From f16edabbb2705c821f24c9425a663952a254d2cf Mon Sep 17 00:00:00 2001 From: Joshua Lambert Date: Thu, 25 Apr 2024 14:43:34 +0100 Subject: [PATCH] update sim_linelist and sim_outbreak tests and snapshots --- tests/testthat/_snaps/sim_linelist.md | 468 ++++++++++++------------- tests/testthat/_snaps/sim_outbreak.md | 486 +++++++++++++------------- tests/testthat/test-sim_linelist.R | 2 + 3 files changed, 479 insertions(+), 477 deletions(-) diff --git a/tests/testthat/_snaps/sim_linelist.md b/tests/testthat/_snaps/sim_linelist.md index ce75f02d..8411350e 100644 --- a/tests/testthat/_snaps/sim_linelist.md +++ b/tests/testthat/_snaps/sim_linelist.md @@ -4,32 +4,32 @@ sim_linelist(contact_distribution = contact_distribution, infect_period = infect_period, prob_infect = 0.5, onset_to_hosp = onset_to_hosp, onset_to_death = onset_to_death) Output - id case_name case_type sex age date_onset date_admission outcome - 1 1 Gabriel Black probable m 35 2023-01-01 recovered - 2 2 Tyler Kelley confirmed m 43 2023-01-01 recovered - 3 3 Cody Morales suspected m 1 2023-01-01 recovered - 4 5 Joewid Le probable m 78 2023-01-01 recovered - 5 6 Carolyn Moore confirmed f 22 2023-01-01 recovered - 6 8 Cheyenne Sayavong confirmed f 28 2023-01-01 recovered - 7 11 Pierce Khanthavong confirmed m 46 2023-01-01 2023-01-13 recovered - 8 12 Kendra To suspected f 67 2023-01-01 recovered - 9 13 Preston Barringer confirmed m 86 2023-01-01 2023-01-01 died - 10 18 Dominique Raymond confirmed f 60 2023-01-02 recovered - 11 20 Bassaam el-Majid probable m 49 2023-01-02 recovered - 12 22 Susana Varela probable f 7 2023-01-02 2023-01-02 recovered - date_outcome date_first_contact date_last_contact ct_value - 1 NA - 2 2022-12-30 2023-01-05 24 - 3 2022-12-30 2023-01-02 NA - 4 2022-12-29 2023-01-02 NA - 5 2023-01-01 2023-01-03 24 - 6 2023-01-03 2023-01-04 24 - 7 2023-01-04 2023-01-05 24 - 8 2023-01-01 2023-01-04 NA - 9 2023-01-09 2022-12-31 2023-01-03 24 - 10 2022-12-30 2023-01-03 24 - 11 2023-01-01 2023-01-04 NA - 12 2023-01-01 2023-01-03 NA + id case_name case_type sex age date_onset date_admission + 1 1 Dominic Sundara probable m 35 2023-01-01 + 2 2 Preston Montgomery suspected m 43 2023-01-01 + 3 3 Reece Chittum probable m 1 2023-01-01 + 4 5 Michael Cheek confirmed m 78 2023-01-01 + 5 6 Jennifer Smith confirmed f 22 2023-01-01 + 6 8 Erika Quintero confirmed f 28 2023-01-01 + 7 11 Isaiah Patterson suspected m 46 2023-01-01 2023-01-13 + 8 12 Cicely Anderson suspected f 67 2023-01-01 + 9 13 Michael John probable m 86 2023-01-01 2023-01-01 + 10 18 Giovana Magana Aguirre suspected f 60 2023-01-02 + 11 20 Mudrik al-Hallal suspected m 49 2023-01-02 + 12 22 Tea Slaughter probable f 7 2023-01-02 2023-01-02 + outcome date_outcome date_first_contact date_last_contact ct_value + 1 recovered NA + 2 recovered 2022-12-30 2023-01-05 NA + 3 recovered 2022-12-30 2023-01-02 NA + 4 recovered 2022-12-29 2023-01-02 23.1 + 5 recovered 2023-01-01 2023-01-03 23.1 + 6 recovered 2023-01-03 2023-01-04 23.1 + 7 recovered 2023-01-04 2023-01-05 NA + 8 recovered 2023-01-01 2023-01-04 NA + 9 died 2023-01-12 2022-12-31 2023-01-03 NA + 10 recovered 2022-12-30 2023-01-03 NA + 11 recovered 2023-01-01 2023-01-04 NA + 12 recovered 2023-01-01 2023-01-03 NA # sim_linelist works as expected with age-strat risks @@ -39,30 +39,30 @@ hosp_risk = age_dep_hosp_risk, hosp_death_risk = age_dep_hosp_death_risk, non_hosp_death_risk = age_dep_non_hosp_death_risk) Output - id case_name case_type sex age date_onset date_admission outcome - 1 1 Micheal Smallwood probable m 35 2023-01-01 recovered - 2 2 Kyle Foster confirmed m 43 2023-01-01 recovered - 3 3 Ghaamid el-Kaiser suspected m 1 2023-01-01 2023-01-11 died - 4 5 Faatih el-Riaz confirmed m 78 2023-01-01 recovered - 5 6 Hope Arshad suspected f 22 2023-01-01 recovered - 6 8 Shanta Holiday probable f 28 2023-01-01 recovered - 7 11 Aiman al-Demian probable m 46 2023-01-01 recovered - 8 12 Chandra Kilian suspected f 67 2023-01-01 recovered - 9 13 Wajdi el-Diab confirmed m 86 2023-01-01 2023-01-01 recovered - 10 18 Kanani Nguyen confirmed f 60 2023-01-02 recovered - 11 20 Raaid el-Vaziri probable m 49 2023-01-02 2023-01-09 recovered - 12 22 Annie Carter probable f 7 2023-01-02 recovered + id case_name case_type sex age date_onset date_admission outcome + 1 1 Cass Duran probable m 35 2023-01-01 recovered + 2 2 Mudrik al-Hallal suspected m 43 2023-01-01 recovered + 3 3 Jareer al-Safar probable m 1 2023-01-01 2023-01-11 recovered + 4 5 Raashid el-Huda confirmed m 78 2023-01-01 recovered + 5 6 Erika Sierra confirmed f 22 2023-01-01 recovered + 6 8 Jennifer Hong confirmed f 28 2023-01-01 recovered + 7 11 Donald Childs suspected m 46 2023-01-01 recovered + 8 12 Kayla Johnson suspected f 67 2023-01-01 died + 9 13 Avery Johnston probable m 86 2023-01-01 2023-01-01 recovered + 10 18 Giovana Segarra suspected f 60 2023-01-02 recovered + 11 20 Donald Root suspected m 49 2023-01-02 2023-01-09 recovered + 12 22 Kiona Dalke probable f 7 2023-01-02 recovered date_outcome date_first_contact date_last_contact ct_value 1 NA - 2 2022-12-30 2023-01-05 24.1 - 3 2023-01-14 2022-12-30 2023-01-02 NA - 4 2022-12-29 2023-01-02 24.1 - 5 2023-01-01 2023-01-03 NA - 6 2023-01-03 2023-01-04 NA + 2 2022-12-30 2023-01-05 NA + 3 2022-12-30 2023-01-02 NA + 4 2022-12-29 2023-01-02 23.1 + 5 2023-01-01 2023-01-03 23.1 + 6 2023-01-03 2023-01-04 23.1 7 2023-01-04 2023-01-05 NA - 8 2023-01-01 2023-01-04 NA - 9 2022-12-31 2023-01-03 24.1 - 10 2022-12-30 2023-01-03 24.1 + 8 2023-01-14 2023-01-01 2023-01-04 NA + 9 2022-12-31 2023-01-03 NA + 10 2022-12-30 2023-01-03 NA 11 2023-01-01 2023-01-04 NA 12 2023-01-01 2023-01-03 NA @@ -73,32 +73,32 @@ prob_infect = 0.5, onset_to_hosp = onset_to_hosp, onset_to_death = onset_to_death, add_ct = FALSE) Output - id case_name case_type sex age date_onset date_admission outcome - 1 1 Gabriel Black probable m 35 2023-01-01 recovered - 2 2 Tyler Kelley confirmed m 43 2023-01-01 recovered - 3 3 Cody Morales suspected m 1 2023-01-01 recovered - 4 5 Joewid Le probable m 78 2023-01-01 recovered - 5 6 Carolyn Moore confirmed f 22 2023-01-01 recovered - 6 8 Cheyenne Sayavong confirmed f 28 2023-01-01 recovered - 7 11 Pierce Khanthavong confirmed m 46 2023-01-01 2023-01-13 recovered - 8 12 Kendra To suspected f 67 2023-01-01 recovered - 9 13 Preston Barringer confirmed m 86 2023-01-01 2023-01-01 died - 10 18 Dominique Raymond confirmed f 60 2023-01-02 recovered - 11 20 Bassaam el-Majid probable m 49 2023-01-02 recovered - 12 22 Susana Varela probable f 7 2023-01-02 2023-01-02 recovered - date_outcome date_first_contact date_last_contact - 1 - 2 2022-12-30 2023-01-05 - 3 2022-12-30 2023-01-02 - 4 2022-12-29 2023-01-02 - 5 2023-01-01 2023-01-03 - 6 2023-01-03 2023-01-04 - 7 2023-01-04 2023-01-05 - 8 2023-01-01 2023-01-04 - 9 2023-01-09 2022-12-31 2023-01-03 - 10 2022-12-30 2023-01-03 - 11 2023-01-01 2023-01-04 - 12 2023-01-01 2023-01-03 + id case_name case_type sex age date_onset date_admission + 1 1 Dominic Sundara probable m 35 2023-01-01 + 2 2 Preston Montgomery suspected m 43 2023-01-01 + 3 3 Reece Chittum probable m 1 2023-01-01 + 4 5 Michael Cheek confirmed m 78 2023-01-01 + 5 6 Jennifer Smith confirmed f 22 2023-01-01 + 6 8 Erika Quintero confirmed f 28 2023-01-01 + 7 11 Isaiah Patterson suspected m 46 2023-01-01 2023-01-13 + 8 12 Cicely Anderson suspected f 67 2023-01-01 + 9 13 Michael John probable m 86 2023-01-01 2023-01-01 + 10 18 Giovana Magana Aguirre suspected f 60 2023-01-02 + 11 20 Mudrik al-Hallal suspected m 49 2023-01-02 + 12 22 Tea Slaughter probable f 7 2023-01-02 2023-01-02 + outcome date_outcome date_first_contact date_last_contact + 1 recovered + 2 recovered 2022-12-30 2023-01-05 + 3 recovered 2022-12-30 2023-01-02 + 4 recovered 2022-12-29 2023-01-02 + 5 recovered 2023-01-01 2023-01-03 + 6 recovered 2023-01-03 2023-01-04 + 7 recovered 2023-01-04 2023-01-05 + 8 recovered 2023-01-01 2023-01-04 + 9 died 2023-01-12 2022-12-31 2023-01-03 + 10 recovered 2022-12-30 2023-01-03 + 11 recovered 2023-01-01 2023-01-04 + 12 recovered 2023-01-01 2023-01-03 # sim_linelist works as expected with anonymous @@ -109,30 +109,30 @@ Output id case_type sex age date_onset date_admission outcome date_outcome 1 1 confirmed m 35 2023-01-01 recovered - 2 2 probable m 43 2023-01-01 recovered + 2 2 suspected m 43 2023-01-01 recovered 3 3 probable m 1 2023-01-01 recovered 4 5 confirmed m 78 2023-01-01 recovered 5 6 confirmed f 22 2023-01-01 recovered 6 8 confirmed f 28 2023-01-01 recovered 7 11 confirmed m 46 2023-01-01 2023-01-13 recovered - 8 12 confirmed f 67 2023-01-01 recovered - 9 13 confirmed m 86 2023-01-01 2023-01-01 died 2023-01-09 - 10 18 confirmed f 60 2023-01-02 recovered + 8 12 suspected f 67 2023-01-01 recovered + 9 13 confirmed m 86 2023-01-01 2023-01-01 died 2023-01-12 + 10 18 suspected f 60 2023-01-02 recovered 11 20 confirmed m 49 2023-01-02 recovered 12 22 confirmed f 7 2023-01-02 2023-01-02 recovered date_first_contact date_last_contact ct_value - 1 24.9 + 1 23.9 2 2022-12-30 2023-01-05 NA 3 2022-12-30 2023-01-02 NA - 4 2022-12-29 2023-01-02 24.9 - 5 2023-01-01 2023-01-03 24.9 - 6 2023-01-03 2023-01-04 24.9 - 7 2023-01-04 2023-01-05 24.9 - 8 2023-01-01 2023-01-04 24.9 - 9 2022-12-31 2023-01-03 24.9 - 10 2022-12-30 2023-01-03 24.9 - 11 2023-01-01 2023-01-04 24.9 - 12 2023-01-01 2023-01-03 24.9 + 4 2022-12-29 2023-01-02 23.9 + 5 2023-01-01 2023-01-03 23.9 + 6 2023-01-03 2023-01-04 23.9 + 7 2023-01-04 2023-01-05 23.9 + 8 2023-01-01 2023-01-04 NA + 9 2022-12-31 2023-01-03 23.9 + 10 2022-12-30 2023-01-03 NA + 11 2023-01-01 2023-01-04 23.9 + 12 2023-01-01 2023-01-03 23.9 # sim_linelist works as expected with age structure @@ -141,32 +141,32 @@ prob_infect = 0.5, onset_to_hosp = onset_to_hosp, onset_to_death = onset_to_death, population_age = age_struct) Output - id case_name case_type sex age date_onset date_admission outcome - 1 1 Gene Than probable m 44 2023-01-01 recovered - 2 2 Caleb Fredericks probable m 13 2023-01-01 recovered - 3 3 Jaisean Venable suspected m 22 2023-01-01 2023-01-09 died - 4 5 Taylor Swift probable m 85 2023-01-01 recovered - 5 6 Korren Bailey confirmed f 41 2023-01-01 recovered - 6 8 Madison Zahn confirmed f 89 2023-01-01 2023-01-02 recovered - 7 11 Dustin Bellow confirmed m 69 2023-01-01 recovered - 8 12 Ryanna Hart confirmed f 23 2023-01-01 recovered - 9 13 Rafael Garcia confirmed m 9 2023-01-01 recovered - 10 18 Ashlan Hendon confirmed f 62 2023-01-02 recovered - 11 20 Tieran Moorer suspected m 52 2023-01-02 2023-01-15 recovered - 12 22 Paige Reich probable f 76 2023-01-02 recovered + id case_name case_type sex age date_onset date_admission outcome + 1 1 Kyle Crane suspected m 44 2023-01-01 recovered + 2 2 Ghaamid el-Ishmael confirmed m 13 2023-01-01 recovered + 3 3 Faatih el-Kaiser confirmed m 22 2023-01-01 2023-01-09 recovered + 4 5 Va'Aahi Galligan suspected m 85 2023-01-01 recovered + 5 6 Katelyn Catlin confirmed f 41 2023-01-01 recovered + 6 8 Lynsey Duron confirmed f 89 2023-01-01 2023-01-02 died + 7 11 Wajdi al-Demian confirmed m 69 2023-01-01 recovered + 8 12 Jacy Cousins confirmed f 23 2023-01-01 recovered + 9 13 Travis Foster confirmed m 9 2023-01-01 recovered + 10 18 Maria Eberhart probable f 62 2023-01-02 recovered + 11 20 Mubarak el-Vaziri suspected m 52 2023-01-02 2023-01-15 recovered + 12 22 Erin Payson confirmed f 76 2023-01-02 recovered date_outcome date_first_contact date_last_contact ct_value 1 NA - 2 2022-12-30 2023-01-05 NA - 3 2023-01-12 2022-12-30 2023-01-02 NA + 2 2022-12-30 2023-01-05 25.1 + 3 2022-12-30 2023-01-02 25.1 4 2022-12-29 2023-01-02 NA - 5 2023-01-01 2023-01-03 24 - 6 2023-01-03 2023-01-04 24 - 7 2023-01-04 2023-01-05 24 - 8 2023-01-01 2023-01-04 24 - 9 2022-12-31 2023-01-03 24 - 10 2022-12-30 2023-01-03 24 + 5 2023-01-01 2023-01-03 25.1 + 6 2023-01-26 2023-01-03 2023-01-04 25.1 + 7 2023-01-04 2023-01-05 25.1 + 8 2023-01-01 2023-01-04 25.1 + 9 2022-12-31 2023-01-03 25.1 + 10 2022-12-30 2023-01-03 NA 11 2023-01-01 2023-01-04 NA - 12 2023-01-01 2023-01-03 NA + 12 2023-01-01 2023-01-03 25.1 # sim_linelist works as expected with age-strat risks & age struct @@ -175,32 +175,32 @@ prob_infect = 0.5, onset_to_hosp = onset_to_hosp, onset_to_death = onset_to_death, hosp_risk = age_dep_hosp_risk, population_age = age_struct) Output - id case_name case_type sex age date_onset date_admission - 1 1 Damion Hamm confirmed m 44 2023-01-01 - 2 2 Ignacio Hernandez confirmed m 13 2023-01-01 - 3 3 Bryce Donnelly confirmed m 22 2023-01-01 - 4 5 David Arrieta confirmed m 85 2023-01-01 2023-01-01 - 5 6 Kristina Vazquez Pallares confirmed f 41 2023-01-01 - 6 8 Nusaiba el-Farah suspected f 89 2023-01-01 - 7 11 Dominic Kills In Sight probable m 69 2023-01-01 - 8 12 Violet Watts confirmed f 23 2023-01-01 - 9 13 Khristopher Cunniff confirmed m 9 2023-01-01 - 10 18 Paige Reich probable f 62 2023-01-02 - 11 20 Jackson Carlson confirmed m 52 2023-01-02 - 12 22 Cassandra Smith suspected f 76 2023-01-02 - outcome date_outcome date_first_contact date_last_contact ct_value - 1 recovered 25.6 - 2 recovered 2022-12-30 2023-01-05 25.6 - 3 recovered 2022-12-30 2023-01-02 25.6 - 4 died 2023-01-25 2022-12-29 2023-01-02 25.6 - 5 recovered 2023-01-01 2023-01-03 25.6 - 6 recovered 2023-01-03 2023-01-04 NA - 7 recovered 2023-01-04 2023-01-05 NA - 8 recovered 2023-01-01 2023-01-04 25.6 - 9 recovered 2022-12-31 2023-01-03 25.6 - 10 recovered 2022-12-30 2023-01-03 NA - 11 recovered 2023-01-01 2023-01-04 25.6 - 12 recovered 2023-01-01 2023-01-03 NA + id case_name case_type sex age date_onset date_admission outcome + 1 1 Maazin el-Othman probable m 44 2023-01-01 recovered + 2 2 Faisal el-Vaziri confirmed m 13 2023-01-01 recovered + 3 3 Jorge Marten suspected m 22 2023-01-01 recovered + 4 5 Kaleb Natarelli confirmed m 85 2023-01-01 2023-01-01 recovered + 5 6 Hope Arshad suspected f 41 2023-01-01 recovered + 6 8 Shanta Holiday probable f 89 2023-01-01 recovered + 7 11 Nicholas Orgill probable m 69 2023-01-01 recovered + 8 12 Chandra Kilian suspected f 23 2023-01-01 recovered + 9 13 Corey Alcala confirmed m 9 2023-01-01 recovered + 10 18 Kanani Nguyen confirmed f 62 2023-01-02 recovered + 11 20 Sean Shrestha probable m 52 2023-01-02 recovered + 12 22 Annie Carter probable f 76 2023-01-02 recovered + date_outcome date_first_contact date_last_contact ct_value + 1 NA + 2 2022-12-30 2023-01-05 24.1 + 3 2022-12-30 2023-01-02 NA + 4 2022-12-29 2023-01-02 24.1 + 5 2023-01-01 2023-01-03 NA + 6 2023-01-03 2023-01-04 NA + 7 2023-01-04 2023-01-05 NA + 8 2023-01-01 2023-01-04 NA + 9 2022-12-31 2023-01-03 24.1 + 10 2022-12-30 2023-01-03 24.1 + 11 2023-01-01 2023-01-04 NA + 12 2023-01-01 2023-01-03 NA # sim_linelist works as expected with modified config @@ -210,32 +210,32 @@ config = create_config(last_contact_distribution = "geom", last_contact_distribution_params = c(prob = 0.5))) Output - id case_name case_type sex age date_onset date_admission outcome - 1 1 Maazina el-Kader probable f 20 2023-01-01 recovered - 2 2 Muneeb al-Youssef confirmed m 24 2023-01-01 recovered - 3 3 Francisco Huerta suspected m 51 2023-01-01 2023-01-07 recovered - 4 5 Sean Sundara confirmed m 16 2023-01-01 recovered - 5 6 Jack Walentine suspected m 83 2023-01-01 recovered - 6 8 Avery Temple probable m 48 2023-01-01 recovered - 7 11 Robert Gonzales probable m 77 2023-01-01 2023-01-01 recovered - 8 12 Timothy Cheek suspected m 90 2023-01-01 recovered - 9 13 Courtney Smith confirmed f 66 2023-01-01 recovered - 10 18 Jasra al-Hadi confirmed f 31 2023-01-02 2023-01-02 recovered - 11 20 Codie Patterson probable m 46 2023-01-02 recovered - 12 22 Eric Childs probable m 75 2023-01-02 recovered + id case_name case_type sex age date_onset date_admission outcome + 1 1 Lily Camacho confirmed f 20 2023-01-01 recovered + 2 2 Sad el-Irani suspected m 24 2023-01-01 recovered + 3 3 Tristan Benjamin suspected m 51 2023-01-01 2023-01-07 recovered + 4 5 Treven Cornejo probable m 16 2023-01-01 recovered + 5 6 Kevin Contreras suspected m 83 2023-01-01 recovered + 6 8 Tyler Garcia suspected m 48 2023-01-01 recovered + 7 11 Royse Beltran probable m 77 2023-01-01 2023-01-01 recovered + 8 12 Clayton Falcon confirmed m 90 2023-01-01 recovered + 9 13 Halle Batchelder confirmed f 66 2023-01-01 recovered + 10 18 Morgan Grant-Perry confirmed f 31 2023-01-02 2023-01-02 recovered + 11 20 Bowen Apodaca confirmed m 46 2023-01-02 recovered + 12 22 Haaroon el-Firman confirmed m 75 2023-01-02 recovered date_outcome date_first_contact date_last_contact ct_value - 1 NA - 2 2022-12-30 2023-01-01 24.1 + 1 24.7 + 2 2022-12-30 2023-01-01 NA 3 2022-12-31 2023-01-02 NA - 4 2022-12-30 2023-01-02 24.1 + 4 2022-12-30 2023-01-02 NA 5 2022-12-31 2023-01-01 NA 6 2022-12-31 2023-01-01 NA 7 2022-12-30 2023-01-02 NA - 8 2022-12-30 2023-01-01 NA - 9 2022-12-29 2023-01-01 24.1 - 10 2022-12-30 2023-01-01 24.1 - 11 2022-12-30 2023-01-01 NA - 12 2022-12-30 2023-01-02 NA + 8 2022-12-30 2023-01-01 24.7 + 9 2022-12-29 2023-01-01 24.7 + 10 2022-12-30 2023-01-01 24.7 + 11 2022-12-30 2023-01-01 24.7 + 12 2022-12-30 2023-01-02 24.7 # sim_linelist works as expected with modified config parameters @@ -244,32 +244,32 @@ prob_infect = 0.5, onset_to_hosp = onset_to_hosp, onset_to_death = onset_to_death, config = create_config(last_contact_distribution_params = c(lambda = 5))) Output - id case_name case_type sex age date_onset date_admission outcome - 1 1 Gabriel Black probable m 35 2023-01-01 recovered - 2 2 Tyler Kelley confirmed m 43 2023-01-01 recovered - 3 3 Cody Morales suspected m 1 2023-01-01 recovered - 4 5 Joewid Le probable m 78 2023-01-01 recovered - 5 6 Carolyn Moore confirmed f 22 2023-01-01 recovered - 6 8 Cheyenne Sayavong confirmed f 28 2023-01-01 recovered - 7 11 Pierce Khanthavong confirmed m 46 2023-01-01 2023-01-13 recovered - 8 12 Kendra To suspected f 67 2023-01-01 recovered - 9 13 Preston Barringer confirmed m 86 2023-01-01 2023-01-01 died - 10 18 Dominique Raymond confirmed f 60 2023-01-02 recovered - 11 20 Bassaam el-Majid probable m 49 2023-01-02 recovered - 12 22 Susana Varela probable f 7 2023-01-02 2023-01-02 recovered - date_outcome date_first_contact date_last_contact ct_value - 1 NA - 2 2023-01-01 2023-01-07 24 - 3 2022-12-31 2023-01-03 NA - 4 2022-12-31 2023-01-04 NA - 5 2023-01-02 2023-01-04 24 - 6 2023-01-06 2023-01-07 24 - 7 2023-01-07 2023-01-08 24 - 8 2023-01-03 2023-01-06 NA - 9 2023-01-09 2023-01-02 2023-01-05 24 - 10 2023-01-01 2023-01-05 24 - 11 2023-01-04 2023-01-07 NA - 12 2023-01-03 2023-01-05 NA + id case_name case_type sex age date_onset date_admission + 1 1 Dominic Sundara probable m 35 2023-01-01 + 2 2 Preston Montgomery suspected m 43 2023-01-01 + 3 3 Reece Chittum probable m 1 2023-01-01 + 4 5 Michael Cheek confirmed m 78 2023-01-01 + 5 6 Jennifer Smith confirmed f 22 2023-01-01 + 6 8 Erika Quintero confirmed f 28 2023-01-01 + 7 11 Isaiah Patterson suspected m 46 2023-01-01 2023-01-13 + 8 12 Cicely Anderson suspected f 67 2023-01-01 + 9 13 Michael John probable m 86 2023-01-01 2023-01-01 + 10 18 Giovana Magana Aguirre suspected f 60 2023-01-02 + 11 20 Mudrik al-Hallal suspected m 49 2023-01-02 + 12 22 Tea Slaughter probable f 7 2023-01-02 2023-01-02 + outcome date_outcome date_first_contact date_last_contact ct_value + 1 recovered NA + 2 recovered 2023-01-01 2023-01-07 NA + 3 recovered 2022-12-31 2023-01-03 NA + 4 recovered 2022-12-31 2023-01-04 23.1 + 5 recovered 2023-01-02 2023-01-04 23.1 + 6 recovered 2023-01-06 2023-01-07 23.1 + 7 recovered 2023-01-07 2023-01-08 NA + 8 recovered 2023-01-03 2023-01-06 NA + 9 died 2023-01-12 2023-01-02 2023-01-05 NA + 10 recovered 2023-01-01 2023-01-05 NA + 11 recovered 2023-01-04 2023-01-07 NA + 12 recovered 2023-01-03 2023-01-05 NA # sim_linelist works as expected with time-varying cfr @@ -279,32 +279,32 @@ config = create_config(time_varying_death_risk = function(risk, time) risk * exp(-time))) Output - id case_name case_type sex age date_onset date_admission - 1 1 Bryce Kelley probable m 35 2023-01-01 - 2 2 Cleatus Kacprowicz confirmed m 43 2023-01-01 - 3 3 Khristopher Carlson suspected m 1 2023-01-01 - 4 5 Raynaldo Grano probable m 78 2023-01-01 - 5 6 Carolyn Moore confirmed f 22 2023-01-01 - 6 8 Cheyenne Sayavong confirmed f 28 2023-01-01 - 7 11 Abdul Maalik al-Chahine confirmed m 46 2023-01-01 2023-01-13 - 8 12 Kendra To suspected f 67 2023-01-01 - 9 13 Joewid Le confirmed m 86 2023-01-01 2023-01-01 - 10 18 Dominique Raymond confirmed f 60 2023-01-02 - 11 20 Jackson Sheek probable m 49 2023-01-02 - 12 22 Susana Varela probable f 7 2023-01-02 2023-01-02 - outcome date_outcome date_first_contact date_last_contact ct_value - 1 recovered NA - 2 recovered 2022-12-30 2023-01-05 24 - 3 recovered 2022-12-30 2023-01-02 NA - 4 recovered 2022-12-29 2023-01-02 NA - 5 recovered 2023-01-01 2023-01-03 24 - 6 recovered 2023-01-03 2023-01-04 24 - 7 recovered 2023-01-04 2023-01-05 24 - 8 recovered 2023-01-01 2023-01-04 NA - 9 recovered 2022-12-31 2023-01-03 24 - 10 recovered 2022-12-30 2023-01-03 24 - 11 recovered 2023-01-01 2023-01-04 NA - 12 recovered 2023-01-01 2023-01-03 NA + id case_name case_type sex age date_onset date_admission outcome + 1 1 Anthony Raigoza suspected m 35 2023-01-01 recovered + 2 2 Joseph Begay probable m 43 2023-01-01 recovered + 3 3 Andi Lee probable m 1 2023-01-01 recovered + 4 5 Robert Duran suspected m 78 2023-01-01 recovered + 5 6 Mikhaila Guyon confirmed f 22 2023-01-01 recovered + 6 8 Kanani Ahn confirmed f 28 2023-01-01 recovered + 7 11 Michael Chittum probable m 46 2023-01-01 2023-01-13 recovered + 8 12 Hope Cobb probable f 67 2023-01-01 recovered + 9 13 Eric Lopez confirmed m 86 2023-01-01 2023-01-01 recovered + 10 18 Kelly Carter probable f 60 2023-01-02 recovered + 11 20 Turki el-Vaziri probable m 49 2023-01-02 recovered + 12 22 Cicely Shangreaux confirmed f 7 2023-01-02 2023-01-02 recovered + date_outcome date_first_contact date_last_contact ct_value + 1 NA + 2 2022-12-30 2023-01-05 NA + 3 2022-12-30 2023-01-02 NA + 4 2022-12-29 2023-01-02 NA + 5 2023-01-01 2023-01-03 25.4 + 6 2023-01-03 2023-01-04 25.4 + 7 2023-01-04 2023-01-05 NA + 8 2023-01-01 2023-01-04 NA + 9 2022-12-31 2023-01-03 25.4 + 10 2022-12-30 2023-01-03 NA + 11 2023-01-01 2023-01-04 NA + 12 2023-01-01 2023-01-03 25.4 # sim_linelist works as expected with time-varying cfr & age-strat @@ -314,30 +314,30 @@ hosp_death_risk = age_dep_hosp_death_risk, config = create_config( time_varying_death_risk = function(risk, time) risk * exp(-time))) Output - id case_name case_type sex age date_onset date_admission - 1 1 Bryce Kelley probable m 35 2023-01-01 - 2 2 Cleatus Kacprowicz confirmed m 43 2023-01-01 - 3 3 Khristopher Carlson suspected m 1 2023-01-01 - 4 5 Raynaldo Grano probable m 78 2023-01-01 - 5 6 Carolyn Moore confirmed f 22 2023-01-01 - 6 8 Cheyenne Sayavong confirmed f 28 2023-01-01 - 7 11 Abdul Maalik al-Chahine confirmed m 46 2023-01-01 2023-01-13 - 8 12 Kendra To suspected f 67 2023-01-01 - 9 13 Joewid Le confirmed m 86 2023-01-01 2023-01-01 - 10 18 Dominique Raymond confirmed f 60 2023-01-02 - 11 20 Jackson Sheek probable m 49 2023-01-02 - 12 22 Susana Varela probable f 7 2023-01-02 2023-01-02 - outcome date_outcome date_first_contact date_last_contact ct_value - 1 recovered NA - 2 recovered 2022-12-30 2023-01-05 24 - 3 recovered 2022-12-30 2023-01-02 NA - 4 recovered 2022-12-29 2023-01-02 NA - 5 recovered 2023-01-01 2023-01-03 24 - 6 recovered 2023-01-03 2023-01-04 24 - 7 recovered 2023-01-04 2023-01-05 24 - 8 recovered 2023-01-01 2023-01-04 NA - 9 recovered 2022-12-31 2023-01-03 24 - 10 recovered 2022-12-30 2023-01-03 24 - 11 recovered 2023-01-01 2023-01-04 NA - 12 recovered 2023-01-01 2023-01-03 NA + id case_name case_type sex age date_onset date_admission outcome + 1 1 Anthony Raigoza suspected m 35 2023-01-01 recovered + 2 2 Joseph Begay probable m 43 2023-01-01 recovered + 3 3 Andi Lee probable m 1 2023-01-01 recovered + 4 5 Robert Duran suspected m 78 2023-01-01 recovered + 5 6 Mikhaila Guyon confirmed f 22 2023-01-01 recovered + 6 8 Kanani Ahn confirmed f 28 2023-01-01 recovered + 7 11 Michael Chittum probable m 46 2023-01-01 2023-01-13 recovered + 8 12 Hope Cobb probable f 67 2023-01-01 recovered + 9 13 Eric Lopez confirmed m 86 2023-01-01 2023-01-01 recovered + 10 18 Kelly Carter probable f 60 2023-01-02 recovered + 11 20 Turki el-Vaziri probable m 49 2023-01-02 recovered + 12 22 Cicely Shangreaux confirmed f 7 2023-01-02 2023-01-02 recovered + date_outcome date_first_contact date_last_contact ct_value + 1 NA + 2 2022-12-30 2023-01-05 NA + 3 2022-12-30 2023-01-02 NA + 4 2022-12-29 2023-01-02 NA + 5 2023-01-01 2023-01-03 25.4 + 6 2023-01-03 2023-01-04 25.4 + 7 2023-01-04 2023-01-05 NA + 8 2023-01-01 2023-01-04 NA + 9 2022-12-31 2023-01-03 25.4 + 10 2022-12-30 2023-01-03 NA + 11 2023-01-01 2023-01-04 NA + 12 2023-01-01 2023-01-03 25.4 diff --git a/tests/testthat/_snaps/sim_outbreak.md b/tests/testthat/_snaps/sim_outbreak.md index 8e97962f..a02f8b01 100644 --- a/tests/testthat/_snaps/sim_outbreak.md +++ b/tests/testthat/_snaps/sim_outbreak.md @@ -5,78 +5,78 @@ prob_infect = 0.5, onset_to_hosp = onset_to_hosp, onset_to_death = onset_to_death) Output $linelist - id case_name case_type sex age date_onset date_admission outcome - 1 1 Gabriel Black probable m 35 2023-01-01 recovered - 2 2 Tyler Kelley confirmed m 43 2023-01-01 recovered - 3 3 Cody Morales suspected m 1 2023-01-01 recovered - 4 5 Joewid Le probable m 78 2023-01-01 recovered - 5 6 Carolyn Moore confirmed f 22 2023-01-01 recovered - 6 8 Cheyenne Sayavong confirmed f 28 2023-01-01 recovered - 7 11 Pierce Khanthavong confirmed m 46 2023-01-01 2023-01-13 recovered - 8 12 Kendra To suspected f 67 2023-01-01 recovered - 9 13 Preston Barringer confirmed m 86 2023-01-01 2023-01-01 died - 10 18 Dominique Raymond confirmed f 60 2023-01-02 recovered - 11 20 Bassaam el-Majid probable m 49 2023-01-02 recovered - 12 22 Susana Varela probable f 7 2023-01-02 2023-01-02 recovered - date_outcome date_first_contact date_last_contact ct_value - 1 NA - 2 2022-12-30 2023-01-05 24 - 3 2022-12-30 2023-01-02 NA - 4 2022-12-29 2023-01-02 NA - 5 2023-01-01 2023-01-03 24 - 6 2023-01-03 2023-01-04 24 - 7 2023-01-04 2023-01-05 24 - 8 2023-01-01 2023-01-04 NA - 9 2023-01-09 2022-12-31 2023-01-03 24 - 10 2022-12-30 2023-01-03 24 - 11 2023-01-01 2023-01-04 NA - 12 2023-01-01 2023-01-03 NA + id case_name case_type sex age date_onset date_admission + 1 1 Dominic Sundara probable m 35 2023-01-01 + 2 2 Preston Montgomery suspected m 43 2023-01-01 + 3 3 Reece Chittum probable m 1 2023-01-01 + 4 5 Michael Cheek confirmed m 78 2023-01-01 + 5 6 Jennifer Smith confirmed f 22 2023-01-01 + 6 8 Erika Quintero confirmed f 28 2023-01-01 + 7 11 Isaiah Patterson suspected m 46 2023-01-01 2023-01-13 + 8 12 Cicely Anderson suspected f 67 2023-01-01 + 9 13 Michael John probable m 86 2023-01-01 2023-01-01 + 10 18 Giovana Magana Aguirre suspected f 60 2023-01-02 + 11 20 Mudrik al-Hallal suspected m 49 2023-01-02 + 12 22 Tea Slaughter probable f 7 2023-01-02 2023-01-02 + outcome date_outcome date_first_contact date_last_contact ct_value + 1 recovered NA + 2 recovered 2022-12-30 2023-01-05 NA + 3 recovered 2022-12-30 2023-01-02 NA + 4 recovered 2022-12-29 2023-01-02 23.1 + 5 recovered 2023-01-01 2023-01-03 23.1 + 6 recovered 2023-01-03 2023-01-04 23.1 + 7 recovered 2023-01-04 2023-01-05 NA + 8 recovered 2023-01-01 2023-01-04 NA + 9 died 2023-01-12 2022-12-31 2023-01-03 NA + 10 recovered 2022-12-30 2023-01-03 NA + 11 recovered 2023-01-01 2023-01-04 NA + 12 recovered 2023-01-01 2023-01-03 NA $contacts - from to age sex date_first_contact - 1 Gabriel Black Tyler Kelley 43 m 2022-12-30 - 2 Gabriel Black Cody Morales 1 m 2022-12-30 - 3 Tyler Kelley Taylor Graves 29 f 2022-12-27 - 4 Tyler Kelley Joewid Le 78 m 2022-12-29 - 5 Cody Morales Carolyn Moore 22 f 2023-01-01 - 6 Cody Morales Rushdi al-Ishak 70 m 2022-12-30 - 7 Cody Morales Cheyenne Sayavong 28 f 2023-01-03 - 8 Joewid Le Mercedes Lovelace 37 f 2023-01-06 - 9 Carolyn Moore Chantelle Vazquez-Luevano 61 f 2023-01-01 - 10 Cheyenne Sayavong Pierce Khanthavong 46 m 2023-01-04 - 11 Cheyenne Sayavong Kendra To 67 f 2023-01-01 - 12 Cheyenne Sayavong Preston Barringer 86 m 2022-12-31 - 13 Pierce Khanthavong Jackson Carlson 71 m 2022-12-28 - 14 Pierce Khanthavong Megan Hayes 51 f 2023-01-01 - 15 Pierce Khanthavong Sam Spencer 44 m 2023-01-02 - 16 Kendra To Amanda Larochelle 49 f 2023-01-02 - 17 Preston Barringer Dominique Raymond 60 f 2022-12-30 - 18 Preston Barringer Natalie Newton 56 f 2023-01-06 - 19 Preston Barringer Bassaam el-Majid 49 m 2023-01-01 - 20 Preston Barringer Qaaid al-Madani 50 m 2023-01-01 - 21 Dominique Raymond Susana Varela 7 f 2023-01-01 - date_last_contact was_case status - 1 2023-01-05 Y case - 2 2023-01-02 Y case - 3 2023-01-03 N unknown - 4 2023-01-02 Y case - 5 2023-01-03 Y case - 6 2023-01-02 N under_followup - 7 2023-01-04 Y case - 8 2023-01-06 N under_followup - 9 2023-01-05 N under_followup - 10 2023-01-05 Y case - 11 2023-01-04 Y case - 12 2023-01-03 Y case - 13 2023-01-05 N under_followup - 14 2023-01-04 N lost_to_followup - 15 2023-01-05 N under_followup - 16 2023-01-03 N under_followup - 17 2023-01-03 Y case - 18 2023-01-09 N unknown - 19 2023-01-04 Y case - 20 2023-01-03 N under_followup - 21 2023-01-03 Y case + from to age sex date_first_contact + 1 Dominic Sundara Preston Montgomery 43 m 2022-12-30 + 2 Dominic Sundara Reece Chittum 1 m 2022-12-30 + 3 Preston Montgomery Kayla Hill 29 f 2022-12-27 + 4 Preston Montgomery Michael Cheek 78 m 2022-12-29 + 5 Reece Chittum Jennifer Smith 22 f 2023-01-01 + 6 Reece Chittum Jaylyn Childs 70 m 2022-12-30 + 7 Reece Chittum Erika Quintero 28 f 2023-01-03 + 8 Michael Cheek Kelly Fitzsimmons 37 f 2023-01-06 + 9 Jennifer Smith Audreon Starkey 61 f 2023-01-01 + 10 Erika Quintero Isaiah Patterson 46 m 2023-01-04 + 11 Erika Quintero Cicely Anderson 67 f 2023-01-01 + 12 Erika Quintero Michael John 86 m 2022-12-31 + 13 Isaiah Patterson Muneeb al-Jamil 71 m 2022-12-28 + 14 Isaiah Patterson Juwairiya el-Abdelrahman 51 f 2023-01-01 + 15 Isaiah Patterson Bishr al-Youssef 44 m 2023-01-02 + 16 Cicely Anderson Samantha Gonzalez 49 f 2023-01-02 + 17 Michael John Giovana Magana Aguirre 60 f 2022-12-30 + 18 Michael John Michiyo Batara 56 f 2023-01-06 + 19 Michael John Mudrik al-Hallal 49 m 2023-01-01 + 20 Michael John Dominic Gonzales 50 m 2023-01-01 + 21 Giovana Magana Aguirre Tea Slaughter 7 f 2023-01-01 + date_last_contact was_case status + 1 2023-01-05 Y case + 2 2023-01-02 Y case + 3 2023-01-03 N under_followup + 4 2023-01-02 Y case + 5 2023-01-03 Y case + 6 2023-01-02 N under_followup + 7 2023-01-04 Y case + 8 2023-01-06 N under_followup + 9 2023-01-05 N under_followup + 10 2023-01-05 Y case + 11 2023-01-04 Y case + 12 2023-01-03 Y case + 13 2023-01-05 N under_followup + 14 2023-01-04 N under_followup + 15 2023-01-05 N under_followup + 16 2023-01-03 N under_followup + 17 2023-01-03 Y case + 18 2023-01-09 N unknown + 19 2023-01-04 Y case + 20 2023-01-03 N under_followup + 21 2023-01-03 Y case # sim_outbreak works as expected with add_names = FALSE @@ -89,76 +89,76 @@ $linelist id case_type sex age date_onset date_admission outcome date_outcome 1 1 confirmed m 35 2023-01-01 recovered - 2 2 probable m 43 2023-01-01 recovered + 2 2 suspected m 43 2023-01-01 recovered 3 3 probable m 1 2023-01-01 recovered 4 5 confirmed m 78 2023-01-01 recovered 5 6 confirmed f 22 2023-01-01 recovered 6 8 confirmed f 28 2023-01-01 recovered 7 11 confirmed m 46 2023-01-01 2023-01-13 recovered - 8 12 confirmed f 67 2023-01-01 recovered - 9 13 confirmed m 86 2023-01-01 2023-01-01 died 2023-01-09 - 10 18 confirmed f 60 2023-01-02 recovered + 8 12 suspected f 67 2023-01-01 recovered + 9 13 confirmed m 86 2023-01-01 2023-01-01 died 2023-01-12 + 10 18 suspected f 60 2023-01-02 recovered 11 20 confirmed m 49 2023-01-02 recovered 12 22 confirmed f 7 2023-01-02 2023-01-02 recovered date_first_contact date_last_contact ct_value - 1 24.9 + 1 23.9 2 2022-12-30 2023-01-05 NA 3 2022-12-30 2023-01-02 NA - 4 2022-12-29 2023-01-02 24.9 - 5 2023-01-01 2023-01-03 24.9 - 6 2023-01-03 2023-01-04 24.9 - 7 2023-01-04 2023-01-05 24.9 - 8 2023-01-01 2023-01-04 24.9 - 9 2022-12-31 2023-01-03 24.9 - 10 2022-12-30 2023-01-03 24.9 - 11 2023-01-01 2023-01-04 24.9 - 12 2023-01-01 2023-01-03 24.9 + 4 2022-12-29 2023-01-02 23.9 + 5 2023-01-01 2023-01-03 23.9 + 6 2023-01-03 2023-01-04 23.9 + 7 2023-01-04 2023-01-05 23.9 + 8 2023-01-01 2023-01-04 NA + 9 2022-12-31 2023-01-03 23.9 + 10 2022-12-30 2023-01-03 NA + 11 2023-01-01 2023-01-04 23.9 + 12 2023-01-01 2023-01-03 23.9 $contacts - from to age sex date_first_contact - 1 Wajdi al-Demian Raaid el-Diab 43 m 2022-12-30 - 2 Wajdi al-Demian Nickolas Nault 1 m 2022-12-30 - 3 Raaid el-Diab Durine Cobb 29 f 2022-12-27 - 4 Raaid el-Diab Hee Kennedy 78 m 2022-12-29 - 5 Nickolas Nault Hope Arshad 22 f 2023-01-01 - 6 Nickolas Nault Mubarak el-Vaziri 70 m 2022-12-30 - 7 Nickolas Nault Shanta Holiday 28 f 2023-01-03 - 8 Hee Kennedy Darian Guyon 37 f 2023-01-06 - 9 Hope Arshad Mackenzie Ahn 61 f 2023-01-01 - 10 Shanta Holiday Raakaan al-Shams 46 m 2023-01-04 - 11 Shanta Holiday Chandra Kilian 67 f 2023-01-01 - 12 Shanta Holiday Ricardo Sanchez 86 m 2022-12-31 - 13 Raakaan al-Shams Tae Woo Nguyen 71 m 2022-12-28 - 14 Raakaan al-Shams Mikhaila Carlson 51 f 2023-01-01 - 15 Raakaan al-Shams Alexander Orio 44 m 2023-01-02 - 16 Chandra Kilian Alexandra Johnson 49 f 2023-01-02 - 17 Ricardo Sanchez Kanani Nguyen 60 f 2022-12-30 - 18 Ricardo Sanchez Nirvana Elizalde Villa 56 f 2023-01-06 - 19 Ricardo Sanchez Jared Chambers 49 m 2023-01-01 - 20 Ricardo Sanchez Thomas Morales 50 m 2023-01-01 - 21 Kanani Nguyen Annie Carter 7 f 2023-01-01 - date_last_contact was_case status - 1 2023-01-05 Y case - 2 2023-01-02 Y case - 3 2023-01-03 N under_followup - 4 2023-01-02 Y case - 5 2023-01-03 Y case - 6 2023-01-02 N under_followup - 7 2023-01-04 Y case - 8 2023-01-06 N unknown - 9 2023-01-05 N under_followup - 10 2023-01-05 Y case - 11 2023-01-04 Y case - 12 2023-01-03 Y case - 13 2023-01-05 N lost_to_followup - 14 2023-01-04 N lost_to_followup - 15 2023-01-05 N under_followup - 16 2023-01-03 N lost_to_followup - 17 2023-01-03 Y case - 18 2023-01-09 N under_followup - 19 2023-01-04 Y case - 20 2023-01-03 N under_followup - 21 2023-01-03 Y case + from to age sex date_first_contact + 1 Jonah Hord Benjamin Flowers 43 m 2022-12-30 + 2 Jonah Hord Rito Cooper 1 m 2022-12-30 + 3 Benjamin Flowers Claire Hicks 29 f 2022-12-27 + 4 Benjamin Flowers Jeremy Loughridge 78 m 2022-12-29 + 5 Rito Cooper Ashwini Ali 22 f 2023-01-01 + 6 Rito Cooper Rory Jumbo 70 m 2022-12-30 + 7 Rito Cooper Danielle Kuhn 28 f 2023-01-03 + 8 Jeremy Loughridge Gicell Cisneros 37 f 2023-01-06 + 9 Ashwini Ali Lauren Nguyen 61 f 2023-01-01 + 10 Danielle Kuhn Thaamir al-Amini 46 m 2023-01-04 + 11 Danielle Kuhn Selena Chun 67 f 2023-01-01 + 12 Danielle Kuhn Charles Stuart Rasi 86 m 2022-12-31 + 13 Thaamir al-Amini Jose Hurtado 71 m 2022-12-28 + 14 Thaamir al-Amini Brianne Shahid 51 f 2023-01-01 + 15 Thaamir al-Amini Efren Armijo 44 m 2023-01-02 + 16 Selena Chun Juanita Martinez 49 f 2023-01-02 + 17 Charles Stuart Rasi Hannah Bodnar 60 f 2022-12-30 + 18 Charles Stuart Rasi Kifaaya el-Ameen 56 f 2023-01-06 + 19 Charles Stuart Rasi Enrique Ponce 49 m 2023-01-01 + 20 Charles Stuart Rasi Jaarallah al-Masood 50 m 2023-01-01 + 21 Hannah Bodnar Ashley Isaac 7 f 2023-01-01 + date_last_contact was_case status + 1 2023-01-05 Y case + 2 2023-01-02 Y case + 3 2023-01-03 N under_followup + 4 2023-01-02 Y case + 5 2023-01-03 Y case + 6 2023-01-02 N under_followup + 7 2023-01-04 Y case + 8 2023-01-06 N under_followup + 9 2023-01-05 N under_followup + 10 2023-01-05 Y case + 11 2023-01-04 Y case + 12 2023-01-03 Y case + 13 2023-01-05 N unknown + 14 2023-01-04 N under_followup + 15 2023-01-05 N under_followup + 16 2023-01-03 N under_followup + 17 2023-01-03 Y case + 18 2023-01-09 N under_followup + 19 2023-01-04 Y case + 20 2023-01-03 N unknown + 21 2023-01-03 Y case # sim_outbreak works as expected with age-strat risks @@ -170,78 +170,78 @@ non_hosp_death_risk = age_dep_non_hosp_death_risk) Output $linelist - id case_name case_type sex age date_onset date_admission outcome - 1 1 Micheal Smallwood probable m 35 2023-01-01 recovered - 2 2 Kyle Foster confirmed m 43 2023-01-01 recovered - 3 3 Ghaamid el-Kaiser suspected m 1 2023-01-01 2023-01-11 died - 4 5 Faatih el-Riaz confirmed m 78 2023-01-01 recovered - 5 6 Hope Arshad suspected f 22 2023-01-01 recovered - 6 8 Shanta Holiday probable f 28 2023-01-01 recovered - 7 11 Aiman al-Demian probable m 46 2023-01-01 recovered - 8 12 Chandra Kilian suspected f 67 2023-01-01 recovered - 9 13 Wajdi el-Diab confirmed m 86 2023-01-01 2023-01-01 recovered - 10 18 Kanani Nguyen confirmed f 60 2023-01-02 recovered - 11 20 Raaid el-Vaziri probable m 49 2023-01-02 2023-01-09 recovered - 12 22 Annie Carter probable f 7 2023-01-02 recovered + id case_name case_type sex age date_onset date_admission outcome + 1 1 Cass Duran probable m 35 2023-01-01 recovered + 2 2 Mudrik al-Hallal suspected m 43 2023-01-01 recovered + 3 3 Jareer al-Safar probable m 1 2023-01-01 2023-01-11 recovered + 4 5 Raashid el-Huda confirmed m 78 2023-01-01 recovered + 5 6 Erika Sierra confirmed f 22 2023-01-01 recovered + 6 8 Jennifer Hong confirmed f 28 2023-01-01 recovered + 7 11 Donald Childs suspected m 46 2023-01-01 recovered + 8 12 Kayla Johnson suspected f 67 2023-01-01 died + 9 13 Avery Johnston probable m 86 2023-01-01 2023-01-01 recovered + 10 18 Giovana Segarra suspected f 60 2023-01-02 recovered + 11 20 Donald Root suspected m 49 2023-01-02 2023-01-09 recovered + 12 22 Kiona Dalke probable f 7 2023-01-02 recovered date_outcome date_first_contact date_last_contact ct_value 1 NA - 2 2022-12-30 2023-01-05 24.1 - 3 2023-01-14 2022-12-30 2023-01-02 NA - 4 2022-12-29 2023-01-02 24.1 - 5 2023-01-01 2023-01-03 NA - 6 2023-01-03 2023-01-04 NA + 2 2022-12-30 2023-01-05 NA + 3 2022-12-30 2023-01-02 NA + 4 2022-12-29 2023-01-02 23.1 + 5 2023-01-01 2023-01-03 23.1 + 6 2023-01-03 2023-01-04 23.1 7 2023-01-04 2023-01-05 NA - 8 2023-01-01 2023-01-04 NA - 9 2022-12-31 2023-01-03 24.1 - 10 2022-12-30 2023-01-03 24.1 + 8 2023-01-14 2023-01-01 2023-01-04 NA + 9 2022-12-31 2023-01-03 NA + 10 2022-12-30 2023-01-03 NA 11 2023-01-01 2023-01-04 NA 12 2023-01-01 2023-01-03 NA $contacts - from to age sex date_first_contact - 1 Micheal Smallwood Kyle Foster 43 m 2022-12-30 - 2 Micheal Smallwood Ghaamid el-Kaiser 1 m 2022-12-30 - 3 Kyle Foster Durine Cobb 29 f 2022-12-27 - 4 Kyle Foster Faatih el-Riaz 78 m 2022-12-29 - 5 Ghaamid el-Kaiser Hope Arshad 22 f 2023-01-01 - 6 Ghaamid el-Kaiser Jonathan Takahashi 70 m 2022-12-30 - 7 Ghaamid el-Kaiser Shanta Holiday 28 f 2023-01-03 - 8 Faatih el-Riaz Darian Guyon 37 f 2023-01-06 - 9 Hope Arshad Mackenzie Ahn 61 f 2023-01-01 - 10 Shanta Holiday Aiman al-Demian 46 m 2023-01-04 - 11 Shanta Holiday Chandra Kilian 67 f 2023-01-01 - 12 Shanta Holiday Wajdi el-Diab 86 m 2022-12-31 - 13 Aiman al-Demian Travis Summers 71 m 2022-12-28 - 14 Aiman al-Demian Mikhaila Carlson 51 f 2023-01-01 - 15 Aiman al-Demian Cory Galligan 44 m 2023-01-02 - 16 Chandra Kilian Alexandra Johnson 49 f 2023-01-02 - 17 Wajdi el-Diab Kanani Nguyen 60 f 2022-12-30 - 18 Wajdi el-Diab Nirvana Elizalde Villa 56 f 2023-01-06 - 19 Wajdi el-Diab Raaid el-Vaziri 49 m 2023-01-01 - 20 Wajdi el-Diab Mubarak al-Shams 50 m 2023-01-01 - 21 Kanani Nguyen Annie Carter 7 f 2023-01-01 - date_last_contact was_case status - 1 2023-01-05 Y case - 2 2023-01-02 Y case - 3 2023-01-03 N under_followup - 4 2023-01-02 Y case - 5 2023-01-03 Y case - 6 2023-01-02 N under_followup - 7 2023-01-04 Y case - 8 2023-01-06 N under_followup - 9 2023-01-05 N lost_to_followup - 10 2023-01-05 Y case - 11 2023-01-04 Y case - 12 2023-01-03 Y case - 13 2023-01-05 N lost_to_followup - 14 2023-01-04 N under_followup - 15 2023-01-05 N under_followup - 16 2023-01-03 N under_followup - 17 2023-01-03 Y case - 18 2023-01-09 N unknown - 19 2023-01-04 Y case - 20 2023-01-03 N lost_to_followup - 21 2023-01-03 Y case + from to age sex date_first_contact + 1 Cass Duran Mudrik al-Hallal 43 m 2022-12-30 + 2 Cass Duran Jareer al-Safar 1 m 2022-12-30 + 3 Mudrik al-Hallal Kaitlynne Rieger 29 f 2022-12-27 + 4 Mudrik al-Hallal Raashid el-Huda 78 m 2022-12-29 + 5 Jareer al-Safar Erika Sierra 22 f 2023-01-01 + 6 Jareer al-Safar Preston Huerta 70 m 2022-12-30 + 7 Jareer al-Safar Jennifer Hong 28 f 2023-01-03 + 8 Raashid el-Huda Kaitlin Gonzalez 37 f 2023-01-06 + 9 Erika Sierra Marissa Slaughter 61 f 2023-01-01 + 10 Jennifer Hong Donald Childs 46 m 2023-01-04 + 11 Jennifer Hong Kayla Johnson 67 f 2023-01-01 + 12 Jennifer Hong Avery Johnston 86 m 2022-12-31 + 13 Donald Childs Lorenzo Gaynor 71 m 2022-12-28 + 14 Donald Childs Michiyo Tran 51 f 2023-01-01 + 15 Donald Childs Ethan Black 44 m 2023-01-02 + 16 Kayla Johnson Marzooqa el-Abdelrahman 49 f 2023-01-02 + 17 Avery Johnston Giovana Segarra 60 f 2022-12-30 + 18 Avery Johnston Kaylie Shangreaux 56 f 2023-01-06 + 19 Avery Johnston Donald Root 49 m 2023-01-01 + 20 Avery Johnston Hunter Simmons 50 m 2023-01-01 + 21 Giovana Segarra Kiona Dalke 7 f 2023-01-01 + date_last_contact was_case status + 1 2023-01-05 Y case + 2 2023-01-02 Y case + 3 2023-01-03 N under_followup + 4 2023-01-02 Y case + 5 2023-01-03 Y case + 6 2023-01-02 N under_followup + 7 2023-01-04 Y case + 8 2023-01-06 N under_followup + 9 2023-01-05 N under_followup + 10 2023-01-05 Y case + 11 2023-01-04 Y case + 12 2023-01-03 Y case + 13 2023-01-05 N under_followup + 14 2023-01-04 N under_followup + 15 2023-01-05 N under_followup + 16 2023-01-03 N under_followup + 17 2023-01-03 Y case + 18 2023-01-09 N unknown + 19 2023-01-04 Y case + 20 2023-01-03 N under_followup + 21 2023-01-03 Y case # sim_outbreak works as expected with age structure @@ -252,56 +252,56 @@ population_age = age_struct) Output $linelist - id case_name case_type sex age date_onset date_admission outcome - 1 1 Gene Than probable m 44 2023-01-01 recovered - 2 2 Caleb Fredericks probable m 13 2023-01-01 recovered - 3 3 Jaisean Venable suspected m 22 2023-01-01 2023-01-09 died - 4 5 Taylor Swift probable m 85 2023-01-01 recovered - 5 6 Korren Bailey confirmed f 41 2023-01-01 recovered - 6 8 Madison Zahn confirmed f 89 2023-01-01 2023-01-02 recovered - 7 11 Dustin Bellow confirmed m 69 2023-01-01 recovered - 8 12 Ryanna Hart confirmed f 23 2023-01-01 recovered - 9 13 Rafael Garcia confirmed m 9 2023-01-01 recovered - 10 18 Ashlan Hendon confirmed f 62 2023-01-02 recovered - 11 20 Tieran Moorer suspected m 52 2023-01-02 2023-01-15 recovered - 12 22 Paige Reich probable f 76 2023-01-02 recovered + id case_name case_type sex age date_onset date_admission outcome + 1 1 Kyle Crane suspected m 44 2023-01-01 recovered + 2 2 Ghaamid el-Ishmael confirmed m 13 2023-01-01 recovered + 3 3 Faatih el-Kaiser confirmed m 22 2023-01-01 2023-01-09 recovered + 4 5 Va'Aahi Galligan suspected m 85 2023-01-01 recovered + 5 6 Katelyn Catlin confirmed f 41 2023-01-01 recovered + 6 8 Lynsey Duron confirmed f 89 2023-01-01 2023-01-02 died + 7 11 Wajdi al-Demian confirmed m 69 2023-01-01 recovered + 8 12 Jacy Cousins confirmed f 23 2023-01-01 recovered + 9 13 Travis Foster confirmed m 9 2023-01-01 recovered + 10 18 Maria Eberhart probable f 62 2023-01-02 recovered + 11 20 Mubarak el-Vaziri suspected m 52 2023-01-02 2023-01-15 recovered + 12 22 Erin Payson confirmed f 76 2023-01-02 recovered date_outcome date_first_contact date_last_contact ct_value 1 NA - 2 2022-12-30 2023-01-05 NA - 3 2023-01-12 2022-12-30 2023-01-02 NA + 2 2022-12-30 2023-01-05 25.1 + 3 2022-12-30 2023-01-02 25.1 4 2022-12-29 2023-01-02 NA - 5 2023-01-01 2023-01-03 24 - 6 2023-01-03 2023-01-04 24 - 7 2023-01-04 2023-01-05 24 - 8 2023-01-01 2023-01-04 24 - 9 2022-12-31 2023-01-03 24 - 10 2022-12-30 2023-01-03 24 + 5 2023-01-01 2023-01-03 25.1 + 6 2023-01-26 2023-01-03 2023-01-04 25.1 + 7 2023-01-04 2023-01-05 25.1 + 8 2023-01-01 2023-01-04 25.1 + 9 2022-12-31 2023-01-03 25.1 + 10 2022-12-30 2023-01-03 NA 11 2023-01-01 2023-01-04 NA - 12 2023-01-01 2023-01-03 NA + 12 2023-01-01 2023-01-03 25.1 $contacts - from to age sex date_first_contact - 1 Gene Than Caleb Fredericks 13 m 2022-12-30 - 2 Gene Than Jaisean Venable 22 m 2022-12-30 - 3 Caleb Fredericks Mawhiba al-Mussa 5 f 2022-12-27 - 4 Caleb Fredericks Taylor Swift 85 m 2022-12-29 - 5 Jaisean Venable Korren Bailey 41 f 2023-01-01 - 6 Jaisean Venable Mustaba al-Sarwar 2 m 2022-12-30 - 7 Jaisean Venable Madison Zahn 89 f 2023-01-03 - 8 Taylor Swift Nicole Perez 86 f 2023-01-06 - 9 Korren Bailey Turfa el-Saab 82 f 2023-01-01 - 10 Madison Zahn Dustin Bellow 69 m 2023-01-04 - 11 Madison Zahn Ryanna Hart 23 f 2023-01-01 - 12 Madison Zahn Rafael Garcia 9 m 2022-12-31 - 13 Dustin Bellow Adrien Leduke 79 m 2022-12-28 - 14 Dustin Bellow Shan Klutke 29 f 2023-01-01 - 15 Dustin Bellow Dennison Kills In Sight 4 m 2023-01-02 - 16 Ryanna Hart Violet Watts 13 f 2023-01-02 - 17 Rafael Garcia Ashlan Hendon 62 f 2022-12-30 - 18 Rafael Garcia Lien Saldanha 24 f 2023-01-06 - 19 Rafael Garcia Tieran Moorer 52 m 2023-01-01 - 20 Rafael Garcia Michael Chavez 74 m 2023-01-01 - 21 Ashlan Hendon Paige Reich 76 f 2023-01-01 + from to age sex date_first_contact + 1 Kyle Crane Ghaamid el-Ishmael 13 m 2022-12-30 + 2 Kyle Crane Faatih el-Kaiser 22 m 2022-12-30 + 3 Ghaamid el-Ishmael Carisa Flores-Gonzalez 5 f 2022-12-27 + 4 Ghaamid el-Ishmael Va'Aahi Galligan 85 m 2022-12-29 + 5 Faatih el-Kaiser Katelyn Catlin 41 f 2023-01-01 + 6 Faatih el-Kaiser Aiman el-Riaz 2 m 2022-12-30 + 7 Faatih el-Kaiser Lynsey Duron 89 f 2023-01-03 + 8 Va'Aahi Galligan Amaani al-Gaber 86 f 2023-01-06 + 9 Katelyn Catlin Lilibeth Black 82 f 2023-01-01 + 10 Lynsey Duron Wajdi al-Demian 69 m 2023-01-04 + 11 Lynsey Duron Jacy Cousins 23 f 2023-01-01 + 12 Lynsey Duron Travis Foster 9 m 2022-12-31 + 13 Wajdi al-Demian Raymond Murray 79 m 2022-12-28 + 14 Wajdi al-Demian Marquaja Johnson 29 f 2023-01-01 + 15 Wajdi al-Demian Raaid el-Diab 4 m 2023-01-02 + 16 Jacy Cousins Kayla Tudor 13 f 2023-01-02 + 17 Travis Foster Maria Eberhart 62 f 2022-12-30 + 18 Travis Foster Katja Muetz 24 f 2023-01-06 + 19 Travis Foster Mubarak el-Vaziri 52 m 2023-01-01 + 20 Travis Foster Alexandre Guerrero 74 m 2023-01-01 + 21 Maria Eberhart Erin Payson 76 f 2023-01-01 date_last_contact was_case status 1 2023-01-05 Y case 2 2023-01-02 Y case @@ -310,17 +310,17 @@ 5 2023-01-03 Y case 6 2023-01-02 N under_followup 7 2023-01-04 Y case - 8 2023-01-06 N unknown - 9 2023-01-05 N lost_to_followup + 8 2023-01-06 N under_followup + 9 2023-01-05 N unknown 10 2023-01-05 Y case 11 2023-01-04 Y case 12 2023-01-03 Y case 13 2023-01-05 N under_followup - 14 2023-01-04 N under_followup - 15 2023-01-05 N under_followup - 16 2023-01-03 N lost_to_followup + 14 2023-01-04 N lost_to_followup + 15 2023-01-05 N lost_to_followup + 16 2023-01-03 N under_followup 17 2023-01-03 Y case - 18 2023-01-09 N under_followup + 18 2023-01-09 N lost_to_followup 19 2023-01-04 Y case 20 2023-01-03 N under_followup 21 2023-01-03 Y case diff --git a/tests/testthat/test-sim_linelist.R b/tests/testthat/test-sim_linelist.R index df58ec38..717d94ed 100644 --- a/tests/testthat/test-sim_linelist.R +++ b/tests/testthat/test-sim_linelist.R @@ -363,6 +363,7 @@ test_that("sim_linelist fails when onset-to-event are given by risk is NA", { }) test_that("sim_linest date_admission column is NA when onset_to_hosp is NA", { + set.seed(1) ll <- suppressWarnings( sim_linelist( contact_distribution = contact_distribution, @@ -388,6 +389,7 @@ test_that("sim_linest date_admission column is NA when onset_to_hosp is NA", { }) test_that("sim_linest date_death column is NA when onset_to_death is NA", { + set.seed(1) ll <- suppressWarnings( sim_linelist( contact_distribution = contact_distribution,