{ "_id": "6a16b57facfb0bcc41d85cbe", "Package": "MicroMoB", "Type": "Package", "Title": "Discrete Time Simulation of Mosquito-Borne Pathogen Transmission", "Version": "0.1.2", "Authors@R": "c(\nperson(\"Sean L.\", \"Wu\", email = \"slwood89@gmail.com\", role = c(\"aut\",\"cre\"), comment = c(ORCID = \"0000-0002-5781-9493\")),\nperson(\"David L.\", \"Smith\", email = \"smitdave@uw.edu\", role = \"aut\", comment = c(ORCID = \"0000-0003-4367-3849\")),\nperson(\"Sophie\", \"Libkind\", role = \"ctb\")\n)", "Description": "Provides a framework based on S3 dispatch for constructing\nmodels of mosquito-borne pathogen transmission which are\nconstructed from submodels of various components (i.e. immature\nand adult mosquitoes, human populations). A consistent\nmathematical expression for the distribution of bites on hosts\nmeans that different models (stochastic, deterministic, etc.)\ncan be coherently incorporated and updated over a discrete time\nstep.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.2.1.9000", "VignetteBuilder": "knitr", "URL": "https://dd-harp.github.io/MicroMoB/,\nhttps://github.com/dd-harp/MicroMoB", "BugReports": "https://github.com/dd-harp/MicroMoB/issues", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-27 09:07:34 UTC", "User": "root" }, "Author": "Sean L. Wu [aut, cre]\n(), David L. Smith [aut]\n(), Sophie Libkind [ctb]", "Maintainer": "Sean L. Wu ", "Repository": "https://slwu89.r-universe.dev", "Date/Publication": "2023-01-17 02:40:02 UTC", "RemoteUrl": "https://github.com/cran/MicroMoB", "RemoteRef": "HEAD", "RemoteSha": "9105166006cda085934ad47ba670e2a16fbecea1", "MD5sum": "9a70ed9bb8b4d7ebe581b947f3c5aae6", "_user": "slwu89", "_type": "src", "_file": "MicroMoB_0.1.2.tar.gz", "_fileid": "49a4be7dea3b5c04798e43eae002e4db775fc37dc4dbc02f20c774daafe9c969", "_filesize": 6754345, "_sha256": "49a4be7dea3b5c04798e43eae002e4db775fc37dc4dbc02f20c774daafe9c969", "_created": "2026-05-27T09:07:34.000Z", "_published": "2026-05-27T09:12:31.382Z", "_distro": "noble", "_jobs": [ { "job": 78044340976, "time": 138, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7236441795" }, { "job": 78044341050, "time": 142, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7236442985" }, { "job": 78044340924, "time": 129, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7236439213" }, { "job": 78044341024, "time": 145, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7236444792" }, { "job": 78044341110, "time": 170, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7236444659" }, { "job": 78044340996, "time": 250, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7236472912" }, { "job": 78044341095, "time": 207, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7236452579" }, { "job": 78044341008, "time": 231, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7236467210" }, { "job": 78043546574, "time": 278, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7236392752" }, { "job": 78044340974, "time": 114, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7236433295" }, { "job": 78044340963, "time": 94, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7236426337" }, { "job": 78044340956, "time": 257, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7236483521" }, { "job": 78044340965, "time": 102, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7236429493" } ], "_buildurl": "https://github.com/r-universe/slwu89/actions/runs/26501683700", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/MicroMoB", "_commit": { "id": "9105166006cda085934ad47ba670e2a16fbecea1", "author": "Sean L. Wu ", "committer": "cran-robot ", "message": "version 0.1.2\n", "time": 1673923202 }, "_maintainer": { "name": "Sean L. Wu", "email": "slwood89@gmail.com", "login": "slwu89", "description": "Y2K survivor", "uuid": 10673535, "orcid": "0000-0002-5781-9493" }, "_registered": true, "_dependencies": [ { "package": "abind", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "data.table", "role": "Suggests" }, { "package": "callr", "role": "Suggests" }, { "package": "httr", "role": "Suggests" }, { "package": "readr", "role": "Suggests" }, { "package": "withr", "role": "Suggests" }, { "package": "plumber", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "slwu89", "count": 5, "uuid": 10673535 } ], "_userbio": { "uuid": 10673535, "type": "user", "name": "Sean", "description": "Y2K survivor" }, "_downloads": { "count": 213, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/MicroMoB" }, "_devurl": "https://github.com/dd-harp/micromob", "_pkgdown": "https://dd-harp.github.io/MicroMoB/", "_searchresults": 32, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MicroMoB.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "slwu89", "_cranurl": false, "_releases": [ { "version": "0.0.9", "date": "2022-02-01" }, { "version": "0.0.11", "date": "2022-03-09" }, { "version": "0.0.12", "date": "2022-03-17" }, { "version": "0.1.0", "date": "2022-07-01" }, { "version": "0.1.2", "date": "2023-01-17" } ], "_exports": [ "api_config_global", "approx_equal", "compute_bloodmeal", "compute_bloodmeal_simple", "compute_emergents", "compute_f", "compute_H", "compute_O", "compute_oviposit", "compute_Psi", "compute_q", "compute_Wd", "compute_wf", "compute_x", "compute_xd", "compute_Z", "distribute", "divmod", "draw_multinom", "get_config_alternative_trace", "get_config_aqua_BH", "get_config_aqua_trace", "get_config_humans_MOI", "get_config_humans_SIR", "get_config_humans_SIS", "get_config_mosquito_RM", "get_config_mosquito_trace", "get_config_visitor_trace", "get_eip_mosquito_RM", "get_f_mosquito_RM", "get_K_aqua_BH", "get_kappa_mosquito_RM", "get_lambda_aqua_trace", "get_molt_aqua_BH", "get_nu_mosquito_RM", "get_p_mosquito_RM", "get_psi_mosquito_RM", "get_q_mosquito_RM", "get_surv_aqua_BH", "get_tmax", "get_tnow", "is_binary", "make_MicroMoB", "observe_pfpr", "output_aqua", "output_mosquitoes", "sample_stochastic_matrix", "sample_stochastic_vector", "set_eip_mosquito_RM", "set_f_mosquito_RM", "set_K_aqua_BH", "set_kappa_mosquito_RM", "set_lambda_aqua_trace", "set_molt_aqua_BH", "set_nu_mosquito_RM", "set_p_mosquito_RM", "set_psi_mosquito_RM", "set_q_mosquito_RM", "set_surv_aqua_BH", "setup_alternative_trace", "setup_aqua_BH", "setup_aqua_trace", "setup_humans_MOI", "setup_humans_SIP", "setup_humans_SIR", "setup_humans_SIS", "setup_mosquito_BQ", "setup_mosquito_RM", "setup_mosquito_trace", "setup_visitor_trace", "step_aqua", "step_humans", "step_mosquitoes", "strata_to_residency_counts", "strata_to_residency_proportion", "time_patch_varying_parameter", "time_varying_parameter" ], "_help": [ { "page": "api_config_global", "title": "Read global configuration options", "topics": [ "api_config_global" ] }, { "page": "approx_equal", "title": "Check if two numeric values are approximately equal", "topics": [ "approx_equal" ] }, { "page": "compute_bloodmeal", "title": "Compute bloodmeals taken by mosquitoes on hosts", "topics": [ "compute_bloodmeal" ] }, { "page": "compute_bloodmeal_simple", "title": "Compute bloodmeals taken by mosquitoes on hosts in simple models", "topics": [ "compute_bloodmeal_simple" ] }, { "page": "compute_emergents", "title": "Compute number of newly emerging adults (lambda)", "topics": [ "compute_emergents" ] }, { "page": "compute_emergents.BH", "title": "Compute number of newly emerging adults from Beverton-Holt dynamics", "topics": [ "compute_emergents.BH" ] }, { "page": "compute_emergents.trace", "title": "Compute number of newly emerging adults from forcing term", "topics": [ "compute_emergents.trace" ] }, { "page": "compute_emergents.trace_deterministic", "title": "Compute number of newly emerging adults from forcing term (deterministic)", "topics": [ "compute_emergents.trace_deterministic" ] }, { "page": "compute_emergents.trace_stochastic", "title": "Compute number of newly emerging adults from forcing term (stochastic)", "topics": [ "compute_emergents.trace_stochastic" ] }, { "page": "compute_f", "title": "Compute mosquito feeding rate (f)", "topics": [ "compute_f" ] }, { "page": "compute_f.BQ", "title": "Compute mosquito feeding rate for BQ model (f)", "topics": [ "compute_f.BQ" ] }, { "page": "compute_f.RM", "title": "Compute mosquito feeding rate for RM model (f)", "topics": [ "compute_f.RM" ] }, { "page": "compute_f.trace", "title": "Compute null mosquito feeding rate (f)", "topics": [ "compute_f.trace" ] }, { "page": "compute_H", "title": "Compute human population strata sizes (H)", "topics": [ "compute_H" ] }, { "page": "compute_H.MOI", "title": "Compute human population strata sizes for MOI model (H)", "topics": [ "compute_H.MOI" ] }, { "page": "compute_H.SIP", "title": "Compute human population strata sizes for SIP model (H)", "topics": [ "compute_H.SIP" ] }, { "page": "compute_H.SIR", "title": "Compute human population strata sizes for SIR model (H)", "topics": [ "compute_H.SIR" ] }, { "page": "compute_H.SIS", "title": "Compute human population strata sizes for SIS model (H)", "topics": [ "compute_H.SIS" ] }, { "page": "compute_O", "title": "Compute available alternative blood hosts (O)", "topics": [ "compute_O" ] }, { "page": "compute_O.trace", "title": "Compute available alternative blood hosts for trace model (O)", "topics": [ "compute_O.trace" ] }, { "page": "compute_oviposit", "title": "Compute number of eggs laid from oviposition for each patch", "topics": [ "compute_oviposit" ] }, { "page": "compute_oviposit.BQ", "title": "Compute number of eggs laid from oviposition for each aquatic habitat for BQ model", "topics": [ "compute_oviposit.BQ" ] }, { "page": "compute_oviposit.BQ_deterministic", "title": "Compute number of eggs laid from oviposition for each patch for deterministic RM model", "topics": [ "compute_oviposit.BQ_deterministic" ] }, { "page": "compute_oviposit.BQ_stochastic", "title": "Compute number of eggs laid from oviposition for each patch for stochastic RM model", "topics": [ "compute_oviposit.BQ_stochastic" ] }, { "page": "compute_oviposit.RM", "title": "Compute number of eggs laid from oviposition for each patch for RM model", "topics": [ "compute_oviposit.RM" ] }, { "page": "compute_oviposit.RM_deterministic", "title": "Compute number of eggs laid from oviposition for each patch for deterministic RM model", "topics": [ "compute_oviposit.RM_deterministic" ] }, { "page": "compute_oviposit.RM_stochastic", "title": "Compute number of eggs laid from oviposition for each patch for stochastic RM model", "topics": [ "compute_oviposit.RM_stochastic" ] }, { "page": "compute_oviposit.trace", "title": "Compute number of eggs laid from oviposition for each patch for null model", "topics": [ "compute_oviposit.trace" ] }, { "page": "compute_Psi", "title": "Compute time at risk matrix (Psi)", "topics": [ "compute_Psi" ] }, { "page": "compute_Psi.MOI", "title": "Compute time at risk matrix for MOI model (Psi)", "topics": [ "compute_Psi.MOI" ] }, { "page": "compute_Psi.SIP", "title": "Compute time at risk matrix for SIP model (Psi)", "topics": [ "compute_Psi.SIP" ] }, { "page": "compute_Psi.SIR", "title": "Compute time at risk matrix for SIR model (Psi)", "topics": [ "compute_Psi.SIR" ] }, { "page": "compute_Psi.SIS", "title": "Compute time at risk matrix for SIS model (Psi)", "topics": [ "compute_Psi.SIS" ] }, { "page": "compute_q", "title": "Compute human blood feeding fraction (q)", "topics": [ "compute_q" ] }, { "page": "compute_q.BQ", "title": "Compute human blood feeding fraction for BQ model (q)", "topics": [ "compute_q.BQ" ] }, { "page": "compute_q.RM", "title": "Compute human blood feeding fraction for RM model (q)", "topics": [ "compute_q.RM" ] }, { "page": "compute_q.trace", "title": "Compute null human blood feeding fraction (q)", "topics": [ "compute_q.trace" ] }, { "page": "compute_Wd", "title": "Compute available visitors (W_{delta})", "topics": [ "compute_Wd" ] }, { "page": "compute_Wd.trace", "title": "Compute available visitors for trace model (W_{delta})", "topics": [ "compute_Wd.trace" ] }, { "page": "compute_wf", "title": "Compute human biting weights (w_{f})", "topics": [ "compute_wf" ] }, { "page": "compute_wf.MOI", "title": "Compute human biting weights for MOI model (w_{f})", "topics": [ "compute_wf.MOI" ] }, { "page": "compute_wf.SIP", "title": "Compute human biting weights for SIP model (w_{f})", "topics": [ "compute_wf.SIP" ] }, { "page": "compute_wf.SIR", "title": "Compute human biting weights for SIR model (w_{f})", "topics": [ "compute_wf.SIR" ] }, { "page": "compute_wf.SIS", "title": "Compute human biting weights for SIS model (w_{f})", "topics": [ "compute_wf.SIS" ] }, { "page": "compute_x", "title": "Compute net infectiousness of humans (x)", "topics": [ "compute_x" ] }, { "page": "compute_x.MOI", "title": "Compute net infectiousness for MOI model (x)", "topics": [ "compute_x.MOI" ] }, { "page": "compute_x.SIP", "title": "Compute net infectiousness for SIP model (x)", "topics": [ "compute_x.SIP" ] }, { "page": "compute_x.SIR", "title": "Compute net infectiousness for SIR model (x)", "topics": [ "compute_x.SIR" ] }, { "page": "compute_x.SIS", "title": "Compute net infectiousness for SIS model (x)", "topics": [ "compute_x.SIS" ] }, { "page": "compute_xd", "title": "Compute net infectiousness of visitors (x_{delta})", "topics": [ "compute_xd" ] }, { "page": "compute_xd.trace", "title": "Compute net infectiousness of visitors for trace model (x_{delta})", "topics": [ "compute_xd.trace" ] }, { "page": "compute_Z", "title": "Compute density of infective mosquitoes (Z)", "topics": [ "compute_Z" ] }, { "page": "compute_Z.BQ", "title": "Compute density of infective mosquitoes for BQ model (Z)", "topics": [ "compute_Z.BQ" ] }, { "page": "compute_Z.RM", "title": "Compute density of infective mosquitoes for RM model (Z)", "topics": [ "compute_Z.RM" ] }, { "page": "compute_Z.trace", "title": "Compute null density of infective mosquitoes (Z)", "topics": [ "compute_Z.trace" ] }, { "page": "distribute", "title": "Distribute items into bins as evenly as possible", "topics": [ "distribute" ] }, { "page": "divmod", "title": "Division of integers", "topics": [ "divmod" ] }, { "page": "draw_multinom", "title": "Draw a multinomially distributed random vector", "topics": [ "draw_multinom" ] }, { "page": "get_config_alternative_trace", "title": "Get parameters for trace driven alternative blood hosts", "topics": [ "get_config_alternative_trace" ] }, { "page": "get_config_aqua_BH", "title": "Get parameters for aquatic (immature) model with Beverton-Holt dynamics", "topics": [ "get_config_aqua_BH" ] }, { "page": "get_config_aqua_trace", "title": "Get parameters for aquatic (immature) model with forced emergence", "topics": [ "get_config_aqua_trace" ] }, { "page": "get_config_humans_MOI", "title": "Get parameters for MOI human model", "topics": [ "get_config_humans_MOI" ] }, { "page": "get_config_humans_SIR", "title": "Get parameters for SIR human model", "topics": [ "get_config_humans_SIR" ] }, { "page": "get_config_humans_SIS", "title": "Get parameters for SIS human model", "topics": [ "get_config_humans_SIS" ] }, { "page": "get_config_mosquito_RM", "title": "Get parameters for generalized Ross-Macdonald mosquito model", "topics": [ "get_config_mosquito_RM" ] }, { "page": "get_config_mosquito_trace", "title": "Get parameters for null mosquito model", "topics": [ "get_config_mosquito_trace" ] }, { "page": "get_config_visitor_trace", "title": "Get parameters for trace driven visitors", "topics": [ "get_config_visitor_trace" ] }, { "page": "get_eip_mosquito_RM", "title": "Get extrinsic incubation period for Ross-Macdonald mosquito model", "topics": [ "get_eip_mosquito_RM" ] }, { "page": "get_f_mosquito_RM", "title": "Get feeding rate for Ross-Macdonald mosquito model", "topics": [ "get_f_mosquito_RM" ] }, { "page": "get_K_aqua_BH", "title": "Get carrying capacity for Beverton-Holt aquatic mosquito model", "topics": [ "get_K_aqua_BH" ] }, { "page": "get_kappa_mosquito_RM", "title": "Get kappa for Ross-Macdonald mosquito model", "topics": [ "get_kappa_mosquito_RM" ] }, { "page": "get_lambda_aqua_trace", "title": "Get daily emergence for Beverton-Holt aquatic mosquito model", "topics": [ "get_lambda_aqua_trace" ] }, { "page": "get_molt_aqua_BH", "title": "Get daily maturation probability for Beverton-Holt aquatic mosquito model", "topics": [ "get_molt_aqua_BH" ] }, { "page": "get_nu_mosquito_RM", "title": "Get number of eggs laid per oviposition for Ross-Macdonald mosquito model", "topics": [ "get_nu_mosquito_RM" ] }, { "page": "get_p_mosquito_RM", "title": "Get daily survival probability for Ross-Macdonald mosquito model", "topics": [ "get_p_mosquito_RM" ] }, { "page": "get_psi_mosquito_RM", "title": "Get mosquito dispersal matrix for Ross-Macdonald mosquito model", "topics": [ "get_psi_mosquito_RM" ] }, { "page": "get_q_mosquito_RM", "title": "Get human blood feeding fraction for Ross-Macdonald mosquito model", "topics": [ "get_q_mosquito_RM" ] }, { "page": "get_surv_aqua_BH", "title": "Get daily survival probability for Beverton-Holt aquatic mosquito model", "topics": [ "get_surv_aqua_BH" ] }, { "page": "get_tmax", "title": "Get maximum time of simulation from model object", "topics": [ "get_tmax" ] }, { "page": "get_tnow", "title": "Get current time of simulation from model object", "topics": [ "get_tnow" ] }, { "page": "is_binary", "title": "Does a numeric object consist of only zeros and ones?", "topics": [ "is_binary" ] }, { "page": "make_MicroMoB", "title": "Make a model object", "topics": [ "make_MicroMoB" ] }, { "page": "MicroMoB", "title": "MicroMoB: Microsimulation for mosquito-borne pathogens", "topics": [ "MicroMoB-package", "MicroMoB" ] }, { "page": "observe_pfpr", "title": "Observe PfPR in human strata", "topics": [ "observe_pfpr" ] }, { "page": "observe_pfpr.SIP", "title": "Observe PfPR in human strata for SIP model", "topics": [ "observe_pfpr.SIP" ] }, { "page": "observe_pfpr.SIS", "title": "Observe PfPR in human strata for SIS model", "topics": [ "observe_pfpr.SIS" ] }, { "page": "output_aqua", "title": "Get output for aquatic (immature) mosquito populations", "topics": [ "output_aqua" ] }, { "page": "output_aqua.BH", "title": "Get output for aquatic (immature) mosquito populations with Beverton-Holt dynamics", "topics": [ "output_aqua.BH" ] }, { "page": "output_aqua.trace", "title": "Get output for aquatic (immature) mosquito populations with forced emergence", "topics": [ "output_aqua.trace" ] }, { "page": "output_mosquitoes", "title": "Get output for mosquito populations", "topics": [ "output_mosquitoes" ] }, { "page": "output_mosquitoes.RM", "title": "Get output for Ross-Macdonald mosquito populations", "topics": [ "output_mosquitoes.RM" ] }, { "page": "output_mosquitoes.trace", "title": "Get output for null mosquito populations", "topics": [ "output_mosquitoes.trace" ] }, { "page": "sample_stochastic_matrix", "title": "Sample a stochastic matrix", "topics": [ "sample_stochastic_matrix" ] }, { "page": "sample_stochastic_vector", "title": "Sample a stochastic vector", "topics": [ "sample_stochastic_vector" ] }, { "page": "set_eip_mosquito_RM", "title": "Set extrinsic incubation period for Ross-Macdonald mosquito model", "topics": [ "set_eip_mosquito_RM" ] }, { "page": "set_f_mosquito_RM", "title": "Set feeding rate for Ross-Macdonald mosquito model", "topics": [ "set_f_mosquito_RM" ] }, { "page": "set_K_aqua_BH", "title": "Set carrying capacity for Beverton-Holt aquatic mosquito model", "topics": [ "set_K_aqua_BH" ] }, { "page": "set_kappa_mosquito_RM", "title": "Set kappa for Ross-Macdonald mosquito model", "topics": [ "set_kappa_mosquito_RM" ] }, { "page": "set_lambda_aqua_trace", "title": "Set daily emergence for trace (forced) aquatic mosquito model", "topics": [ "set_lambda_aqua_trace" ] }, { "page": "set_molt_aqua_BH", "title": "Set daily maturation probability for Beverton-Holt aquatic mosquito model", "topics": [ "set_molt_aqua_BH" ] }, { "page": "set_nu_mosquito_RM", "title": "Set number of eggs laid per oviposition for Ross-Macdonald mosquito model", "topics": [ "set_nu_mosquito_RM" ] }, { "page": "set_p_mosquito_RM", "title": "Set daily survival probability for Ross-Macdonald mosquito model", "topics": [ "set_p_mosquito_RM" ] }, { "page": "set_psi_mosquito_RM", "title": "Set mosquito dispersal matrix for Ross-Macdonald mosquito model", "topics": [ "set_psi_mosquito_RM" ] }, { "page": "set_q_mosquito_RM", "title": "Set human blood feeding fraction for Ross-Macdonald mosquito model", "topics": [ "set_q_mosquito_RM" ] }, { "page": "set_surv_aqua_BH", "title": "Set daily survival probability for Beverton-Holt aquatic mosquito model", "topics": [ "set_surv_aqua_BH" ] }, { "page": "setup_alternative_trace", "title": "Setup trace driven alternative blood hosts", "topics": [ "setup_alternative_trace" ] }, { "page": "setup_aqua_BH", "title": "Setup aquatic (immature) mosquito model with Beverton-Holt dynamics", "topics": [ "setup_aqua_BH" ] }, { "page": "setup_aqua_trace", "title": "Setup aquatic (immature) mosquito model with trace (forced) emergence", "topics": [ "setup_aqua_trace" ] }, { "page": "setup_humans_MOI", "title": "Setup humans with MOI (multiplicity of infection) pathogen model", "topics": [ "setup_humans_MOI" ] }, { "page": "setup_humans_SIP", "title": "Setup humans with SIP pathogen model", "topics": [ "setup_humans_SIP" ] }, { "page": "setup_humans_SIR", "title": "Setup humans with SIR infection model", "topics": [ "setup_humans_SIR" ] }, { "page": "setup_humans_SIS", "title": "Setup humans with SIS pathogen model", "topics": [ "setup_humans_SIS" ] }, { "page": "setup_mosquito_BQ", "title": "Setup blood feeding & oviposition (BQ) behavioral state mosquito model", "topics": [ "setup_mosquito_BQ" ] }, { "page": "setup_mosquito_RM", "title": "Setup generalized Ross-Macdonald mosquito model", "topics": [ "setup_mosquito_RM" ] }, { "page": "setup_mosquito_trace", "title": "Setup null mosquito model", "topics": [ "setup_mosquito_trace" ] }, { "page": "setup_visitor_trace", "title": "Setup trace driven visitors", "topics": [ "setup_visitor_trace" ] }, { "page": "step_aqua", "title": "Update aquatic (immature) mosquito populations", "topics": [ "step_aqua" ] }, { "page": "step_aqua.BH", "title": "Update aquatic (immature) mosquito populations for Beverton-Holt dynamics", "topics": [ "step_aqua.BH" ] }, { "page": "step_aqua.BH_deterministic", "title": "Update aquatic (immature) mosquito populations for deterministic Beverton-Holt dynamics", "topics": [ "step_aqua.BH_deterministic" ] }, { "page": "step_aqua.BH_stochastic", "title": "Update aquatic (immature) mosquito populations for stochastic Beverton-Holt dynamics", "topics": [ "step_aqua.BH_stochastic" ] }, { "page": "step_aqua.trace", "title": "Update aquatic (immature) mosquito populations for forced emergence", "topics": [ "step_aqua.trace" ] }, { "page": "step_humans", "title": "Update human population", "topics": [ "step_humans" ] }, { "page": "step_humans.MOI", "title": "Update MOI human model", "topics": [ "step_humans.MOI" ] }, { "page": "step_humans.MOI_deterministic", "title": "Update MOI human model (deterministic)", "topics": [ "step_humans.MOI_deterministic" ] }, { "page": "step_humans.MOI_stochastic", "title": "Update MOI human model (stochastic)", "topics": [ "step_humans.MOI_stochastic" ] }, { "page": "step_humans.SIP", "title": "Update SIP human model", "topics": [ "step_humans.SIP" ] }, { "page": "step_humans.SIP_deterministic", "title": "Update SIP human model (deterministic)", "topics": [ "step_humans.SIP_deterministic" ] }, { "page": "step_humans.SIP_stochastic", "title": "Update SIP human model (stochastic)", "topics": [ "step_humans.SIP_stochastic" ] }, { "page": "step_humans.SIR", "title": "Update SIR human model", "topics": [ "step_humans.SIR" ] }, { "page": "step_humans.SIR_deterministic", "title": "Update SIR human model (deterministic)", "topics": [ "step_humans.SIR_deterministic" ] }, { "page": "step_humans.SIR_stochastic", "title": "Update SIR human model (stochastic)", "topics": [ "step_humans.SIR_stochastic" ] }, { "page": "step_humans.SIS", "title": "Update SIS human model", "topics": [ "step_humans.SIS" ] }, { "page": "step_humans.SIS_deterministic", "title": "Update SIS human model (deterministic)", "topics": [ "step_humans.SIS_deterministic" ] }, { "page": "step_humans.SIS_stochastic", "title": "Update SIS human model (stochastic)", "topics": [ "step_humans.SIS_stochastic" ] }, { "page": "step_mosquitoes", "title": "Update mosquito population", "topics": [ "step_mosquitoes" ] }, { "page": "step_mosquitoes.BQ", "title": "Update blood feeding & oviposition (BQ) behavioral state mosquitoes", "topics": [ "step_mosquitoes.BQ" ] }, { "page": "step_mosquitoes.BQ_deterministic", "title": "Update blood feeding & oviposition (BQ) behavioral state mosquitoes (deterministic)", "topics": [ "step_mosquitoes.BQ_deterministic" ] }, { "page": "step_mosquitoes.BQ_stochastic", "title": "Update blood feeding & oviposition (BQ) behavioral state mosquitoes (stochastic)", "topics": [ "step_mosquitoes.BQ_stochastic" ] }, { "page": "step_mosquitoes.RM", "title": "Update Ross-Macdonald mosquitoes", "topics": [ "step_mosquitoes.RM" ] }, { "page": "step_mosquitoes.RM_deterministic", "title": "Update Ross-Macdonald mosquitoes (deterministic)", "topics": [ "step_mosquitoes.RM_deterministic" ] }, { "page": "step_mosquitoes.RM_stochastic", "title": "Update Ross-Macdonald mosquitoes (stochastic)", "topics": [ "step_mosquitoes.RM_stochastic" ] }, { "page": "step_mosquitoes.trace", "title": "Update null mosquito population", "topics": [ "step_mosquitoes.trace" ] }, { "page": "strata_to_residency_counts", "title": "Helper function for lumped population strata (counts)", "topics": [ "strata_to_residency_counts" ] }, { "page": "strata_to_residency_proportion", "title": "Helper function for lumped population strata (proportional assignment)", "topics": [ "strata_to_residency_proportion" ] }, { "page": "time_patch_varying_parameter", "title": "Input parameters that may vary by time and patch", "topics": [ "time_patch_varying_parameter" ] }, { "page": "time_varying_parameter", "title": "Input parameters that may vary by time", "topics": [ "time_varying_parameter" ] } ], "_readme": "https://github.com/cran/MicroMoB/raw/HEAD/README.md", "_rundeps": [ "abind", "jsonlite" ], "_vignettes": [ { "source": "Advanced.Rmd", "filename": "Advanced.html", "title": "Advanced topics", "engine": "knitr::rmarkdown", "headings": [ "Writing new packages", "Writing new models", "Plumber web API" ], "created": "2022-03-08 23:50:02", "modified": "2022-03-08 23:50:02", "commits": 1 }, { "source": "BH_aqua.Rmd", "filename": "BH_aqua.html", "title": "Beverton-Holt aquatic model", "engine": "knitr::rmarkdown", "headings": [ "Deterministic model", "Stochastic model", "Deterministic equilibrium" ], "created": "2022-02-01 08:00:04", "modified": "2022-07-01 18:10:02", "commits": 2 }, { "source": "bloodmeal.Rmd", "filename": "bloodmeal.html", "title": "Blood feeding", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Schematic", "Human component", "Mosquito component", "Other components", "Biting distribution matrix ($\\beta$)", "Entomological inoculation rate ($EIR$)", "Net infectiousness of the human population ($\\kappa$)", "Directed wiring diagram" ], "created": "2022-02-01 08:00:04", "modified": "2022-02-01 08:00:04", "commits": 1 }, { "source": "Contributing.Rmd", "filename": "Contributing.html", "title": "Contributing", "engine": "knitr::rmarkdown", "headings": [ "Issues", "Git", "Continuous integration", "Pull Requests" ], "created": "2022-02-01 08:00:04", "modified": "2022-02-01 08:00:04", "commits": 1 }, { "source": "MicroMoB.Rmd", "filename": "MicroMoB.html", "title": "Micro-MoB (Microsimulation for mosquito-borne pathogens)", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Software design", "Dynamics", "Components", "Mosquitoes", "Aquatic", "Humans", "Visitor", "Other blood hosts", "Dynamics between components" ], "created": "2022-02-01 08:00:04", "modified": "2022-03-08 23:50:02", "commits": 2 }, { "source": "MOI_human.Rmd", "filename": "MOI_human.html", "title": "Queueing model for human superinfection", "engine": "knitr::rmarkdown", "headings": [ "Simulation" ], "created": "2022-02-01 08:00:04", "modified": "2022-07-01 18:10:02", "commits": 2 }, { "source": "RM_mosquito.Rmd", "filename": "RM_mosquito.html", "title": "Ross-Macdonald mosquito model", "engine": "knitr::rmarkdown", "headings": [ "Deterministic model", "Stochastic model", "Example", "Deterministic simulation", "Stochastic simulation" ], "created": "2022-02-01 08:00:04", "modified": "2022-07-01 18:10:02", "commits": 2 }, { "source": "RM_transmission.Rmd", "filename": "RM_transmission.html", "title": "Ross-Macdonald transmission model", "engine": "knitr::rmarkdown", "headings": [ "Endemic equilibrium solution", "MicroMoB simulation" ], "created": "2022-02-01 08:00:04", "modified": "2022-07-01 18:10:02", "commits": 2 }, { "source": "BQ_mosquito.Rmd", "filename": "BQ_mosquito.html", "title": "Simple behavioral state mosquito model", "engine": "knitr::rmarkdown", "headings": [ "Deterministic model", "\\begin{equation}\\left[\\begin{array}{cc}B_{t+1} \\Q_{t+1} \\\\end{array}\\right]", "Stochastic model", "Simulation" ], "created": "2022-03-08 23:50:02", "modified": "2022-07-01 18:10:02", "commits": 2 } ], "_score": 4.158362492095249, "_indexed": true, "_nocasepkg": "micromob", "_universes": [ "slwu89", "dd-harp" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.2", "date": "2026-05-27T09:09:54.000Z", "distro": "noble", "arch": "aarch64", "commit": "9105166006cda085934ad47ba670e2a16fbecea1", "fileid": "67140153981f3dc5314ce1a3dde0dc81d3c2134a1e2eb758923a264a118de18a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/slwu89/actions/runs/26501683700" }, { "r": "4.7.0", "os": "linux", "version": "0.1.2", "date": "2026-05-27T09:09:53.000Z", "distro": "noble", "arch": "x86_64", "commit": "9105166006cda085934ad47ba670e2a16fbecea1", "fileid": "9d17eca5dc01bef6f3d6467bcad5b2f791102dff04c65892a3bcac052ce17f2c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/slwu89/actions/runs/26501683700" }, { "r": "4.6.0", "os": "linux", "version": "0.1.2", "date": "2026-05-27T09:09:46.000Z", "distro": "noble", "arch": "aarch64", "commit": "9105166006cda085934ad47ba670e2a16fbecea1", "fileid": "44673c4fbe176d6e60508aa4ab74453a0d7f6286c38622e0c5932066399586ee", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/slwu89/actions/runs/26501683700" }, { "r": "4.6.0", "os": "linux", "version": "0.1.2", "date": "2026-05-27T09:09:57.000Z", "distro": "noble", "arch": "x86_64", "commit": "9105166006cda085934ad47ba670e2a16fbecea1", "fileid": "247d9151adc40a74d67afb5ac02bb9adef4ce96f9a2e501176a8824d5cf500cf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/slwu89/actions/runs/26501683700" }, { "r": "4.5.3", "os": "mac", "version": "0.1.2", "date": "2026-05-27T09:09:57.000Z", "arch": "aarch64", "commit": "9105166006cda085934ad47ba670e2a16fbecea1", "fileid": "179ffdce145960cb3badc83ec245547afc918797965b3cd6fcb1a4868fb15e93", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/slwu89/actions/runs/26501683700" }, { "r": "4.5.3", "os": "mac", "version": "0.1.2", "date": "2026-05-27T09:11:07.000Z", "arch": "x86_64", "commit": "9105166006cda085934ad47ba670e2a16fbecea1", "fileid": "0cd5b925ea8d02a477f7a8cd414aa97af7da874b7baac6632e4b8a47f574fce3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/slwu89/actions/runs/26501683700" }, { "r": "4.6.0", "os": "mac", "version": "0.1.2", "date": "2026-05-27T09:10:18.000Z", "arch": "aarch64", "commit": "9105166006cda085934ad47ba670e2a16fbecea1", "fileid": "750384b89eda75397ed82d3cd11f25f6ebc4cf711cf504c6579f538fb8e7b1cf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/slwu89/actions/runs/26501683700" }, { "r": "4.6.0", "os": "mac", "version": "0.1.2", "date": "2026-05-27T09:10:48.000Z", "arch": "x86_64", "commit": "9105166006cda085934ad47ba670e2a16fbecea1", "fileid": "d28364a1fbba2c3ac08c9d0348ec7c89aaca682461b06d79dfc87f7174ded33c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/slwu89/actions/runs/26501683700" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.2", "date": "2026-05-27T09:09:49.000Z", "arch": "emscripten", "commit": "9105166006cda085934ad47ba670e2a16fbecea1", "fileid": "862dd9d4498589e04281481f7e3258aadf516adc858ccca2a165df5314f40abe", "status": "success", "buildurl": "https://github.com/r-universe/slwu89/actions/runs/26501683700" }, { "r": "4.7.0", "os": "win", "version": "0.1.2", "date": "2026-05-27T09:08:51.000Z", "arch": "x86_64", "commit": "9105166006cda085934ad47ba670e2a16fbecea1", "fileid": "12d6564140817b2c9aea87c1b0d8411334ba2b95e519e9a50074fb2afc7f30c8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/slwu89/actions/runs/26501683700" }, { "r": "4.5.3", "os": "win", "version": "0.1.2", "date": "2026-05-27T09:09:31.000Z", "arch": "x86_64", "commit": "9105166006cda085934ad47ba670e2a16fbecea1", "fileid": "9933cc0e26e19af44c16a9f8dde80f8673f22bac5d1a0ef336a66eff52756b84", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/slwu89/actions/runs/26501683700" }, { "r": "4.6.0", "os": "win", "version": "0.1.2", "date": "2026-05-27T09:09:02.000Z", "arch": "x86_64", "commit": "9105166006cda085934ad47ba670e2a16fbecea1", "fileid": "654e6a0ad4ecfa34da07cf931045b713c6722ac3fba115a92caa32c4ca529cc4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/slwu89/actions/runs/26501683700" } ] }