{ "_id": "6acce484a14063b82c3aa530", "Package": "MIPanalyzer", "Type": "Package", "Title": "Filtering and analysis of MIP data", "Version": "1.1.0", "Authors@R": "as.person(c(\n\"Bob Verity [aut, cre]\"\n))", "Description": "Filtering and analysis of MIP data.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "SystemRequirements": "C++11", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libgdal-dev gdal-bin libgeos-dev make\nlibicu-dev libuv1-dev libssl-dev libproj-dev libsqlite3-dev", "Repository": "https://plasmogenepi.r-universe.dev", "Date/Publication": "2023-12-12 13:45:23 UTC", "RemoteUrl": "https://github.com/mrc-ide/MIPanalyzer", "RemoteRef": "HEAD", "RemoteSha": "72f692e8c70b607f8ae65dfaf3d2e417acb8582d", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-12 13:32:28 UTC", "User": "root" }, "Author": "Bob Verity [aut, cre]", "Maintainer": "Bob Verity ", "_user": "plasmogenepi", "_type": "src", "_file": "MIPanalyzer_1.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/65c2ddc620e0fd6f0d80ba70d25ef8a545d9e5fc2cc5e41e2933f9285686c38f", "_filesize": 2750271, "_sha256": "65c2ddc620e0fd6f0d80ba70d25ef8a545d9e5fc2cc5e41e2933f9285686c38f", "_expires": "2027-01-20T13:45:38.000Z", "_created": "2026-10-12T13:32:28.000Z", "_published": "2026-10-12T13:45:40.371Z", "_buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38255866882", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 114835837267, "time": 254, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "11750497889" }, { "job": 114835837150, "time": 267, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11750922440" }, { "job": 114835837129, "time": 227, "config": "linux-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11750917275" }, { "job": 114835837128, "time": 245, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11750917313" }, { "job": 114835837051, "time": 195, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11749844198" }, { "job": 114835837142, "time": 712, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11750933225" }, { "job": 114835837262, "time": 264, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11749729590" }, { "job": 114835837099, "time": 509, "config": "macos-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11750743374" }, { "job": 114833780239, "time": 312, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11749663658" }, { "job": 114835837065, "time": 170, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11749569137" }, { "job": 114835837109, "time": 350, "config": "windows-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "11750752982" }, { "job": 114835837151, "time": 300, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11750692862" }, { "job": 114835837238, "time": 263, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11750897455" }, { "job": 114835837182, "time": 339, "config": "windows-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11750673052" }, { "job": 114835837153, "time": 261, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11750652838" } ], "_upstream": "https://github.com/mrc-ide/MIPanalyzer", "_commit": { "id": "72f692e8c70b607f8ae65dfaf3d2e417acb8582d", "author": "bobverity ", "committer": "GitHub ", "message": "Merge pull request #17 from mrc-ide/develop\n\nDevelop", "time": 1702388723 }, "_maintainer": { "name": "Bob Verity", "email": "r.verity@imperial.ac.uk", "login": "bobverity", "description": "", "uuid": 9216594 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "role": "Imports" }, { "package": "vcfR", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "plotly", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ape", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "rworldmap", "role": "Imports" }, { "package": "coda", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "here", "role": "Suggests" }, { "package": "kableExtra", "role": "Suggests" }, { "package": "tidyverse", "role": "Suggests" } ], "_owner": "mrc-ide", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 2, "_contributors": [ { "user": "bobverity", "count": 45, "uuid": 9216594 }, { "user": "ojwatson", "count": 10, "uuid": 15249565 } ], "_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/MIPanalyzer" }, "_devurl": "https://github.com/mrc-ide/mipanalyzer", "_searchresults": 39, "_topics": [ "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/MIPanalyzer.html", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_cranurl": false, "_exports": [ "check_MIPanalyzer_loaded", "explore_filter_coverage_loci", "explore_filter_coverage_samples", "filter_counts", "filter_coverage_loci", "filter_coverage_samples", "filter_loci", "filter_loci_invariant", "filter_overcounts", "filter_samples", "filter_wsaf", "get_genomic_distance", "get_IB_mixture", "get_IBS_distance", "get_spatial_distance", "get_wsaf", "inbreeding_mle", "is.mipanalyzer_biallelic", "is.mipanalyzer_multiallelic", "lonlat_to_bearing", "mipanalyzer_biallelic_to_vcfR", "mipanalyzer_file", "pca_wsaf", "pcoa_genomic_distance", "Pf_chrom_lengths", "plot_coverage", "plot_distance", "plot_map", "plot_pca", "plot_pca_contribution", "plot_pca_variance", "plot_pcoa", "plot_wsaf", "rbetabinom", "rdirichlet", "sim_biallelic", "vcf_to_mipanalyzer_biallelic", "vcf_to_mipanalyzer_multiallelic" ], "_help": [ { "page": "check_MIPanalyzer_loaded", "title": "Check that MIPanalyzer package has loaded successfully", "topics": [ "check_MIPanalyzer_loaded" ] }, { "page": "explore_filter_coverage_loci", "title": "Explore locus coverage prior to filtering", "topics": [ "explore_filter_coverage_loci" ] }, { "page": "explore_filter_coverage_samples", "title": "Explore sample coverage prior to filtering", "topics": [ "explore_filter_coverage_samples" ] }, { "page": "filter_counts", "title": "Filter alleles based on raw counts", "topics": [ "filter_counts" ] }, { "page": "filter_coverage_loci", "title": "Filter loci based on coverage", "topics": [ "filter_coverage_loci" ] }, { "page": "filter_coverage_samples", "title": "Filter samples based on coverage", "topics": [ "filter_coverage_samples" ] }, { "page": "filter_loci", "title": "Filter out some loci", "topics": [ "filter_loci" ] }, { "page": "filter_loci_invariant", "title": "Filter loci to drop invariant sites", "topics": [ "filter_loci_invariant" ] }, { "page": "filter_overcounts", "title": "Filter out over-counts", "topics": [ "filter_overcounts" ] }, { "page": "filter_samples", "title": "Filter out some samples", "topics": [ "filter_samples" ] }, { "page": "filter_wsaf", "title": "Filter alleles based on within-sample allele frequencies", "topics": [ "filter_wsaf" ] }, { "page": "get_genomic_distance", "title": "Get genomic distance between samples", "topics": [ "get_genomic_distance" ] }, { "page": "get_IB_mixture", "title": "Get identity by mixture", "topics": [ "get_IB_mixture" ] }, { "page": "get_IBS_distance", "title": "Get identity by state (IBS) distance", "topics": [ "get_IBS_distance" ] }, { "page": "get_spatial_distance", "title": "Get great circle distance between spatial points", "topics": [ "get_spatial_distance" ] }, { "page": "get_wsaf", "title": "Get within-sample allele frequencies", "topics": [ "get_wsaf" ] }, { "page": "inbreeding_mle", "title": "Estimate pairwise inbreeding coefficient F by maximum likelihood", "topics": [ "inbreeding_mle" ] }, { "page": "is.mipanalyzer_biallelic", "title": "Determine if object is of class mipanalyzer_biallelic", "topics": [ "is.mipanalyzer_biallelic" ] }, { "page": "is.mipanalyzer_multiallelic", "title": "Determine if object is of class mipanalyzer_multiallelic", "topics": [ "is.mipanalyzer_multiallelic" ] }, { "page": "lonlat_to_bearing", "title": "Calculate great circle distance and bearing between coordinates", "topics": [ "lonlat_to_bearing" ] }, { "page": "MIPanalyzer", "title": "MIPanalyzer", "topics": [ "MIPanalyzer-package", "MIPanalyzer" ] }, { "page": "mipanalyzer_biallelic_to_vcfR", "title": "Converts a MIPanalyzer biallelic object to vcfR", "topics": [ "mipanalyzer_biallelic_to_vcfR" ] }, { "page": "mipanalyzer_file", "title": "Load system file", "topics": [ "mipanalyzer_file" ] }, { "page": "pca_wsaf", "title": "PCA of within-sample allele frequencies", "topics": [ "pca_wsaf" ] }, { "page": "pcoa_genomic_distance", "title": "PCoA of genomic distances between samples", "topics": [ "pcoa_genomic_distance" ] }, { "page": "Pf_chrom_lengths", "title": "Get dataframe of P.falciparum chromosome lengths", "topics": [ "Pf_chrom_lengths" ] }, { "page": "plot_coverage", "title": "Plot coverage matrix", "topics": [ "plot_coverage" ] }, { "page": "plot_distance", "title": "Plot a distance matrix", "topics": [ "plot_distance" ] }, { "page": "plot_map", "title": "Produce ggplot map", "topics": [ "plot_map" ] }, { "page": "plot_pca", "title": "Plot PCA", "topics": [ "plot_pca" ] }, { "page": "plot_pca_contribution", "title": "Plot PCA contribution of each variable", "topics": [ "plot_pca_contribution" ] }, { "page": "plot_pca_variance", "title": "Plot variance explained by PCA components", "topics": [ "plot_pca_variance" ] }, { "page": "plot_pcoa", "title": "Plot PCoA", "topics": [ "plot_pcoa" ] }, { "page": "plot_wsaf", "title": "Plot within-sample allele frequencies", "topics": [ "plot_wsaf" ] }, { "page": "print.mipanalyzer_biallelic", "title": "Custom print function for class mipanalyzer_biallelic", "topics": [ "print.mipanalyzer_biallelic" ] }, { "page": "print.mipanalyzer_multiallelic", "title": "Custom print function for class mipanalyzer_multiallelic", "topics": [ "print.mipanalyzer_multiallelic" ] }, { "page": "rbetabinom", "title": "Draw from Beta-binomial distribution", "topics": [ "rbetabinom" ] }, { "page": "rdirichlet", "title": "Draw from Dirichlet distribution", "topics": [ "rdirichlet" ] }, { "page": "sim_biallelic", "title": "Simulate biallelic data", "topics": [ "sim_biallelic" ] }, { "page": "summary.mipanalyzer_biallelic", "title": "Print summary for class mipanalyzer_biallelic", "topics": [ "summary.mipanalyzer_biallelic" ] }, { "page": "summary.mipanalyzer_multiallelic", "title": "Print summary for class mipanalyzer_multiallelic", "topics": [ "summary.mipanalyzer_multiallelic" ] }, { "page": "vcf_to_mipanalyzer_biallelic", "title": "Convert vcf to biallelic mipanalyzer data class", "topics": [ "vcf_to_mipanalyzer_biallelic" ] }, { "page": "vcf_to_mipanalyzer_multiallelic", "title": "Convert vcf to multiallelic mipanalyzer data class", "topics": [ "vcf_to_mipanalyzer_multiallelic" ] } ], "_readme": "https://github.com/mrc-ide/MIPanalyzer/raw/HEAD/README.md", "_rundeps": [ "ape", "askpass", "base64enc", "bslib", "cachem", "cli", "cluster", "coda", "cpp11", "crosstalk", "curl", "data.table", "digest", "dotCall64", "dplyr", "evaluate", "farver", "fastmap", "fields", "fontawesome", "fs", "generics", "ggplot2", "glue", "gtable", "highr", "htmltools", "htmlwidgets", "httr", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "magrittr", "maps", "MASS", "Matrix", "memoise", "memuse", "mgcv", "mime", "nlme", "openssl", "otel", "permute", "pillar", "pinfsc50", "pkgconfig", "plotly", "plyr", "promises", "purrr", "R6", "rappdirs", "raster", "RColorBrewer", "Rcpp", "reshape2", "rlang", "rmarkdown", "rworldmap", "S7", "sass", "scales", "sp", "spam", "stringi", "stringr", "sys", "terra", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vcfR", "vctrs", "vegan", "viridisLite", "withr", "xfun", "yaml" ], "_sysdeps": [ { "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": "structure_analysis.Rmd", "filename": "structure_analysis.html", "title": "Analysis of population structure", "author": "Bob Verity", "engine": "knitr::rmarkdown", "headings": [ "Principal Component Analysis (PCA)", "Principal Coordinates Analysis (PCoA) from genetic distances" ], "created": "2023-12-12 12:28:14", "modified": "2023-12-12 13:43:50", "commits": 2 }, { "source": "genetic_distances.Rmd", "filename": "genetic_distances.html", "title": "Comparing genetic distances", "author": "Bob Verity", "engine": "knitr::rmarkdown", "headings": [ "Estimating relatedness between samples", "Comparing different distance metrics" ], "created": "2023-12-12 12:28:14", "modified": "2023-12-12 13:43:50", "commits": 2 }, { "source": "installation.Rmd", "filename": "installation.html", "title": "Installation", "engine": "knitr::knitr", "headings": [ "Installing Rcpp", "Installing and loading MIPanalyzer" ], "created": "2023-12-11 05:02:11", "modified": "2023-12-12 13:43:50", "commits": 2 }, { "source": "filtering_data.Rmd", "filename": "filtering_data.html", "title": "Reading in and filtering data", "author": "Bob Verity", "engine": "knitr::rmarkdown", "headings": [ "Reading in data and understanding the mipanalyzer_biallelic format", "Filtering data based on coverage", "Filtering based on other criteria" ], "created": "2023-12-11 05:02:11", "modified": "2023-12-12 12:28:14", "commits": 2 } ], "_score": 4.193124598354462, "_indexed": false, "_nocasepkg": "mipanalyzer", "_universes": [ "plasmogenepi" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.0", "date": "2026-10-12T13:35:27.000Z", "distro": "resolute", "arch": "aarch64", "commit": "72f692e8c70b607f8ae65dfaf3d2e417acb8582d", "fileid": "https://r2.ropensci.org/3f79af7d509ed62976d5f15ef147b04a44f82f7e57b6e7060dafece085172e94", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38255866882" }, { "r": "4.7.0", "os": "linux", "version": "1.1.0", "date": "2026-10-12T13:35:40.000Z", "distro": "resolute", "arch": "x86_64", "commit": "72f692e8c70b607f8ae65dfaf3d2e417acb8582d", "fileid": "https://r2.ropensci.org/f2f35998b6f7127f101c8bd3f0a2d6ed944826d0ac8e80ee19f1efec121d97cb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38255866882" }, { "r": "4.6.1", "os": "linux", "version": "1.1.0", "date": "2026-10-12T13:35:11.000Z", "distro": "resolute", "arch": "aarch64", "commit": "72f692e8c70b607f8ae65dfaf3d2e417acb8582d", "fileid": "https://r2.ropensci.org/6b844aa78808031948755ca9be8762a0de4a4e47d0fd9311b2b75d679dd11d78", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38255866882" }, { "r": "4.6.1", "os": "linux", "version": "1.1.0", "date": "2026-10-12T13:35:26.000Z", "distro": "resolute", "arch": "x86_64", "commit": "72f692e8c70b607f8ae65dfaf3d2e417acb8582d", "fileid": "https://r2.ropensci.org/d20f50ec914476e30aeed23c1871692c6ae0850b60e6647118166509c825e980", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38255866882" }, { "r": "4.5.3", "os": "mac", "version": "1.1.0", "date": "2026-10-12T13:34:53.000Z", "arch": "aarch64", "commit": "72f692e8c70b607f8ae65dfaf3d2e417acb8582d", "fileid": "https://r2.ropensci.org/31edf3477a8b0a61d9ac1cb8be8b9b57dc7808100e1c31e5631da679d0b8f0e4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38255866882" }, { "r": "4.5.3", "os": "mac", "version": "1.1.0", "date": "2026-10-12T13:38:07.000Z", "arch": "x86_64", "commit": "72f692e8c70b607f8ae65dfaf3d2e417acb8582d", "fileid": "https://r2.ropensci.org/7e174db35c16a0ebe75287f9bd141a4c0449d25a49189fa8ca5393ec685d2bd9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38255866882" }, { "r": "4.6.1", "os": "mac", "version": "1.1.0", "date": "2026-10-12T13:35:26.000Z", "arch": "aarch64", "commit": "72f692e8c70b607f8ae65dfaf3d2e417acb8582d", "fileid": "https://r2.ropensci.org/2f4103a61e3287b2457d1a3f14cdff38d823c4ccddbfe8cbcff25690ee7c4924", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38255866882" }, { "r": "4.6.1", "os": "mac", "version": "1.1.0", "date": "2026-10-12T13:37:47.000Z", "arch": "x86_64", "commit": "72f692e8c70b607f8ae65dfaf3d2e417acb8582d", "fileid": "https://r2.ropensci.org/cf3b3ae3ab5fdd1976a23441c67e48af42df1acc8612b4401ac09f4cc4af9ce1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38255866882" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.0", "date": "2026-10-12T13:35:53.000Z", "arch": "emscripten", "commit": "72f692e8c70b607f8ae65dfaf3d2e417acb8582d", "fileid": "https://r2.ropensci.org/9eb54aa684b8b39febc07af077abd1ba2f38ba61635c324a9dfb1d2e03e4ec74", "status": "success", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38255866882" }, { "r": "4.7.0", "os": "win", "version": "1.1.0", "date": "2026-10-12T13:36:38.000Z", "arch": "aarch64", "commit": "72f692e8c70b607f8ae65dfaf3d2e417acb8582d", "fileid": "https://r2.ropensci.org/72544360e5ec854536a7ccf76659a5922cfe26b6ce502e39914515be61ff65e0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38255866882" }, { "r": "4.7.0", "os": "win", "version": "1.1.0", "date": "2026-10-12T13:34:22.000Z", "arch": "x86_64", "commit": "72f692e8c70b607f8ae65dfaf3d2e417acb8582d", "fileid": "https://r2.ropensci.org/c54fc5dbc01e14c2d8c940bc30fd6126095201fbe15567bcfc522df65e570e54", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38255866882" }, { "r": "4.5.3", "os": "win", "version": "1.1.0", "date": "2026-10-12T13:34:31.000Z", "arch": "x86_64", "commit": "72f692e8c70b607f8ae65dfaf3d2e417acb8582d", "fileid": "https://r2.ropensci.org/dcf1dfe5f9c2efaf322ac247c9e9084c0ed2527e66c1e04a0afad523bbf6171d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38255866882" }, { "r": "4.6.1", "os": "win", "version": "1.1.0", "date": "2026-10-12T13:36:20.000Z", "arch": "aarch64", "commit": "72f692e8c70b607f8ae65dfaf3d2e417acb8582d", "fileid": "https://r2.ropensci.org/ce4596c9aff8567bca01d733c442907f9b4905eeab534f6230c301ab9af4f74c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38255866882" }, { "r": "4.6.1", "os": "win", "version": "1.1.0", "date": "2026-10-12T13:34:35.000Z", "arch": "x86_64", "commit": "72f692e8c70b607f8ae65dfaf3d2e417acb8582d", "fileid": "https://r2.ropensci.org/5e89c253f053e72be014241598b28de263eb2f42f9d91959686e3da1abc8a58b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38255866882" } ] }