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actions-user committed May 20, 2024
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Expand Up @@ -66,6 +66,9 @@ contact_distribution <- epiparameter::epidist(
prob_distribution_params = c(mean = 2)
)
#> Citation cannot be created as author, year, journal or title is missing
```

``` r

# create COVID-19 infectious period
infect_period <- epiparameter::epidist(
Expand All @@ -75,6 +78,9 @@ infect_period <- epiparameter::epidist(
prob_distribution_params = c(shape = 1, scale = 1)
)
#> Citation cannot be created as author, year, journal or title is missing
```

``` r

# get onset to hospital admission from {epiparameter} database
onset_to_hosp <- epiparameter::epidist_db(
Expand All @@ -89,6 +95,9 @@ onset_to_hosp <- epiparameter::epidist_db(
#> Case Data." _Journal of Clinical Medicine_. doi:10.3390/jcm9020538
#> <https://doi.org/10.3390/jcm9020538>..
#> To retrieve the citation use the 'get_citation' function
```

``` r

# get onset to death from {epiparameter} database
onset_to_death <- epiparameter::epidist_db(
Expand Down Expand Up @@ -240,6 +249,9 @@ head(outbreak$linelist)
#> 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
```

``` r
head(outbreak$contacts)
#> from to age sex date_first_contact
#> 1 Elshadaii Rivers Gerardo Hernandez 63 m 2022-12-28
Expand Down Expand Up @@ -311,7 +323,9 @@ simulation is one part of a wider R package (e.g. {EpiNow}).

- [`{LLsim}`](https://github.com/jrcpulliam/LLsim) simulates line list
data using a stochastic SIR model with a fixed population with
observation and reporting delays.
observation and reporting delays. Line list data is generated in two
steps, 1) the SIR model simulates the outbreak (`simpleSim()`), 2) the
outbreak data is converted into a line list (`createLineList()`).
- [`{simulacr}`](https://github.com/reconhub/simulacr) uses a branching
process model to simulate cases and contacts for an outbreak. It
simulates transmission of infections using other epidemiological R
Expand Down Expand Up @@ -339,20 +353,17 @@ simulation is one part of a wider R package (e.g. {EpiNow}).
Table of line list simulator features
</summary>

| | {simulist} | {LLsim} | {simulacr} | {epidict} | {EpiNow} | generative-nowcasting |
|--------------------------------------|--------------------|--------------------|--------------------|--------------------|--------------------|-----------------------|
| Simulates line list | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
| Simulates contacts | :white_check_mark: | :white_check_mark: | :white_check_mark: | :x: | :x: | :x: |
| Parameterised with epi distributions | :white_check_mark: | :white_check_mark: | :white_check_mark: | :x: | :white_check_mark: | :white_check_mark: |
| Interoperable with {epicontacts} | :white_check_mark: | :white_check_mark: | :white_check_mark: | :x: | :x: | :x: |
| Explicit population size | :x: | :white_check_mark: | :white_check_mark: | :x: | :x: | :x: |
| R package | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: | :x: |
| Actively maintained\* | :white_check_mark: | :x: | :x: | :x: | :x: | :white_check_mark: |
| On CRAN | :x: | :x: | :x: | :x: | :x: | NA |
| Unit testing | :white_check_mark: | :white_check_mark: | :x: | :white_check_mark: | :x: | NA |

\* We define actively maintained as the repository having a commit to
the main branch within the last 12 months
| | {simulist} | {LLsim} | {simulacr} | {epidict} | {EpiNow} | generative-nowcasting |
|------------------------------------------|--------------------|--------------------|--------------------|--------------------|--------------------|-----------------------|
| Simulates line list | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
| Simulates contacts | :white_check_mark: | :white_check_mark: | :white_check_mark: | :x: | :x: | :x: |
| Parameterised with epi distributions[^1] | :white_check_mark: | :white_check_mark: | :white_check_mark: | :x: | :white_check_mark: | :white_check_mark: |
| Interoperable with {epicontacts} | :white_check_mark: | :white_check_mark: | :white_check_mark: | :x: | :x: | :x: |
| Explicit population size[^2] | :x: | :white_check_mark: | :white_check_mark: | :x: | :x: | :x: |
| R package | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: | :x: |
| Actively maintained[^3] | :white_check_mark: | :x: | :x: | :x: | :x: | :white_check_mark: |
| On CRAN | :x: | :x: | :x: | :x: | :x: | NA |
| Unit testing[^4] | :white_check_mark: | :white_check_mark: | :x: | :white_check_mark: | :x: | NA |

</details>

Expand All @@ -361,3 +372,39 @@ list that should be added, or if a package included in this list has
been updated and the table should reflect this please contribute by
making an [issue](https://github.com/epiverse-trace/simulist/issues) or
a [pull request](https://github.com/epiverse-trace/simulist/pulls).

Some packages are related to {simulist} but do not simulate line list
data. These include:

- [`{outbreaks}`](https://CRAN.R-project.org/package=outbreaks) an R
package containing a library of outbreak data sets, including line
list data, for a variety of past and simulated outbreaks, e.g. Ebola
and MERS.
- [`{ringbp}`](https://github.com/epiforecasts/ringbp) an R package to
simulate cases using an individual-level transmission model with
contact tracing.
- [`{epichains}`](https://github.com/epiverse-trace/epichains) an R
package with functionality to simulate transmission chains using a
branching process model.

The {outbreaks} package is useful if data from a past outbreak data or
generic line list data is required. The {ringbp} and {epichains}
packages can be used to generate case data over time which can then be
converted into a line list with some manual post-processing.

[^1]: In this context *Parameterised with epi distributions* means that
the simulation uses epidemiological distributions (e.g. serial
interval, infectious period) to parameterise the model and the
parameters of these epi distributions can be modified by the user.

[^2]: *Explicit population size* refers to the simulation using a finite
population size which is controlled by the user for the depletion of
susceptible individuals in the model.

[^3]: We define *Actively maintained* as the repository having a commit
to the main branch within the last 12 months.

[^4]: *Unit testing* is ticked if the package contains any form of
testing, this can use any testing framework, for example
[{testthat}](https://CRAN.R-project.org/package=testthat) or
[{tinytest}](https://CRAN.R-project.org/package=tinytest).

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