{ "_id": "6ad0b88bb0a1b4b4099d7529", "Package": "moire", "Title": "Multiplicity of Infection and Allele Frequency Recovery from\nNoisy Polyallelic Genetics Data", "Version": "3.7.0", "Authors@R": "c(\nperson(given = \"Maxwell\",\nfamily = \"Murphy\",\nrole = c(\"aut\", \"cre\"),\nemail = \"mm@maxmurphy.dev\",\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. Implements the model\ndescribed in Murphy and Greenhouse (2024)\n.", "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": "cmake make libicu-dev", "Repository": "https://plasmogenepi.r-universe.dev", "Date/Publication": "2026-09-15 17:50:47 UTC", "RemoteUrl": "https://github.com/eppicenter/moire", "RemoteRef": "HEAD", "RemoteSha": "6ae03862fe1be61a85e715ce359f613658cf142e", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-15 11:20:29 UTC", "User": "root" }, "Author": "Maxwell Murphy [aut, cre] (ORCID:\n),\nBryan Greenhouse [aut, ths] (ORCID:\n)", "Maintainer": "Maxwell Murphy ", "_user": "plasmogenepi", "_type": "src", "_file": "moire_3.7.0.tar.gz", "_fileid": "https://r2.ropensci.org/131286289ac5572c53816b32a5e87954a0fc3d7a0ffe82c5f09dac94cb098f1c", "_filesize": 4507196, "_sha256": "131286289ac5572c53816b32a5e87954a0fc3d7a0ffe82c5f09dac94cb098f1c", "_expires": "2027-01-23T11:27:05.000Z", "_created": "2026-10-15T11:20:29.000Z", "_published": "2026-10-15T11:27:07.637Z", "_buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38726170480", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 116394385257, "time": 152, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11968353834" }, { "job": 116394385307, "time": 196, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11968214056" }, { "job": 116394385458, "time": 240, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11968229085" }, { "job": 116394385386, "time": 190, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11967709539" }, { "job": 116394385416, "time": 151, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11968488641" }, { "job": 116394385561, "time": 315, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11967899524" }, { "job": 116394385395, "time": 162, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11967689545" }, { "job": 116394385445, "time": 247, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11967449756" }, { "job": 116392571338, "time": 275, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11968473204" }, { "job": 116394385502, "time": 153, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11967584554" }, { "job": 116394385630, "time": 281, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11968479176" }, { "job": 116394385783, "time": 220, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11968269050" }, { "job": 116394385623, "time": 232, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11968084216" }, { "job": 116394385574, "time": 306, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11968059344" }, { "job": 116394385565, "time": 193, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11967844254" } ], "_upstream": "https://github.com/eppicenter/moire", "_commit": { "id": "6ae03862fe1be61a85e715ce359f613658cf142e", "author": "Maxwell Murphy ", "committer": "Maxwell Murphy ", "message": "Update maintainer email to mm@maxmurphy.dev\n", "time": 1789494647 }, "_maintainer": { "name": "Maxwell Murphy", "email": "mm@maxmurphy.dev", "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": "parallel", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "forcats", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "parallelly", "role": "Suggests" } ], "_owner": "eppicenter", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-29", "n": 2 }, { "week": "2026-37", "n": 1 }, { "week": "2026-38", "n": 2 } ], "_tags": [ { "name": "v3.6.0", "date": "2026-07-17" }, { "name": "v3.7.0", "date": "2026-09-15" } ], "_topics": [ "genomics", "malaria", "mcmc", "cpp", "openmp" ], "_stars": 8, "_contributors": [ { "user": "m-murphy", "count": 153, "uuid": 5225200 }, { "user": "nickjhathaway", "count": 1, "uuid": 2828038 } ], "_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": 439, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/moire" }, "_devurl": "https://github.com/eppicenter/moire", "_pkgdown": "https://eppicenter.github.io/moire/", "_searchresults": 27, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/moire.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/eppicenter/moire", "_realowner": "eppicenter", "_cranurl": true, "_releases": [ { "version": "3.7.0", "date": "2026-09-26" } ], "_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": "2026-09-10 00:12:20", "commits": 15 } ], "_score": 5.811575005870593, "_indexed": false, "_nocasepkg": "moire", "_universes": [ "plasmogenepi" ], "_indexurl": "https://eppicenter.r-universe.dev/moire", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.7.0", "date": "2026-10-15T11:23:06.000Z", "distro": "resolute", "arch": "aarch64", "commit": "6ae03862fe1be61a85e715ce359f613658cf142e", "fileid": "https://r2.ropensci.org/2eed00c8835cafded71a167d0bff117fac604f32a9b1e3597f4cffcf93fa4ba1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38726170480" }, { "r": "4.7.0", "os": "linux", "version": "3.7.0", "date": "2026-10-15T11:23:27.000Z", "distro": "resolute", "arch": "x86_64", "commit": "6ae03862fe1be61a85e715ce359f613658cf142e", "fileid": "https://r2.ropensci.org/29c608c1f908c2e650eabe41ddee65b6b4abf88ce35dc191b00515469f91ebf1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38726170480" }, { "r": "4.6.1", "os": "linux", "version": "3.7.0", "date": "2026-10-15T11:24:25.000Z", "distro": "resolute", "arch": "aarch64", "commit": "6ae03862fe1be61a85e715ce359f613658cf142e", "fileid": "https://r2.ropensci.org/6e27ef9a0e889e6ab0900b274f4e03cbe4f75b2b72a7c4df724e88c78f04e4a5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38726170480" }, { "r": "4.6.1", "os": "linux", "version": "3.7.0", "date": "2026-10-15T11:23:35.000Z", "distro": "resolute", "arch": "x86_64", "commit": "6ae03862fe1be61a85e715ce359f613658cf142e", "fileid": "https://r2.ropensci.org/b56a7cfe497fa420c36ccea8b11244639640b09607fe33a5b3f30fdcbb6f957f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38726170480" }, { "r": "4.5.3", "os": "mac", "version": "3.7.0", "date": "2026-10-15T11:22:52.000Z", "arch": "aarch64", "commit": "6ae03862fe1be61a85e715ce359f613658cf142e", "fileid": "https://r2.ropensci.org/a72cd69a6b2eb0c25ca062d0fc11bed76d09a8ad9986dec9f53e31aa0ae8e6d4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38726170480" }, { "r": "4.5.3", "os": "mac", "version": "3.7.0", "date": "2026-10-15T11:24:06.000Z", "arch": "x86_64", "commit": "6ae03862fe1be61a85e715ce359f613658cf142e", "fileid": "https://r2.ropensci.org/c1e749a6bf0113fc4821a379570fb970eec845c7947f1230cc7c58f75c37cfeb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38726170480" }, { "r": "4.6.1", "os": "mac", "version": "3.7.0", "date": "2026-10-15T11:23:05.000Z", "arch": "aarch64", "commit": "6ae03862fe1be61a85e715ce359f613658cf142e", "fileid": "https://r2.ropensci.org/a6557f2a17af53cb539030859f2c90131bbf07b4d6a6ade773d3e7b6da1856fb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38726170480" }, { "r": "4.6.1", "os": "mac", "version": "3.7.0", "date": "2026-10-15T11:23:54.000Z", "arch": "x86_64", "commit": "6ae03862fe1be61a85e715ce359f613658cf142e", "fileid": "https://r2.ropensci.org/34c7ecaed6611d53c92d79978afc52f3106d07be4981f83af085394f22e0173c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38726170480" }, { "r": "4.6.0", "os": "wasm", "version": "3.7.0", "date": "2026-10-15T11:23:19.000Z", "arch": "emscripten", "commit": "6ae03862fe1be61a85e715ce359f613658cf142e", "fileid": "https://r2.ropensci.org/7e4144c16b27b5fe099fae8c8d66304c9f8461893c8aec7a0e121d2a99a1e13b", "status": "success", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38726170480" }, { "r": "4.7.0", "os": "win", "version": "3.7.0", "date": "2026-10-15T11:24:30.000Z", "arch": "aarch64", "commit": "6ae03862fe1be61a85e715ce359f613658cf142e", "fileid": "https://r2.ropensci.org/df77433a108cb160c635a1115680acfe52d4242cbc55fdd05b82e4591a84b79d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38726170480" }, { "r": "4.7.0", "os": "win", "version": "3.7.0", "date": "2026-10-15T11:23:02.000Z", "arch": "x86_64", "commit": "6ae03862fe1be61a85e715ce359f613658cf142e", "fileid": "https://r2.ropensci.org/a03a6213b0238686640114f97f06599eba07ced6e7c0e87c028519321edd97cc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38726170480" }, { "r": "4.5.3", "os": "win", "version": "3.7.0", "date": "2026-10-15T11:23:12.000Z", "arch": "x86_64", "commit": "6ae03862fe1be61a85e715ce359f613658cf142e", "fileid": "https://r2.ropensci.org/6257ba0eb229271daac5aded3722b492a17bd9086b1b4d8e6c6b0fa8477fb878", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38726170480" }, { "r": "4.6.1", "os": "win", "version": "3.7.0", "date": "2026-10-15T11:25:02.000Z", "arch": "aarch64", "commit": "6ae03862fe1be61a85e715ce359f613658cf142e", "fileid": "https://r2.ropensci.org/c4181e2f4a789dc0c3ea5ce9af11e2e826ba6aef29c9557fdf6e203af9985dfb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38726170480" }, { "r": "4.6.1", "os": "win", "version": "3.7.0", "date": "2026-10-15T11:22:35.000Z", "arch": "x86_64", "commit": "6ae03862fe1be61a85e715ce359f613658cf142e", "fileid": "https://r2.ropensci.org/88518dbdd67cbc3b29bc2cbfed511a01ea51fc8d14f805c7f1cca604c9a36833", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/plasmogenepi/actions/runs/38726170480" } ] }