R Under development (unstable) (2026-02-18 r89435 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. > > if (requireNamespace("tinytest", quietly = TRUE)) { + + test_tmat_matches_expected <- function(tmat) { + # Check for out of bounds values + tinytest::expect_false(any(tmat < 0)) + tinytest::expect_false(any(tmat > 1)) + } + + tinytest::test_package("measles") + } Loading required package: epiworldR Thank you for using epiworldR! Please consider citing it in your work. You can find the citation information by running citation("epiworldR") test-contact-matrix.R......... 0 tests test-contact-matrix.R......... 0 tests test-contact-matrix.R......... 0 tests test-contact-matrix.R......... 0 tests test-contact-matrix.R......... 0 tests test-contact-matrix.R......... 0 tests test-contact-matrix.R......... 0 tests test-contact-matrix.R......... 0 tests test-contact-matrix.R......... 1 tests OK test-contact-matrix.R......... 1 tests OK _________________________________________________________________________ |||||||Running the model... |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. ||||||| test-contact-matrix.R......... 1 tests OK test-contact-matrix.R......... 1 tests OK test-contact-matrix.R......... 2 tests OK test-contact-matrix.R......... 2 tests OK test-contact-matrix.R......... 2 tests OK test-contact-matrix.R......... 2 tests OK test-contact-matrix.R......... 2 tests OK test-contact-matrix.R......... 3 tests OK test-contact-matrix.R......... 3 tests OK test-contact-matrix.R......... 3 tests OK test-contact-matrix.R......... 3 tests OK test-contact-matrix.R......... 3 tests OK test-contact-matrix.R......... 3 tests OK test-contact-matrix.R......... 4 tests OK test-contact-matrix.R......... 4 tests OK _________________________________________________________________________ |||||||Running the model... |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. ||||||| test-contact-matrix.R......... 4 tests OK test-contact-matrix.R......... 4 tests OK test-contact-matrix.R......... 5 tests OK test-contact-matrix.R......... 5 tests OK test-contact-matrix.R......... 5 tests OK test-contact-matrix.R......... 5 tests OK test-contact-matrix.R......... 5 tests OK test-contact-matrix.R......... 6 tests OK test-contact-matrix.R......... 7 tests OK test-contact-matrix.R......... 8 tests OK 72ms test-hospitalization.R........ 0 tests test-hospitalization.R........ 0 tests test-hospitalization.R........ 0 tests test-hospitalization.R........ 0 tests test-hospitalization.R........ 0 tests Starting multiple runs (1000) using 2 thread(s) _________________________________________________________________________ _________________________________________________________________________ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. test-hospitalization.R........ 0 tests test-hospitalization.R........ 0 tests Attaching package: 'data.table' The following object is masked from 'package:base': %notin% test-hospitalization.R........ 0 tests test-hospitalization.R........ 0 tests test-hospitalization.R........ 0 tests test-hospitalization.R........ 0 tests test-hospitalization.R........ 0 tests test-hospitalization.R........ 0 tests test-hospitalization.R........ 0 tests test-hospitalization.R........ 1 tests OK test-hospitalization.R........ 1 tests OK test-hospitalization.R........ 1 tests OK test-hospitalization.R........ 1 tests OK test-hospitalization.R........ 1 tests OK test-hospitalization.R........ 1 tests OK test-hospitalization.R........ 2 tests OK test-hospitalization.R........ 2 tests OK test-hospitalization.R........ 2 tests OK test-hospitalization.R........ 3 tests OK 8.4s test-measles-quarantine-errors.R 0 tests test-measles-quarantine-errors.R 1 tests OK test-measles-quarantine-errors.R 2 tests OK test-measles-quarantine-errors.R 2 tests OK test-measles-quarantine-errors.R 3 tests OK test-measles-quarantine-errors.R 4 tests OK test-measles-quarantine-errors.R 5 tests OK test-measles-quarantine-errors.R 6 tests OK test-measles-quarantine-errors.R 7 tests OK test-measles-quarantine-errors.R 8 tests OK test-measles-quarantine-errors.R 9 tests OK test-measles-quarantine-errors.R 9 tests OK test-measles-quarantine-errors.R 9 tests OK test-measles-quarantine-errors.R 9 tests OK test-measles-quarantine-errors.R 9 tests OK test-measles-quarantine-errors.R 9 tests OK test-measles-quarantine-errors.R 10 tests OK test-measles-quarantine-errors.R 11 tests OK test-measles-quarantine-errors.R 12 tests OK test-measles-quarantine-errors.R 13 tests OK test-measles-quarantine-errors.R 14 tests OK test-measles-quarantine-errors.R 15 tests OK test-measles-quarantine-errors.R 16 tests OK test-measles-quarantine-errors.R 17 tests OK test-measles-quarantine-errors.R 18 tests OK test-measles-quarantine-errors.R 19 tests OK test-measles-quarantine-errors.R 20 tests OK test-measles-quarantine-errors.R 21 tests OK test-measles-quarantine-errors.R 22 tests OK test-measles-quarantine-errors.R 23 tests OK test-measles-quarantine-errors.R 24 tests OK test-measles-quarantine-errors.R 25 tests OK test-measles-quarantine-errors.R 26 tests OK test-measles-quarantine-errors.R 27 tests OK test-measles-quarantine-errors.R 28 tests OK test-measles-quarantine-errors.R 29 tests OK test-measles-quarantine-errors.R 30 tests OK test-measles-quarantine-errors.R 31 tests OK test-measles-quarantine-errors.R 32 tests OK test-measles-quarantine-errors.R 33 tests OK test-measles-quarantine-errors.R 34 tests OK test-measles-quarantine-errors.R 35 tests OK test-measles-quarantine-errors.R 36 tests OK test-measles-quarantine-errors.R 37 tests OK test-measles-quarantine-errors.R 38 tests OK test-measles-quarantine-errors.R 39 tests OK 32ms test-measles-quarantine-math.R 0 tests Starting multiple runs (200) using 2 thread(s) _________________________________________________________________________ _________________________________________________________________________ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. ----- PASSED : test-measles-quarantine-math.R<4--39> call| expect_equal(r0_obs, R0, tolerance = 0.1) Starting multiple runs (200) using 2 thread(s) _________________________________________________________________________ _________________________________________________________________________ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. ----- PASSED : test-measles-quarantine-math.R<4--39> call| expect_equal(r0_obs, R0, tolerance = 0.1) Starting multiple runs (200) using 2 thread(s) _________________________________________________________________________ _________________________________________________________________________ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. ----- PASSED : test-measles-quarantine-math.R<4--39> call| expect_equal(r0_obs, R0, tolerance = 0.1) test-measles-quarantine-math.R 3 tests OK 2.3s test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests _________________________________________________________________________ Running the model... ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. test-measlesmixing.R.......... 0 tests ________________________________________________________________________________ ________________________________________________________________________________ SIMULATION STUDY Name of the model : Measles with Mixing and Quarantine Population size : 9000 Agents' data : (none) Number of entities : 3 Days (duration) : 100 (of 100) Number of viruses : 1 Last run elapsed t : 23.00ms Last run speed : 37.54 million agents x day / second Rewiring : off Global events: - Update infected individuals (runs daily) Virus(es): - Measles Tool(s): - Vaccine Model parameters: - (IGNORED) Vax improved recovery : 0.8000 - Contact rate : 15.0000 - Contact tracing days prior : 4.0000 - Contact tracing success rate : 0.8000 - Days undetected : 2.0000 - Hospitalization period : 10.0000 - Hospitalization rate : 0.1000 - Incubation period : 10.0000 - Isolation period : 10.0000 - Isolation willingness : 0.8000 - Prodromal period : 3.0000 - Quarantine period : 14.0000 - Quarantine willingness : 0.9000 - Rash period : 7.0000 - Transmission rate : 0.9000 - Vaccination rate : 0.9500 - Vax efficacy : 0.9700 Distribution of the population at time 100: - ( 0) Susceptible : 8999 -> 8997 - ( 1) Exposed : 1 -> 0 - ( 2) Prodromal : 0 -> 0 - ( 3) Rash : 0 -> 0 - ( 4) Isolated : 0 -> 0 - ( 5) Isolated Recovered : 0 -> 0 - ( 6) Detected Hospitalized : 0 -> 0 - ( 7) Quarantined Exposed : 0 -> 0 - ( 8) Quarantined Susceptible : 0 -> 0 - ( 9) Quarantined Prodromal : 0 -> 0 - (10) Quarantined Recovered : 0 -> 0 - (11) Hospitalized : 0 -> 0 - (12) Recovered : 0 -> 3 Transition Probabilities: - Susceptible 1.00 0.00 - - - - - - - - - - - - Exposed - 0.91 0.06 - - - - 0.03 - - - - - - Prodromal - - 0.50 0.50 - - - - - - - - - - Rash - - - - 0.50 0.50 - - - - - - - - Isolated - - - - - 1.00 - - - - - - - - Isolated Recovered - - - - - 0.88 - - - - - - 0.12 - Detected Hospitalized - - - - - - - - - - - - - - Quarantined Exposed - - - - - - - 0.83 - 0.17 - - - - Quarantined Susceptible - - - - - - - - - - - - - - Quarantined Prodromal - - - - 1.00 - - - - - - - - - Quarantined Recovered - - - - - - - - - - - - - - Hospitalized - - - - - - - - - - - - - - Recovered - - - - - - - - - - - - 1.00 test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 0 tests test-measlesmixing.R.......... 1 tests OK test-measlesmixing.R.......... 2 tests OK test-measlesmixing.R.......... 3 tests OK test-measlesmixing.R.......... 4 tests OK test-measlesmixing.R.......... 5 tests OK test-measlesmixing.R.......... 6 tests OK test-measlesmixing.R.......... 7 tests OK test-measlesmixing.R.......... 8 tests OK 61ms test-measlesmixingriskquarantine-multiple.R 0 tests test-measlesmixingriskquarantine-multiple.R 0 tests test-measlesmixingriskquarantine-multiple.R 0 tests test-measlesmixingriskquarantine-multiple.R 0 tests test-measlesmixingriskquarantine-multiple.R 0 tests test-measlesmixingriskquarantine-multiple.R 0 tests test-measlesmixingriskquarantine-multiple.R 0 tests test-measlesmixingriskquarantine-multiple.R 0 tests test-measlesmixingriskquarantine-multiple.R 0 tests Starting multiple runs (50) using 2 thread(s) _________________________________________________________________________ _________________________________________________________________________ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. test-measlesmixingriskquarantine-multiple.R 0 tests Starting multiple runs (50) using 2 thread(s) _________________________________________________________________________ _________________________________________________________________________ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. test-measlesmixingriskquarantine-multiple.R 0 tests Starting multiple runs (50) using 2 thread(s) _________________________________________________________________________ _________________________________________________________________________ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. test-measlesmixingriskquarantine-multiple.R 0 tests Starting multiple runs (50) using 2 thread(s) _________________________________________________________________________ _________________________________________________________________________ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. test-measlesmixingriskquarantine-multiple.R 0 tests Starting multiple runs (50) using 2 thread(s) _________________________________________________________________________ _________________________________________________________________________ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. test-measlesmixingriskquarantine-multiple.R 0 tests test-measlesmixingriskquarantine-multiple.R 1 tests OK test-measlesmixingriskquarantine-multiple.R 2 tests OK test-measlesmixingriskquarantine-multiple.R 3 tests OK test-measlesmixingriskquarantine-multiple.R 4 tests OK test-measlesmixingriskquarantine-multiple.R 5 tests OK test-measlesmixingriskquarantine-multiple.R 6 tests OK test-measlesmixingriskquarantine-multiple.R 7 tests OK 1.3s test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 0 tests _________________________________________________________________________ Running the model... ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done. test-measlesmixingriskquarantine.R 0 tests ________________________________________________________________________________ ________________________________________________________________________________ SIMULATION STUDY Name of the model : Measles with Mixing and Risk-based Quarantine Population size : 9000 Agents' data : (none) Number of entities : 3 Days (duration) : 100 (of 100) Number of viruses : 1 Last run elapsed t : 49.00ms Last run speed : 18.35 million agents x day / second Rewiring : off Global events: - Update infected individuals (runs daily) Virus(es): - Measles Tool(s): - Vaccine Model parameters: - Contact rate : 15.0000 - Contact tracing days prior : 4.0000 - Contact tracing success rate : 0.8000 - Days undetected : 2.0000 - Detection rate quarantine : 0.5000 - Hospitalization period : 10.0000 - Hospitalization rate : 0.1000 - Incubation period : 10.0000 - Isolation period : 10.0000 - Isolation willingness : 0.8000 - Prodromal period : 3.0000 - Quarantine period high : 21.0000 - Quarantine period low : 7.0000 - Quarantine period medium : 14.0000 - Quarantine willingness : 0.9000 - Rash period : 7.0000 - Transmission rate : 0.9000 - Vaccination rate : 0.9500 - Vax efficacy : 0.9700 Distribution of the population at time 100: - ( 0) Susceptible : 8999 -> 8578 - ( 1) Exposed : 1 -> 3 - ( 2) Prodromal : 0 -> 0 - ( 3) Rash : 0 -> 0 - ( 4) Isolated : 0 -> 0 - ( 5) Isolated Recovered : 0 -> 2 - ( 6) Detected Hospitalized : 0 -> 0 - ( 7) Quarantined Exposed : 0 -> 0 - ( 8) Quarantined Susceptible : 0 -> 402 - ( 9) Quarantined Prodromal : 0 -> 0 - (10) Quarantined Recovered : 0 -> 0 - (11) Hospitalized : 0 -> 0 - (12) Recovered : 0 -> 15 Transition Probabilities: - Susceptible 1.00 0.00 - - - - - 0.00 0.00 - - - - - Exposed - 0.90 0.08 - - - - 0.02 - - - - - - Prodromal - - 0.68 0.18 0.13 - - - - - - - - - Rash - - - 0.12 - 0.75 - - - - - - 0.12 - Isolated - - - - 0.23 0.69 0.08 - - - - - - - Isolated Recovered - - - - - 0.89 - - - - - - 0.11 - Detected Hospitalized - - - - - - 0.75 - - - - - 0.25 - Quarantined Exposed - 0.03 - - - - - 0.91 - 0.07 - - - - Quarantined Susceptible 0.08 - - - - - - - 0.92 - - - - - Quarantined Prodromal - - - - 0.33 - - - - 0.67 - - - - Quarantined Recovered - - - - - - - - - - - - - - Hospitalized - - - - - - - - - - - - - - Recovered - - - - - - - - - - - - 1.00 test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 0 tests test-measlesmixingriskquarantine.R 1 tests OK test-measlesmixingriskquarantine.R 2 tests OK test-measlesmixingriskquarantine.R 3 tests OK test-measlesmixingriskquarantine.R 4 tests OK test-measlesmixingriskquarantine.R 5 tests OK test-measlesmixingriskquarantine.R 6 tests OK test-measlesmixingriskquarantine.R 7 tests OK test-measlesmixingriskquarantine.R 8 tests OK test-measlesmixingriskquarantine.R 9 tests OK test-measlesmixingriskquarantine.R 10 tests OK test-measlesmixingriskquarantine.R 11 tests OK test-measlesmixingriskquarantine.R 12 tests OK test-measlesmixingriskquarantine.R 13 tests OK test-measlesmixingriskquarantine.R 14 tests OK test-measlesmixingriskquarantine.R 15 tests OK test-measlesmixingriskquarantine.R 16 tests OK test-measlesmixingriskquarantine.R 17 tests OK test-measlesmixingriskquarantine.R 18 tests OK test-measlesmixingriskquarantine.R 19 tests OK test-measlesmixingriskquarantine.R 20 tests OK test-measlesmixingriskquarantine.R 21 tests OK test-measlesmixingriskquarantine.R 22 tests OK test-measlesmixingriskquarantine.R 23 tests OK test-measlesmixingriskquarantine.R 24 tests OK test-measlesmixingriskquarantine.R 25 tests OK test-measlesmixingriskquarantine.R 26 tests OK 86ms All ok, 94 results (12.2s) > > proc.time() user system elapsed 15.43 1.93 12.40