{
"package": "R6",
"role": "Imports"
},
{
"package": "Rcpp",
"version": ">= 0.12.11",
"role": "Imports"
},
{
"package": "coala",
"role": "Suggests"
},
{
"package": "knitr",
"role": "Suggests"
},
{
"package": "markdown",
"role": "Suggests"
},
{
"package": "rmarkdown",
"role": "Suggests"
},
{
"package": "scrm",
"role": "Suggests"
},
{
"package": "testthat",
"role": "Suggests"
}
],
"_owner": "lucasnell",
"_selfowned": true,
"_usedby": 0,
"_updates": [],
"_tags": [],
"_stars": 8,
"_contributors": [
{
"user": "lucasnell",
"count": 904,
"uuid": 15268280
},
{
"user": "eddelbuettel",
"count": 1,
"uuid": 673121
}
],
"_userbio": {
"uuid": 15268280,
"type": "user",
"name": "Lucas Nell",
"followers": 6
},
"_downloads": {
"count": 547,
"source": "https://cranlogs.r-pkg.org/downloads/total/last-month/jackalope"
},
"_devurl": "https://github.com/lucasnell/jackalope",
"_searchresults": 39,
"_topics": [
"zlib",
"openblas",
"curl",
"bzip2",
"xz-utils",
"cpp"
],
"_rbuild": "4.6.1",
"_assets": [
"extra/citation.cff",
"extra/citation.html",
"extra/citation.json",
"extra/citation.txt",
"extra/contents.json",
"extra/jackalope.html",
"extra/manual.pdf",
"extra/NEWS.html",
"extra/NEWS.txt",
"extra/readme.html",
"extra/readme.md",
"LICENSE"
],
"_homeurl": "https://github.com/lucasnell/jackalope",
"_realowner": "lucasnell",
"_cranurl": true,
"_releases": [
{
"version": "0.1.0",
"date": "2019-06-04"
},
{
"version": "0.1.1",
"date": "2019-06-12"
},
{
"version": "0.1.2",
"date": "2019-07-11"
},
{
"version": "0.1.3",
"date": "2019-10-17"
},
{
"version": "1.0.0",
"date": "2019-11-22"
},
{
"version": "1.1.0",
"date": "2020-02-28"
},
{
"version": "1.1.1",
"date": "2020-06-15"
},
{
"version": "1.1.2",
"date": "2021-02-10"
},
{
"version": "1.1.3",
"date": "2021-07-06"
},
{
"version": "1.1.4",
"date": "2023-10-15"
},
{
"version": "1.1.5",
"date": "2023-11-28"
},
{
"version": "1.1.6",
"date": "2025-09-29"
}
],
"_exports": [
"create_genome",
"create_haplotypes",
"haplotypes",
"haps_gtrees",
"haps_phylo",
"haps_ssites",
"haps_theta",
"haps_vcf",
"illumina",
"indels",
"pacbio",
"read_fasta",
"ref_genome",
"sub_F81",
"sub_F84",
"sub_GTR",
"sub_HKY85",
"sub_JC69",
"sub_K80",
"sub_TN93",
"sub_UNREST",
"write_fasta",
"write_gtrees",
"write_vcf"
],
"_datasets": [
{
"name": "evo_rates",
"title": "Table of evolutionary rates.",
"object": "evo_rates",
"class": [
"data.frame"
],
"fields": [
"domain",
"species",
"Ge",
"Gc_Gnc",
"indels",
"subs",
"Ne",
"pi_s",
"theta_s"
],
"rows": 15,
"table": true,
"tojson": true
}
],
"_help": [
{
"page": "create_genome",
"title": "Create a reference genome.",
"topics": [
"create_genome"
]
},
{
"page": "create_haplotypes",
"title": "Create haplotypes from a reference genome.",
"topics": [
"create_haplotypes"
]
},
{
"page": "evo_rates",
"title": "Table of evolutionary rates.",
"topics": [
"evo_rates"
]
},
{
"page": "haplotypes",
"title": "An R6 Class Representing Haploid Variants",
"topics": [
"haplotypes"
]
},
{
"page": "haps_functions",
"title": "Organize higher-level information for creating haplotypes.",
"topics": [
"haps_functions"
]
},
{
"page": "haps_gtrees",
"title": "Organize information to create haplotypes using gene trees",
"topics": [
"haps_gtrees",
"write_gtrees"
]
},
{
"page": "haps_phylo",
"title": "Organize information to create haplotypes using phylogenetic tree(s)",
"topics": [
"haps_phylo"
]
},
{
"page": "haps_ssites",
"title": "Organize information to create haplotypes using segregating sites matrices",
"topics": [
"haps_ssites"
]
},
{
"page": "haps_theta",
"title": "Organize information to create haplotypes using theta parameter",
"topics": [
"haps_theta"
]
},
{
"page": "haps_vcf",
"title": "Organize information to create haplotypes using a VCF file",
"topics": [
"haps_vcf"
]
},
{
"page": "illumina",
"title": "Create and write Illumina reads to FASTQ file(s).",
"topics": [
"illumina"
]
},
{
"page": "indels",
"title": "Insertions and deletions (indels) specification",
"topics": [
"indels"
]
},
{
"page": "pacbio",
"title": "Create and write PacBio reads to FASTQ file(s).",
"topics": [
"pacbio"
]
},
{
"page": "read_fasta",
"title": "Read a fasta file.",
"topics": [
"read_fasta"
]
},
{
"page": "ref_genome",
"title": "R6 Class Representing a Reference Genome",
"topics": [
"ref_genome"
]
},
{
"page": "sub_models",
"title": "Construct necessary information for substitution models.",
"topics": [
"sub_F81",
"sub_F84",
"sub_GTR",
"sub_HKY85",
"sub_JC69",
"sub_K80",
"sub_models",
"sub_TN93",
"sub_UNREST"
]
},
{
"page": "write_fasta",
"title": "Write a 'ref_genome' or 'haplotypes' object to a FASTA file.",
"topics": [
"write_fasta"
]
},
{
"page": "write_vcf",
"title": "Write haplotype info from a 'haplotypes' object to a VCF file.",
"topics": [
"write_vcf"
]
}
],
"_pkglogo": "https://github.com/lucasnell/jackalope/raw/HEAD/man/figures/logo.png",
"_readme": "https://github.com/lucasnell/jackalope/raw/HEAD/README.md",
"_rundeps": [
"ape",
"digest",
"lattice",
"nlme",
"R6",
"Rcpp",
"RcppArmadillo",
"RcppProgress",
"Rhtslib"
],
"_sysdeps": [
{
"shlib": "libz",
"package": "zlib1g",
"headers": "zlib1g-dev",
"source": "zlib",
"version": "1:1.3.dfsg+really1.3.1-1ubuntu3.1",
"name": "zlib",
"homepage": "http://zlib.net/",
"description": "compression library - runtime"
},
{
"shlib": "liblapack",
"package": "libopenblas0-pthread",
"source": "openblas",
"version": "0.3.32+ds-5",
"name": "openblas",
"homepage": "https://www.openblas.net/",
"description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
},
{
"shlib": "libblas",
"package": "libopenblas0-pthread",
"source": "openblas",
"version": "0.3.32+ds-5",
"name": "openblas",
"homepage": "https://www.openblas.net/",
"description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
},
{
"shlib": "libcurl",
"package": "libcurl4t64",
"headers": "libcurl4-openssl-dev",
"source": "curl",
"version": "8.18.0-1ubuntu2.7",
"name": "curl",
"homepage": "https://curl.se/",
"description": "easy-to-use client-side URL transfer library (OpenSSL flavour)"
},
{
"shlib": "libbz2",
"package": "libbz2-1.0",
"headers": "libbz2-dev",
"source": "bzip2",
"version": "1.0.8-6ubuntu0.1",
"name": "bzip2",
"homepage": "https://sourceware.org/bzip2/",
"description": "high-quality block-sorting file compressor library - runtime"
},
{
"shlib": "liblzma",
"package": "liblzma5",
"headers": "liblzma-dev",
"source": "xz-utils",
"version": "5.8.3-1",
"name": "xz-utils",
"homepage": "https://tukaani.org/xz/",
"description": "XZ-format compression library"
},
{
"shlib": "libstdc++",
"package": "libstdc++6",
"source": "gcc",
"version": "16-20260322-1ubuntu1",
"name": "c++",
"homepage": "http://gcc.gnu.org/",
"description": "GNU Standard C++ Library v3"
}
],
"_vignettes": [
{
"source": "jackalope-intro.Rmd",
"filename": "jackalope-intro.html",
"title": "Intro to jackalope",
"engine": "knitr::rmarkdown",
"headings": [
"Generating reference genome",
"Molecular evolution information",
"Assembling a genome",
"Based on a reference",
"Based on a diploid individual",
"Estimating divergence between populations",
"Constructing a phylogeny",
"From one phylogenetic tree",
"From gene trees"
],
"created": "2019-05-24 20:19:35",
"modified": "2023-11-28 18:14:13",
"commits": 7
},
{
"source": "sub-models.Rmd",
"filename": "sub-models.html",
"title": "Models of nucleotide substitution",
"engine": "knitr::rmarkdown",
"headings": [
"Introduction",
"JC69",
"K80",
"F81",
"HKY85",
"TN93",
"F84",
"GTR",
"UNREST",
"References"
],
"created": "2018-09-18 20:47:50",
"modified": "2020-02-28 15:14:00",
"commits": 7
}
],
"_score": 5.494154594018443,
"_indexed": true,
"_nocasepkg": "jackalope",
"_universes": [
"lucasnell"
],
"_binaries": [
{
"r": "4.7.0",
"os": "linux",
"version": "1.1.6",
"date": "2026-10-13T12:18:40.000Z",
"distro": "resolute",
"arch": "aarch64",
"commit": "b119c7728dc909e12347dbb2165309756d7cf84f",
"fileid": "https://r2.ropensci.org/a9593a1b80d00f09bbb5e2d9360849b85e07db1c0ce934275f1ec613b0772d24",
"status": "success",
"check": "OK",
"buildurl": "https://github.com/r-universe/lucasnell/actions/runs/38395421687"
},
{
"r": "4.7.0",
"os": "linux",
"version": "1.1.6",
"date": "2026-10-13T12:19:00.000Z",
"distro": "resolute",
"arch": "x86_64",
"commit": "b119c7728dc909e12347dbb2165309756d7cf84f",
"fileid": "https://r2.ropensci.org/dba496374d54854c62d064f6938be5122baad5240ab24f38d898063900890dca",
"status": "success",
"check": "OK",
"buildurl": "https://github.com/r-universe/lucasnell/actions/runs/38395421687"
},
{
"r": "4.6.1",
"os": "linux",
"version": "1.1.6",
"date": "2026-10-13T12:18:37.000Z",
"distro": "resolute",
"arch": "aarch64",
"commit": "b119c7728dc909e12347dbb2165309756d7cf84f",
"fileid": "https://r2.ropensci.org/8b8e48aa1809163e985352842b35a94ae8baf479b80a4b99d7774c2e3c8b2036",
"status": "success",
"check": "OK",
"buildurl": "https://github.com/r-universe/lucasnell/actions/runs/38395421687"
},
{
"r": "4.6.1",
"os": "linux",
"version": "1.1.6",
"date": "2026-10-13T12:19:02.000Z",
"distro": "resolute",
"arch": "x86_64",
"commit": "b119c7728dc909e12347dbb2165309756d7cf84f",
"fileid": "https://r2.ropensci.org/bd5ae8ef41590bffddc705512a1c8539f18f92b10b657586aacf7640620d2be9",
"status": "success",
"check": "OK",
"buildurl": "https://github.com/r-universe/lucasnell/actions/runs/38395421687"
},
{
"r": "4.5.3",
"os": "mac",
"version": "1.1.6",
"date": "2026-10-13T12:39:24.000Z",
"arch": "aarch64",
"commit": "b119c7728dc909e12347dbb2165309756d7cf84f",
"fileid": "https://r2.ropensci.org/f5a5a6cae9789992c14c550fe8a8636a3cbd49a26dbc18fb988a707ff860ccc3",
"status": "success",
"check": "OK",
"buildurl": "https://github.com/r-universe/lucasnell/actions/runs/38395421687"
},
{
"r": "4.5.3",
"os": "mac",
"version": "1.1.6",
"date": "2026-10-13T12:35:42.000Z",
"arch": "x86_64",
"commit": "b119c7728dc909e12347dbb2165309756d7cf84f",
"fileid": "https://r2.ropensci.org/0976ccac54274030eea32c42e4a28758a51bcb7d882b3a7b8da3e7201ae8b3a7",
"status": "success",
"check": "OK",
"buildurl": "https://github.com/r-universe/lucasnell/actions/runs/38395421687"
},
{
"r": "4.6.1",
"os": "mac",
"version": "1.1.6",
"date": "2026-10-13T12:38:11.000Z",
"arch": "aarch64",
"commit": "b119c7728dc909e12347dbb2165309756d7cf84f",
"fileid": "https://r2.ropensci.org/1a3010bea4b02c1b200f5021f99e3a024c32ff5342360c57fa85f7fb7882481c",
"status": "success",
"check": "OK",
"buildurl": "https://github.com/r-universe/lucasnell/actions/runs/38395421687"
},
{
"r": "4.6.1",
"os": "mac",
"version": "1.1.6",
"date": "2026-10-13T12:39:34.000Z",
"arch": "x86_64",
"commit": "b119c7728dc909e12347dbb2165309756d7cf84f",
"fileid": "https://r2.ropensci.org/40780373697d8225e0bbb3f019d41a3693c54cd0ab991f71d032b3eb57770226",
"status": "success",
"check": "OK",
"buildurl": "https://github.com/r-universe/lucasnell/actions/runs/38395421687"
},
{
"r": "4.7.0",
"os": "win",
"version": "1.1.6",
"date": "2026-10-13T12:21:53.000Z",
"arch": "aarch64",
"commit": "b119c7728dc909e12347dbb2165309756d7cf84f",
"fileid": "https://r2.ropensci.org/0c62bfaeb500441d68288de2f98bb3e462650bf84fb91360902c2c829f3c7709",
"status": "success",
"check": "OK",
"buildurl": "https://github.com/r-universe/lucasnell/actions/runs/38395421687"
},
{
"r": "4.7.0",
"os": "win",
"version": "1.1.6",
"date": "2026-10-13T12:18:15.000Z",
"arch": "x86_64",
"commit": "b119c7728dc909e12347dbb2165309756d7cf84f",
"fileid": "https://r2.ropensci.org/bcbcd8ac372d3678e78c755c45a6370562b759ce7b13f0140ec6a87d548c4dbe",
"status": "success",
"check": "OK",
"buildurl": "https://github.com/r-universe/lucasnell/actions/runs/38395421687"
},
{
"r": "4.5.3",
"os": "win",
"version": "1.1.6",
"date": "2026-10-13T12:18:05.000Z",
"arch": "x86_64",
"commit": "b119c7728dc909e12347dbb2165309756d7cf84f",
"fileid": "https://r2.ropensci.org/7664fd615a3fbb1d9fd1e16c31b7b6d8746500128f54a720f456556c4195b99c",
"status": "success",
"check": "OK",
"buildurl": "https://github.com/r-universe/lucasnell/actions/runs/38395421687"
},
{
"r": "4.6.1",
"os": "win",
"version": "1.1.6",
"date": "2026-10-13T12:22:05.000Z",
"arch": "aarch64",
"commit": "b119c7728dc909e12347dbb2165309756d7cf84f",
"fileid": "https://r2.ropensci.org/1fa3f20f6c0c1a1d6d79e8987634462e10fce5a2269a44a064945b0a14dc637d",
"status": "success",
"check": "OK",
"buildurl": "https://github.com/r-universe/lucasnell/actions/runs/38395421687"
},
{
"r": "4.6.1",
"os": "win",
"version": "1.1.6",
"date": "2026-10-13T12:18:10.000Z",
"arch": "x86_64",
"commit": "b119c7728dc909e12347dbb2165309756d7cf84f",
"fileid": "https://r2.ropensci.org/a5bb24b715804302230f5f2ce0e3143a1ecc89660a5bbb3f3ecbb6083c9d1323",
"status": "success",
"check": "OK",
"buildurl": "https://github.com/r-universe/lucasnell/actions/runs/38395421687"
}
]
}