{ "_id": "6a310a173efcd9bda4357252", "Package": "isoRelate", "Title": "Identity-by-Descent Inference of Haploid Recombining Organisms", "Version": "0.1.0", "Authors@R": "person(\"Lyndal\", \"Henden\", email = \"lyndal_henden@hotmail.com\", role = c(\"aut\", \"cre\"))", "Description": "Pairwise identity by descent inference of haploid species\nusing single nucleotide polymorphism data. isoRelate can detect\nIBD in the presence of multi-clonal infections and also\nprovides a function for identifying loci under recent positive\nselection.", "License": "MIT + file LICENSE", "LazyData": "TRUE", "RoxygenNote": "6.0.1.9000", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://plasmogenepi.r-universe.dev", "Date/Publication": "2018-03-19 05:48:43 UTC", "RemoteUrl": "https://github.com/bahlolab/isoRelate", "RemoteRef": "HEAD", "RemoteSha": "109ee470f1d1e9e4cd131045c23eea7047cff649", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-16 08:26:14 UTC", "User": "root" }, "Author": "Lyndal Henden [aut, cre]", "Maintainer": "Lyndal Henden ", "MD5sum": "0a1a52d7de99dbf55fea2dff1f40695b", "_user": "plasmogenepi", "_type": "src", "_file": "isoRelate_0.1.0.tar.gz", "_fileid": "7ceb76b3c951df81ac93604ca5456232615d3170ba2baec367da105202f7b2a9", "_filesize": 1355580, "_sha256": "7ceb76b3c951df81ac93604ca5456232615d3170ba2baec367da105202f7b2a9", "_created": "2026-06-16T08:26:14.000Z", "_published": "2026-06-16T08:32:23.155Z", "_distro": "noble", "_jobs": [ { "job": 81613251934, "time": 178, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "7661328439" }, { "job": 81613251941, "time": 176, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7661327583" }, { "job": 81613251921, "time": 170, "config": "linux-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7661325310" }, { "job": 81613251989, "time": 164, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7661322769" }, { "job": 81613252083, "time": 142, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7661313051" }, { "job": 81613251949, "time": 286, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "7661370377" }, { "job": 81613251939, "time": 130, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7661308691" }, { "job": 81613251924, "time": 293, "config": "macos-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7661373661" }, { "job": 81612521058, "time": 238, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7661256154" }, { "job": 81613251913, "time": 137, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7661311381" }, { "job": 81613251928, "time": 237, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7661353267" }, { "job": 81613251927, "time": 161, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7661321130" }, { "job": 81613251932, "time": 160, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7661320989" } ], "_buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27604304497", "_status": "failure", "_host": "GitHub-Actions", "_upstream": "https://github.com/bahlolab/isoRelate", "_commit": { "id": "109ee470f1d1e9e4cd131045c23eea7047cff649", "author": "Lyndal Henden ", "committer": "Lyndal Henden ", "message": "added citation file\n", "time": 1521438523 }, "_maintainer": { "name": "Lyndal Henden", "email": "lyndal_henden@hotmail.com", "login": "lyndal-h", "description": "", "uuid": 90087687 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.2.1", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 0.12.5", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "ggplot2", "version": ">= 2.1.0", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "intergraph", "role": "Imports" }, { "package": "ggnetwork", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bahlolab", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "performs", "cpp" ], "_stars": 7, "_contributors": [ { "user": "lyndal", "count": 29, "uuid": 13774769 } ], "_userbio": { "uuid": 140542976, "type": "organization", "name": "PlasmoGenEpi", "followers": 1, "description": "We are a network of scientists who have come together since 2018 to address challenges in malaria genomic epidemiology." }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/isoRelate" }, "_devurl": "https://github.com/bahlolab/isorelate", "_searchresults": 8, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/isoRelate.html", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_cranurl": false, "_exports": [ "calculateMissingness", "calculatePopAlleleFreq", "getGenotypes", "getIBDiclusters", "getIBDiR", "getIBDmatrix", "getIBDparameters", "getIBDpclusters", "getIBDposterior", "getIBDproportion", "getIBDsegments", "getIBDsummary", "groupPairs", "IBDMatrix", "isolatePairs", "plotIBDclusters", "plotIBDiR", "plotIBDproportions", "plotIBDsegments" ], "_datasets": [ { "name": "annotation_genes", "title": "Plasmodium Falciparum Gene Annotation Dataset", "object": "annotation_genes", "class": [ "data.frame" ], "fields": [ "chr", "start", "end", "strand", "name", "gene_id" ], "rows": 5777, "table": true, "tojson": true }, { "name": "highlight_genes", "title": "Plasmodium Falciparum Gene Highlight Dataset", "object": "highlight_genes", "class": [ "data.frame" ], "fields": [ "chr", "start", "end", "name", "gene_id" ], "rows": 31, "table": true, "tojson": true }, { "name": "my_ibd", "title": "IBD Segments For The Papua New Guinea Dataset", "object": "my_ibd", "class": [ "data.frame" ], "fields": [ "fid1", "iid1", "fid2", "iid2", "chr", "start_snp", "end_snp", "start_position_bp", "end_position_bp", "start_position_M", "end_position_M", "number_snps", "length_bp", "length_M", "ibd_status" ], "rows": 331, "table": true, "tojson": true }, { "name": "png_genotypes", "title": "Filtered Genotypes For The Papua New Guinea Dataset", "object": "png_genotypes", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "png_ibd", "title": "IBD Segments For The Papua New Guinea Dataset", "object": "png_ibd", "class": [ "data.frame" ], "fields": [ "fid1", "iid1", "fid2", "iid2", "chr", "start_snp", "end_snp", "start_position_bp", "end_position_bp", "start_position_M", "end_position_M", "number_snps", "length_bp", "length_M", "ibd_status" ], "rows": 331, "table": true, "tojson": true }, { "name": "png_parameters", "title": "IBD Parameter Estimates For The Papua New Guinea Dataset", "object": "png_parameters", "class": [ "data.frame" ], "fields": [ "fid1", "iid1", "fid2", "iid2", "m", "ibd0", "ibd1", "ibd2" ], "rows": 666, "table": true, "tojson": true }, { "name": "png_pedmap", "title": "Papua New Guinea Plasmodium Falciparum Dataset", "object": "png_pedmap", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "AmatrixDD", "title": "The matrix A in the equation Ax=b for 2 diploid chromosomes", "topics": [ "AmatrixDD" ] }, { "page": "AmatrixHD", "title": "The matrix A in the equation Ax=b for 1 haploid and 1 diploid chromosome", "topics": [ "AmatrixHD" ] }, { "page": "AmatrixHH", "title": "The matrix A in the equation Ax=b for 2 haploid chromosomes", "topics": [ "AmatrixHH" ] }, { "page": "annotation_genes", "title": "Plasmodium Falciparum Gene Annotation Dataset", "topics": [ "annotation_genes" ] }, { "page": "areColors", "title": "Internal function", "topics": [ "areColors" ] }, { "page": "bVectorDD", "title": "The vector b in the equation Ax=b for 2 diploid chromosomes", "topics": [ "bVectorDD" ] }, { "page": "bVectorHD", "title": "The vector b in the equation Ax=b for 1 haploid chromosome and 1 diploid chromosome", "topics": [ "bVectorHD" ] }, { "page": "bVectorHH", "title": "The vector b in the equation Ax=b for 2 haploid chromosomes", "topics": [ "bVectorHH" ] }, { "page": "calculateAlpha", "title": "Calculate alpha", "topics": [ "calculateAlpha" ] }, { "page": "calculateBeta", "title": "Calculate beta", "topics": [ "calculateBeta" ] }, { "page": "calculateGamma", "title": "Calculate gamma", "topics": [ "calculateGamma" ] }, { "page": "calculateLogLikelihood", "title": "Calculate the log-likelihood of the data", "topics": [ "calculateLogLikelihood" ] }, { "page": "calculateMeiosis", "title": "Estimation of Meiosis", "topics": [ "calculateMeiosis" ] }, { "page": "calculateMissingness", "title": "Calculate Missingness Proportions", "topics": [ "calculateMissingness" ] }, { "page": "calculatePopAlleleFreq", "title": "Calculate Allele Frequencies for SNPs from Genotype Data", "topics": [ "calculatePopAlleleFreq" ] }, { "page": "calculateScale", "title": "Calculate scale", "topics": [ "calculateScale" ] }, { "page": "calculateViterbi", "title": "Calculate the Viterbi sequence", "topics": [ "calculateViterbi" ] }, { "page": "clusterSummary", "title": "A function that prints summary information of clusters", "topics": [ "clusterSummary" ] }, { "page": "emissionProbDD", "title": "The emission probabilities for 2 diploid chromosomes", "topics": [ "emissionProbDD" ] }, { "page": "emissionProbHD", "title": "The emission probabilities for 1 haploid chromosome and 1 diploid chromosome", "topics": [ "emissionProbHD" ] }, { "page": "emissionProbHH", "title": "The emission probabilities for 2 haploid chromosomes", "topics": [ "emissionProbHH" ] }, { "page": "emissionProbMissingGeno", "title": "Calculating the emission probability sumation when missing genotype calls present", "topics": [ "emissionProbMissingGeno" ] }, { "page": "genotypeErrorD", "title": "The genotyping error probability for 1 diploid chromosome", "topics": [ "genotypeErrorD" ] }, { "page": "genotypeErrorH", "title": "The genotyping error probability for 1 haploid chromosome", "topics": [ "genotypeErrorH" ] }, { "page": "getColourPaletteMajor", "title": "IsoRelate Colour Palette for groups", "topics": [ "getColourPaletteMajor" ] }, { "page": "getColourPaletteMinor", "title": "'getColourPaletteMinor()' generates a specified number of shades of a given colour.", "topics": [ "getColourPaletteMinor" ] }, { "page": "getGenotypes", "title": "Pre-Analysis Data Processing", "topics": [ "getGenotypes" ] }, { "page": "getIBDiclusters", "title": "Interval Cluster Networks", "topics": [ "getIBDiclusters" ] }, { "page": "getIBDiR", "title": "Selection Significance Statistic", "topics": [ "getIBDiR" ] }, { "page": "getIBDmatrix", "title": "Binary IBD Matrix", "topics": [ "getIBDmatrix" ] }, { "page": "getIBDparameters", "title": "Parameter Estimation", "topics": [ "getIBDparameters" ] }, { "page": "getIBDpclusters", "title": "Genome Cluster Networks", "topics": [ "getIBDpclusters" ] }, { "page": "getIBDposterior", "title": "IBD Posterior Probabilities", "topics": [ "getIBDposterior" ] }, { "page": "getIBDproportion", "title": "Proportion of Pairs IBD", "topics": [ "getIBDproportion" ] }, { "page": "getIBDsegments", "title": "IBD Segment Detection", "topics": [ "getIBDsegments" ] }, { "page": "getIBDsummary", "title": "IBD Segment Summary", "topics": [ "getIBDsummary" ] }, { "page": "getOverlap", "title": "function to find IBD that overlap interval", "topics": [ "getOverlap" ] }, { "page": "groupPairs", "title": "Group Combinations for Analysis", "topics": [ "groupPairs" ] }, { "page": "haplotypeToGenotype", "title": "Call Genotypes from Haplotype Data", "topics": [ "haplotypeToGenotype" ] }, { "page": "highlight_genes", "title": "Plasmodium Falciparum Gene Highlight Dataset", "topics": [ "highlight_genes" ] }, { "page": "IBDLabel", "title": "Internal Function", "topics": [ "IBDLabel" ] }, { "page": "IBDMatrix", "title": "Binary Matrix of IBD", "topics": [ "IBDMatrix" ] }, { "page": "IBDparameters", "title": "IBDparameters() calculates IBD probabilities then estimates the number of meiosis for an isolate pair.", "topics": [ "IBDparameters" ] }, { "page": "IBDTable", "title": "Internal Function", "topics": [ "IBDTable" ] }, { "page": "iRfunction", "title": "Internal Function", "topics": [ "iRfunction" ] }, { "page": "isolatePairs", "title": "Pair Combinations for Analysis", "topics": [ "isolatePairs" ] }, { "page": "merge_lists", "title": "Internal Function", "topics": [ "merge_lists" ] }, { "page": "my_ibd", "title": "IBD Segments For The Papua New Guinea Dataset", "topics": [ "my_ibd" ] }, { "page": "plotIBDclusters", "title": "Plot Cluster Networks", "topics": [ "plotIBDclusters" ] }, { "page": "plotIBDiR", "title": "Plot iR Statistics", "topics": [ "plotIBDiR" ] }, { "page": "plotIBDproportions", "title": "Plot The Proportion of Pairs IBD", "topics": [ "plotIBDproportions" ] }, { "page": "plotIBDsegments", "title": "Plot IBD Segments", "topics": [ "plotIBDsegments" ] }, { "page": "png_genotypes", "title": "Filtered Genotypes For The Papua New Guinea Dataset", "topics": [ "png_genotypes" ] }, { "page": "png_ibd", "title": "IBD Segments For The Papua New Guinea Dataset", "topics": [ "png_ibd" ] }, { "page": "png_parameters", "title": "IBD Parameter Estimates For The Papua New Guinea Dataset", "topics": [ "png_parameters" ] }, { "page": "png_pedmap", "title": "Papua New Guinea Plasmodium Falciparum Dataset", "topics": [ "png_pedmap" ] }, { "page": "roundDecimal", "title": "Round digits to specified decimal places", "topics": [ "roundDecimal" ] }, { "page": "transitionProbDD", "title": "The transition probabilities for 2 diploid chromosomes", "topics": [ "transitionProbDD" ] }, { "page": "transitionProbHD", "title": "The transition probabilities for 1 haploid and 1 diploid chromosome", "topics": [ "transitionProbHD" ] }, { "page": "transitionProbHH", "title": "The transition probabilities for 2 haploid chromosomes", "topics": [ "transitionProbHH" ] }, { "page": "trueGenotypes", "title": "Matrices of all possible genotype combinations between pairs, given MOI", "topics": [ "trueGenotypes" ] } ], "_readme": "https://github.com/bahlolab/isoRelate/raw/HEAD/README.md", "_rundeps": [ "cli", "coda", "codetools", "cpp11", "data.table", "doParallel", "farver", "foreach", "ggnetwork", "ggplot2", "ggrepel", "glue", "gtable", "igraph", "intergraph", "isoband", "iterators", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "network", "pillar", "pkgconfig", "R6", "RColorBrewer", "Rcpp", "rlang", "S7", "scales", "sna", "statnet.common", "tibble", "utf8", "vctrs", "viridisLite", "withr" ], "_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" } ], "_score": 2.5440680443502757, "_indexed": false, "_nocasepkg": "isorelate", "_universes": [ "plasmogenepi" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.0", "date": "2026-06-16T08:29:04.000Z", "distro": "noble", "arch": "aarch64", "commit": "109ee470f1d1e9e4cd131045c23eea7047cff649", "fileid": "8690a04c4a35e0a55ebd0cf8e02195abad3641843e9132954361aafc2549759b", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27604304497" }, { "r": "4.7.0", "os": "linux", "version": "0.1.0", "date": "2026-06-16T08:28:55.000Z", "distro": "noble", "arch": "x86_64", "commit": "109ee470f1d1e9e4cd131045c23eea7047cff649", "fileid": "8c24737dfeba7173de99da5ec6298ac26d4475f1afe773c5e0a13a3c7eefe2c1", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27604304497" }, { "r": "4.6.0", "os": "linux", "version": "0.1.0", "date": "2026-06-16T08:28:59.000Z", "distro": "noble", "arch": "aarch64", "commit": "109ee470f1d1e9e4cd131045c23eea7047cff649", "fileid": "85c5d2922c0bd7c3e592449439061b382a191bbcf416f6a93993e9b29b176df5", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27604304497" }, { "r": "4.6.0", "os": "linux", "version": "0.1.0", "date": "2026-06-16T08:28:49.000Z", "distro": "noble", "arch": "x86_64", "commit": "109ee470f1d1e9e4cd131045c23eea7047cff649", "fileid": "de1d32c8a6c14240efa35cfb4d4c9fc1a34b9ff4f621aa81b76a4560b47ec31d", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27604304497" }, { "r": "4.5.3", "os": "mac", "version": "0.1.0", "date": "2026-06-16T08:28:34.000Z", "arch": "aarch64", "commit": "109ee470f1d1e9e4cd131045c23eea7047cff649", "fileid": "242461ab03f843f3c986eb20711cd5ec4d033565bf67c9f32b20b68833db9112", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27604304497" }, { "r": "4.5.3", "os": "mac", "version": "0.1.0", "date": "2026-06-16T08:30:10.000Z", "arch": "x86_64", "commit": "109ee470f1d1e9e4cd131045c23eea7047cff649", "fileid": "3779e14234496fbfcc37639117895d5dfbb7b25ce95363c78addaadeb841517b", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27604304497" }, { "r": "4.6.0", "os": "mac", "version": "0.1.0", "date": "2026-06-16T08:28:27.000Z", "arch": "aarch64", "commit": "109ee470f1d1e9e4cd131045c23eea7047cff649", "fileid": "2106d9ab0125e5780da987c531d5fb578fb8b8fe5bf64a57a7c86a3364098b10", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27604304497" }, { "r": "4.6.0", "os": "mac", "version": "0.1.0", "date": "2026-06-16T08:30:07.000Z", "arch": "x86_64", "commit": "109ee470f1d1e9e4cd131045c23eea7047cff649", "fileid": "6c26aedb23bf1e006e025d5de87c986c0e47c5f910b6d87ffd89d169635d8dac", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27604304497" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.0", "date": "2026-06-16T08:28:54.000Z", "arch": "emscripten", "commit": "109ee470f1d1e9e4cd131045c23eea7047cff649", "fileid": "95aa4c3dce04f8cf8bec934ce214d17bb73c8ba486b12a2604aa3cfb5d4d7240", "status": "success", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27604304497" }, { "r": "4.7.0", "os": "win", "version": "0.1.0", "date": "2026-06-16T08:29:03.000Z", "arch": "x86_64", "commit": "109ee470f1d1e9e4cd131045c23eea7047cff649", "fileid": "c2d9472300820b6fc6d9cbaa86fed9c2571b50dfe7e7d3eebf7bf2d83c3a3057", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27604304497" }, { "r": "4.5.3", "os": "win", "version": "0.1.0", "date": "2026-06-16T08:28:08.000Z", "arch": "x86_64", "commit": "109ee470f1d1e9e4cd131045c23eea7047cff649", "fileid": "ecb7ae7fc64cf9c1a177775268dec8b2e0f35788080ae1aa37b1b790d1fb6569", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27604304497" }, { "r": "4.6.0", "os": "win", "version": "0.1.0", "date": "2026-06-16T08:28:00.000Z", "arch": "x86_64", "commit": "109ee470f1d1e9e4cd131045c23eea7047cff649", "fileid": "275f04742365f455349d417c1443ca4051eee34a4728aa5e344f90a1e65b1606", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/27604304497" } ] }