From d9f82305c22bd303ba2df451add32c3fd053e318 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Thu, 4 Jan 2024 16:21:19 +0000 Subject: [PATCH] Automatic readme update --- README.md | 134 +++++++++++++++++++++++++++--------------------------- 1 file changed, 67 insertions(+), 67 deletions(-) diff --git a/README.md b/README.md index 267047a0..a0a799d0 100644 --- a/README.md +++ b/README.md @@ -110,20 +110,20 @@ linelist <- sim_linelist( onset_to_death = onset_to_death ) head(linelist) -#> id case_name case_type gender age date_onset date_admission -#> 1 1 Brian Murphy confirmed m 87 2023-01-01 -#> 2 2 Benjamin Brooks probable m 13 2023-01-01 -#> 3 3 Zoe Turner probable f 6 2023-01-01 -#> 4 4 Hannah Butler confirmed f 32 2023-01-02 -#> 5 5 Daris Villalobos-Corral confirmed m 50 2023-01-03 -#> 6 6 Zachary Lapre probable m 34 2023-01-01 -#> date_death date_first_contact date_last_contact ct_value -#> 1 27.9 -#> 2 2023-01-01 2023-01-05 NA -#> 3 2022-12-31 2023-01-05 NA -#> 4 2022-12-30 2023-01-03 27.9 -#> 5 2022-12-27 2023-01-03 27.9 -#> 6 2023-01-02 2023-01-05 NA +#> id case_name case_type gender age date_onset date_admission date_death +#> 1 1 Justin Murphy suspected m 8 2023-01-01 +#> 2 2 Mahmood al-Badie confirmed m 66 2023-01-02 +#> 3 3 Hannah Dice suspected f 81 2023-01-01 +#> 4 4 Simey Vu confirmed f 55 2023-01-02 +#> 5 5 Ira Francis confirmed m 26 2023-01-03 +#> 6 6 Jacob Sumners probable m 13 2023-01-03 +#> date_first_contact date_last_contact ct_value +#> 1 NA +#> 2 2022-12-31 2023-01-02 22.7 +#> 3 2023-01-01 2023-01-03 NA +#> 4 2023-01-01 2023-01-04 22.7 +#> 5 2023-01-02 2023-01-06 22.7 +#> 6 2023-01-03 2023-01-06 NA ``` In this example, the line list is simulated using the default values @@ -143,26 +143,26 @@ linelist <- sim_linelist( ) head(linelist) #> id case_name case_type gender age date_onset date_admission -#> 1 1 Luc James confirmed m 43 2019-12-01 -#> 2 2 Ernestina Espinoza confirmed f 24 2019-12-02 -#> 3 3 Nicholas Krishnaswamy confirmed m 53 2019-12-01 -#> 4 4 Ian Lewis probable m 24 2019-12-02 -#> 5 5 Antonio Alvarez probable m 11 2019-12-02 -#> 6 6 Abdul Haleem al-Youssef suspected m 45 2019-12-03 +#> 1 1 Cheyenne Espino Aguilar probable f 5 2019-12-01 +#> 2 2 Muhjar al-Nawaz confirmed f 37 2019-12-01 +#> 3 3 Crystal Spleen probable f 41 2019-12-01 +#> 4 4 Nohemy Montano suspected f 36 2019-12-01 +#> 5 5 Malik Fuller suspected m 5 2019-12-01 +#> 6 6 Lavelle Snow probable m 86 2019-12-01 #> date_death date_first_contact date_last_contact ct_value -#> 1 25.2 -#> 2 2019-12-04 2019-12-07 25.2 -#> 3 2019-12-02 2019-12-03 25.2 -#> 4 2019-12-04 2019-12-06 NA -#> 5 2019-11-30 2019-12-02 NA +#> 1 2019-12-26 NA +#> 2 2019-12-01 2019-12-08 26.3 +#> 3 2019-12-02 2019-12-04 NA +#> 4 2019-12-02 2019-12-05 NA +#> 5 2019-11-29 2019-12-03 NA #> 6 2019-12-01 2019-12-04 NA ``` To simulate a table of contacts of cases (i.e. to reflect a contact tracing dataset) we can use the same serial interval defined for the example above. We additionally need a contact distribution, which -represents the probability that each person in the population will be a -given number of contacts on a given day. +represents the probability that each person that infected an individual, +also had a given number of contacts that did not become infected. ``` r contact_distribution <- epiparameter::epidist( @@ -179,20 +179,20 @@ contacts <- sim_contacts( contact_distribution = contact_distribution ) head(contacts) -#> from to cnt_age cnt_gender date_first_contact -#> 1 Jacob Camacho Fiona Dall 55 f 2022-12-31 -#> 2 Jacob Camacho Chandan Vang 36 m 2022-12-30 -#> 3 Jacob Camacho Troy Choi 70 m 2023-01-01 -#> 4 Jacob Camacho Fateena al-Hamdan 74 f 2023-01-04 -#> 5 Jacob Camacho Abdul Baasid el-Asad 48 m 2023-01-03 -#> 6 Fiona Dall Jeremy Moreno 83 m 2022-12-31 -#> date_last_contact was_case status -#> 1 2023-01-06 Y case -#> 2 2023-01-01 N under_followup -#> 3 2023-01-02 N under_followup -#> 4 2023-01-06 N under_followup -#> 5 2023-01-04 N under_followup -#> 6 2023-01-04 Y case +#> from to cnt_age cnt_gender date_first_contact +#> 1 Lauren Gurreri Raeanna Riley 9 f 2022-12-30 +#> 2 Lauren Gurreri Breann Huff 53 f 2023-01-04 +#> 3 Lauren Gurreri Talaal el-Attar 83 m 2023-01-01 +#> 4 Lauren Gurreri Austin Martinez 47 m 2022-12-29 +#> 5 Lauren Gurreri Theodora Fox 37 f 2022-12-30 +#> 6 Lauren Gurreri Ashleigh Reiter 89 f 2023-01-01 +#> date_last_contact was_case status +#> 1 2023-01-04 Y case +#> 2 2023-01-05 Y case +#> 3 2023-01-04 Y case +#> 4 2023-01-02 N under_followup +#> 5 2023-01-03 N under_followup +#> 6 2023-01-03 N lost_to_followup ``` If both the line list and contacts table are required, they can be @@ -210,35 +210,35 @@ outbreak <- sim_outbreak( contact_distribution = contact_distribution ) head(outbreak$linelist) -#> id case_name case_type gender age date_onset date_admission -#> 1 1 Amanda Mills suspected f 72 2023-01-01 -#> 2 2 Anthony San Miguel confirmed m 32 2023-01-01 -#> 3 3 Calista Silva confirmed f 57 2023-01-03 -#> 4 4 Alia Strover confirmed f 1 2023-01-01 2023-01-03 -#> 5 5 Justin Burchfield probable m 48 2023-01-03 -#> 6 6 Cody Nguyen confirmed m 1 2023-01-06 +#> id case_name case_type gender age date_onset date_admission +#> 1 1 Celsa Davis probable f 86 2023-01-01 2023-01-06 +#> 2 2 Tatyanna Yarbrough-Montoya suspected f 56 2023-01-01 2023-01-01 +#> 3 3 Erika Cordova suspected f 84 2023-01-01 +#> 4 4 Nakheel al-Amara confirmed f 48 2023-01-01 +#> 5 5 Ayanna Roberts probable f 65 2023-01-01 +#> 6 6 Matthew Apodaca confirmed m 11 2023-01-02 #> date_death date_first_contact date_last_contact ct_value #> 1 NA -#> 2 2023-01-01 2023-01-04 23.5 -#> 3 2023-01-01 2023-01-05 23.5 -#> 4 2022-12-31 2023-01-05 23.5 -#> 5 2023-01-03 2023-01-07 NA -#> 6 2023-01-01 2023-01-04 23.5 +#> 2 2023-01-02 2023-01-03 NA +#> 3 2022-12-29 2023-01-02 NA +#> 4 2023-01-02 2023-01-06 25.4 +#> 5 2022-12-30 2023-01-03 NA +#> 6 2022-12-29 2023-01-02 25.4 head(outbreak$contacts) -#> from to cnt_age cnt_gender date_first_contact -#> 1 Amanda Mills Anthony San Miguel 32 m 2023-01-01 -#> 2 Amanda Mills Corey Dunlap 37 m 2023-01-01 -#> 3 Amanda Mills Fendi Saldanha 82 f 2023-01-01 -#> 4 Anthony San Miguel Calista Silva 57 f 2023-01-01 -#> 5 Anthony San Miguel Alia Strover 1 f 2022-12-31 -#> 6 Anthony San Miguel Justin Burchfield 48 m 2023-01-03 -#> date_last_contact was_case status -#> 1 2023-01-04 Y case -#> 2 2023-01-04 N lost_to_followup -#> 3 2023-01-03 N lost_to_followup -#> 4 2023-01-05 Y case -#> 5 2023-01-05 Y case -#> 6 2023-01-07 Y case +#> from to cnt_age cnt_gender +#> 1 Celsa Davis Tatyanna Yarbrough-Montoya 56 f +#> 2 Celsa Davis Erika Cordova 84 f +#> 3 Celsa Davis Mawzoona al-Vaziri 71 f +#> 4 Celsa Davis Masood al-Ramin 82 m +#> 5 Celsa Davis Akshitsinh Vang 16 m +#> 6 Tatyanna Yarbrough-Montoya Nakheel al-Amara 48 f +#> date_first_contact date_last_contact was_case status +#> 1 2023-01-02 2023-01-03 Y case +#> 2 2022-12-29 2023-01-02 Y case +#> 3 2023-01-01 2023-01-03 N under_followup +#> 4 2023-01-01 2023-01-03 N under_followup +#> 5 2023-01-05 2023-01-08 N under_followup +#> 6 2023-01-02 2023-01-06 Y case ``` ## Help