{ "_id": "6a1e99021d7bb097a0a6dae9", "Package": "moire", "Title": "Multiplicity of Infection and Allele Frequency Recovery from\nNoisy Polyallelic Genetics Data", "Version": "3.5.0", "Authors@R": "c(\nperson(given = \"Maxwell\",\nfamily = \"Murphy\",\nrole = c(\"aut\", \"cre\"),\nemail = \"murphy2122@berkeley.edu\",\ncomment = c(ORCID = \"0000-0003-0332-4388\")),\nperson(given = \"Bryan\",\nfamily = \"Greenhouse\",\nrole = c(\"aut\", \"ths\"),\nemail = \"bryan.greenhouse@ucsf.edu\",\ncomment = c(ORCID = \"0000-0003-0287-9111\")))", "Description": "A Markov Chain Monte Carlo (MCMC) based approach to\nBayesian estimation of individual level multiplicity of\ninfection, within host relatedness, and population allele\nfrequencies from polyallelic genetic data.", "License": "GPL (>= 3)", "Encoding": "UTF-8", "LazyData": "true", "LazyDataCompression": "bzip2", "SystemRequirements": "C++17, GNU make", "URL": "https://github.com/EPPIcenter/moire,\nhttps://eppicenter.github.io/moire/,\nhttps://eppicenter.ucsf.edu/resources", "BugReports": "https://github.com/EPPIcenter/moire/issues", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.1", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "make libicu-dev", "Repository": "https://eppicenter.r-universe.dev", "Date/Publication": "2024-11-06 21:35:57 UTC", "RemoteUrl": "https://github.com/eppicenter/moire", "RemoteRef": "HEAD", "RemoteSha": "656dcfbb827430edeffa40a0af7b44cc89f689bd", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-02 08:40:34 UTC", "User": "root" }, "Author": "Maxwell Murphy [aut, cre] (ORCID:\n),\nBryan Greenhouse [aut, ths] (ORCID:\n)", "Maintainer": "Maxwell Murphy ", "MD5sum": "f49eca448b7651e718a04c37c4528fa7", "_user": "eppicenter", "_type": "src", "_file": "moire_3.5.0.tar.gz", "_fileid": "611892f7d1af136baab1ed7132df7cab0a49b07f3c486cd454427b9177f50031", "_filesize": 4489034, "_sha256": "611892f7d1af136baab1ed7132df7cab0a49b07f3c486cd454427b9177f50031", "_created": "2026-06-02T08:40:34.000Z", "_published": "2026-06-02T08:49:06.258Z", "_distro": "noble", "_jobs": [ { "job": 79032465456, "time": 209, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7353035537" }, { "job": 79032465552, "time": 208, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7353034057" }, { "job": 79032465445, "time": 189, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7353028508" }, { "job": 79032465457, "time": 202, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7353032292" }, { "job": 79032465531, "time": 151, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7353025650" }, { "job": 79032465461, "time": 271, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7353069088" }, { "job": 79032465453, "time": 146, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7353028071" }, { "job": 79032465465, "time": 401, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7353110401" }, { "job": 79031697754, "time": 270, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7352960273" }, { "job": 79032465336, "time": 182, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7353028740" }, { "job": 79032465423, "time": 186, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7353026878" }, { "job": 79032465363, "time": 171, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7353020895" }, { "job": 79032465480, "time": 236, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7353043754" } ], "_buildurl": "https://github.com/r-universe/eppicenter/actions/runs/26808376544", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/eppicenter/moire", "_commit": { "id": "656dcfbb827430edeffa40a0af7b44cc89f689bd", "author": "Maxwell Murphy ", "committer": "Maxwell Murphy ", "message": "update article\n", "time": 1730928957 }, "_maintainer": { "name": "Maxwell Murphy", "email": "murphy2122@berkeley.edu", "login": "m-murphy", "orcid": "0000-0003-0332-4388", "twitter": "@MxMrphy", "description": "", "uuid": 5225200 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppProgress", "role": "LinkingTo" }, { "package": "RcppParallel", "role": "LinkingTo" }, { "package": "BH", "role": "LinkingTo" }, { "package": "Rcpp", "role": "Imports" }, { "package": "RcppProgress", "role": "Imports" }, { "package": "RcppParallel", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "markdown", "role": "Suggests" }, { "package": "forcats", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "parallelly", "role": "Suggests" } ], "_owner": "eppicenter", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "genomics", "malaria", "mcmc", "cpp", "openmp" ], "_stars": 7, "_contributors": [ { "user": "m-murphy", "count": 149, "uuid": 5225200 } ], "_userbio": { "uuid": 14140677, "type": "organization", "name": "EPPIcenter", "description": "A systems epidemiology approach to complex infectious disease dynamics: state-of-the-art data collection, molecular technologies, & computational analysis" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/moire" }, "_devurl": "https://github.com/eppicenter/moire", "_pkgdown": "https://eppicenter.github.io/moire/", "_searchresults": 25, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/moire.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "calculate_he", "calculate_med_allele_freqs", "calculate_naive_allele_frequencies", "calculate_naive_coi", "calculate_naive_coi_offset", "load_delimited_data", "load_long_form_data", "plot_chain_swaps", "rdirichlet", "run_mcmc", "simulate_allele_frequencies", "simulate_data", "simulate_observed_allele", "simulate_observed_genotype", "simulate_sample_coi", "simulate_sample_genotype", "summarize_allele_freq_fn", "summarize_allele_freqs", "summarize_coi", "summarize_effective_coi", "summarize_epsilon_neg", "summarize_epsilon_pos", "summarize_he", "summarize_relatedness" ], "_datasets": [ { "name": "mcmc_results", "title": "MCMC results from using the packaged simulated data and calling 'run_mcmc()'", "object": "mcmc_results", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "namibia_data", "title": "Genetic and epidemiological data from Namibia", "object": "namibia_data", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "sample_id", "HealthFacility", "HealthDistrict", "Region", "Country", "locus", "allele" ], "rows": 97214, "table": true, "tojson": true }, { "name": "regional_allele_frequencies", "title": "Allele frequencies for different regions", "object": "regional_allele_frequencies", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "simulated_data", "title": "Simulated genotyping data", "object": "simulated_data", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "calculate_he", "title": "Calculate the expected heterozygosity from allele frequencies", "topics": [ "calculate_he" ] }, { "page": "calculate_med_allele_freqs", "title": "Calculate the geometric median of the posterior distribution of allele frequencies", "topics": [ "calculate_med_allele_freqs" ] }, { "page": "calculate_naive_allele_frequencies", "title": "Calculate naive allele frequencies", "topics": [ "calculate_naive_allele_frequencies" ] }, { "page": "calculate_naive_coi", "title": "Calculate naive COI", "topics": [ "calculate_naive_coi" ] }, { "page": "calculate_naive_coi_offset", "title": "Calculate naive COI offset", "topics": [ "calculate_naive_coi_offset" ] }, { "page": "load_delimited_data", "title": "Load delimited data", "topics": [ "load_delimited_data" ] }, { "page": "load_long_form_data", "title": "Load long form data", "topics": [ "load_long_form_data" ] }, { "page": "mcmc_results", "title": "MCMC results from using the packaged simulated data and calling 'run_mcmc()'", "topics": [ "mcmc_results" ] }, { "page": "namibia_data", "title": "Genetic and epidemiological data from Namibia", "topics": [ "namibia_data" ] }, { "page": "plot_chain_swaps", "title": "Plot chain swap acceptance rates", "topics": [ "plot_chain_swaps" ] }, { "page": "rdirichlet", "title": "Dirichlet distribution", "topics": [ "rdirichlet" ] }, { "page": "regional_allele_frequencies", "title": "Allele frequencies for different regions", "topics": [ "regional_allele_frequencies" ] }, { "page": "run_mcmc", "title": "Sample from the target distribution using MCMC", "topics": [ "run_mcmc" ] }, { "page": "simulate_allele_frequencies", "title": "Simulate allele frequencies", "topics": [ "simulate_allele_frequencies" ] }, { "page": "simulate_data", "title": "Simulate data generated according to the assumed model", "topics": [ "simulate_data" ] }, { "page": "simulate_observed_allele", "title": "Simulates the observation process", "topics": [ "simulate_observed_allele" ] }, { "page": "simulate_observed_genotype", "title": "Simulate observed genotypes", "topics": [ "simulate_observed_genotype" ] }, { "page": "simulate_sample_coi", "title": "Simulate sample COI", "topics": [ "simulate_sample_coi" ] }, { "page": "simulate_sample_genotype", "title": "Simulate sample genotype", "topics": [ "simulate_sample_genotype" ] }, { "page": "simulated_data", "title": "Simulated genotyping data", "topics": [ "simulated_data" ] }, { "page": "summarize_allele_freq_fn", "title": "Summarize Function of Allele Frequencies", "topics": [ "summarize_allele_freq_fn" ] }, { "page": "summarize_allele_freqs", "title": "Summarize allele frequencies", "topics": [ "summarize_allele_freqs" ] }, { "page": "summarize_coi", "title": "Summarize COI", "topics": [ "summarize_coi" ] }, { "page": "summarize_effective_coi", "title": "Summarize effective COI", "topics": [ "summarize_effective_coi" ] }, { "page": "summarize_epsilon_neg", "title": "Summarize epsilon_neg", "topics": [ "summarize_epsilon_neg" ] }, { "page": "summarize_epsilon_pos", "title": "Summarize epsilon_pos", "topics": [ "summarize_epsilon_pos" ] }, { "page": "summarize_he", "title": "Summarize locus heterozygosity", "topics": [ "summarize_he" ] }, { "page": "summarize_relatedness", "title": "Summarize relatedness", "topics": [ "summarize_relatedness" ] } ], "_pkglogo": "https://github.com/eppicenter/moire/raw/HEAD/man/figures/logo.svg", "_readme": "https://github.com/eppicenter/moire/raw/HEAD/README.md", "_rundeps": [ "BH", "cli", "cpp11", "dplyr", "farver", "generics", "ggplot2", "glue", "gtable", "isoband", "labeling", "lifecycle", "magrittr", "pillar", "pkgconfig", "purrr", "R6", "RColorBrewer", "Rcpp", "RcppParallel", "RcppProgress", "rlang", "S7", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "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" }, { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_vignettes": [ { "source": "namibia.Rmd", "filename": "namibia.html", "title": "Application to Namibia", "engine": "knitr::rmarkdown", "headings": [ "Running MOIRE on Namibia data" ], "created": "2024-03-18 22:03:28", "modified": "2024-08-01 01:36:32", "commits": 3 }, { "source": "mcmc_demo.Rmd", "filename": "mcmc_demo.html", "title": "MCMC Demonstration", "engine": "knitr::rmarkdown", "headings": [ "Simulation and MCMC", "Estimating COI", "Estimating effective COI", "What is effective COI?", "Estimating Relatedness", "Estimating allele frequencies", "Estimating expected heterozygosity" ], "created": "2020-08-24 22:23:04", "modified": "2023-12-19 19:37:25", "commits": 14 } ], "_score": 4.243038048686294, "_indexed": true, "_nocasepkg": "moire", "_universes": [ "eppicenter", "m-murphy" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.5.0", "date": "2026-06-02T08:44:00.000Z", "distro": "noble", "arch": "aarch64", "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd", "fileid": "87b5692c716a508e05427dcfce3d49d2efb1274a18b8fe409e5ad744e07efcc3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/26808376544" }, { "r": "4.7.0", "os": "linux", "version": "3.5.0", "date": "2026-06-02T08:43:48.000Z", "distro": "noble", "arch": "x86_64", "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd", "fileid": "50a5ca136917548f93fd674b77c0d540c8053b5be8c26c3e2a24383ec1046785", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/26808376544" }, { "r": "4.6.0", "os": "linux", "version": "3.5.0", "date": "2026-06-02T08:43:40.000Z", "distro": "noble", "arch": "aarch64", "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd", "fileid": "7f516839932f512d7f73fda43e42f10435fe9304b5383c58a7e23324b7e2239f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/26808376544" }, { "r": "4.6.0", "os": "linux", "version": "3.5.0", "date": "2026-06-02T08:43:45.000Z", "distro": "noble", "arch": "x86_64", "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd", "fileid": "49d686eae89f17682955244f5b8f68754f6f84a5eff7fd872e7f4b70301f16d4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/26808376544" }, { "r": "4.5.3", "os": "mac", "version": "3.5.0", "date": "2026-06-02T08:43:38.000Z", "arch": "aarch64", "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd", "fileid": "ab622ff627fbe765eed45483acd69281d1f58157c9439fb865f4cd37eec979b2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/26808376544" }, { "r": "4.5.3", "os": "mac", "version": "3.5.0", "date": "2026-06-02T08:44:50.000Z", "arch": "x86_64", "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd", "fileid": "ed705b231cdb4d9507bf7a86eb87d63d4ce00d40a843404f308b471c1b7eb164", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/26808376544" }, { "r": "4.6.0", "os": "mac", "version": "3.5.0", "date": "2026-06-02T08:43:46.000Z", "arch": "aarch64", "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd", "fileid": "8bb5aae84ee8c71c720792c72a7ba108231259db2b9fc684515dbbd3835be0ea", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/26808376544" }, { "r": "4.6.0", "os": "mac", "version": "3.5.0", "date": "2026-06-02T08:46:08.000Z", "arch": "x86_64", "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd", "fileid": "8b2ae467d9b9c05385a3aeb727101a595a39ab7a9e9b03e0048ec19294470e39", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/26808376544" }, { "r": "4.6.0", "os": "wasm", "version": "3.5.0", "date": "2026-06-02T08:43:59.000Z", "arch": "emscripten", "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd", "fileid": "d092582168bcbf443166f01771ddefda551779700ec4aebae234b6c1b05919c9", "status": "success", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/26808376544" }, { "r": "4.7.0", "os": "win", "version": "3.5.0", "date": "2026-06-02T08:42:42.000Z", "arch": "x86_64", "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd", "fileid": "22800fa964347e4cf26557d87b9ccb2ba12c36c76eac9846ca237fdc56bd278e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/26808376544" }, { "r": "4.5.3", "os": "win", "version": "3.5.0", "date": "2026-06-02T08:42:33.000Z", "arch": "x86_64", "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd", "fileid": "2be5a115f24eb59ad175136730c73583d6ff9eacce4a8e158aad0dc0bf764c3d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/26808376544" }, { "r": "4.6.0", "os": "win", "version": "3.5.0", "date": "2026-06-02T08:43:09.000Z", "arch": "x86_64", "commit": "656dcfbb827430edeffa40a0af7b44cc89f689bd", "fileid": "49f3a63213fdbc50df194144ba229bb5df97c17488d3a5ea629d76eff45fe260", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/26808376544" } ] }