{ "_id": "6a1f1966b401979e7341ef63", "Package": "DESA", "Title": "Detecting Epidemics using School Absenteeism", "Version": "1.0.0", "Date": "2025-05-01", "Authors@R": "c(\nperson(\"Vinay\", \"Joshy\", email = \"joshy@uoguelph.ca\", role = c(\"aut\", \"cre\", \"cph\")),\nperson(\"Zeny\", \"Feng\", email = \"zfeng@uoguelph.ca\", role = c(\"aut\", \"cph\", \"ths\")),\nperson(\"Lorna\", \"Deeth\", email = \"ldeeth@uoguelph.ca\", role = c(\"aut\", \"cph\", \"ths\")),\nperson(\"Justin\", \"Slater\", email = \"jslate04@uoguelph.ca\", role = c(\"aut\", \"cph\", \"ths\")),\nperson(\"Kayla\", \"Vanderkruk\", email = \"kayla.vanderkruk@gmail.com\", role = c(\"aut\", \"com\", \"ctb\")))", "Description": "Provides a comprehensive framework for early epidemic\ndetection through school absenteeism surveillance. The package\noffers three core functionalities: (1) simulation of population\nstructures, epidemic spread, and resulting school absenteeism\npatterns; (2) implementation of surveillance models that\ngenerate alerts for impending epidemics based on absenteeism\ndata and (3) evaluation of alert timeliness and accuracy\nthrough alert time quality metrics to optimize model\nparameters. These tools enable public health officials and\nresearchers to develop and assess early warning systems before\nimplementation. Methods are based on research published in\nVanderkruk et al. (2023) and\nWard et al. (2019) .", "License": "GPL (>= 3)", "URL": "https://github.com/vjoshy/DESA", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "BugReports": "https://github.com/vjoshy/DESA/issues", "Repository": "https://vjoshy.r-universe.dev", "Date/Publication": "2025-12-18 00:47:10 UTC", "RemoteUrl": "https://github.com/vjoshy/desa", "RemoteRef": "HEAD", "RemoteSha": "5f647b7df6fad5b2fab2c8cde882c2603d0db246", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-17 05:22:14 UTC", "User": "root" }, "Author": "Vinay Joshy [aut, cre, cph],\nZeny Feng [aut, cph, ths],\nLorna Deeth [aut, cph, ths],\nJustin Slater [aut, cph, ths],\nKayla Vanderkruk [aut, com, ctb]", "Maintainer": "Vinay Joshy ", "MD5sum": "7113e1aee01eeb24bb6737ffe58dc0e7", "_user": "vjoshy", "_type": "src", "_file": "DESA_1.0.0.tar.gz", "_fileid": "c09ffc9fa4eadf4b9e645fb87cbe8c1410e9627e754c5a6a6ce57738edb201f3", "_filesize": 364248, "_sha256": "c09ffc9fa4eadf4b9e645fb87cbe8c1410e9627e754c5a6a6ce57738edb201f3", "_created": "2026-05-17T05:22:14.000Z", "_published": "2026-06-02T17:56:54.000Z", "_distro": "noble", "_jobs": [ { "job": 79137308002, "time": 170, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7039593894" }, { "job": 79137307661, "time": 174, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7039594407" }, { "job": 79137308141, "time": 172, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7039590901" }, { "job": 79137307826, "time": 168, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7039590600" }, { "job": 79137307251, "time": 190, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7039574714" }, { "job": 79137306898, "time": 120, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7365750046" }, { "job": 79137307554, "time": 120, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7039588583" }, { "job": 79137307785, "time": 191, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7039596080" }, { "job": 79137308101, "time": 116, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7039588876" } ], "_buildurl": "https://github.com/r-universe/vjoshy/actions/runs/25982210121", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/vjoshy/desa", "_commit": { "id": "5f647b7df6fad5b2fab2c8cde882c2603d0db246", "author": "Vinay Joshy <80487875+unmaskedcrusader@users.noreply.github.com>", "committer": "Vinay Joshy <80487875+unmaskedcrusader@users.noreply.github.com>", "message": "remove pkgcheck\n", "time": 1766018830 }, "_maintainer": { "name": "Vinay Joshy", "email": "joshy@uoguelph.ca", "login": "vjoshy", "description": "", "uuid": 80487875 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "zoo", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "gridExtra", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "cli", "role": "Suggests" }, { "package": "fansi", "role": "Suggests" }, { "package": "farver", "role": "Suggests" }, { "package": "utf8", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "vjoshy", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-51", "n": 4 } ], "_tags": [], "_stars": 2, "_contributors": [ { "user": "vjoshy", "count": 129, "uuid": 80487875 } ], "_userbio": { "uuid": 80487875, "type": "user", "name": "Vinay Joshy" }, "_downloads": { "count": 561, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/DESA" }, "_devurl": "https://github.com/vjoshy/desa", "_searchresults": 3, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/DESA.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/vjoshy/desa", "_realowner": "vjoshy", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2025-05-07" } ], "_exports": [ "alarm_metrics", "alarm_plot_data", "best_model", "catchment_sim", "compile_epi", "create_alarm_metrics_summary", "elementary_pop", "eval_metrics", "plot_single_epidemic", "simulate_households", "ssir", "subpop_children", "subpop_noChildren" ], "_help": [ { "page": "alarm_metrics", "title": "Create an Alarm Metrics Object", "topics": [ "alarm_metrics" ] }, { "page": "alarm_plot_data", "title": "Create Alarm Plot Data Object", "topics": [ "alarm_plot_data" ] }, { "page": "best_model", "title": "Create Best Model", "topics": [ "best_model" ] }, { "page": "catchment_sim", "title": "Simulating catchment areas", "topics": [ "catchment_sim" ] }, { "page": "compile_epi", "title": "Compile Epidemic Data", "topics": [ "compile_epi" ] }, { "page": "create_alarm_metrics_summary", "title": "Create Alarm Metrics Summary", "topics": [ "create_alarm_metrics_summary" ] }, { "page": "elementary_pop", "title": "Create Elementary Schools population size", "topics": [ "elementary_pop" ] }, { "page": "eval_metrics", "title": "Evaluate Alarm Metrics for Epidemic Models", "topics": [ "eval_metrics" ] }, { "page": "plot_single_epidemic", "title": "Plot a single epidemic simulation", "topics": [ "plot_single_epidemic" ] }, { "page": "plot.alarm_metrics", "title": "Plot Heatmap of Alarm Metrics", "topics": [ "plot.alarm_metrics" ] }, { "page": "plot.alarm_plot_data", "title": "Plot Epidemic Data with Alarm Metrics", "topics": [ "plot.alarm_plot_data" ] }, { "page": "plot.ssir_epidemic", "title": "Plot method for a single SSIR epidemic simulation", "topics": [ "plot.ssir_epidemic" ] }, { "page": "plot.ssir_epidemic_multi", "title": "Plot method for multiple SSIR epidemic simulations", "topics": [ "plot.ssir_epidemic_multi" ] }, { "page": "simulate_households", "title": "Simulate total households and individuals data", "topics": [ "simulate_households" ] }, { "page": "ssir", "title": "Stochastic SIR simulation", "topics": [ "ssir" ] }, { "page": "subpop_children", "title": "Simulate households with children", "topics": [ "subpop_children" ] }, { "page": "subpop_noChildren", "title": "Simulate households without children", "topics": [ "subpop_noChildren" ] }, { "page": "summary.alarm_metrics_summary", "title": "Summary of Alarm Metrics", "topics": [ "summary.alarm_metrics_summary" ] }, { "page": "summary.ssir_epidemic", "title": "S3 Summary method for epidemic Simulation", "topics": [ "summary.ssir_epidemic" ] }, { "page": "summary.ssir_epidemic_multi", "title": "S3 Summary method for multiple epidemic simulations", "topics": [ "summary.ssir_epidemic_multi" ] } ], "_readme": "https://github.com/vjoshy/desa/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "dplyr", "farver", "generics", "ggplot2", "glue", "gridExtra", "gtable", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "pillar", "pkgconfig", "purrr", "R6", "RColorBrewer", "rlang", "S7", "scales", "tibble", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "zoo" ], "_score": 3, "_indexed": true, "_nocasepkg": "desa", "_universes": [ "vjoshy" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-05-17T05:24:40.000Z", "distro": "noble", "commit": "5f647b7df6fad5b2fab2c8cde882c2603d0db246", "fileid": "a4c028967bc12a6a613803233d044a381068108c7f8ebba0f1b83c517aa84c5f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vjoshy/actions/runs/25982210121" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-05-17T05:24:38.000Z", "distro": "noble", "commit": "5f647b7df6fad5b2fab2c8cde882c2603d0db246", "fileid": "c0dee5a62586a2b2e0f9b906d6b0e5a9a00bedc6aaaf86c4ecf37eb6ac2fe173", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vjoshy/actions/runs/25982210121" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-05-17T05:24:19.000Z", "commit": "5f647b7df6fad5b2fab2c8cde882c2603d0db246", "fileid": "e6729ef7d38b7eb6d77ece2d62c851e7f59b4752cf1a744c8a2e7733c45429c5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vjoshy/actions/runs/25982210121" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0", "date": "2026-05-17T05:24:15.000Z", "commit": "5f647b7df6fad5b2fab2c8cde882c2603d0db246", "fileid": "4274242f78814fd162ec3481ff8fa1ec42f7f89d1681f91f43cc380754961b70", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vjoshy/actions/runs/25982210121" }, { "r": "4.7.0", "os": "win", "version": "1.0.0", "date": "2026-05-17T05:23:41.000Z", "commit": "5f647b7df6fad5b2fab2c8cde882c2603d0db246", "fileid": "65c6f3bc672ee8bc7b91fdda0af9821be4c1beab94b7a8d303c942b2bcac3d39", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vjoshy/actions/runs/25982210121" }, { "r": "4.5.3", "os": "win", "version": "1.0.0", "date": "2026-05-17T05:24:27.000Z", "commit": "5f647b7df6fad5b2fab2c8cde882c2603d0db246", "fileid": "b899fc130591977f991f83cfa2578b28999ff322ab628ceec837fa0c0f248b54", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vjoshy/actions/runs/25982210121" }, { "r": "4.6.0", "os": "win", "version": "1.0.0", "date": "2026-05-17T05:23:35.000Z", "commit": "5f647b7df6fad5b2fab2c8cde882c2603d0db246", "fileid": "b6d273b2dc9e8b75856bd81f83b00f505942cf635954d208b36c9c9604d0f801", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vjoshy/actions/runs/25982210121" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-06-02T17:56:36.000Z", "commit": "5f647b7df6fad5b2fab2c8cde882c2603d0db246", "fileid": "a4a0e3359e03de6431d6b95d1d4679e564606389de0eebf7c015e68a65931ef9", "status": "success", "buildurl": "https://github.com/r-universe/vjoshy/actions/runs/25982210121" } ] }