simulist: Simulate line list data

License: MIT R-CMD-check Codecov test coverage Lifecycle: stable Project Status: Active – The project has reached a stable, usable state and is being actively developed. DOI CRAN status CRAN downloads

{simulist} is an R package to simulate individual-level infectious disease outbreak data, including line lists and contact tracing data. It can often be useful to have synthetic datasets like these available when demonstrating outbreak analytics techniques or testing new analysis methods.

{simulist} is developed at the Centre for the Mathematical Modelling of Infectious Diseases at the London School of Hygiene and Tropical Medicine as part of Epiverse-TRACE.

Key features

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

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

Post-process simulated line list data for:

:date: Real-time outbreak snapshots with right-truncation
:memo: Messy data with inconsistencies, mistakes and missing values
:ledger: Censor dates to daily, epi- and iso-weekly, yearly and other groupings

Installation

The package can be installed from CRAN using

install.packages("simulist")

You can install the development version of {simulist} from GitHub with:

# check whether {pak} is installed
if(!require("pak")) install.packages("pak")
pak::pak("epiverse-trace/simulist")

Alternatively, install pre-compiled binaries from the Epiverse TRACE R-universe

install.packages("simulist", repos = c("https://epiverse-trace.r-universe.dev", "https://cloud.r-project.org"))

Quick start

library(simulist)

A line list can be simulated by calling sim_linelist(). The function provides sensible defaults to quickly generate a epidemiologically valid data set.

set.seed(1)
linelist <- sim_linelist()
head(linelist)
#>   id          case_name case_type sex age date_onset date_reporting
#> 1  1        James Manis suspected   m  59 2023-01-01     2023-01-01
#> 2  2          Chen Moua confirmed   m  90 2023-01-01     2023-01-01
#> 3  3       David Welter confirmed   m   4 2023-01-02     2023-01-02
#> 4  5 Christopher Turner confirmed   m  29 2023-01-04     2023-01-04
#> 5  6        Morgan Bohn suspected   f  14 2023-01-05     2023-01-05
#> 6  7    Yutitham Corpuz  probable   m  85 2023-01-06     2023-01-06
#>   date_admission   outcome date_outcome date_first_contact date_last_contact
#> 1     2023-01-09      died   2023-01-13               <NA>              <NA>
#> 2           <NA> recovered         <NA>         2022-12-29        2023-01-03
#> 3           <NA> recovered         <NA>         2022-12-28        2023-01-01
#> 4           <NA> recovered         <NA>         2022-12-28        2023-01-04
#> 5     2023-01-09      died   2023-01-23         2022-12-31        2023-01-04
#> 6     2023-01-08 recovered         <NA>         2022-12-31        2023-01-06
#>   ct_value
#> 1       NA
#> 2     24.5
#> 3     24.8
#> 4     25.4
#> 5       NA
#> 6       NA

However, to simulate a more realistic line list using epidemiological parameters estimated for an infectious disease outbreak we can use previously estimated epidemiological parameters. These can be from the {epiparameter} R package if available, or if these are not in the {epiparameter} database yet (such as the contact distribution for COVID-19) we can define them ourselves. Here we define a contact distribution, period of infectiousness, onset-to-hospitalisation delay, and onset-to-death delay.

library(epiparameter)
# create COVID-19 contact distribution
contact_distribution <- epiparameter::epiparameter(
  disease = "COVID-19",
  epi_name = "contact distribution",
  prob_distribution = create_prob_distribution(
    prob_distribution = "pois",
    prob_distribution_params = c(mean = 2)
  )
)
#> Citation cannot be created as author, year, journal or title is missing

# create COVID-19 infectious period
infectious_period <- epiparameter::epiparameter(
  disease = "COVID-19",
  epi_name = "infectious period",
  prob_distribution = create_prob_distribution(
    prob_distribution = "gamma",
    prob_distribution_params = c(shape = 1, scale = 1)
  )
)
#> Citation cannot be created as author, year, journal or title is missing

# create COVID-19 onset to hospital admission
onset_to_hosp <- epiparameter(
  disease = "COVID-19",
  epi_name = "onset to hospitalisation",
  prob_distribution = create_prob_distribution(
    prob_distribution = "lnorm",
    prob_distribution_params = c(meanlog = 1, sdlog = 0.5)
  )
)
#> Citation cannot be created as author, year, journal or title is missing

# get onset to death from {epiparameter} database
onset_to_death <- epiparameter::epiparameter_db(
  disease = "COVID-19",
  epi_name = "onset to death",
  single_epiparameter = TRUE
)
#> Using Linton N, Kobayashi T, Yang Y, Hayashi K, Akhmetzhanov A, Jung S, Yuan
#> B, Kinoshita R, Nishiura H (2020). "Incubation Period and Other
#> Epidemiological Characteristics of 2019 Novel Coronavirus Infections
#> with Right Truncation: A Statistical Analysis of Publicly Available
#> 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

To simulate a line list for COVID-19 with an Poisson contact distribution with a mean number of contacts of 2 and a probability of infection per contact of 0.5, we use the sim_linelist() function. The mean number of contacts and probability of infection determine the outbreak reproduction number, if the resulting reproduction number is around one it means we will likely get a reasonably sized outbreak (10 - 1,000 cases, varying due to the stochastic simulation).

Warning: the reproduction number of the simulation results from the contact distribution (contact_distribution) and the probability of infection (prob_infection); the number of infections is a binomial sample of the number of contacts for each case with the probability of infection (i.e. being sampled) given by prob_infection. If the average number of secondary infections from each primary case is greater than 1 then this can lead to the outbreak becoming extremely large. There is currently no depletion of susceptible individuals in the simulation model, so the maximum outbreak size (second element of the vector supplied to the outbreak_size argument) can be used to return a line list early without producing an excessively large data set.

set.seed(1)
linelist <- sim_linelist(
  contact_distribution = contact_distribution,
  infectious_period = infectious_period,
  prob_infection = 0.5,
  onset_to_hosp = onset_to_hosp,
  onset_to_death = onset_to_death
)
head(linelist)
#>   id            case_name case_type sex age date_onset date_reporting
#> 1  1   Jennifer Pritchett confirmed   f   1 2023-01-01     2023-01-01
#> 2  2         Tyler Payson confirmed   f  29 2023-01-01     2023-01-01
#> 3  3            Sean Wong confirmed   m  78 2023-01-01     2023-01-01
#> 4  5       Bishr al-Safar confirmed   m  70 2023-01-01     2023-01-01
#> 5  6 Francisco Montgomery  probable   m  28 2023-01-01     2023-01-01
#> 6  8         Jack Millard suspected   m  61 2023-01-01     2023-01-01
#>   date_admission   outcome date_outcome date_first_contact date_last_contact
#> 1     2023-01-03      died   2023-01-18               <NA>              <NA>
#> 2     2023-01-03      died   2023-02-09         2022-12-30        2023-01-08
#> 3           <NA> recovered         <NA>         2022-12-31        2023-01-05
#> 4     2023-01-04 recovered         <NA>         2022-12-31        2023-01-04
#> 5     2023-01-05 recovered         <NA>         2022-12-29        2023-01-02
#> 6           <NA> recovered         <NA>         2022-12-28        2023-01-05
#>   ct_value
#> 1     27.1
#> 2     25.2
#> 3     24.8
#> 4     26.2
#> 5       NA
#> 6       NA

In this example, the line list is simulated using the default values (see ?sim_linelist). The default hospitalisation risk is assumed to be 0.2 (i.e. there is a 20% probability an infected individual becomes hospitalised) and the start date of the outbreak is 1st January 2023. To modify either of these, we can specify them in the function.

linelist <- sim_linelist(
  contact_distribution = contact_distribution,
  infectious_period = infectious_period,
  prob_infection = 0.5,
  onset_to_hosp = onset_to_hosp,
  onset_to_death = onset_to_death,
  hosp_risk = 0.01,
  outbreak_start_date = as.Date("2019-12-01")
)
head(linelist)
#>   id           case_name case_type sex age date_onset date_reporting
#> 1  1         Odessa Haid suspected   f  32 2019-12-01     2019-12-01
#> 2  3         Amanda Chen confirmed   f  48 2019-12-01     2019-12-01
#> 3  4        Shelby Miles  probable   f   3 2019-12-01     2019-12-01
#> 4  5     Tharwa el-Pasha suspected   f  25 2019-12-01     2019-12-01
#> 5  6       Kelly Laroche confirmed   f  57 2019-12-01     2019-12-01
#> 6  7 Katelynn Montgomery confirmed   f   9 2019-12-01     2019-12-01
#>   date_admission   outcome date_outcome date_first_contact date_last_contact
#> 1           <NA> recovered         <NA>               <NA>              <NA>
#> 2           <NA> recovered         <NA>         2019-11-28        2019-12-03
#> 3           <NA> recovered         <NA>         2019-11-28        2019-12-07
#> 4           <NA> recovered         <NA>         2019-11-26        2019-12-02
#> 5           <NA> recovered         <NA>         2019-11-28        2019-12-04
#> 6           <NA> recovered         <NA>         2019-11-30        2019-12-05
#>   ct_value
#> 1       NA
#> 2     25.3
#> 3       NA
#> 4       NA
#> 5     22.3
#> 6     29.0

To simulate a table of contacts of cases (i.e. to reflect a contact tracing dataset) we can use the same parameters defined for the example above.

contacts <- sim_contacts(
  contact_distribution = contact_distribution,
  infectious_period = infectious_period,
  prob_infection = 0.5
)
head(contacts)
#>               from               to age sex date_first_contact
#> 1     Kevin Sablan Kelcee Goldsmith  75   f         2022-12-29
#> 2     Kevin Sablan  Itzel Ontiveros  33   f         2022-12-30
#> 3 Kelcee Goldsmith          Alex Wu  46   m         2022-12-25
#> 4 Kelcee Goldsmith   Xavier Kennedy  53   m         2022-12-27
#> 5 Kelcee Goldsmith   Kimber Nemecek  81   f         2022-12-29
#> 6 Kelcee Goldsmith     Samuel Stott  89   m         2022-12-28
#>   date_last_contact was_case         status
#> 1        2023-01-03     TRUE           case
#> 2        2023-01-03    FALSE under_followup
#> 3        2023-01-04    FALSE under_followup
#> 4        2023-01-03     TRUE           case
#> 5        2023-01-02     TRUE           case
#> 6        2023-01-05     TRUE           case

If both the line list and contacts table are required, they can be jointly simulated using the sim_outbreak() function. This uses the same inputs as sim_linelist() and sim_contacts() to produce a line list and contacts table of the same outbreak (the arguments also have the same default settings as the other functions).

outbreak <- sim_outbreak(
  contact_distribution = contact_distribution,
  infectious_period = infectious_period,
  prob_infection = 0.5,
  onset_to_hosp = onset_to_hosp,
  onset_to_death = onset_to_death
)
head(outbreak$linelist)
#>   id          case_name case_type sex age date_onset date_reporting
#> 1  1     Waseef el-Abad  probable   m  39 2023-01-01     2023-01-01
#> 2  2      Anthony Vigil confirmed   m  47 2023-01-01     2023-01-01
#> 3  3  Jonathan Regalado  probable   m  59 2023-01-01     2023-01-01
#> 4  4    Josephine Zhang suspected   f  20 2023-01-02     2023-01-02
#> 5  6 Husain al-Ebrahimi confirmed   m  41 2023-01-02     2023-01-02
#> 6 12   Alexandria Meier confirmed   f  39 2023-01-02     2023-01-02
#>   date_admission   outcome date_outcome date_first_contact date_last_contact
#> 1           <NA> recovered         <NA>               <NA>              <NA>
#> 2           <NA> recovered         <NA>         2022-12-30        2023-01-02
#> 3           <NA> recovered         <NA>         2023-01-01        2023-01-05
#> 4           <NA> recovered         <NA>         2022-12-30        2023-01-04
#> 5           <NA> recovered         <NA>         2022-12-28        2023-01-02
#> 6           <NA> recovered         <NA>         2022-12-31        2023-01-03
#>   ct_value
#> 1       NA
#> 2     25.0
#> 3       NA
#> 4       NA
#> 5     26.5
#> 6     24.0
head(outbreak$contacts)
#>             from                 to age sex date_first_contact
#> 1 Waseef el-Abad      Anthony Vigil  47   m         2022-12-30
#> 2 Waseef el-Abad  Jonathan Regalado  59   m         2023-01-01
#> 3  Anthony Vigil    Josephine Zhang  20   f         2022-12-30
#> 4  Anthony Vigil  Manuella Mitchell  56   f         2022-12-30
#> 5  Anthony Vigil Husain al-Ebrahimi  41   m         2022-12-28
#> 6  Anthony Vigil   Qamraaa al-Bacho   8   f         2022-12-27
#>   date_last_contact was_case         status
#> 1        2023-01-02     TRUE           case
#> 2        2023-01-05     TRUE           case
#> 3        2023-01-04     TRUE           case
#> 4        2023-01-04    FALSE under_followup
#> 5        2023-01-02     TRUE           case
#> 6        2023-01-07    FALSE under_followup

Help

To report a bug please open an issue.

Contribute

Contributions to {simulist} are welcomed. Please follow the package contributing guide.

Code of Conduct

Please note that the {simulist} project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Citing this package

citation("simulist")
#> To cite package 'simulist' in publications use:
#> 
#>   Lambert J, Tamayo Cuartero C (2026). _simulist: Simulate Disease
#>   Outbreak Line List and Contacts Data_. doi:10.5281/zenodo.10471458
#>   <https://doi.org/10.5281/zenodo.10471458>,
#>   <https://epiverse-trace.github.io/simulist/>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {simulist: Simulate Disease Outbreak Line List and Contacts Data},
#>     author = {Joshua W. Lambert and Carmen {Tamayo Cuartero}},
#>     year = {2026},
#>     doi = {10.5281/zenodo.10471458},
#>     url = {https://epiverse-trace.github.io/simulist/},
#>   }

Complimentary R packages

:package: :left_right_arrow: :package: {epiparameter}
:package: :left_right_arrow: :package: {epicontacts}
:package: :left_right_arrow: :package: {incidence2}
:package: :left_right_arrow: :package: {cleanepi}

This project has some overlap with other R packages. Here we list these packages and provide a table of features and attributes that are present for each package to help decide which package is appropriate for each use-case.

In some cases the packages are dedicated to simulating line list and other epidemiological data (e.g. {simulist}), in others the line list 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 distributions1 :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 size2 :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 maintained3 :white_check_mark: :x: :x: :x: :x: :white_check_mark:
On CRAN :white_check_mark: :x: :x: :x: :x: NA
Unit testing4 :white_check_mark: :white_check_mark: :x: :white_check_mark: :x: NA

If there is another package with this functionality missing from the 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 or a pull request.

Other R packages for simulating epidemic dynamics can be found in the Epidemic simulation models section of the Epidemiology CRAN task view.

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

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.

Another package for creating messy data is the {messy} package. This can be used, either independently or in combination with messy_linelist(), to create messy line list and contacts data.

  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} or {tinytest}.↩︎