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Expand Up @@ -32,6 +32,18 @@ at the [London School of Hygiene and Tropical
Medicine](https://www.lshtm.ac.uk/) as part of
[Epiverse-TRACE](https://data.org/initiatives/epiverse/).

## Key features

`{simulist}` allows you to simulate realistic line list and contact
tracing data, with:

:hourglass_flowing_sand: Parameterised epidemiological delay
distributions <br> :hospital: Population-wide or age-stratified
hospitalisation and death risks <br> :bar_chart: Uniform or
age-structured populations <br> :chart_with_upwards_trend: Constant or
time-varying case fatality risk <br> :clipboard: Customisable
probability of case types and contact tracing follow-up <br>

## Installation

You can install the development version of `{simulist}` from
Expand Down Expand Up @@ -144,20 +156,20 @@ linelist <- sim_linelist(
onset_to_death = onset_to_death
)
head(linelist)
#> id case_name case_type sex age date_onset date_admission outcome
#> 1 1 Dominic Sundara probable m 35 2023-01-01 <NA> recovered
#> 2 2 Preston Montgomery suspected m 43 2023-01-01 <NA> recovered
#> 3 3 Reece Chittum probable m 1 2023-01-01 <NA> recovered
#> 4 5 Michael Cheek confirmed m 78 2023-01-01 <NA> recovered
#> 5 6 Jennifer Smith confirmed f 22 2023-01-01 <NA> recovered
#> 6 8 Erika Quintero confirmed f 28 2023-01-01 <NA> recovered
#> id case_name case_type sex age date_onset date_admission outcome
#> 1 1 Rushdi al-Ishak probable m 35 2023-01-01 <NA> recovered
#> 2 2 Jeffrey Le confirmed m 43 2023-01-01 <NA> recovered
#> 3 3 Dominic Barringer suspected m 1 2023-01-01 <NA> recovered
#> 4 5 Tyler Kelley probable m 78 2023-01-01 <NA> recovered
#> 5 6 Carolyn Moore confirmed f 22 2023-01-01 <NA> recovered
#> 6 8 Cheyenne Sayavong confirmed f 28 2023-01-01 2023-01-04 died
#> date_outcome date_first_contact date_last_contact ct_value
#> 1 <NA> <NA> <NA> NA
#> 2 <NA> 2022-12-30 2023-01-05 NA
#> 2 <NA> 2022-12-30 2023-01-05 24
#> 3 <NA> 2022-12-30 2023-01-02 NA
#> 4 <NA> 2022-12-29 2023-01-02 23.1
#> 5 <NA> 2023-01-01 2023-01-03 23.1
#> 6 <NA> 2023-01-03 2023-01-04 23.1
#> 4 <NA> 2022-12-29 2023-01-02 NA
#> 5 <NA> 2023-01-01 2023-01-03 24
#> 6 2023-01-16 2023-01-03 2023-01-04 24
```

In this example, the line list is simulated using the default values
Expand All @@ -177,20 +189,20 @@ linelist <- sim_linelist(
outbreak_start_date = as.Date("2019-12-01")
)
head(linelist)
#> id case_name case_type sex age date_onset date_admission outcome
#> 1 1 Ya'qoob el-Firman probable m 80 2019-12-01 <NA> recovered
#> 2 2 Cassandra Martinez confirmed f 85 2019-12-01 2019-12-03 died
#> 3 4 Andrea Richards confirmed f 76 2019-12-01 <NA> recovered
#> 4 8 Dalany Whitesides confirmed f 12 2019-12-01 <NA> recovered
#> 5 11 Amanda Cali confirmed f 50 2019-12-01 <NA> recovered
#> 6 14 Linh Farmer probable f 54 2019-12-01 <NA> recovered
#> id case_name case_type sex age date_onset date_admission outcome
#> 1 1 Kiersten Matthews confirmed f 72 2019-12-01 <NA> recovered
#> 2 2 Omar Cruz confirmed m 85 2019-12-01 <NA> recovered
#> 3 3 Emilio Alvarado suspected m 24 2019-12-01 <NA> recovered
#> 4 4 Sonya Santiago confirmed f 67 2019-12-01 2019-12-03 recovered
#> 5 5 Michelle Brooks probable f 37 2019-12-02 <NA> recovered
#> 6 6 Anastasia Hamlin confirmed f 14 2019-12-02 <NA> recovered
#> date_outcome date_first_contact date_last_contact ct_value
#> 1 <NA> <NA> <NA> NA
#> 2 2019-12-05 2019-12-04 2019-12-06 23.6
#> 3 <NA> 2019-11-29 2019-12-03 23.6
#> 4 <NA> 2019-12-05 2019-12-05 23.6
#> 5 <NA> 2019-12-03 2019-12-05 23.6
#> 6 <NA> 2019-11-30 2019-12-02 NA
#> 1 <NA> <NA> <NA> 23.5
#> 2 <NA> 2019-11-30 2019-12-06 23.5
#> 3 <NA> 2019-11-30 2019-12-01 NA
#> 4 <NA> 2019-12-07 2019-12-09 23.5
#> 5 <NA> 2019-12-01 2019-12-04 NA
#> 6 <NA> 2019-12-01 2019-12-04 23.5
```

To simulate a table of contacts of cases (i.e. to reflect a contact
Expand All @@ -203,21 +215,26 @@ contacts <- sim_contacts(
infect_period = infect_period,
prob_infect = 0.5
)
#> Warning: Number of cases exceeds maximum outbreak size.
#> Returning data early with 10176 cases and 20217 total contacts (including cases).
```

``` r
head(contacts)
#> from to age sex date_first_contact date_last_contact
#> 1 Jada Cardona Tyray Jackson 50 m 2023-01-03 2023-01-04
#> 2 Tyray Jackson Karol Alcon 4 f 2023-01-02 2023-01-03
#> 3 Tyray Jackson Hishaam al-Khawaja 82 m 2022-12-31 2023-01-03
#> 4 Tyray Jackson Jessica Cunningham 64 f 2023-01-04 2023-01-05
#> 5 Tyray Jackson Danyell Ricks 12 f 2023-01-03 2023-01-05
#> 6 Karol Alcon Thalia Williams 22 f 2023-01-05 2023-01-07
#> was_case status
#> 1 Y case
#> 2 Y case
#> 3 Y case
#> 4 N under_followup
#> 5 Y case
#> 6 Y case
#> from to age sex date_first_contact date_last_contact
#> 1 Brandon Byrnes Mustaba el-Wahba 14 m 2023-01-01 2023-01-03
#> 2 Brandon Byrnes Lonnie Williams 33 m 2022-12-31 2023-01-05
#> 3 Brandon Byrnes Robert Brown 34 m 2022-12-28 2023-01-02
#> 4 Brandon Byrnes Desiree Mabry 76 f 2023-01-03 2023-01-06
#> 5 Brandon Byrnes Salvador Trevino 73 m 2023-01-05 2023-01-07
#> 6 Desiree Mabry Gina Yu 90 f 2023-01-05 2023-01-06
#> was_case status
#> 1 N under_followup
#> 2 N lost_to_followup
#> 3 N under_followup
#> 4 Y case
#> 5 N under_followup
#> 6 N under_followup
```

If both the line list and contacts table are required, they can be
Expand All @@ -235,38 +252,38 @@ outbreak <- sim_outbreak(
onset_to_death = onset_to_death
)
head(outbreak$linelist)
#> id case_name case_type sex age date_onset date_admission outcome
#> 1 1 Elshadaii Rivers confirmed f 46 2023-01-01 2023-01-01 recovered
#> 2 2 Gerardo Hernandez probable m 63 2023-01-01 <NA> recovered
#> 3 3 Evan Whitmore confirmed m 22 2023-01-01 <NA> recovered
#> 4 5 Louis Heredia probable m 75 2023-01-01 <NA> recovered
#> 5 7 Steven Byers confirmed m 84 2023-01-02 <NA> recovered
#> 6 8 Derrick Mackey confirmed m 56 2023-01-02 <NA> recovered
#> id case_name case_type sex age date_onset date_admission outcome
#> 1 1 Annnees al-Nazir probable m 24 2023-01-01 <NA> recovered
#> 2 2 Muammar al-Miah probable m 46 2023-01-02 <NA> recovered
#> 3 4 Melina Tarin probable f 71 2023-01-02 <NA> recovered
#> 4 6 Alysh Lovejoy suspected f 13 2023-01-03 <NA> recovered
#> 5 9 Dylan Scanlon confirmed m 28 2023-01-03 <NA> recovered
#> 6 11 Nikolay Mcinnis suspected m 15 2023-01-03 <NA> recovered
#> date_outcome date_first_contact date_last_contact ct_value
#> 1 <NA> <NA> <NA> 25.8
#> 2 <NA> 2022-12-28 2023-01-02 NA
#> 3 <NA> 2023-01-04 2023-01-06 25.8
#> 4 <NA> 2023-01-01 2023-01-03 NA
#> 5 <NA> 2023-01-02 2023-01-05 25.8
#> 6 <NA> 2023-01-03 2023-01-06 25.8
#> 1 <NA> <NA> <NA> NA
#> 2 <NA> 2023-01-04 2023-01-07 NA
#> 3 <NA> 2023-01-03 2023-01-05 NA
#> 4 <NA> 2023-01-04 2023-01-06 NA
#> 5 <NA> 2023-01-04 2023-01-07 25.6
#> 6 <NA> 2023-01-05 2023-01-06 NA
```

``` r
head(outbreak$contacts)
#> from to age sex date_first_contact
#> 1 Elshadaii Rivers Gerardo Hernandez 63 m 2022-12-28
#> 2 Elshadaii Rivers Evan Whitmore 22 m 2023-01-04
#> 3 Elshadaii Rivers Hunter Wells 77 m 2023-01-01
#> 4 Gerardo Hernandez Louis Heredia 75 m 2023-01-01
#> 5 Gerardo Hernandez Ronald Phanekham 23 m 2023-01-02
#> 6 Gerardo Hernandez Steven Byers 84 m 2023-01-02
#> date_last_contact was_case status
#> 1 2023-01-02 Y case
#> 2 2023-01-06 Y case
#> 3 2023-01-05 N under_followup
#> 4 2023-01-03 Y case
#> 5 2023-01-04 N under_followup
#> 6 2023-01-05 Y case
#> from to age sex date_first_contact date_last_contact
#> 1 Annnees al-Nazir Muammar al-Miah 46 m 2023-01-04 2023-01-07
#> 2 Annnees al-Nazir Siena Quimby 76 f 2022-12-27 2023-01-02
#> 3 Muammar al-Miah Melina Tarin 71 f 2023-01-03 2023-01-05
#> 4 Muammar al-Miah Destinee Embry 49 f 2023-01-01 2023-01-04
#> 5 Melina Tarin Alysh Lovejoy 13 f 2023-01-04 2023-01-06
#> 6 Alysh Lovejoy Andrew Knott 55 m 2023-01-03 2023-01-05
#> was_case status
#> 1 Y case
#> 2 N lost_to_followup
#> 3 Y case
#> 4 N under_followup
#> 5 Y case
#> 6 N under_followup
```

## Help
Expand All @@ -293,23 +310,31 @@ By contributing to this project, you agree to abide by its terms.
citation("simulist")
#> To cite package 'simulist' in publications use:
#>
#> Lambert J, Tamayo C (2024). _simulist: Tools to Simulate Line List
#> and Contacts Data_. doi:10.5281/zenodo.10471458
#> Lambert J, Tamayo C (2024). _simulist: Simulate Disease Outbreak Line
#> List and Contacts Data_. doi:10.5281/zenodo.10471458
#> <https://doi.org/10.5281/zenodo.10471458>,
#> <https://github.com/epiverse-trace/simulist,https://epiverse-trace.github.io/simulist/>.
#> <https://epiverse-trace.github.io/simulist/>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {simulist: Tools to Simulate Line List and Contacts Data},
#> title = {simulist: Simulate Disease Outbreak Line List and Contacts Data},
#> author = {Joshua W. Lambert and Carmen Tamayo},
#> year = {2024},
#> doi = {10.5281/zenodo.10471458},
#> url = {https://github.com/epiverse-trace/simulist,
#> https://epiverse-trace.github.io/simulist/},
#> url = {https://epiverse-trace.github.io/simulist/},
#> }
```

## Complimentary R packages

:package: :left_right_arrow: :package:
[{epiparameter}](https://epiverse-trace.github.io/epiparameter/) <br>
:package: :left_right_arrow: :package:
[{epicontacts}](https://www.repidemicsconsortium.org/epicontacts/) <br>
:package: :left_right_arrow: :package:
[{incidence2}](https://www.reconverse.org/incidence2/) <br>

## Related projects

This project has some overlap with other R packages. Here we list these
Expand Down

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