{ "_id": "69a044bb239241465c36a179", "Package": "leapfrog", "Title": "Multistate Population Projection Model for Demographic and HIV\nEstimation", "Version": "0.1.8", "Authors@R": "c(\nperson(given = \"Jeffrey\",\nfamily = \"Imai-Eaton\",\nrole = c(\"aut\"),\nemail = \"jeffrey.eaton@imperial.ac.uk\",\ncomment = c(ORCID = \"0000-0001-7728-728X\")),\nperson(given = \"Magdalene\",\nfamily = \"Walters\",\nrole = c(\"aut\"),\nemail = \"m.walters@imperial.ac.uk\"),\nperson(given = \"Robert\",\nfamily = \"Ashton\",\nrole = c(\"aut\", \"cre\"),\nemail = \"robertashton94@gmail.com\"),\nperson(given = \"Mantra\",\nfamily = \"Kusumgar\",\nrole = c(\"aut\"),\nemail = \"m.kusumgar@imperial.ac.uk\"))", "Description": "Leapfrog is a multistate population projection model for\nestimating population, demographic indicators, and HIV\nepidemic. The model combines a standard cohort component model\nof population projection (CCMPP) with a multistate model for\nHIV infection, disease progression, and treatment. Statistical\ntools are implemented for joint inference from multiple\ndemographic and epidemiologic data sources.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "URL": "https://github.com/hivtools/leapfrog", "BugReports": "https://github.com/hivtools/leapfrog/issues", "Config/testthat/edition": "3", "Additional_repositories": "https://mrc-ide.r-universe.dev", "Remotes": [ "rlglaubius/SpectrumUtils", "" ], "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libhdf5-dev", "Repository": "https://mrc-ide.r-universe.dev", "Date/Publication": "2026-02-26 11:43:03 UTC", "RemoteUrl": "https://github.com/hivtools/leapfrog", "RemoteRef": "main", "RemoteSha": "36ab3d2337a8f1f8fd004bb523dbb1db16556d25", "RemoteSubdir": "leapfrogr", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-02-26 12:56:24 UTC", "User": "root" }, "Author": "Jeffrey Imai-Eaton [aut] (ORCID:\n),\nMagdalene Walters [aut],\nRobert Ashton [aut, cre],\nMantra Kusumgar [aut]", "Maintainer": "Robert Ashton ", "MD5sum": "0c9db0df1205ea262a54a8b7c68d6a04", "_user": "mrc-ide", "_type": "src", "_file": "leapfrog_0.1.8.tar.gz", "_fileid": "459cf93312985d8f4c33445978ac65b125da92c4a98dc757426915692ae05030", "_filesize": 5984446, "_sha256": "459cf93312985d8f4c33445978ac65b125da92c4a98dc757426915692ae05030", "_created": "2026-02-26T12:56:24.000Z", "_distro": "noble", "_jobs": [ { "job": 64990228517, "time": 185, "config": "linux-devel-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "5672264141" }, { "job": 64990228531, "time": 196, "config": "linux-devel-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "5672266292" }, { "job": 64990228535, "time": 187, "config": "linux-release-arm64", "r": "4.5.2", "check": "ERROR", "artifact": "5672264759" }, { "job": 64990228569, "time": 198, "config": "linux-release-x86_64", "r": "4.5.2", "check": "ERROR", "artifact": "5672266570" }, { "job": 64990228534, "time": 130, "config": "macos-devel-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "5672250910" }, { "job": 64990228512, "time": 260, "config": "macos-devel-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "5672281669" }, { "job": 64990228571, "time": 185, "config": "macos-release-arm64", "r": "4.5.2", "check": "ERROR", "artifact": "5672263788" }, { "job": 64990228536, "time": 382, "config": "macos-release-x86_64", "r": "4.5.2", "check": "ERROR", "artifact": "5672312405" }, { "job": 64989662954, "time": 285, "config": "source", "r": "4.5.2", "check": "OK", "artifact": "5672220065" }, { "job": 64990228523, "time": 171, "config": "wasm-release", "r": "4.5.1", "check": "OK", "artifact": "5672260439" }, { "job": 64990228543, "time": 207, "config": "windows-devel", "r": "4.6.0", "check": "ERROR", "artifact": "5672268938" }, { "job": 64990228563, "time": 212, "config": "windows-oldrel", "r": "4.4.3", "check": "ERROR", "artifact": "5672270161" }, { "job": 64990228491, "time": 205, "config": "windows-release", "r": "4.5.2", "check": "ERROR", "artifact": "5672268375" } ], "_buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/22442891957", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/hivtools/leapfrog", "_commit": { "id": "36ab3d2337a8f1f8fd004bb523dbb1db16556d25", "author": "Rob <39248272+r-ash@users.noreply.github.com>", "committer": "GitHub ", "message": "Merge pull request #320 from hivtools/update-docs\n\nUpdate stale development doc to work with new model config setup", "time": 1772106183 }, "_maintainer": { "name": "Robert Ashton", "email": "robertashton94@gmail.com", "login": "r-ash", "uuid": 39248272 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.3.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "beers", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "hdf5r", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "abind", "role": "Suggests" }, { "package": "docopt", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "plyr", "role": "Suggests" }, { "package": "RcppEigen", "role": "Suggests" }, { "package": "readxl", "role": "Suggests" }, { "package": "reshape2", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "SpectrumUtils", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "withr", "role": "Suggests" }, { "package": "xml2", "role": "Suggests" } ], "_owner": "hivtools", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-12", "n": 1 }, { "week": "2025-13", "n": 2 }, { "week": "2025-15", "n": 4 }, { "week": "2025-16", "n": 3 }, { "week": "2025-17", "n": 3 }, { "week": "2025-19", "n": 1 }, { "week": "2025-20", "n": 1 }, { "week": "2025-21", "n": 3 }, { "week": "2025-22", "n": 3 }, { "week": "2025-23", "n": 4 }, { "week": "2025-24", "n": 3 }, { "week": "2025-25", "n": 2 }, { "week": "2025-26", "n": 3 }, { "week": "2025-30", "n": 1 }, { "week": "2025-31", "n": 1 }, { "week": "2025-34", "n": 5 }, { "week": "2025-38", "n": 1 }, { "week": "2025-42", "n": 4 }, { "week": "2025-45", "n": 5 }, { "week": "2025-46", "n": 5 }, { "week": "2025-47", "n": 2 }, { "week": "2025-51", "n": 7 }, { "week": "2026-02", "n": 1 }, { "week": "2026-03", "n": 1 }, { "week": "2026-05", "n": 4 }, { "week": "2026-06", "n": 1 }, { "week": "2026-09", "n": 1 } ], "_tags": [ { "name": "v0.1.0", "date": "2025-07-23" }, { "name": "v0.1.0-2", "date": "2025-07-23" }, { "name": "v1.0.0", "date": "2025-11-12" }, { "name": "v1.0.1", "date": "2026-02-05" } ], "_stars": 0, "_contributors": [ { "user": "r-ash", "count": 643, "uuid": 39248272 }, { "user": "m-kusumgar", "count": 250, "uuid": 98405247 }, { "user": "mwalte10", "count": 167, "uuid": 24323420 }, { "user": "jeffeaton", "count": 56, "uuid": 7427899 }, { "user": "richfitz", "count": 15, "uuid": 1558093 } ], "_userbio": { "uuid": 25453642, "type": "organization", "name": "MRC Centre for Global Infectious Disease Analysis", "description": "MRC Centre hosted within the Department of Infectious Disease Epidemiology at Imperial College London" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/leapfrog" }, "_devurl": "https://github.com/hivtools/leapfrog", "_searchresults": 18, "_topics": [ "cpp" ], "_rbuild": "4.5.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/leapfrog.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "%>%", "get_leapfrog_ss", "get_state_space", "get_time_slice", "list_model_configurations", "process_parameters_to_cpp", "process_parameters_to_r", "process_pjnz", "read_parameters", "run_model", "run_model_from_state", "run_model_single_year", "save_parameters" ], "_help": [ { "page": "beers_open_ended", "title": "Beers Ordinary Graduation with Open-Ended Age Group", "topics": [ "beers_open_ended" ] }, { "page": "get_leapfrog_ss", "title": "Get the state space dimensions for a particular model configuration", "topics": [ "get_leapfrog_ss" ] }, { "page": "get_state_space", "title": "Run leapfrog model fit", "topics": [ "get_state_space" ] }, { "page": "get_time_slice", "title": "Slice a single year from model state", "topics": [ "get_time_slice" ] }, { "page": "list_model_configurations", "title": "List the avaialble model configurations", "topics": [ "list_model_configurations" ] }, { "page": "process_parameters_to_cpp", "title": "Process parameters and convert from 1 based indexing in R to 0 based indexing in C++. Also add in any defaults/extra parameters, e.g. 'h_art_stage_dur'.", "topics": [ "process_parameters_to_cpp" ] }, { "page": "process_parameters_to_r", "title": "Process parameters and convert from 0 based indexing for C++ to 1 based indexing in R.", "topics": [ "process_parameters_to_r" ] }, { "page": "process_pjnz", "title": "Prepare inputs from Spectrum PJNZ", "topics": [ "process_pjnz" ] }, { "page": "read_parameters", "title": "Read parameters from HDF5 file format. This implicitly processes the parameters from C++ 0 based indexing to R 1 based indexing.", "topics": [ "read_parameters" ] }, { "page": "run_model", "title": "Run leapfrog model fit", "topics": [ "run_model" ] }, { "page": "run_model_from_state", "title": "Run leapfrog model fit from initial state", "topics": [ "run_model_from_state" ] }, { "page": "run_model_single_year", "title": "Run leapfrog model fit for a single year", "topics": [ "run_model_single_year" ] }, { "page": "save_parameters", "title": "Save parameters to HDF5 file format. This implicitly processes the parameters to C++ 0 based indexing.", "topics": [ "save_parameters" ] } ], "_readme": "https://github.com/hivtools/leapfrog/raw/main/leapfrogr/README.md", "_rundeps": [ "beers", "bit", "bit64", "cli", "dplyr", "generics", "glue", "hdf5r", "lifecycle", "magrittr", "pillar", "pkgconfig", "R6", "Rcpp", "rlang", "tibble", "tidyselect", "utf8", "vctrs", "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" } ], "_vignettes": [ { "source": "development.Rmd", "filename": "development.html", "title": "Developing leapfrog", "engine": "knitr::rmarkdown", "headings": [ "Structure", "Model variants", "State saving", "Modifying config to add new input, output or intermediate data", "Config structure", "Adding a new model variant" ], "created": "2025-11-20 18:15:01", "modified": "2026-02-26 11:43:03", "commits": 3 }, { "source": "variables.Rmd", "filename": "variables.html", "title": "Variable naming conventions", "engine": "knitr::rmarkdown", "headings": [ "Leapfrog naming rules", "Rules for unpacking structs", "Leaptfrog to Leapfrog glossary", "State space", "Loop variable convention", "Key indices in state space or other options controlling fit", "Input data", "Outputs", "Intermediate data" ], "created": "2025-11-20 18:15:01", "modified": "2025-11-20 18:15:01", "commits": 1 } ], "_score": 5.288696260590256, "_indexed": false, "_nocasepkg": "leapfrog", "_universes": [ "mrc-ide" ], "_indexurl": "https://hivtools.r-universe.dev/leapfrog", "_failure": { "version": "0.1.10", "commit": { "id": "66b296cb6502fc8d02f65f1349ba8ba9bfb290a7", "author": "Rob Ashton ", "committer": "Rob Ashton ", "message": "Ensure pwid_sex_ratio is a time series of correct length\n", "time": 1780592354 }, "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/26974169878", "date": "2026-06-04T19:24:59.816Z", "job": { "job": 79596851045, "time": 200, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7420954064" } }, "_binaries": [ { "r": "4.6.0", "os": "linux", "version": "0.1.8", "date": "2026-02-26T12:59:27.000Z", "distro": "noble", "arch": "aarch64", "commit": "36ab3d2337a8f1f8fd004bb523dbb1db16556d25", "fileid": "3edd0628784962a3e4b3db0b3c12a2172bf2ba05b19bedcb6a0cbed161027a0e", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/22442891957" }, { "r": "4.6.0", "os": "linux", "version": "0.1.8", "date": "2026-02-26T12:59:36.000Z", "distro": "noble", "arch": "x86_64", "commit": "36ab3d2337a8f1f8fd004bb523dbb1db16556d25", "fileid": "caa9f9db1e717df353c19bef6bab41fb05eea83f83559394628eae09f90024c2", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/22442891957" }, { "r": "4.6.0", "os": "mac", "version": "0.1.8", "date": "2026-02-26T12:58:36.000Z", "arch": "aarch64", "commit": "36ab3d2337a8f1f8fd004bb523dbb1db16556d25", "fileid": "fd25cefc5b93d12a265e700221ad69da562826621c45dea995d9f632462705ce", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/22442891957" }, { "r": "4.6.0", "os": "mac", "version": "0.1.8", "date": "2026-02-26T12:59:58.000Z", "arch": "x86_64", "commit": "36ab3d2337a8f1f8fd004bb523dbb1db16556d25", "fileid": "94da1854b6e16ccc05ef559f66947ecfcc6a7e0ad6fc7719a68950c80ea98f55", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/22442891957" }, { "r": "4.5.2", "os": "mac", "version": "0.1.8", "date": "2026-02-26T12:59:05.000Z", "arch": "aarch64", "commit": "36ab3d2337a8f1f8fd004bb523dbb1db16556d25", "fileid": "59d74638a692d04ad383cd3b88af34460dbdc0d5821f37c1003edd95fae40b2d", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/22442891957" }, { "r": "4.5.2", "os": "mac", "version": "0.1.8", "date": "2026-02-26T13:01:37.000Z", "arch": "x86_64", "commit": "36ab3d2337a8f1f8fd004bb523dbb1db16556d25", "fileid": "69435c4558f9939698fcd00fa93adb8eae1f50b491c235e93c3338f9f9b8ce3a", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/22442891957" }, { "r": "4.5.1", "os": "wasm", "version": "0.1.8", "date": "2026-02-26T12:59:34.000Z", "arch": "emscripten", "commit": "36ab3d2337a8f1f8fd004bb523dbb1db16556d25", "fileid": "e0a2f951a0949bb0b7d80ebfbc19f1b7e0afe036856968d6dbc9b6c1d7b6c86c", "status": "success", "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/22442891957" }, { "r": "4.6.0", "os": "win", "version": "0.1.8", "date": "2026-02-26T12:59:01.000Z", "arch": "x86_64", "commit": "36ab3d2337a8f1f8fd004bb523dbb1db16556d25", "fileid": "9ea6e329db41cd111463905b368eeaa99e74fd6e88a423c450847a8c71368398", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/22442891957" }, { "r": "4.5.2", "os": "win", "version": "0.1.8", "date": "2026-02-26T12:58:59.000Z", "arch": "x86_64", "commit": "36ab3d2337a8f1f8fd004bb523dbb1db16556d25", "fileid": "56882fa212f7c58eb42469ef38a5871ec7c380721530ef06e2931104b0f0e8be", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/22442891957" } ] }