diff --git a/README.md b/README.md index e119fb28..b7e6d9aa 100644 --- a/README.md +++ b/README.md @@ -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( @@ -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( @@ -89,6 +95,9 @@ onset_to_hosp <- epiparameter::epidist_db( #> Case Data." _Journal of Clinical Medicine_. doi: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( @@ -240,6 +249,9 @@ head(outbreak$linelist) #> 4 2023-01-01 2023-01-03 NA #> 5 2023-01-02 2023-01-05 25.8 #> 6 2023-01-03 2023-01-06 25.8 +``` + +``` r head(outbreak$contacts) #> from to age sex date_first_contact #> 1 Elshadaii Rivers Gerardo Hernandez 63 m 2022-12-28 @@ -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 @@ -339,20 +353,17 @@ simulation is one part of a wider R package (e.g. {EpiNow}). Table of line list simulator features -| | {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 | @@ -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).