R Under development (unstable) (2026-01-20 r89309 ucrt) -- "Unsuffered Consequences" Copyright (C) 2026 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(DepMod) > > test_check("DepMod") Saving _problems/test-run_model-2.R [ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-run_model.R:2:3'): run_model returns base and alt results ────── Error in `(function (death_rate, retirement_rate, excess_mortality, increased_relapse_1, increased_relapse_2, increased_relapse_3, increased_relapse_4, increased_relapse_5, mean_dur_chron, leavemodel, incidence_no_history, pmild, pmoderate, psevere, mildrecovery, mildpartial, mildchronic, moderaterecovery, moderatepartial, moderatechronic, severerecovery, severepartial, severechronic, mildrecoverycured, mildrecoveryrelapse, mildpartialcured, mildpartialrelapse, moderaterecoveryrelapse, moderaterecoverycured, moderatepartialcured, moderatepartialrelapse, severerecoverycured, severerecoveryrelapse, severepartialcured, severepartialrelapse) { transition_matrix <- array(0, dim = c(length(states), length(states), 47), dimnames = list(from = states, to = states, year = 0:46)) transition_matrix["mild_incidence", "mild_incidence", ] <- 1 transition_matrix["mild_incidence", "mild_cured", ] <- leavemodel/pmild * ((pmild * mildrecovery * (1 - mildrecoveryrelapse * relapsecure) + pmild * mildpartial * (1 - mildpartialrelapse * relapsecure))) transition_matrix["mild_incidence", "mild_1x_1_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * mildrecoveryrelapse + pmild * mildpartial * mildpartialrelapse)) * 0.4 transition_matrix["mild_incidence", "mild_1x_2_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * mildrecoveryrelapse + pmild * mildpartial * mildpartialrelapse)) * 0.3 transition_matrix["mild_incidence", "mild_1x_3_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * mildrecoveryrelapse + pmild * mildpartial * mildpartialrelapse)) * 0.2 transition_matrix["mild_incidence", "mild_1x_4_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * mildrecoveryrelapse + pmild * mildpartial * mildpartialrelapse)) * 0.07 transition_matrix["mild_incidence", "mild_1x_5_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * mildrecoveryrelapse + pmild * mildpartial * mildpartialrelapse)) * 0.03 transition_matrix["mild_incidence", "mild_chronic", ] <- leavemodel/pmild * ((pmild * mildchronic)) transition_matrix["mild_incidence", "mild_mortality", ] <- 1 - leavemodel transition_matrix["moderate_incidence", "moderate_incidence", ] <- 1 transition_matrix["moderate_incidence", "moderate_cured", ] <- leavemodel/pmoderate * ((pmoderate * moderaterecovery * (1 - moderaterecoveryrelapse * relapsecure * moderatecure) + pmoderate * moderatepartial * (1 - moderatepartialrelapse * relapsecure * moderatecure))) transition_matrix["moderate_incidence", "moderate_1x_1_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * moderaterecoveryrelapse * moderatecure + pmoderate * moderatepartial * moderatepartialrelapse * moderatecure)) * 0.4 transition_matrix["moderate_incidence", "moderate_1x_2_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * moderaterecoveryrelapse * moderatecure + pmoderate * moderatepartial * moderatepartialrelapse * moderatecure)) * 0.3 transition_matrix["moderate_incidence", "moderate_1x_3_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * moderaterecoveryrelapse * moderatecure + pmoderate * moderatepartial * moderatepartialrelapse * moderatecure)) * 0.2 transition_matrix["moderate_incidence", "moderate_1x_4_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * moderaterecoveryrelapse * moderatecure + pmoderate * moderatepartial * moderatepartialrelapse * moderatecure)) * 0.07 transition_matrix["moderate_incidence", "moderate_1x_5_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * moderaterecoveryrelapse * moderatecure + pmoderate * moderatepartial * moderatepartialrelapse * moderatecure)) * 0.03 transition_matrix["moderate_incidence", "moderate_chronic", ] <- leavemodel/pmoderate * ((pmoderate * moderatechronic)) transition_matrix["moderate_incidence", "moderate_mortality", ] <- 1 - leavemodel transition_matrix["severe_incidence", "severe_incidence", ] <- 1 transition_matrix["severe_incidence", "severe_cured", ] <- leavemodel/psevere * ((psevere * severerecovery * (1 - severerecoveryrelapse * relapsecure * severecure) + psevere * severepartial * (1 - severepartialrelapse * relapsecure * severecure))) transition_matrix["severe_incidence", "severe_1x_1_year", ] <- leavemodel/psevere * (relapsecure * (psevere * severerecovery * severerecoveryrelapse * severecure + psevere * severepartial * severepartialrelapse * severecure)) * 0.4 transition_matrix["severe_incidence", "severe_1x_2_year", ] <- leavemodel/psevere * (relapsecure * (psevere * severerecovery * severerecoveryrelapse * severecure + psevere * severepartial * severepartialrelapse * severecure)) * 0.3 transition_matrix["severe_incidence", "severe_1x_3_year", ] <- leavemodel/psevere * (relapsecure * (psevere * severerecovery * severerecoveryrelapse * severecure + psevere * severepartial * severepartialrelapse * severecure)) * 0.2 transition_matrix["severe_incidence", "severe_1x_4_year", ] <- leavemodel/psevere * (relapsecure * (psevere * severerecovery * severerecoveryrelapse * severecure + psevere * severepartial * severepartialrelapse * severecure)) * 0.07 transition_matrix["severe_incidence", "severe_1x_5_year", ] <- leavemodel/psevere * (relapsecure * (psevere * severerecovery * severerecoveryrelapse * severecure + psevere * severepartial * severepartialrelapse * severecure)) * 0.03 transition_matrix["severe_incidence", "severe_chronic", ] <- leavemodel/psevere * ((psevere * severechronic)) transition_matrix["severe_incidence", "severe_mortality", ] <- 1 - leavemodel transition_matrix["mild_cured", "mild_cured", ] <- leavemodel transition_matrix["mild_cured", "mild_mortality", ] <- 1 - leavemodel transition_matrix["moderate_cured", "moderate_cured", ] <- leavemodel transition_matrix["moderate_cured", "moderate_mortality", ] <- 1 - leavemodel transition_matrix["severe_cured", "severe_cured", ] <- leavemodel transition_matrix["severe_cured", "severe_mortality", ] <- 1 - leavemodel transition_matrix["mild_1x_1_year", "mild_cured", ] <- leavemodel/pmild * ((pmild * mildrecovery * (1 - (1 - (mildrecoverycured * (1 - increased_relapse_1))) * relapsecure) + pmild * mildpartial * (1 - (1 - (mildpartialcured * (1 - increased_relapse_1))) * relapsecure))) transition_matrix["mild_1x_1_year", "mild_2x_1_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * (1 - (mildrecoverycured * (1 - increased_relapse_1))) + pmild * mildpartial * (1 - (mildpartialcured * (1 - increased_relapse_1))))) * 0.4 transition_matrix["mild_1x_1_year", "mild_2x_2_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * (1 - (mildrecoverycured * (1 - increased_relapse_1))) + pmild * mildpartial * (1 - (mildpartialcured * (1 - increased_relapse_1))))) * 0.3 transition_matrix["mild_1x_1_year", "mild_2x_3_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * (1 - (mildrecoverycured * (1 - increased_relapse_1))) + pmild * mildpartial * (1 - (mildpartialcured * (1 - increased_relapse_1))))) * 0.2 transition_matrix["mild_1x_1_year", "mild_2x_4_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * (1 - (mildrecoverycured * (1 - increased_relapse_1))) + pmild * mildpartial * (1 - (mildpartialcured * (1 - increased_relapse_1))))) * 0.07 transition_matrix["mild_1x_1_year", "mild_2x_5_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * (1 - (mildrecoverycured * (1 - increased_relapse_1))) + pmild * mildpartial * (1 - (mildpartialcured * (1 - increased_relapse_1))))) * 0.03 transition_matrix["mild_1x_1_year", "mild_chronic", ] <- leavemodel/pmild * ((pmild * mildchronic)) transition_matrix["mild_1x_1_year", "mild_mortality", ] <- 1 - leavemodel transition_matrix["moderate_1x_1_year", "moderate_cured", ] <- leavemodel/pmoderate * ((pmoderate * moderaterecovery * (1 - (1 - (moderaterecoverycured * (1 - increased_relapse_1))) * relapsecure * moderatecure) + pmoderate * moderatepartial * (1 - (1 - (moderatepartialcured * (1 - increased_relapse_1))) * relapsecure * moderatecure))) transition_matrix["moderate_1x_1_year", "moderate_2x_1_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * (1 - (moderaterecoverycured * (1 - increased_relapse_1))) + pmoderate * moderatepartial * (1 - (moderatepartialcured * (1 - increased_relapse_1))))) * 0.4 transition_matrix["moderate_1x_1_year", "moderate_2x_2_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * (1 - (moderaterecoverycured * (1 - increased_relapse_1))) + pmoderate * moderatepartial * (1 - (moderatepartialcured * (1 - increased_relapse_1))))) * 0.3 transition_matrix["moderate_1x_1_year", "moderate_2x_3_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * (1 - (moderaterecoverycured * (1 - increased_relapse_1))) + pmoderate * moderatepartial * (1 - (moderatepartialcured * (1 - increased_relapse_1))))) * 0.2 transition_matrix["moderate_1x_1_year", "moderate_2x_4_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * (1 - (moderaterecoverycured * (1 - increased_relapse_1))) + pmoderate * moderatepartial * (1 - (moderatepartialcured * (1 - increased_relapse_1))))) * 0.07 transition_matrix["moderate_1x_1_year", "moderate_2x_5_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * (1 - (moderaterecoverycured * (1 - increased_relapse_1))) + pmoderate * moderatepartial * (1 - (moderatepartialcured * (1 - increased_relapse_1))))) * 0.03 transition_matrix["moderate_1x_1_year", "moderate_chronic", ] <- leavemodel/pmoderate * ((pmoderate * moderatechronic)) transition_matrix["moderate_1x_1_year", "moderate_mortality", ] <- 1 - leavemodel transition_matrix["severe_1x_1_year", "severe_cured", ] <- leavemodel/psevere * ((psevere * severerecovery * (1 - (1 - (severerecoverycured * (1 - increased_relapse_1))) * relapsecure * severecure) + psevere * severepartial * (1 - (1 - (severepartialcured * (1 - increased_relapse_1))) * relapsecure * severecure))) transition_matrix["severe_1x_1_year", "severe_2x_1_year", ] <- leavemodel/psevere * ((relapsecure * (psevere * severerecovery * (1 - (severerecoverycured * (1 - increased_relapse_1))) * severecure + psevere * severepartial * (1 - severepartialcured * (1 - increased_relapse_1))) * severecure)) * 0.4 transition_matrix["severe_1x_1_year", "severe_2x_2_year", ] <- leavemodel/psevere * ((relapsecure * (psevere * severerecovery * (1 - (severerecoverycured * (1 - increased_relapse_1))) * severecure + psevere * severepartial * (1 - severepartialcured * (1 - increased_relapse_1))) * severecure)) * 0.3 transition_matrix["severe_1x_1_year", "severe_2x_3_year", ] <- leavemodel/psevere * ((relapsecure * (psevere * severerecovery * (1 - (severerecoverycured * (1 - increased_relapse_1))) * severecure + psevere * severepartial * (1 - severepartialcured * (1 - increased_relapse_1))) * severecure)) * 0.2 transition_matrix["severe_1x_1_year", "severe_2x_4_year", ] <- leavemodel/psevere * ((relapsecure * (psevere * severerecovery * (1 - (severerecoverycured * (1 - increased_relapse_1))) * severecure + psevere * severepartial * (1 - severepartialcured * (1 - increased_relapse_1))) * severecure)) * 0.07 transition_matrix["severe_1x_1_year", "severe_2x_5_year", ] <- leavemodel/psevere * ((relapsecure * (psevere * severerecovery * (1 - (severerecoverycured * (1 - increased_relapse_1))) * severecure + psevere * severepartial * (1 - severepartialcured * (1 - increased_relapse_1))) * severecure)) * 0.03 transition_matrix["severe_1x_1_year", "severe_chronic", ] <- leavemodel/psevere * ((psevere * severechronic)) transition_matrix["severe_1x_1_year", "severe_mortality", ] <- 1 - leavemodel transition_matrix["mild_1x_2_year", "mild_1x_1_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_1x_2_year", "mild_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_1x_2_year", "moderate_1x_1_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_1x_2_year", "moderate_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_1x_2_year", "severe_1x_1_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_1x_2_year", "severe_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_1x_3_year", "mild_1x_2_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_1x_3_year", "mild_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_1x_3_year", "moderate_1x_2_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_1x_3_year", "moderate_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_1x_3_year", "severe_1x_2_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_1x_3_year", "severe_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_1x_4_year", "mild_1x_3_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_1x_4_year", "mild_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_1x_4_year", "moderate_1x_3_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_1x_4_year", "moderate_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_1x_4_year", "severe_1x_3_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_1x_4_year", "severe_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_1x_5_year", "mild_1x_4_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_1x_5_year", "mild_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_1x_5_year", "moderate_1x_4_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_1x_5_year", "moderate_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_1x_5_year", "severe_1x_4_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_1x_5_year", "severe_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_2x_1_year", "mild_cured", ] <- leavemodel/pmild * ((pmild * mildrecovery * (1 - (1 - (mildrecoverycured * (1 - increased_relapse_2))) * relapsecure) + pmild * mildpartial * (1 - (1 - (mildpartialcured * (1 - increased_relapse_2))) * relapsecure))) transition_matrix["mild_2x_1_year", "mild_3x_1_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * (1 - (mildrecoverycured * (1 - increased_relapse_2))) + pmild * mildpartial * (1 - (mildpartialcured * (1 - increased_relapse_2))))) * 0.4 transition_matrix["mild_2x_1_year", "mild_3x_2_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * (1 - (mildrecoverycured * (1 - increased_relapse_2))) + pmild * mildpartial * (1 - (mildpartialcured * (1 - increased_relapse_2))))) * 0.3 transition_matrix["mild_2x_1_year", "mild_3x_3_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * (1 - (mildrecoverycured * (1 - increased_relapse_2))) + pmild * mildpartial * (1 - (mildpartialcured * (1 - increased_relapse_2))))) * 0.2 transition_matrix["mild_2x_1_year", "mild_3x_4_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * (1 - (mildrecoverycured * (1 - increased_relapse_2))) + pmild * mildpartial * (1 - (mildpartialcured * (1 - increased_relapse_2))))) * 0.07 transition_matrix["mild_2x_1_year", "mild_3x_5_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * (1 - (mildrecoverycured * (1 - increased_relapse_2))) + pmild * mildpartial * (1 - (mildpartialcured * (1 - increased_relapse_2))))) * 0.03 transition_matrix["mild_2x_1_year", "mild_chronic", ] <- leavemodel/pmild * ((pmild * mildchronic)) transition_matrix["mild_2x_1_year", "mild_mortality", ] <- 1 - leavemodel transition_matrix["moderate_2x_1_year", "moderate_cured", ] <- leavemodel/pmoderate * ((pmoderate * moderaterecovery * (1 - (1 - (moderaterecoverycured * (1 - increased_relapse_2))) * relapsecure * moderatecure) + pmoderate * moderatepartial * (1 - (1 - (moderatepartialcured * (1 - increased_relapse_2))) * relapsecure * moderatecure))) transition_matrix["moderate_2x_1_year", "moderate_3x_1_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * (1 - (moderaterecoverycured * (1 - increased_relapse_2))) + pmoderate * moderatepartial * (1 - (moderatepartialcured * (1 - increased_relapse_2))))) * 0.4 transition_matrix["moderate_2x_1_year", "moderate_3x_2_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * (1 - (moderaterecoverycured * (1 - increased_relapse_2))) + pmoderate * moderatepartial * (1 - (moderatepartialcured * (1 - increased_relapse_2))))) * 0.3 transition_matrix["moderate_2x_1_year", "moderate_3x_3_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * (1 - (moderaterecoverycured * (1 - increased_relapse_2))) + pmoderate * moderatepartial * (1 - (moderatepartialcured * (1 - increased_relapse_2))))) * 0.2 transition_matrix["moderate_2x_1_year", "moderate_3x_4_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * (1 - (moderaterecoverycured * (1 - increased_relapse_2))) + pmoderate * moderatepartial * (1 - (moderatepartialcured * (1 - increased_relapse_2))))) * 0.07 transition_matrix["moderate_2x_1_year", "moderate_3x_5_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * (1 - (moderaterecoverycured * (1 - increased_relapse_2))) + pmoderate * moderatepartial * (1 - (moderatepartialcured * (1 - increased_relapse_2))))) * 0.03 transition_matrix["moderate_2x_1_year", "moderate_chronic", ] <- leavemodel/pmoderate * ((pmoderate * moderatechronic)) transition_matrix["moderate_2x_1_year", "moderate_mortality", ] <- 1 - leavemodel transition_matrix["severe_2x_1_year", "severe_cured", ] <- leavemodel/psevere * ((psevere * severerecovery * (1 - (1 - (severerecoverycured * (1 - increased_relapse_2))) * relapsecure * severecure) + psevere * severepartial * (1 - (1 - (severepartialcured * (1 - increased_relapse_2))) * relapsecure * severecure))) transition_matrix["severe_2x_1_year", "severe_3x_1_year", ] <- leavemodel/psevere * ((relapsecure * (psevere * severerecovery * (1 - (severerecoverycured * (1 - increased_relapse_2))) * severecure + psevere * severepartial * (1 - severepartialcured * (1 - increased_relapse_2))) * severecure)) * 0.4 transition_matrix["severe_2x_1_year", "severe_3x_2_year", ] <- leavemodel/psevere * ((relapsecure * (psevere * severerecovery * (1 - (severerecoverycured * (1 - increased_relapse_2))) * severecure + psevere * severepartial * (1 - severepartialcured * (1 - increased_relapse_2))) * severecure)) * 0.3 transition_matrix["severe_2x_1_year", "severe_3x_3_year", ] <- leavemodel/psevere * ((relapsecure * (psevere * severerecovery * (1 - (severerecoverycured * (1 - increased_relapse_2))) * severecure + psevere * severepartial * (1 - severepartialcured * (1 - increased_relapse_2))) * severecure)) * 0.2 transition_matrix["severe_2x_1_year", "severe_3x_4_year", ] <- leavemodel/psevere * ((relapsecure * (psevere * severerecovery * (1 - (severerecoverycured * (1 - increased_relapse_2))) * severecure + psevere * severepartial * (1 - severepartialcured * (1 - increased_relapse_2))) * severecure)) * 0.07 transition_matrix["severe_2x_1_year", "severe_3x_5_year", ] <- leavemodel/psevere * ((relapsecure * (psevere * severerecovery * (1 - (severerecoverycured * (1 - increased_relapse_2))) * severecure + psevere * severepartial * (1 - severepartialcured * (1 - increased_relapse_2))) * severecure)) * 0.03 transition_matrix["severe_2x_1_year", "severe_chronic", ] <- leavemodel/psevere * ((psevere * severechronic)) transition_matrix["severe_2x_1_year", "severe_mortality", ] <- 1 - leavemodel transition_matrix["mild_2x_2_year", "mild_2x_1_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_2x_2_year", "mild_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_2x_2_year", "moderate_2x_1_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_2x_2_year", "moderate_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_2x_2_year", "severe_2x_1_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_2x_2_year", "severe_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_2x_3_year", "mild_2x_2_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_2x_3_year", "mild_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_2x_3_year", "moderate_2x_2_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_2x_3_year", "moderate_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_2x_3_year", "severe_2x_2_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_2x_3_year", "severe_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_2x_4_year", "mild_2x_3_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_2x_4_year", "mild_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_2x_4_year", "moderate_2x_3_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_2x_4_year", "moderate_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_2x_4_year", "severe_2x_3_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_2x_4_year", "severe_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_2x_5_year", "mild_2x_4_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_2x_5_year", "mild_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_2x_5_year", "moderate_2x_4_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_2x_5_year", "moderate_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_2x_5_year", "severe_2x_4_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_2x_5_year", "severe_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_3x_1_year", "mild_cured", ] <- leavemodel/pmild * ((pmild * mildrecovery * (1 - (1 - (mildrecoverycured * (1 - increased_relapse_3))) * relapsecure) + pmild * mildpartial * (1 - (1 - (mildpartialcured * (1 - increased_relapse_3))) * relapsecure))) transition_matrix["mild_3x_1_year", "mild_4x_1_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * (1 - (mildrecoverycured * (1 - increased_relapse_3))) + pmild * mildpartial * (1 - (mildpartialcured * (1 - increased_relapse_3))))) * 0.4 transition_matrix["mild_3x_1_year", "mild_4x_2_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * (1 - (mildrecoverycured * (1 - increased_relapse_3))) + pmild * mildpartial * (1 - (mildpartialcured * (1 - increased_relapse_3))))) * 0.3 transition_matrix["mild_3x_1_year", "mild_4x_3_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * (1 - (mildrecoverycured * (1 - increased_relapse_3))) + pmild * mildpartial * (1 - (mildpartialcured * (1 - increased_relapse_3))))) * 0.2 transition_matrix["mild_3x_1_year", "mild_4x_4_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * (1 - (mildrecoverycured * (1 - increased_relapse_3))) + pmild * mildpartial * (1 - (mildpartialcured * (1 - increased_relapse_3))))) * 0.07 transition_matrix["mild_3x_1_year", "mild_4x_5_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * (1 - (mildrecoverycured * (1 - increased_relapse_3))) + pmild * mildpartial * (1 - (mildpartialcured * (1 - increased_relapse_3))))) * 0.03 transition_matrix["mild_3x_1_year", "mild_chronic", ] <- leavemodel/pmild * ((pmild * mildchronic)) transition_matrix["mild_3x_1_year", "mild_mortality", ] <- 1 - leavemodel transition_matrix["moderate_3x_1_year", "moderate_cured", ] <- leavemodel/pmoderate * ((pmoderate * moderaterecovery * (1 - (1 - (moderaterecoverycured * (1 - increased_relapse_3))) * relapsecure * moderatecure) + pmoderate * moderatepartial * (1 - (1 - (moderatepartialcured * (1 - increased_relapse_3))) * relapsecure * moderatecure))) transition_matrix["moderate_3x_1_year", "moderate_4x_1_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * (1 - (moderaterecoverycured * (1 - increased_relapse_3))) + pmoderate * moderatepartial * (1 - (moderatepartialcured * (1 - increased_relapse_3))))) * 0.4 transition_matrix["moderate_3x_1_year", "moderate_4x_2_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * (1 - (moderaterecoverycured * (1 - increased_relapse_3))) + pmoderate * moderatepartial * (1 - (moderatepartialcured * (1 - increased_relapse_3))))) * 0.3 transition_matrix["moderate_3x_1_year", "moderate_4x_3_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * (1 - (moderaterecoverycured * (1 - increased_relapse_3))) + pmoderate * moderatepartial * (1 - (moderatepartialcured * (1 - increased_relapse_3))))) * 0.2 transition_matrix["moderate_3x_1_year", "moderate_4x_4_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * (1 - (moderaterecoverycured * (1 - increased_relapse_3))) + pmoderate * moderatepartial * (1 - (moderatepartialcured * (1 - increased_relapse_3))))) * 0.07 transition_matrix["moderate_3x_1_year", "moderate_4x_5_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * (1 - (moderaterecoverycured * (1 - increased_relapse_3))) + pmoderate * moderatepartial * (1 - (moderatepartialcured * (1 - increased_relapse_3))))) * 0.03 transition_matrix["moderate_3x_1_year", "moderate_chronic", ] <- leavemodel/pmoderate * ((pmoderate * moderatechronic)) transition_matrix["moderate_3x_1_year", "moderate_mortality", ] <- 1 - leavemodel transition_matrix["severe_3x_1_year", "severe_cured", ] <- leavemodel/psevere * ((psevere * severerecovery * (1 - (1 - (severerecoverycured * (1 - increased_relapse_3))) * relapsecure * severecure) + psevere * severepartial * (1 - (1 - (severepartialcured * (1 - increased_relapse_3))) * relapsecure * severecure))) transition_matrix["severe_3x_1_year", "severe_4x_1_year", ] <- leavemodel/psevere * ((relapsecure * (psevere * severerecovery * (1 - (severerecoverycured * (1 - increased_relapse_3))) * severecure + psevere * severepartial * (1 - severepartialcured * (1 - increased_relapse_3))) * severecure)) * 0.4 transition_matrix["severe_3x_1_year", "severe_4x_2_year", ] <- leavemodel/psevere * ((relapsecure * (psevere * severerecovery * (1 - (severerecoverycured * (1 - increased_relapse_3))) * severecure + psevere * severepartial * (1 - severepartialcured * (1 - increased_relapse_3))) * severecure)) * 0.3 transition_matrix["severe_3x_1_year", "severe_4x_3_year", ] <- leavemodel/psevere * ((relapsecure * (psevere * severerecovery * (1 - (severerecoverycured * (1 - increased_relapse_3))) * severecure + psevere * severepartial * (1 - severepartialcured * (1 - increased_relapse_3))) * severecure)) * 0.2 transition_matrix["severe_3x_1_year", "severe_4x_4_year", ] <- leavemodel/psevere * ((relapsecure * (psevere * severerecovery * (1 - (severerecoverycured * (1 - increased_relapse_3))) * severecure + psevere * severepartial * (1 - severepartialcured * (1 - increased_relapse_3))) * severecure)) * 0.07 transition_matrix["severe_3x_1_year", "severe_4x_5_year", ] <- leavemodel/psevere * ((relapsecure * (psevere * severerecovery * (1 - (severerecoverycured * (1 - increased_relapse_3))) * severecure + psevere * severepartial * (1 - severepartialcured * (1 - increased_relapse_3))) * severecure)) * 0.03 transition_matrix["severe_3x_1_year", "severe_chronic", ] <- leavemodel/psevere * ((psevere * severechronic)) transition_matrix["severe_3x_1_year", "severe_mortality", ] <- 1 - leavemodel transition_matrix["mild_3x_2_year", "mild_3x_1_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_3x_2_year", "mild_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_3x_2_year", "moderate_3x_1_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_3x_2_year", "moderate_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_3x_2_year", "severe_3x_1_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_3x_2_year", "severe_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_3x_3_year", "mild_3x_2_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_3x_3_year", "mild_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_3x_3_year", "moderate_3x_2_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_3x_3_year", "moderate_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_3x_3_year", "severe_3x_2_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_3x_3_year", "severe_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_3x_4_year", "mild_3x_3_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_3x_4_year", "mild_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_3x_4_year", "moderate_3x_3_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_3x_4_year", "moderate_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_3x_4_year", "severe_3x_3_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_3x_4_year", "severe_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_3x_5_year", "mild_3x_4_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_3x_5_year", "mild_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_3x_5_year", "moderate_3x_4_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_3x_5_year", "moderate_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_3x_5_year", "severe_3x_4_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_3x_5_year", "severe_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_4x_1_year", "mild_cured", ] <- leavemodel/pmild * ((pmild * mildrecovery * (1 - (1 - (mildrecoverycured * (1 - increased_relapse_4))) * relapsecure) + pmild * mildpartial * (1 - (1 - (mildpartialcured * (1 - increased_relapse_4))) * relapsecure))) transition_matrix["mild_4x_1_year", "mild_5x_1_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * (1 - (mildrecoverycured * (1 - increased_relapse_4))) + pmild * mildpartial * (1 - (mildpartialcured * (1 - increased_relapse_4))))) * 0.4 transition_matrix["mild_4x_1_year", "mild_5x_2_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * (1 - (mildrecoverycured * (1 - increased_relapse_4))) + pmild * mildpartial * (1 - (mildpartialcured * (1 - increased_relapse_4))))) * 0.3 transition_matrix["mild_4x_1_year", "mild_5x_3_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * (1 - (mildrecoverycured * (1 - increased_relapse_4))) + pmild * mildpartial * (1 - (mildpartialcured * (1 - increased_relapse_4))))) * 0.2 transition_matrix["mild_4x_1_year", "mild_5x_4_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * (1 - (mildrecoverycured * (1 - increased_relapse_4))) + pmild * mildpartial * (1 - (mildpartialcured * (1 - increased_relapse_4))))) * 0.07 transition_matrix["mild_4x_1_year", "mild_5x_5_year", ] <- leavemodel/pmild * (relapsecure * (pmild * mildrecovery * (1 - (mildrecoverycured * (1 - increased_relapse_4))) + pmild * mildpartial * (1 - (mildpartialcured * (1 - increased_relapse_4))))) * 0.03 transition_matrix["mild_4x_1_year", "mild_chronic", ] <- leavemodel/pmild * ((pmild * mildchronic)) transition_matrix["mild_4x_1_year", "mild_mortality", ] <- 1 - leavemodel transition_matrix["moderate_4x_1_year", "moderate_cured", ] <- leavemodel/pmoderate * ((pmoderate * moderaterecovery * (1 - (1 - (moderaterecoverycured * (1 - increased_relapse_4))) * relapsecure * moderatecure) + pmoderate * moderatepartial * (1 - (1 - (moderatepartialcured * (1 - increased_relapse_4))) * relapsecure * moderatecure))) transition_matrix["moderate_4x_1_year", "moderate_5x_1_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * (1 - (moderaterecoverycured * (1 - increased_relapse_4))) + pmoderate * moderatepartial * (1 - (moderatepartialcured * (1 - increased_relapse_4))))) * 0.4 transition_matrix["moderate_4x_1_year", "moderate_5x_2_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * (1 - (moderaterecoverycured * (1 - increased_relapse_4))) + pmoderate * moderatepartial * (1 - (moderatepartialcured * (1 - increased_relapse_4))))) * 0.3 transition_matrix["moderate_4x_1_year", "moderate_5x_3_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * (1 - (moderaterecoverycured * (1 - increased_relapse_4))) + pmoderate * moderatepartial * (1 - (moderatepartialcured * (1 - increased_relapse_4))))) * 0.2 transition_matrix["moderate_4x_1_year", "moderate_5x_4_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * (1 - (moderaterecoverycured * (1 - increased_relapse_4))) + pmoderate * moderatepartial * (1 - (moderatepartialcured * (1 - increased_relapse_4))))) * 0.07 transition_matrix["moderate_4x_1_year", "moderate_5x_5_year", ] <- leavemodel/pmoderate * (relapsecure * (pmoderate * moderaterecovery * (1 - (moderaterecoverycured * (1 - increased_relapse_4))) + pmoderate * moderatepartial * (1 - (moderatepartialcured * (1 - increased_relapse_4))))) * 0.03 transition_matrix["moderate_4x_1_year", "moderate_chronic", ] <- leavemodel/pmoderate * ((pmoderate * moderatechronic)) transition_matrix["moderate_4x_1_year", "moderate_mortality", ] <- 1 - leavemodel transition_matrix["severe_4x_1_year", "severe_cured", ] <- leavemodel/psevere * ((psevere * severerecovery * (1 - (1 - (severerecoverycured * (1 - increased_relapse_4))) * relapsecure * severecure) + psevere * severepartial * (1 - (1 - (severepartialcured * (1 - increased_relapse_4))) * relapsecure * severecure))) transition_matrix["severe_4x_1_year", "severe_5x_1_year", ] <- leavemodel/psevere * ((relapsecure * (psevere * severerecovery * (1 - (severerecoverycured * (1 - increased_relapse_4))) * severecure + psevere * severepartial * (1 - severepartialcured * (1 - increased_relapse_4))) * severecure)) * 0.4 transition_matrix["severe_4x_1_year", "severe_5x_2_year", ] <- leavemodel/psevere * ((relapsecure * (psevere * severerecovery * (1 - (severerecoverycured * (1 - increased_relapse_4))) * severecure + psevere * severepartial * (1 - severepartialcured * (1 - increased_relapse_4))) * severecure)) * 0.3 transition_matrix["severe_4x_1_year", "severe_5x_3_year", ] <- leavemodel/psevere * ((relapsecure * (psevere * severerecovery * (1 - (severerecoverycured * (1 - increased_relapse_4))) * severecure + psevere * severepartial * (1 - severepartialcured * (1 - increased_relapse_4))) * severecure)) * 0.2 transition_matrix["severe_4x_1_year", "severe_5x_4_year", ] <- leavemodel/psevere * ((relapsecure * (psevere * severerecovery * (1 - (severerecoverycured * (1 - increased_relapse_4))) * severecure + psevere * severepartial * (1 - severepartialcured * (1 - increased_relapse_4))) * severecure)) * 0.07 transition_matrix["severe_4x_1_year", "severe_5x_5_year", ] <- leavemodel/psevere * ((relapsecure * (psevere * severerecovery * (1 - (severerecoverycured * (1 - increased_relapse_4))) * severecure + psevere * severepartial * (1 - severepartialcured * (1 - increased_relapse_4))) * severecure)) * 0.03 transition_matrix["severe_4x_1_year", "severe_chronic", ] <- leavemodel/psevere * ((psevere * severechronic)) transition_matrix["severe_4x_1_year", "severe_mortality", ] <- 1 - leavemodel transition_matrix["mild_4x_2_year", "mild_4x_1_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_4x_2_year", "mild_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_4x_2_year", "moderate_4x_1_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_4x_2_year", "moderate_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_4x_2_year", "severe_4x_1_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_4x_2_year", "severe_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_4x_3_year", "mild_4x_2_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_4x_3_year", "mild_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_4x_3_year", "moderate_4x_2_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_4x_3_year", "moderate_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_4x_3_year", "severe_4x_2_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_4x_3_year", "severe_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_4x_4_year", "mild_4x_3_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_4x_4_year", "mild_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_4x_4_year", "moderate_4x_3_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_4x_4_year", "moderate_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_4x_4_year", "severe_4x_3_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_4x_4_year", "severe_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_4x_5_year", "mild_4x_4_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_4x_5_year", "mild_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_4x_5_year", "moderate_4x_4_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_4x_5_year", "moderate_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_4x_5_year", "severe_4x_4_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_4x_5_year", "severe_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_5x_1_year", "mild_cured", ] <- leavemodel/pmild * ((pmild * mildrecovery * (1 - (1 - (mildrecoverycured * (1 - increased_relapse_5))) * relapsecure) + pmild * mildpartial * (1 - (1 - (mildpartialcured * (1 - increased_relapse_5))) * relapsecure))) + `Fifth episode to chronic` transition_matrix["mild_5x_1_year", "mild_mortality", ] <- 1 - leavemodel transition_matrix["mild_5x_1_year", "mild_chronic", ] <- 1 - (1 - leavemodel) - (leavemodel/pmild * ((pmild * mildrecovery * (1 - (1 - (mildrecoverycured * (1 - increased_relapse_5))) * relapsecure) + pmild * mildpartial * (1 - (1 - (mildpartialcured * (1 - increased_relapse_5))) * relapsecure))) + `Fifth episode to chronic`) transition_matrix["moderate_5x_1_year", "moderate_cured", ] <- leavemodel/pmoderate * ((pmoderate * moderaterecovery * (1 - (1 - (moderaterecoverycured * (1 - increased_relapse_5))) * relapsecure * moderatecure) + pmoderate * moderatepartial * (1 - (1 - (moderatepartialcured * (1 - increased_relapse_5))) * relapsecure * moderatecure))) + `Fifth episode to chronic` transition_matrix["moderate_5x_1_year", "moderate_mortality", ] <- 1 - leavemodel transition_matrix["moderate_5x_1_year", "moderate_chronic", ] <- 1 - (1 - leavemodel) - (leavemodel/pmoderate * ((pmoderate * moderaterecovery * (1 - (1 - (moderaterecoverycured * (1 - increased_relapse_5))) * relapsecure * moderatecure) + pmoderate * moderatepartial * (1 - (1 - (moderatepartialcured * (1 - increased_relapse_5))) * relapsecure * moderatecure))) + `Fifth episode to chronic`) transition_matrix["severe_5x_1_year", "severe_cured", ] <- `Fifth episode to chronic` transition_matrix["severe_5x_1_year", "severe_mortality", ] <- 1 - leavemodel transition_matrix["severe_5x_1_year", "severe_chronic", ] <- 1 - (1 - leavemodel) - (`Fifth episode to chronic`) transition_matrix["mild_5x_2_year", "mild_5x_1_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_5x_2_year", "mild_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_5x_2_year", "moderate_5x_1_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_5x_2_year", "moderate_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_5x_2_year", "severe_5x_1_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_5x_2_year", "severe_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_5x_3_year", "mild_5x_2_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_5x_3_year", "mild_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_5x_3_year", "moderate_5x_2_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_5x_3_year", "moderate_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_5x_3_year", "severe_5x_2_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_5x_3_year", "severe_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_5x_4_year", "mild_5x_3_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_5x_4_year", "mild_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_5x_4_year", "moderate_5x_3_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_5x_4_year", "moderate_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_5x_4_year", "severe_5x_3_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_5x_4_year", "severe_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_5x_5_year", "mild_5x_4_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_5x_5_year", "mild_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_5x_5_year", "moderate_5x_4_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["moderate_5x_5_year", "moderate_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_5x_5_year", "severe_5x_4_year", ] <- (1 - retirement_rate) * (1 - death_rate) transition_matrix["severe_5x_5_year", "severe_mortality", ] <- 1 - (1 - retirement_rate) * (1 - death_rate) transition_matrix["mild_chronic", "mild_cured", ] <- (1 - 2^(-1/(mean_dur_chron * log(2)))) * (leavemodel) transition_matrix["mild_chronic", "mild_chronic", ] <- 2^(-1/(mean_dur_chron * log(2))) * (leavemodel) transition_matrix["mild_chronic", "mild_mortality", ] <- 1 - leavemodel transition_matrix["moderate_chronic", "moderate_cured", ] <- (1 - 2^(-1/(mean_dur_chron * log(2)))) * (leavemodel) transition_matrix["moderate_chronic", "moderate_chronic", ] <- 2^(-1/(mean_dur_chron * log(2))) * (leavemodel) transition_matrix["moderate_chronic", "moderate_mortality", ] <- 1 - leavemodel transition_matrix["severe_chronic", "severe_cured", ] <- (1 - 2^(-1/(mean_dur_chron * log(2)))) * (leavemodel) transition_matrix["severe_chronic", "severe_chronic", ] <- 2^(-1/(mean_dur_chron * log(2))) * (leavemodel) transition_matrix["severe_chronic", "severe_mortality", ] <- 1 - leavemodel transition_matrix["mild_mortality", "mild_mortality", ] <- 1 transition_matrix["moderate_mortality", "moderate_mortality", ] <- 1 transition_matrix["severe_mortality", "severe_mortality", ] <- 1 return(transition_matrix) })(death_rate = 0.00198371022638523, retirement_rate = 0.02128, excess_mortality = 1.65, increased_relapse_1 = 0.5, increased_relapse_2 = 0.7, increased_relapse_3 = 0.899999976158142, increased_relapse_4 = 0.949999988079071, increased_relapse_5 = 0.990000009536743, mean_dur_chron = 3.95964163041925, leavemodel = 0.975516530159933, incidence_no_history = 0.0128446472713444, pmild = 0.3, pmoderate = 0.47, psevere = 0.23, mildrecovery = 0.6, mildpartial = 0.37, mildchronic = 0.03, moderaterecovery = 0.475, moderatepartial = 0.495, moderatechronic = 0.03, severerecovery = 0.51, severepartial = 0.46, severechronic = 0.03, mildrecoverycured = 0.458333, mildrecoveryrelapse = 0.5416666, mildpartialcured = 0.2, mildpartialrelapse = 0.8, moderaterecoverycured = 0.49, moderaterecoveryrelapse = 0.51, moderatepartialcured = 0.25, moderatepartialrelapse = 0.75, severerecoverycured = 0.49, severerecoveryrelapse = 0.51, severepartialcured = 0.25, severepartialrelapse = 0.75)`: object 'relapsecure' not found Backtrace: ▆ 1. └─DepMod::run_model(sim_runs = 1, total_population = 100) at test-run_model.R:2:3 2. ├─base::do.call(func_first_part_model, parameters_first) 3. └─DepMod (local) ``(...) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ] Error: ! Test failures. Execution halted