sim_contacts.md
In simulist: Simulate Disease Outbreak Line List and Contacts Data

sim_contacts works as expected with defaults

Code
  sim_contacts()
Output
                         from                     to age sex date_first_contact
  1  Louis Baltazar-Francisco        Masooma Sheldon  58   f         2022-12-27
  2  Louis Baltazar-Francisco      Rachel Fredericks  29   f         2022-12-30
  3         Rachel Fredericks          Makiah Thomas  24   f         2023-01-12
  4         Rachel Fredericks         Mersadez Swift  42   f         2023-01-11
  5         Rachel Fredericks      Mitchell Sandoval  48   m         2023-01-09
  6             Makiah Thomas       Saahira el-Laham  76   f         2023-01-11
  7             Makiah Thomas           Celsa Bellow  39   f         2023-01-14
  8             Makiah Thomas Stephanie Garcia Mayen  24   f         2023-01-12
  9          Saahira el-Laham        Laurel Lehmkuhl  53   f         2023-01-20
  10   Stephanie Garcia Mayen           Cade Amerson  86   m         2023-01-17
  11   Stephanie Garcia Mayen         Tristan Thomas  40   m         2023-01-16
  12             Cade Amerson Nohelia Kills In Sight  83   f         2023-01-21
  13             Cade Amerson       Sage Wachtendorf  90   m         2023-01-21
  14   Nohelia Kills In Sight        Faalih al-Saleh  35   m         2023-01-28
  15          Faalih al-Saleh            Nasteh Long  43   f         2023-02-01
  16          Faalih al-Saleh        Dominica Abeyta   1   f         2023-01-30
  17          Faalih al-Saleh         Patrick Martin  29   m         2023-02-02
  18          Dominica Abeyta          Bryant Taylor  78   m         2023-02-03
  19          Dominica Abeyta        Arkaan al-Faris  22   m         2023-02-04
  20          Dominica Abeyta          Olivia Carson  70   f         2023-02-03
     date_last_contact was_case           status
  1         2023-01-04        N   under_followup
  2         2023-01-06        Y             case
  3         2023-01-18        Y             case
  4         2023-01-18        N lost_to_followup
  5         2023-01-17        N   under_followup
  6         2023-01-18        Y             case
  7         2023-01-20        N lost_to_followup
  8         2023-01-19        Y             case
  9         2023-01-30        N   under_followup
  10        2023-01-22        Y             case
  11        2023-01-22        N   under_followup
  12        2023-01-31        Y             case
  13        2023-01-26        N   under_followup
  14        2023-02-03        Y             case
  15        2023-02-04        N lost_to_followup
  16        2023-02-06        Y             case
  17        2023-02-09        N   under_followup
  18        2023-02-08        N   under_followup
  19        2023-02-12        Y             case
  20        2023-02-09        N lost_to_followup

sim_contacts works as expected

Code
  sim_contacts(contact_distribution = contact_distribution, infectious_period = infectious_period,
    prob_infection = 0.5)
Output
                 from                      to age sex date_first_contact
  1      Alivia Perez      Barrington Johnson  44   m         2022-12-29
  2      Alivia Perez          Madison Krause  49   f         2022-12-27
  3    Madison Krause            Ashlan Allen  60   f         2022-12-29
  4    Madison Krause          Turfa el-Farah  56   f         2022-12-29
  5    Madison Krause       Nykalous Shumpert  49   m         2022-12-30
  6      Ashlan Allen          Arshad al-Basa  50   m         2022-12-31
  7      Ashlan Allen            Destiny Hart   7   f         2022-12-29
  8      Ashlan Allen            Ronald Welch  20   m         2022-12-30
  9      Ashlan Allen           Simon Pickett  24   m         2022-12-29
  10     Ashlan Allen            Jeramy Fitch  51   m         2022-12-31
  11     Ashlan Allen          Joshua Ryckman  53   m         2022-12-31
  12     Destiny Hart        Janayva Ambrozic  16   f         2022-12-25
  13     Destiny Hart Nicole Vazquez Pallares  83   f         2022-12-30
  14     Jeramy Fitch        Nusaiba al-Rassi   2   f         2022-12-31
  15     Jeramy Fitch            Korren Watts  48   f         2023-01-01
  16     Jeramy Fitch           Shan Saldanha  65   f         2022-12-30
  17 Janayva Ambrozic             Adrian Wang  44   m         2022-12-28
  18 Nusaiba al-Rassi           Luis Quintana  77   m         2022-12-31
  19 Nusaiba al-Rassi       Jonathan Krishnan  90   m         2022-12-27
  20 Nusaiba al-Rassi        Ryanna Vialpando  66   f         2022-12-30
  21 Nusaiba al-Rassi         Alexander Brown  19   m         2023-01-01
  22     Korren Watts          Cruz Hernandez  17   m         2022-12-31
  23    Shan Saldanha        Breanna Crandall  34   f         2023-01-02
  24    Shan Saldanha           Preston Miles  75   m         2023-01-03
  25  Alexander Brown              Drue White  31   m         2022-12-30
     date_last_contact was_case           status
  1         2023-01-04        N   under_followup
  2         2023-01-04        Y             case
  3         2023-01-10        Y             case
  4         2023-01-05        N   under_followup
  5         2023-01-05        N   under_followup
  6         2023-01-03        N          unknown
  7         2023-01-06        Y             case
  8         2023-01-05        Y             case
  9         2023-01-05        N lost_to_followup
  10        2023-01-04        Y             case
  11        2023-01-04        N   under_followup
  12        2023-01-05        Y             case
  13        2023-01-05        N   under_followup
  14        2023-01-03        Y             case
  15        2023-01-02        Y             case
  16        2023-01-05        Y             case
  17        2023-01-09        N   under_followup
  18        2023-01-06        N   under_followup
  19        2023-01-06        N          unknown
  20        2023-01-06        N lost_to_followup
  21        2023-01-10        Y             case
  22        2023-01-06        N   under_followup
  23        2023-01-07        N   under_followup
  24        2023-01-06        Y             case
  25        2023-01-05        N   under_followup

sim_contacts works as expected with modified config

Code
  sim_contacts(contact_distribution = contact_distribution, infectious_period = infectious_period,
    prob_infection = 0.5, config = create_config(last_contact_distribution = function(
      x) stats::rgeom(n = x, prob = 0.5)))
Output
                        from                      to age sex date_first_contact
  1            Gabriel Berry          Preston Larson  16   m         2022-12-28
  2            Gabriel Berry        Kaitlynne Rieger  40   f         2022-12-29
  3         Kaitlynne Rieger          Jackson Foster   9   m         2022-12-31
  4         Kaitlynne Rieger       Danika Shangreaux  50   f         2022-12-29
  5         Kaitlynne Rieger            Hope Johnson  24   f         2022-12-30
  6           Jackson Foster             Kanani Hong  10   f         2022-12-29
  7           Jackson Foster             Sam Summers  79   m         2022-12-31
  8           Jackson Foster          Nirvana Sierra  32   f         2022-12-31
  9           Jackson Foster           Walter Mcgill  39   m         2022-12-25
  10          Jackson Foster            Brandon Hall  37   m         2022-12-30
  11          Jackson Foster             Kelly Dalke  12   f         2022-12-31
  12             Sam Summers      Alexandra Clements  14   f         2023-01-01
  13             Sam Summers            Jose Sanchez  16   m         2022-12-30
  14            Brandon Hall         Cicely Anderson  15   f         2022-12-27
  15            Brandon Hall Marzooqa el-Abdelrahman   2   f         2022-12-30
  16            Brandon Hall        Kaitlin Gonzalez  65   f         2022-12-26
  17      Alexandra Clements             Gienry Sena  67   m         2022-12-30
  18         Cicely Anderson       Khaleel al-Demian  73   m         2023-01-01
  19         Cicely Anderson           Erika Segarra  17   f         2022-12-31
  20         Cicely Anderson         Raymond Kennedy  84   m         2023-01-02
  21         Cicely Anderson            Jakob Galvan   5   m         2023-01-03
  22 Marzooqa el-Abdelrahman               Kyle Orio  41   m         2022-12-30
  23        Kaitlin Gonzalez         Travis Chambers  31   m         2023-01-02
  24        Kaitlin Gonzalez           Jennifer Tran  72   f         2022-12-31
  25            Jakob Galvan           Alawi el-Diab  36   m         2022-12-31
     date_last_contact was_case           status
  1         2023-01-01        N   under_followup
  2         2023-01-01        Y             case
  3         2023-01-02        Y             case
  4         2023-01-03        N lost_to_followup
  5         2023-01-02        N lost_to_followup
  6         2023-01-03        N   under_followup
  7         2023-01-02        Y             case
  8         2023-01-02        Y             case
  9         2023-01-03        N   under_followup
  10        2023-01-02        Y             case
  11        2023-01-02        N   under_followup
  12        2023-01-03        Y             case
  13        2023-01-03        N          unknown
  14        2023-01-03        Y             case
  15        2023-01-03        Y             case
  16        2023-01-02        Y             case
  17        2023-01-05        N lost_to_followup
  18        2023-01-04        N lost_to_followup
  19        2023-01-05        N          unknown
  20        2023-01-04        N          unknown
  21        2023-01-03        Y             case
  22        2023-01-04        N   under_followup
  23        2023-01-03        N   under_followup
  24        2023-01-06        Y             case
  25        2023-01-05        N   under_followup

sim_contacts works as expected with modified config parameters

Code
  sim_contacts(contact_distribution = contact_distribution, infectious_period = infectious_period,
    prob_infection = 0.5, config = create_config(last_contact_distribution = function(
      x) stats::rpois(n = x, lambda = 5)))
Output
                 from                      to age sex date_first_contact
  1      Alivia Perez      Barrington Johnson  44   m         2022-12-29
  2      Alivia Perez          Madison Krause  49   f         2022-12-27
  3    Madison Krause            Ashlan Allen  60   f         2022-12-29
  4    Madison Krause          Turfa el-Farah  56   f         2022-12-29
  5    Madison Krause       Nykalous Shumpert  49   m         2022-12-30
  6      Ashlan Allen          Arshad al-Basa  50   m         2022-12-31
  7      Ashlan Allen            Destiny Hart   7   f         2022-12-29
  8      Ashlan Allen            Ronald Welch  20   m         2022-12-30
  9      Ashlan Allen           Simon Pickett  24   m         2022-12-29
  10     Ashlan Allen            Jeramy Fitch  51   m         2022-12-31
  11     Ashlan Allen          Joshua Ryckman  53   m         2022-12-31
  12     Destiny Hart        Janayva Ambrozic  16   f         2022-12-25
  13     Destiny Hart Nicole Vazquez Pallares  83   f         2022-12-30
  14     Jeramy Fitch        Nusaiba al-Rassi   2   f         2022-12-31
  15     Jeramy Fitch            Korren Watts  48   f         2023-01-01
  16     Jeramy Fitch           Shan Saldanha  65   f         2022-12-30
  17 Janayva Ambrozic             Adrian Wang  44   m         2022-12-28
  18 Nusaiba al-Rassi           Luis Quintana  77   m         2022-12-31
  19 Nusaiba al-Rassi       Jonathan Krishnan  90   m         2022-12-27
  20 Nusaiba al-Rassi        Ryanna Vialpando  66   f         2022-12-30
  21 Nusaiba al-Rassi         Alexander Brown  19   m         2023-01-01
  22     Korren Watts          Cruz Hernandez  17   m         2022-12-31
  23    Shan Saldanha        Breanna Crandall  34   f         2023-01-02
  24    Shan Saldanha           Preston Miles  75   m         2023-01-03
  25  Alexander Brown              Drue White  31   m         2022-12-30
     date_last_contact was_case           status
  1         2023-01-06        N   under_followup
  2         2023-01-07        Y             case
  3         2023-01-13        Y             case
  4         2023-01-07        N   under_followup
  5         2023-01-07        N   under_followup
  6         2023-01-05        N          unknown
  7         2023-01-08        Y             case
  8         2023-01-07        Y             case
  9         2023-01-07        N lost_to_followup
  10        2023-01-05        Y             case
  11        2023-01-05        N   under_followup
  12        2023-01-07        Y             case
  13        2023-01-07        N   under_followup
  14        2023-01-04        Y             case
  15        2023-01-03        Y             case
  16        2023-01-08        Y             case
  17        2023-01-11        N   under_followup
  18        2023-01-08        N   under_followup
  19        2023-01-08        N          unknown
  20        2023-01-08        N lost_to_followup
  21        2023-01-13        Y             case
  22        2023-01-08        N   under_followup
  23        2023-01-09        N   under_followup
  24        2023-01-08        Y             case
  25        2023-01-06        N   under_followup

sim_contacts works as expected with age structure

Code
  sim_contacts(contact_distribution = contact_distribution, infectious_period = infectious_period,
    prob_infection = 0.5, population_age = age_struct)
Output
                  from                  to age sex date_first_contact
  1    Lilliana Urbina    Christian Havlik  51   m         2022-12-29
  2    Lilliana Urbina   Raihaana al-Samra  73   f         2022-12-27
  3  Raihaana al-Samra         Carina Baca  75   f         2022-12-29
  4  Raihaana al-Samra     Tiffanie Cahill  25   f         2022-12-29
  5  Raihaana al-Samra    Antonio Quintana  48   m         2022-12-30
  6        Carina Baca         Austin John  79   m         2022-12-31
  7        Carina Baca      Jamie Stilwell  52   f         2022-12-29
  8        Carina Baca      Luis Hernandez  63   m         2022-12-30
  9        Carina Baca       Hyungu Dorado  37   m         2022-12-29
  10       Carina Baca     Brentt Spangler  34   m         2022-12-31
  11       Carina Baca        Matthew Cree  88   m         2022-12-31
  12    Jamie Stilwell       Rebeca Chavez  80   f         2022-12-25
  13    Jamie Stilwell     Katelyn Harrier  78   f         2022-12-30
  14   Brentt Spangler         Ruby Gaspar  10   f         2022-12-31
  15   Brentt Spangler     Mufeeda el-Ozer  77   f         2023-01-01
  16   Brentt Spangler       Natasha Vigil  80   f         2022-12-30
  17     Rebeca Chavez         Neil Yousaf  18   m         2022-12-28
  18       Ruby Gaspar        Shympia Kwak  61   m         2022-12-31
  19       Ruby Gaspar        Julian Berry  33   m         2022-12-27
  20       Ruby Gaspar          Sara Young  42   f         2022-12-30
  21       Ruby Gaspar     Wallace Eriacho  60   m         2023-01-01
  22   Mufeeda el-Ozer            Andy Lee  25   m         2022-12-31
  23     Natasha Vigil     Adrianna Torres  81   f         2023-01-02
  24     Natasha Vigil James Wilson-Parson  66   m         2023-01-03
  25   Wallace Eriacho     Anthony Johnson  88   m         2022-12-30
     date_last_contact was_case         status
  1         2023-01-04        N under_followup
  2         2023-01-04        Y           case
  3         2023-01-10        Y           case
  4         2023-01-05        N under_followup
  5         2023-01-05        N under_followup
  6         2023-01-03        N under_followup
  7         2023-01-06        Y           case
  8         2023-01-05        Y           case
  9         2023-01-05        N under_followup
  10        2023-01-04        Y           case
  11        2023-01-04        N under_followup
  12        2023-01-05        Y           case
  13        2023-01-05        N under_followup
  14        2023-01-03        Y           case
  15        2023-01-02        Y           case
  16        2023-01-05        Y           case
  17        2023-01-09        N        unknown
  18        2023-01-06        N under_followup
  19        2023-01-06        N under_followup
  20        2023-01-06        N        unknown
  21        2023-01-10        Y           case
  22        2023-01-06        N under_followup
  23        2023-01-07        N under_followup
  24        2023-01-06        Y           case
  25        2023-01-05        N under_followup