{ "_id": "6adcd25836cb6c0442e4f5da", "Package": "msdes", "Title": "CE Model", "Author": "Ayman Sadek", "Maintainer": "Ayman Sadek ", "Description": "This is the Multiple Sclerosis MS Multiple Technology\nAppraisal MTA ID6369 Descrete Event Simulation DES Model.", "Config/roxygen2/version": "8.1.0", "Version": "1.0.0", "Roxygen": "list(markdown = TRUE)", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "License": "GPL (>= 3)", "LazyData": "true", "URL": "https://daysnmake.github.io/msdes/", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev", "Repository": "https://daysnmake.r-universe.dev", "Date/Publication": "2026-10-24 15:24:30 UTC", "RemoteUrl": "https://github.com/daysNmake/msdes", "RemoteRef": "HEAD", "RemoteSha": "ca33cc2d38b5fe60c48a1a8197101bcbf691d4aa", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-24 15:40:53 UTC", "User": "root" }, "_user": "daysnmake", "_type": "src", "_file": "msdes_1.0.0.tar.gz", "_fileid": "https://r2.ropensci.org/e7062e8da08e90ebccfec8d24cb1f4e696f3c67eb9b1395da24623a331a77369", "_filesize": 3345454, "_sha256": "e7062e8da08e90ebccfec8d24cb1f4e696f3c67eb9b1395da24623a331a77369", "_expires": "2027-02-01T15:44:22.000Z", "_created": "2026-10-24T15:40:53.000Z", "_published": "2026-10-24T15:44:24.105Z", "_upstream": "https://github.com/daysNmake/msdes", "_status": "success", "_maintainer": { "name": "Ayman Sadek", "email": "ayman.sadek@bristol.ac.uk", "login": "daysnmake", "description": "I'm a health economic modeller and medical statistician.", "uuid": 169648739 }, "_jobs": [ { "job": 120913918270, "time": 169, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "12565089297" }, { "job": 120913918263, "time": 160, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "12565258617" }, { "job": 120913918308, "time": 101, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "12565806073" }, { "job": 120913918209, "time": 79, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "12565750728" }, { "job": 120911545542, "time": 628, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12564599428" }, { "job": 120913918206, "time": 148, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12565388072" }, { "job": 120913918249, "time": 89, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "12564758870" }, { "job": 120913918217, "time": 81, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "12565472890" }, { "job": 120913918283, "time": 97, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "12565806069" } ], "_buildurl": "https://github.com/r-universe/daysnmake/actions/runs/40107286819", "_commit": { "id": "ca33cc2d38b5fe60c48a1a8197101bcbf691d4aa", "author": "daysNmake ", "committer": "daysNmake ", "message": "update.\n", "time": 1792855470 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "hesim", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "progressr", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "flexsurv", "role": "Imports" }, { "package": "BCEA", "role": "Imports" }, { "package": "voi", "role": "Imports" }, { "package": "VGAM", "role": "Imports" }, { "package": "WARDEN", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "daysnmake", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-04", "n": 10 }, { "week": "2026-05", "n": 1 }, { "week": "2026-07", "n": 5 }, { "week": "2026-09", "n": 1 }, { "week": "2026-10", "n": 9 }, { "week": "2026-11", "n": 3 }, { "week": "2026-27", "n": 1 }, { "week": "2026-28", "n": 1 }, { "week": "2026-29", "n": 7 }, { "week": "2026-35", "n": 3 }, { "week": "2026-36", "n": 6 }, { "week": "2026-39", "n": 3 }, { "week": "2026-40", "n": 11 }, { "week": "2026-41", "n": 10 }, { "week": "2026-42", "n": 9 }, { "week": "2026-43", "n": 28 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "daysnmake", "count": 292, "uuid": 169648739 }, { "user": "bogdasayen", "count": 49, "uuid": 7103613 }, { "user": "catalopez2809", "count": 5, "uuid": 183820782 } ], "_userbio": { "uuid": 169648739, "type": "user", "name": "Ayman Sadek", "followers": 0, "description": "I'm a health economic modeller and medical statistician." }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/msdes" }, "_devurl": "https://github.com/daysnmake/msdes", "_pkgdown": "https://daysnmake.github.io/msdes/", "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/msdes.html", "extra/readme.html", "extra/readme.md" ], "_cranurl": false, "_exports": [ "draw_tte_new_warden", "gen_common_all_inputs", "gen_init_events", "gen_inputs", "gen_react_events", "gen_unique_pt_inputs", "rrmsdesmodel", "rrmsdessetup", "run_sim_new", "summarise_ce_results", "summarise_samples" ], "_datasets": [ { "name": "df_baseline_severity", "title": "", "object": "df_baseline_severity", "class": [ "data.frame" ], "fields": [ "X.EDSS.0.EDSS.1.EDSS.2.EDSS.3.EDSS.4.EDSS.5.EDSS.6.EDSS.7.EDSS.8.EDSS.9" ], "rows": 6, "table": true, "tojson": true }, { "name": "df_c_spms", "title": "", "object": "df_c_spms", "class": [ "data.frame" ], "fields": [ "PegIFN.β.1.SC.125μg", "Siponimod" ], "rows": 3, "table": true, "tojson": true }, { "name": "df_c_tx", "title": "DMT costs by year", "object": "df_c_tx", "class": [ "matrix", "array" ], "fields": [ "Natalizumab-IV", "Natalizumab-SC", "Natalizumab biosimilar-IV", "Natalizumab biosimilar-SC", "Fingolimod", "Alemtuzumab", "Cladribine", "Ublituximab", "Ofatumumab", "Ocrelizumab", "PegIFN-?-1 SC 125?g", "IFN?-1a SC 44?g", "IFN?-1a SC 22?g", "IFN?-1a IM 30?g", "IFN?-1b SC 250?g", "Glatiramer Acetate 20mg", "Glatiramer Acetate 40mg" ], "rows": 3, "table": true, "tojson": true }, { "name": "df_c_tx_admin", "title": "Treatment administration costs by year", "object": "df_c_tx_admin", "class": [ "matrix", "array" ], "fields": [ "Natalizumab-IV", "Natalizumab-SC", "Natalizumab biosimilar-IV", "Natalizumab biosimilar-SC", "Fingolimod", "Alemtuzumab", "Cladribine", "Ublituximab", "Ofatumumab", "Ocrelizumab", "PegIFN-?-1 SC 125?g", "IFN?-1a SC 44?g", "IFN?-1a SC 22?g", "IFN?-1a IM 30?g", "IFN?-1b SC 250?g", "Glatiramer Acetate 20mg", "Glatiramer Acetate 40mg" ], "rows": 3, "table": true, "tojson": true }, { "name": "df_c_tx_load", "title": "Annual treatment scheduled load factors years 1-5", "object": "df_c_tx_load", "class": [ "matrix", "array" ], "fields": [ "Natalizumab-IV", "Natalizumab-SC", "Natalizumab biosimilar-IV", "Natalizumab biosimilar-SC", "Fingolimod", "Alemtuzumab", "Cladribine", "Ublituximab", "Ofatumumab", "Ocrelizumab", "PegIFN-?-1 SC 125?g", "IFN?-1a SC 44?g", "IFN?-1a SC 22?g", "IFN?-1a IM 30?g", "IFN?-1b SC 250?g", "Glatiramer Acetate 20mg", "Glatiramer Acetate 40mg" ], "rows": 5, "table": true, "tojson": true }, { "name": "df_c_tx_monitor", "title": "Treatment monitoring costs by year", "object": "df_c_tx_monitor", "class": [ "matrix", "array" ], "fields": [ "Natalizumab-IV", "Natalizumab-SC", "Natalizumab biosimilar-IV", "Natalizumab biosimilar-SC", "Fingolimod", "Alemtuzumab", "Cladribine", "Ublituximab", "Ofatumumab", "Ocrelizumab", "PegIFN-?-1 SC 125?g", "IFN?-1a SC 44?g", "IFN?-1a SC 22?g", "IFN?-1a IM 30?g", "IFN?-1b SC 250?g", "Glatiramer Acetate 20mg", "Glatiramer Acetate 40mg" ], "rows": 3, "table": true, "tojson": true }, { "name": "df_duration_relapse", "title": "", "object": "df_duration_relapse", "class": [ "data.frame" ], "fields": [ "X.days_relapse_hospital.sd_days_relapse_hospital.days_relapse.sd_days_relapse.n_group" ], "rows": 3, "table": true, "tojson": true }, { "name": "df_r_all_cause_mortality", "title": "", "object": "df_r_all_cause_mortality", "class": [ "data.frame" ], "fields": [ "X.age.mx.qx.lx.dx.ex.age.1.mx.1.qx.1.lx.1.dx.1.ex.1" ], "rows": 101, "table": true, "tojson": true }, { "name": "df_u_relapse", "title": "", "object": "df_u_relapse", "class": [ "matrix", "array" ], "fields": [ "u_mean_relapse_hospital", "u_sd_relapse_hospital" ], "rows": 3, "table": true, "tojson": true }, { "name": "hr_rrms_arr_fe", "title": "", "object": "hr_rrms_arr_fe", "class": [ "data.frame" ], "fields": [ ".trta", "parameter", "mean", "sd", "X2.5.", "X25.", "X50.", "X75.", "X97.5.", "Bulk_ESS", "Tail_ESS", "Rhat" ], "rows": 16, "table": true, "tojson": true }, { "name": "hr_rrms_cdp3_fe", "title": "", "object": "hr_rrms_cdp3_fe", "class": [ "data.frame" ], "fields": [ ".trta", "parameter", "mean", "sd", "X2.5.", "X25.", "X50.", "X75.", "X97.5.", "Bulk_ESS", "Tail_ESS", "Rhat" ], "rows": 11, "table": true, "tojson": true }, { "name": "hr_rrms_cdp6_fe", "title": "", "object": "hr_rrms_cdp6_fe", "class": [ "data.frame" ], "fields": [ ".trta", "parameter", "mean", "sd", "X2.5.", "X25.", "X50.", "X75.", "X97.5.", "Bulk_ESS", "Tail_ESS", "Rhat" ], "rows": 10, "table": true, "tojson": true }, { "name": "hr_rrms_discontinuation_fe", "title": "", "object": "hr_rrms_discontinuation_fe", "class": [ "data.frame" ], "fields": [ ".trta", "parameter", "mean", "sd", "X2.5.", "X25.", "X50.", "X75.", "X97.5.", "Bulk_ESS", "Tail_ESS", "Rhat" ], "rows": 12, "table": true, "tojson": true }, { "name": "hr_rrms_saes_fe", "title": "", "object": "hr_rrms_saes_fe", "class": [ "data.frame" ], "fields": [ ".trta", "parameter", "mean", "sd", "X2.5.", "X25.", "X50.", "X75.", "X97.5.", "Bulk_ESS", "Tail_ESS", "Rhat" ], "rows": 14, "table": true, "tojson": true }, { "name": "m_c_edss", "title": "", "object": "m_c_edss", "class": [ "matrix", "array" ], "fields": [ "rrms_mean", "rrms_se", "spms_mean", "spms_se" ], "rows": 10, "table": true, "tojson": true }, { "name": "m_c_relapse", "title": "", "object": "m_c_relapse", "class": [ "data.frame" ], "fields": [ "mean", "sd" ], "rows": 6, "table": true, "tojson": true }, { "name": "m_discontinuation", "title": "", "object": "m_discontinuation", "class": [ "matrix", "array" ], "fields": [ "alpha", "beta", "follow_up", "mean", "sd" ], "rows": 4, "table": true, "tojson": true }, { "name": "m_n_patients_edss", "title": "Patient counts by EDSS score", "object": "m_n_patients_edss", "class": [ "matrix", "array" ], "fields": [ "X0", "X1", "X2", "X3", "X4", "X5", "X6", "X7", "X8", "X9" ], "rows": 2, "table": true, "tojson": true }, { "name": "m_proportion_ontrtline", "title": "A matrix of patient counts stratified by treatment", "object": "m_proportion_ontrtline", "class": [ "matrix", "array" ], "fields": [ "Natalizumab.IV", "Natalizumab.SC", "Natalizumab.biosimilar.IV", "Natalizumab.biosimilar.SC", "Cladribine", "Ublituximab", "Ofatumumab", "Ocrelizumab" ], "rows": 4, "table": true, "tojson": true }, { "name": "m_r_mortality", "title": "", "object": "m_r_mortality", "class": [ "matrix", "array" ], "fields": [ "age", "mx", "qx", "lx", "dx", "ex", "age.1", "mx.1", "qx.1", "lx.1", "dx.1", "ex.1" ], "rows": 101, "table": true, "tojson": true }, { "name": "m_saes", "title": "", "object": "m_saes", "class": [ "matrix", "array" ], "fields": [ "alpha", "beta", "follow_up", "mean", "sd" ], "rows": 2, "table": true, "tojson": true }, { "name": "m_tto_edss_decrease_rrms_sigma", "title": "Natural history variance covariance.", "object": "m_tto_edss_decrease_rrms_sigma", "class": [ "matrix", "array" ], "fields": [ "rate", "BaselineWebEDSS" ], "rows": 2, "table": true, "tojson": true }, { "name": "m_tto_edss_decrease_spms_sigma", "title": "Natural history variance covariance.", "object": "m_tto_edss_decrease_spms_sigma", "class": [ "matrix", "array" ], "fields": [ "rate", "BaselineWebEDSS" ], "rows": 2, "table": true, "tojson": true }, { "name": "m_tto_edss_increase_harrms_sigma", "title": "Natural history treatment dependent variance covariance.", "object": "m_tto_edss_increase_harrms_sigma", "class": [ "matrix", "array" ], "fields": [ "rate", "BaselineWebEDSS", "DMTNatalizumab" ], "rows": 3, "table": true, "tojson": true }, { "name": "m_tto_edss_increase_rrms_sigma", "title": "Natural history treatment dependent variance covariance.", "object": "m_tto_edss_increase_rrms_sigma", "class": [ "matrix", "array" ], "fields": [ "rate", "BaselineWebEDSS", "DMTNatalizumab" ], "rows": 3, "table": true, "tojson": true }, { "name": "m_tto_edss_increase_spms_sigma", "title": "Natural history variance covariance.", "object": "m_tto_edss_increase_spms_sigma", "class": [ "matrix", "array" ], "fields": [ "rate", "BaselineWebEDSS" ], "rows": 2, "table": true, "tojson": true }, { "name": "m_tto_relapse_spms_sigma", "title": "Natural history variance covariance.", "object": "m_tto_relapse_spms_sigma", "class": [ "matrix", "array" ], "fields": [ "rate", "BaselineWebEDSS" ], "rows": 2, "table": true, "tojson": true }, { "name": "m_tto_sp_conversion_harrms_sigma", "title": "Natural history treatment dependent variance covariance.", "object": "m_tto_sp_conversion_harrms_sigma", "class": [ "matrix", "array" ], "fields": [ "rate", "BaselineWebEDSS", "DMTNatalizumab" ], "rows": 3, "table": true, "tojson": true }, { "name": "m_u_carer", "title": "", "object": "m_u_carer", "class": [ "matrix", "array" ], "fields": [ "Mean", "SE" ], "rows": 10, "table": true, "tojson": true }, { "name": "m_u_carer_ta127", "title": "", "object": "m_u_carer_ta127", "class": [ "data.frame" ], "fields": [ "X.Mean.SE" ], "rows": 10, "table": true, "tojson": true }, { "name": "m_u_edss_clarity", "title": "", "object": "m_u_edss_clarity", "class": [ "data.frame" ], "fields": [ "X.rrms_mean.rrms_sd.spms_mean.spms_sd" ], "rows": 10, "table": true, "tojson": true }, { "name": "m_u_edss_opera", "title": "", "object": "m_u_edss_opera", "class": [ "data.frame" ], "fields": [ "X.rrms_mean.rrms_sd.spms_mean.spms_sd" ], "rows": 10, "table": true, "tojson": true }, { "name": "r_sae", "title": "", "object": "r_sae", "class": [ "data.frame" ], "fields": [ "X.x" ], "rows": 1, "table": true, "tojson": true }, { "name": "Releff_HA_ARR_FE", "title": "", "object": "Releff_HA_ARR_FE", "class": [ "data.frame" ], "fields": [ ".trtb..trta.parameter.mean.sd.2.5..25..50..75..97.5..Bulk_ESS.Tail_ESS.Rhat" ], "rows": 6, "table": true, "tojson": true }, { "name": "Releff_RRMS_ARR_RE", "title": "", "object": "Releff_RRMS_ARR_RE", "class": [ "data.frame" ], "fields": [ ".trtb..trta.parameter.mean.sd.2.5..25..50..75..97.5..Bulk_ESS.Tail_ESS.Rhat" ], "rows": 16, "table": true, "tojson": true }, { "name": "Releff_RRMS_CDP3_RE", "title": "", "object": "Releff_RRMS_CDP3_RE", "class": [ "data.frame" ], "fields": [ ".trtb..trta.parameter.mean.sd.2.5..25..50..75..97.5..Bulk_ESS.Tail_ESS.Rhat" ], "rows": 11, "table": true, "tojson": true }, { "name": "Releff_RRMS_CDP6_3_FE", "title": "", "object": "Releff_RRMS_CDP6_3_FE", "class": [ "data.frame" ], "fields": [ ".trtb..trta.parameter.mean.sd.2.5..25..50..75..97.5..Bulk_ESS.Tail_ESS.Rhat" ], "rows": 11, "table": true, "tojson": true }, { "name": "Releff_RRMS_CDP6_3_RE", "title": "", "object": "Releff_RRMS_CDP6_3_RE", "class": [ "data.frame" ], "fields": [ ".trtb..trta.parameter.mean.sd.2.5..25..50..75..97.5..Bulk_ESS.Tail_ESS.Rhat" ], "rows": 11, "table": true, "tojson": true }, { "name": "Releff_RRMS_CDP6_RE", "title": "", "object": "Releff_RRMS_CDP6_RE", "class": [ "data.frame" ], "fields": [ ".trtb..trta.parameter.mean.sd.2.5..25..50..75..97.5..Bulk_ESS.Tail_ESS.Rhat" ], "rows": 9, "table": true, "tojson": true }, { "name": "Releff_RRMS_Discontinuation_RE", "title": "", "object": "Releff_RRMS_Discontinuation_RE", "class": [ "data.frame" ], "fields": [ ".trtb..trta.parameter.mean.sd.2.5..25..50..75..97.5..Bulk_ESS.Tail_ESS.Rhat" ], "rows": 12, "table": true, "tojson": true }, { "name": "Releff_RRMS_SeriousAEs_RE", "title": "", "object": "Releff_RRMS_SeriousAEs_RE", "class": [ "data.frame" ], "fields": [ ".trtb..trta.parameter.mean.sd.2.5..25..50..75..97.5..Bulk_ESS.Tail_ESS.Rhat" ], "rows": 13, "table": true, "tojson": true }, { "name": "saes_data", "title": "", "object": "saes_data", "class": [ "data.frame" ], "fields": [ "Serious.Adverse.events", "Incidence", "Weight", "Cost", "Utility.decrement" ], "rows": 9, "table": true, "tojson": true }, { "name": "tto_relapse_harrms_sigma", "title": "Natural history treatment dependent variance covariance.", "object": "tto_relapse_harrms_sigma", "class": [ "matrix", "array" ], "fields": [ "rate", "BaselineWebEDSS", "DMTNatalizumab" ], "rows": 3, "table": true, "tojson": true }, { "name": "u_edss", "title": "", "object": "u_edss", "class": [ "matrix", "array" ], "fields": [ "rrms_mean", "rrms_sd", "spms_mean", "spms_sd" ], "rows": 10, "table": true, "tojson": true }, { "name": "v_p_relapse_severity", "title": "", "object": "v_p_relapse_severity", "class": [ "data.frame" ], "fields": [ "No_relapse", "untreated", "limited_activities", "oral_steroids", "intravenous_steroids", "hospital_admission" ], "rows": 1, "table": true, "tojson": true }, { "name": "v_r_relapse_severity", "title": "", "object": "v_r_relapse_severity", "class": [ "data.frame" ], "fields": [ "X.No_relapse.untreated.limited_activities.oral_steroids.intravenous_steroids.hospital_admission" ], "rows": 1, "table": true, "tojson": true }, { "name": "v_smr", "title": "", "object": "v_smr", "class": [ "matrix", "array" ], "fields": [ "x" ], "rows": 2, "table": true, "tojson": true }, { "name": "v_smr_severity", "title": "", "object": "v_smr_severity", "class": [ "data.frame" ], "fields": [ "X.0.1.2.3.4.5.6.7.8.9" ], "rows": 1, "table": true, "tojson": true }, { "name": "v_smr_severity_harding", "title": "A matrix of excess all cause mortality for MS patients by severity", "object": "v_smr_severity_harding", "class": [ "matrix", "array" ], "fields": [ "X0", "X1", "X2", "X3", "X4", "X5", "X6", "X7", "X8", "X9" ], "rows": 3, "table": true, "tojson": true }, { "name": "v_smr_severity_Jick_Harding", "title": "", "object": "v_smr_severity_Jick_Harding", "class": [ "data.frame" ], "fields": [ "X.0.1.2.3.4.5.6.7.8.9" ], "rows": 2, "table": true, "tojson": true }, { "name": "v_tto_edss_decrease_rrms_mu", "title": "Natural history coefficients.", "object": "v_tto_edss_decrease_rrms_mu", "class": [ "matrix", "array" ], "fields": [ "rate", "BaselineWebEDSS" ], "rows": 1, "table": true, "tojson": true }, { "name": "v_tto_edss_decrease_spms_mu", "title": "Natural history coefficients.", "object": "v_tto_edss_decrease_spms_mu", "class": [ "matrix", "array" ], "fields": [ "rate", "BaselineWebEDSS" ], "rows": 1, "table": true, "tojson": true }, { "name": "v_tto_edss_increase_harrms_mu", "title": "Natural history treatment dependent coefficients.", "object": "v_tto_edss_increase_harrms_mu", "class": [ "matrix", "array" ], "fields": [ "rate", "BaselineWebEDSS", "DMTNatalizumab" ], "rows": 1, "table": true, "tojson": true }, { "name": "v_tto_edss_increase_rrms_mu", "title": "Natural history treatment dependent coefficients.", "object": "v_tto_edss_increase_rrms_mu", "class": [ "matrix", "array" ], "fields": [ "rate", "BaselineWebEDSS", "DMTNatalizumab" ], "rows": 1, "table": true, "tojson": true }, { "name": "v_tto_edss_increase_spms_mu", "title": "Natural history coefficients.", "object": "v_tto_edss_increase_spms_mu", "class": [ "matrix", "array" ], "fields": [ "rate", "BaselineWebEDSS" ], "rows": 1, "table": true, "tojson": true }, { "name": "v_tto_relapse_harrms_mu", "title": "Natural history treatment dependent coefficients.", "object": "v_tto_relapse_harrms_mu", "class": [ "matrix", "array" ], "fields": [ "V1" ], "rows": 3, "table": true, "tojson": true }, { "name": "v_tto_relapse_spms_mu", "title": "Natural history coefficients.", "object": "v_tto_relapse_spms_mu", "class": [ "matrix", "array" ], "fields": [ "V1" ], "rows": 2, "table": true, "tojson": true }, { "name": "v_tto_sp_conversion_harrms_mu", "title": "Natural history treatment dependent coefficients.", "object": "v_tto_sp_conversion_harrms_mu", "class": [ "matrix", "array" ], "fields": [ "V1" ], "rows": 3, "table": true, "tojson": true }, { "name": "vv_smr", "title": "", "object": "vv_smr", "class": [ "data.frame" ], "fields": [ "X.x" ], "rows": 2, "table": true, "tojson": true } ], "_help": [ { "page": "df_c_tx", "title": "DMT costs by year", "topics": [ "df_c_tx" ] }, { "page": "df_c_tx_admin", "title": "Treatment administration costs by year", "topics": [ "df_c_tx_admin" ] }, { "page": "df_c_tx_load", "title": "Annual treatment scheduled load factors years 1-5", "topics": [ "df_c_tx_load" ] }, { "page": "df_c_tx_monitor", "title": "Treatment monitoring costs by year", "topics": [ "df_c_tx_monitor" ] }, { "page": "draw_tte_new_warden", "title": "Draw time to Event custom function", "topics": [ "draw_tte_new_warden" ] }, { "page": "gen_common_all_inputs", "title": "Generate Global inputs", "topics": [ "gen_common_all_inputs" ] }, { "page": "gen_init_events", "title": "Generate initial events", "topics": [ "gen_init_events" ] }, { "page": "gen_inputs", "title": "generate inputs", "topics": [ "gen_inputs" ] }, { "page": "gen_react_events", "title": "Generate reaction events", "topics": [ "gen_react_events" ] }, { "page": "gen_unique_pt_inputs", "title": "Generate Individual inputs", "topics": [ "gen_unique_pt_inputs" ] }, { "page": "m_n_patients_edss", "title": "Patient counts by EDSS score", "topics": [ "m_n_patients_edss" ] }, { "page": "m_proportion_ontrtline", "title": "A matrix of patient counts stratified by treatment", "topics": [ "m_proportion_ontrtline" ] }, { "page": "m_tto_edss_increase_harrms_sigma", "title": "Natural history treatment dependent variance covariance.", "topics": [ "m_tto_edss_increase_harrms_sigma", "m_tto_edss_increase_rrms_sigma", "m_tto_sp_conversion_harrms_sigma", "tto_relapse_harrms_sigma" ] }, { "page": "m_tto_edss_increase_spms_sigma", "title": "Natural history variance covariance.", "topics": [ "m_tto_edss_decrease_rrms_sigma", "m_tto_edss_decrease_spms_sigma", "m_tto_edss_increase_spms_sigma", "m_tto_relapse_spms_sigma" ] }, { "page": "rrmsdesmodel", "title": "RunModel as a function", "topics": [ "rrmsdesmodel" ] }, { "page": "rrmsdessetup", "title": "SetupModel as a function", "topics": [ "rrmsdessetup" ] }, { "page": "run_sim_new", "title": "Run Sim new", "topics": [ "run_sim_new" ] }, { "page": "summarise_ce_results", "title": "Summarise Cost-effectiveness results", "topics": [ "summarise_ce_results" ] }, { "page": "summarise_samples", "title": "Summarise Samples", "topics": [ "summarise_samples" ] }, { "page": "v_smr_severity_harding", "title": "A matrix of excess all cause mortality for MS patients by severity", "topics": [ "v_smr_severity_harding" ] }, { "page": "v_tto_edss_increase_harrms_mu", "title": "Natural history treatment dependent coefficients.", "topics": [ "v_tto_edss_increase_harrms_mu", "v_tto_edss_increase_rrms_mu", "v_tto_relapse_harrms_mu", "v_tto_sp_conversion_harrms_mu" ] }, { "page": "v_tto_edss_increase_spms_mu", "title": "Natural history coefficients.", "topics": [ "v_tto_edss_decrease_rrms_mu", "v_tto_edss_decrease_spms_mu", "v_tto_edss_increase_spms_mu", "v_tto_relapse_spms_mu" ] } ], "_pkglogo": "https://github.com/daysNmake/msdes/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/daysNmake/msdes/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "assertthat", "backports", "base64enc", "bbmle", "BCEA", "bdsmatrix", "bslib", "cachem", "checkmate", "cli", "codetools", "cpp11", "crayon", "crosstalk", "curl", "data.table", "dbarts", "deSolve", "digest", "distributional", "doFuture", "dplyr", "earth", "evaluate", "expm", "farver", "fastGHQuad", "fastmap", "flexsurv", "fontawesome", "foreach", "Formula", "fs", "future", "future.apply", "generics", "ggplot2", "globals", "glue", "gridExtra", "gtable", "hesim", "highr", "hms", "htmltools", "htmlwidgets", "httr", "isoband", "iterators", "jquerylib", "jsonlite", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "listenv", "lsoda", "magrittr", "MASS", "Matrix", "matrixStats", "memoise", "mgcv", "mime", "msm", "mstate", "muhaz", "mvtnorm", "nlme", "numDeriv", "openssl", "otel", "parallelly", "pillar", "pkgconfig", "plotly", "plotmo", "plotrix", "posterior", "prettyunits", "progress", "progressr", "promises", "purrr", "quadprog", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "Rdpack", "rlang", "rmarkdown", "rstpm2", "S7", "sass", "scales", "statmod", "stringi", "stringr", "survival", "sys", "tensorA", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "VGAM", "viridisLite", "voi", "WARDEN", "withr", "xfun", "yaml", "zoo" ], "_vignettes": [ { "source": "msdes.Rmd", "filename": "msdes.html", "title": "msdes", "author": "Ayman Sadek", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Main options", "model setup", "Run Model", "Plot Results" ], "created": "2026-10-21 13:24:52", "modified": "2026-10-24 15:08:30", "commits": 6 }, { "source": "simple.Rmd", "filename": "simple.html", "title": "simple", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Main options", "model setup", "Load Data", "Run Model", "Plot Results" ], "created": "2026-10-24 14:00:06", "modified": "2026-10-24 15:08:30", "commits": 2 } ], "_score": 4.505149978319906, "_indexed": true, "_nocasepkg": "msdes", "_universes": [ "daysnmake" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-10-24T15:43:34.000Z", "distro": "resolute", "commit": "ca33cc2d38b5fe60c48a1a8197101bcbf691d4aa", "fileid": "https://r2.ropensci.org/ec5844b37f5a96dba5937d98bf0b7ac2c1b66843895f4f64b7660dc013440a10", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/daysnmake/actions/runs/40107286819" }, { "r": "4.6.1", "os": "linux", "version": "1.0.0", "date": "2026-10-24T15:43:37.000Z", "distro": "resolute", "commit": "ca33cc2d38b5fe60c48a1a8197101bcbf691d4aa", "fileid": "https://r2.ropensci.org/bbc28a07e55568407291b2b4ca0748603f28fd45d30dcc3fcb78689b700e88cd", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/daysnmake/actions/runs/40107286819" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-10-24T15:42:42.000Z", "commit": "ca33cc2d38b5fe60c48a1a8197101bcbf691d4aa", "fileid": "https://r2.ropensci.org/3eb73ef1e62f271239337807451dc903bdeef0ae0aa4c62ecff11ad429fd18e2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/daysnmake/actions/runs/40107286819" }, { "r": "4.6.1", "os": "mac", "version": "1.0.0", "date": "2026-10-24T15:42:19.000Z", "commit": "ca33cc2d38b5fe60c48a1a8197101bcbf691d4aa", "fileid": "https://r2.ropensci.org/59cc941b36854fb807ecaf3af9d90d552189a878122d07da6bd5fa06c3f332b0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/daysnmake/actions/runs/40107286819" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-10-24T15:43:37.000Z", "commit": "ca33cc2d38b5fe60c48a1a8197101bcbf691d4aa", "fileid": "https://r2.ropensci.org/59b889c04ee67dfa27f0071e9fe7e8c70f2d453417665edac7141b997e5eff2f", "status": "success", "buildurl": "https://github.com/r-universe/daysnmake/actions/runs/40107286819" }, { "r": "4.7.0", "os": "win", "version": "1.0.0", "date": "2026-10-24T15:42:13.000Z", "commit": "ca33cc2d38b5fe60c48a1a8197101bcbf691d4aa", "fileid": "https://r2.ropensci.org/2e5daf0604620386735da5119fa3de373a5fe45e6f7163a35487ff9ae808660d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/daysnmake/actions/runs/40107286819" }, { "r": "4.5.3", "os": "win", "version": "1.0.0", "date": "2026-10-24T15:42:10.000Z", "commit": "ca33cc2d38b5fe60c48a1a8197101bcbf691d4aa", "fileid": "https://r2.ropensci.org/f51f3ee24a35bfd7ff4324f134f20796148c9ca079e94645e3c099b8b3df3899", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/daysnmake/actions/runs/40107286819" }, { "r": "4.6.1", "os": "win", "version": "1.0.0", "date": "2026-10-24T15:42:30.000Z", "commit": "ca33cc2d38b5fe60c48a1a8197101bcbf691d4aa", "fileid": "https://r2.ropensci.org/02cb1bd77aa9a80cd6132fec01a81742a8eb9f4da35954acd378cf7a42223f5c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/daysnmake/actions/runs/40107286819" } ] }