{ "_id": "6a5a9b1109eb0996dd691116", "Package": "moire", "Title": "Multiplicity of Infection and Allele Frequency Recovery from\nNoisy Polyallelic Genetics Data", "Version": "3.6.0", "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": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "make libicu-dev", "Repository": "https://eppicenter.r-universe.dev", "Date/Publication": "2026-07-17 20:39:05 UTC", "RemoteUrl": "https://github.com/eppicenter/moire", "RemoteRef": "HEAD", "RemoteSha": "e04d9d67addee1fdbf091c3fed688199128450b7", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-17 21:05:03 UTC", "User": "root" }, "Author": "Maxwell Murphy [aut, cre] (ORCID:\n),\nBryan Greenhouse [aut, ths] (ORCID:\n)", "Maintainer": "Maxwell Murphy ", "_user": "eppicenter", "_type": "src", "_file": "moire_3.6.0.tar.gz", "_fileid": "https://r2.ropensci.org/b54e9fc3e4dbe4cfe8102f57a7349835f99f539c7024eb3ebb589c9440d50b81", "_filesize": 4498928, "_sha256": "b54e9fc3e4dbe4cfe8102f57a7349835f99f539c7024eb3ebb589c9440d50b81", "_expires": "2026-10-25T21:13:50.000Z", "_created": "2026-07-17T21:05:03.000Z", "_published": "2026-07-17T21:13:52.731Z", "_jobs": [ { "job": 87993490465, "time": 253, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8419711924" }, { "job": 87993490535, "time": 238, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8419705864" }, { "job": 87993490455, "time": 235, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8419705604" }, { "job": 87993490414, "time": 214, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8419697362" }, { "job": 87993490437, "time": 162, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8419673435" }, { "job": 87993490331, "time": 457, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "8419765024" }, { "job": 87993490339, "time": 170, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8419675688" }, { "job": 87993490394, "time": 249, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8419704821" }, { "job": 87992573017, "time": 291, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8419620894" }, { "job": 87993490303, "time": 193, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8419690153" }, { "job": 87993490264, "time": 200, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8419692906" }, { "job": 87993490386, "time": 180, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8419686214" }, { "job": 87993490314, "time": 210, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8419696224" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/eppicenter/actions/runs/29613237434", "_status": "success", "_upstream": "https://github.com/eppicenter/moire", "_commit": { "id": "e04d9d67addee1fdbf091c3fed688199128450b7", "author": "Maxwell Murphy ", "committer": "Maxwell Murphy ", "message": "CI: update GitHub Actions to current r-lib/r-wasm patterns\n\nBump checkout and Pages actions, move to build-rwasm@v3 with pkgdown-first\nsingle-job layout, and allow docs deploy if the Wasm step flakes.\n", "time": 1784320745 }, "_maintainer": { "name": "Maxwell Murphy", "email": "murphy2122@berkeley.edu", "login": "m-murphy", "orcid": "0000-0003-0332-4388", "twitter": "@MxMrphy", "description": "", "uuid": 5225200 }, "_distro": "resolute", "_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": [ { "week": "2026-29", "n": 2 } ], "_tags": [ { "name": "v3.6.0", "date": "2026-07-17" } ], "_topics": [ "genomics", "malaria", "mcmc", "cpp", "openmp" ], "_stars": 7, "_contributors": [ { "user": "m-murphy", "count": 151, "uuid": 5225200 } ], "_userbio": { "uuid": 14140677, "type": "organization", "name": "EPPIcenter", "followers": 23, "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": 28, "_rbuild": "4.6.1", "_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": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" }, { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "16-20260322-1ubuntu1", "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": 4.292256071356476, "_indexed": true, "_nocasepkg": "moire", "_universes": [ "eppicenter", "m-murphy" ], "_previous": "3.5.0", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.6.0", "date": "2026-07-17T21:09:16.000Z", "distro": "resolute", "arch": "aarch64", "commit": "e04d9d67addee1fdbf091c3fed688199128450b7", "fileid": "https://r2.ropensci.org/3c68c950cf1bb2166fe4983d05e8c061376c67e86cdbfcb02e04f2be73e31b1d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/29613237434" }, { "r": "4.7.0", "os": "linux", "version": "3.6.0", "date": "2026-07-17T21:08:53.000Z", "distro": "resolute", "arch": "x86_64", "commit": "e04d9d67addee1fdbf091c3fed688199128450b7", "fileid": "https://r2.ropensci.org/e713d0e3000ea5cffc78e3d657153f7601ffabfa3e7690fc1b6d0b4c0e1ad8ec", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/29613237434" }, { "r": "4.6.1", "os": "linux", "version": "3.6.0", "date": "2026-07-17T21:09:00.000Z", "distro": "resolute", "arch": "aarch64", "commit": "e04d9d67addee1fdbf091c3fed688199128450b7", "fileid": "https://r2.ropensci.org/3603c82b4ba6ff0dbfe82fab0630da101292de8c8d1faa942eb1cceab7cc9834", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/29613237434" }, { "r": "4.6.1", "os": "linux", "version": "3.6.0", "date": "2026-07-17T21:08:26.000Z", "distro": "resolute", "arch": "x86_64", "commit": "e04d9d67addee1fdbf091c3fed688199128450b7", "fileid": "https://r2.ropensci.org/fa3faa05746358cb566990f066030eff46aab436b4e33d537b006073091bd7ec", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/29613237434" }, { "r": "4.5.3", "os": "mac", "version": "3.6.0", "date": "2026-07-17T21:07:37.000Z", "arch": "aarch64", "commit": "e04d9d67addee1fdbf091c3fed688199128450b7", "fileid": "https://r2.ropensci.org/3c4cc869ba0b21b1f61d92bc4fa778bace7c5a4631086b000dc5988022c6c5dd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/29613237434" }, { "r": "4.5.3", "os": "mac", "version": "3.6.0", "date": "2026-07-17T21:10:54.000Z", "arch": "x86_64", "commit": "e04d9d67addee1fdbf091c3fed688199128450b7", "fileid": "https://r2.ropensci.org/4f9b4bcd87207fcd66566bbaf2158d20a42c0610c1c903a24fdac6bcd0917cf1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/29613237434" }, { "r": "4.6.1", "os": "mac", "version": "3.6.0", "date": "2026-07-17T21:07:42.000Z", "arch": "aarch64", "commit": "e04d9d67addee1fdbf091c3fed688199128450b7", "fileid": "https://r2.ropensci.org/ccf90e455b5dc211f8a7ccd90e12442b957d77e2bc0969603dbfb1bf4ba82965", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/29613237434" }, { "r": "4.6.1", "os": "mac", "version": "3.6.0", "date": "2026-07-17T21:08:20.000Z", "arch": "x86_64", "commit": "e04d9d67addee1fdbf091c3fed688199128450b7", "fileid": "https://r2.ropensci.org/91d833f50931cabc4fd63e0fe59663ba5d700004580a4ff21cd3b6cbf8f92b4c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/29613237434" }, { "r": "4.6.0", "os": "wasm", "version": "3.6.0", "date": "2026-07-17T21:08:24.000Z", "arch": "emscripten", "commit": "e04d9d67addee1fdbf091c3fed688199128450b7", "fileid": "https://r2.ropensci.org/ff96c895adcc7aa4f6a6c03da85544643e91f0988e0717b421dcbffd0bf9d2df", "status": "success", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/29613237434" }, { "r": "4.7.0", "os": "win", "version": "3.6.0", "date": "2026-07-17T21:07:24.000Z", "arch": "x86_64", "commit": "e04d9d67addee1fdbf091c3fed688199128450b7", "fileid": "https://r2.ropensci.org/998348f8ae0a54daf22a1b28f2f189bf6f10c35216d114a65269c726247fb6b6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/29613237434" }, { "r": "4.5.3", "os": "win", "version": "3.6.0", "date": "2026-07-17T21:07:07.000Z", "arch": "x86_64", "commit": "e04d9d67addee1fdbf091c3fed688199128450b7", "fileid": "https://r2.ropensci.org/9228c635877c2d0510f6651b21b3c7847741a18084fe23f581c27f9eb38a2d27", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/29613237434" }, { "r": "4.6.1", "os": "win", "version": "3.6.0", "date": "2026-07-17T21:07:29.000Z", "arch": "x86_64", "commit": "e04d9d67addee1fdbf091c3fed688199128450b7", "fileid": "https://r2.ropensci.org/c48adb2fe94ac5b13b3dfb6ad55b27ed9c85dceeb65c2c9281847a9d4999c6f7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/eppicenter/actions/runs/29613237434" } ] }