{ "_id": "6acf49dbd9de2f3f33fca372", "Package": "REffectivePred", "Type": "Package", "Title": "Pandemic Prediction Model in an SIRS Framework", "Version": "1.0.1", "Authors@R": "c(person(given = \"Razvan\", \nfamily = \"Romanescu\",\nrole = c(\"aut\", \"cre\"),\nemail = \"razvan_romanescu@hotmail.com\"),\nperson(given = \"Songdi\",\nfamily = \"Hu\",\nrole = \"aut\"),\nperson(given = \"Md Ashiqul\",\nfamily = \"Haque\",\nrole = \"aut\"),\nperson(given = \"Olivier\",\nfamily = \"Tremblay-Savard\",\nrole = \"aut\"))", "Description": "A suite of methods to fit and predict case count data\nusing a compartmental SIRS (Susceptible – Infectious –\nRecovered – Susceptible) model, based on an assumed\nspecification of the effective reproduction number. The\nsignificance of this approach is that it relates epidemic\nprogression to the average number of contacts of infected\nindividuals, which decays as a function of the total\nsusceptible fraction remaining in the population. The main\nfunctions are pred.curve(), which computes the epidemic curve\nfor a set of parameters, and estimate.mle(), which finds the\nbest fitting curve to observed data. The easiest way to pass\narguments to the functions is via a config file, which contains\ninput settings required for prediction, and the package offers\ntwo methods, navigate_to_config() which points the user to the\nconfiguration file, and re_predict() for starting the\nfit-predict process. The main model was published in Razvan G.\nRomanescu et al. .", "License": "GPL (>= 2)", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "Collate": "'prediction_model.v16.R' 'executions.v16.R'", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-14 08:18:44 UTC", "User": "root" }, "Author": "Razvan Romanescu [aut, cre], Songdi Hu [aut], Md Ashiqul Haque\n[aut], Olivier Tremblay-Savard [aut]", "Maintainer": "Razvan Romanescu ", "Repository": "https://rootofunity.r-universe.dev", "Date/Publication": "2024-11-12 09:50:05 UTC", "RemoteUrl": "https://github.com/cran/REffectivePred", "RemoteRef": "HEAD", "RemoteSha": "3fa466aeb3e10e28f28775dbd08f7aacdb5d14b9", "_user": "rootofunity", "_type": "src", "_file": "REffectivePred_1.0.1.tar.gz", "_fileid": "https://r2.ropensci.org/fbcc20990dd8b06cc363fccc7aa833fbefac5c68adb3ba453edc8568b56695ab", "_filesize": 229823, "_sha256": "fbcc20990dd8b06cc363fccc7aa833fbefac5c68adb3ba453edc8568b56695ab", "_expires": "2027-01-22T09:22:29.000Z", "_created": "2026-10-14T08:18:44.000Z", "_published": "2026-10-14T09:22:35.383Z", "_buildurl": "https://github.com/r-universe/rootofunity/actions/runs/38533938887", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 115753272604, "time": 107, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11879212002" }, { "job": 115753272439, "time": 98, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11879772022" }, { "job": 115753272443, "time": 199, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11881799529" }, { "job": 115753272449, "time": 164, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11882073294" }, { "job": 115752278640, "time": 153, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11879281687" }, { "job": 115753272414, "time": 76, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11879572226" }, { "job": 115753272540, "time": 74, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11879970958" }, { "job": 115753272494, "time": 71, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11879436669" }, { "job": 115753272496, "time": 60, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11879537220" } ], "_upstream": "https://github.com/cran/REffectivePred", "_commit": { "id": "3fa466aeb3e10e28f28775dbd08f7aacdb5d14b9", "author": "Razvan Romanescu ", "committer": "cran-robot ", "message": "version 1.0.1\n", "time": 1731405005 }, "_maintainer": { "name": "Razvan Romanescu", "email": "razvan_romanescu@hotmail.com", "login": "rootofunity", "description": "", "uuid": 85967756 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "yaml", "role": "Imports" }, { "package": "config", "role": "Imports" }, { "package": "zoo", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "utils", "role": "Imports" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 1, "_contributors": [ { "user": "rootofunity", "count": 1, "uuid": 85967756 } ], "_userbio": { "uuid": 85967756, "type": "user", "name": "rootOfUnity", "followers": 0 }, "_downloads": { "count": 318, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/REffectivePred" }, "_searchresults": 6, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/REffectivePred.html" ], "_realowner": "rootofunity", "_cranurl": false, "_releases": [ { "version": "1.0.0", "date": "2024-02-02" }, { "version": "1.0.1", "date": "2024-11-14" } ], "_exports": [ "c_helper", "ci.curve", "estimate.mle", "find_ends", "find_starts", "load_config", "log_lklh", "navigate_to_config", "plot_outputs", "pred.curve", "ranges_to_waves", "re_predict", "rt_empirical", "waves_1d_list" ], "_help": [ { "page": "c_helper", "title": "Contact rate function.", "topics": [ "c_helper" ] }, { "page": "ci.curve", "title": "Confidence bands", "topics": [ "ci.curve" ] }, { "page": "estimate.mle", "title": "Fit the Model", "topics": [ "estimate.mle" ] }, { "page": "find_ends", "title": "Detect end of waves", "topics": [ "find_ends" ] }, { "page": "find_starts", "title": "Detect start of waves", "topics": [ "find_starts" ] }, { "page": "load_config", "title": "Load configuration file", "topics": [ "load_config" ] }, { "page": "log_lklh", "title": "The likelihood function", "topics": [ "log_lklh" ] }, { "page": "navigate_to_config", "title": "Navigate to the config file", "topics": [ "navigate_to_config" ] }, { "page": "plot_outputs", "title": "Plotting function", "topics": [ "plot_outputs" ] }, { "page": "pred.curve", "title": "Epidemic Curve Model", "topics": [ "pred.curve" ] }, { "page": "ranges_to_waves", "title": "Utility function for range manipulation", "topics": [ "ranges_to_waves" ] }, { "page": "re_predict", "title": "Demo of main functions", "topics": [ "re_predict" ] }, { "page": "rt_empirical", "title": "Empirical estimate of R_t", "topics": [ "rt_empirical" ] }, { "page": "serial.helper", "title": "Serial interval", "topics": [ "serial.helper" ] }, { "page": "waves_1d_list", "title": "Utility function for range manipulation", "topics": [ "waves_1d_list" ] } ], "_rundeps": [ "config", "lattice", "yaml", "zoo" ], "_score": 1, "_indexed": true, "_nocasepkg": "reffectivepred", "_universes": [ "rootofunity" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.1", "date": "2026-10-14T08:20:51.000Z", "distro": "resolute", "commit": "3fa466aeb3e10e28f28775dbd08f7aacdb5d14b9", "fileid": "https://r2.ropensci.org/fc06a7cc7bd3728b2b1990884b1bd29bd7680cc22d31b03050dfa2dec52e3295", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rootofunity/actions/runs/38533938887" }, { "r": "4.6.1", "os": "linux", "version": "1.0.1", "date": "2026-10-14T08:20:40.000Z", "distro": "resolute", "commit": "3fa466aeb3e10e28f28775dbd08f7aacdb5d14b9", "fileid": "https://r2.ropensci.org/272d19d70895fdfb3f509ec1de47151c50a66f6aaa5700424805611b8c693d0c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rootofunity/actions/runs/38533938887" }, { "r": "4.5.3", "os": "mac", "version": "1.0.1", "date": "2026-10-14T09:20:49.000Z", "commit": "3fa466aeb3e10e28f28775dbd08f7aacdb5d14b9", "fileid": "https://r2.ropensci.org/e5eeb6c69e1d4a1bd91b780238887fbea1fa0f4c2abb09392818a88283a5ca9f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rootofunity/actions/runs/38533938887" }, { "r": "4.6.1", "os": "mac", "version": "1.0.1", "date": "2026-10-14T09:18:36.000Z", "commit": "3fa466aeb3e10e28f28775dbd08f7aacdb5d14b9", "fileid": "https://r2.ropensci.org/d91645bcbaa0ac1843770f6b02814f987e790c3530d391fcbf3748838feaf754", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rootofunity/actions/runs/38533938887" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.1", "date": "2026-10-14T08:20:36.000Z", "commit": "3fa466aeb3e10e28f28775dbd08f7aacdb5d14b9", "fileid": "https://r2.ropensci.org/37649724d899bccc75ac0c1866932cefc8a56a0a9da0f2b6faa20cd60a983817", "status": "success", "buildurl": "https://github.com/r-universe/rootofunity/actions/runs/38533938887" }, { "r": "4.7.0", "os": "win", "version": "1.0.1", "date": "2026-10-14T08:20:12.000Z", "commit": "3fa466aeb3e10e28f28775dbd08f7aacdb5d14b9", "fileid": "https://r2.ropensci.org/bde01dd71e4573039613191b7771c41e84a1bac7fda4a9c34f3b7df70e6792e0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rootofunity/actions/runs/38533938887" }, { "r": "4.5.3", "os": "win", "version": "1.0.1", "date": "2026-10-14T08:20:12.000Z", "commit": "3fa466aeb3e10e28f28775dbd08f7aacdb5d14b9", "fileid": "https://r2.ropensci.org/8395daf1a144a98b80b1d0b9de3afd3ab7685092a7835d6103066f296d585b41", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rootofunity/actions/runs/38533938887" }, { "r": "4.6.1", "os": "win", "version": "1.0.1", "date": "2026-10-14T08:19:59.000Z", "commit": "3fa466aeb3e10e28f28775dbd08f7aacdb5d14b9", "fileid": "https://r2.ropensci.org/30025cce1eaa6b3ab016c7c3ceef01ffd97326d8d836599e3e8655e5c4f0550c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rootofunity/actions/runs/38533938887" } ] }