Package: idmodelr 0.4.0

idmodelr: Infectious Disease Model Library and Utilities

Explore a range of infectious disease models in a consistent framework. The primary aim of 'idmodelr' is to provide a library of infectious disease models for researchers, students, and other interested individuals. These models can be used to understand the underlying dynamics and as a reference point when developing models for research. 'idmodelr' also provides a range of utilities. These include: plotting functionality; a simulation wrapper; scenario analysis tooling; an interactive dashboard; tools for handling mult-dimensional models; and both model and parameter look up tables. Unlike other modelling packages such as 'pomp' (<https://kingaa.github.io/pomp/>), 'libbi' (<http://libbi.org>) and 'EpiModel' (<http://www.epimodel.org>), 'idmodelr' serves primarily as an educational resource. It is most comparable to epirecipes (<http://epirecip.es/epicookbook/chapters/simple>) but provides a more consistent framework, an R based workflow, and additional utility tooling. After users have explored model dynamics with 'idmodelr' they may then implement their model using one of these packages in order to utilise the model fitting tools they provide. For newer modellers, this package reduces the barrier to entry by containing multiple infectious disease models, providing a consistent framework for simulation and visualisation, and signposting towards other, more research focussed, resources.

Authors:Sam Abbott [aut, cre], Akira Endo [aut]

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idmodelr.pdf |idmodelr.html
idmodelr/json (API)
NEWS

# Install 'idmodelr' in R:
install.packages('idmodelr', repos = c('https://seabbs.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/seabbs/idmodelr/issues

Datasets:

On CRAN:

diseaseepidemiologyinfectiousinfectious-disease-modelsmodellingopen-scienceutliities

44 exports 15 stars 1.81 score 46 dependencies 191 downloads

Last updated 2 years agofrom:52c4ad1972

Exports:add_pointer_structaggregate_modelaggregate_model_internalcombine_strat_model_outputcombine_to_age_modelestimate_norm_dist_from_cigather_strat_multi_variablegather_strat_variablegenerate_parameter_permutationsmodel_df_to_vectorplot_modelrequired_parametersscenario_analysisSEI_demographics_odeSEI_odeSEIR_demographics_odeSEIR_odeSEIRS_demographics_odeSEIRS_odeSEIS_demographics_odeSEIS_odeSHLIR_demographics_odeSHLIR_odeSHLITR_demographics_odeSHLITR_odeSHLITR_risk_demographics_odeSHLITR_risk_odeSI_demographics_odeSI_odesimulate_modelSIR_demographics_odeSIR_odeSIR_vaccination_demographics_odeSIR_vaccination_odeSIRS_demographics_odeSIRS_odeSIRS_vaccination_demographics_odeSIRS_vaccination_odeSIS_demographics_odeSIS_odesolve_odesummarise_modelsummarise_strat_varsummarise_var_by_strat

Dependencies:clicodetoolscolorspacecpp11deSolvedigestdplyrfansifarverfurrrfuturegenericsggplot2globalsgluegridExtragtableisobandlabelinglatticelifecyclelistenvmagrittrMASSMatrixmgcvmunsellnlmeparallellypillarpkgconfigpurrrR6RColorBrewerrlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisviridisLitewithr

Model details

Rendered frommodel_details.Rmdusingknitr::rmarkdownon Jun 23 2024.

Last update: 2019-07-19
Started: 2019-07-19

Other resources

Rendered fromresources.Rmdusingknitr::rmarkdownon Jun 23 2024.

Last update: 2022-09-02
Started: 2019-07-23

Parameter details

Rendered fromparameter_details.Rmdusingknitr::rmarkdownon Jun 23 2024.

Last update: 2019-07-19
Started: 2019-07-19

Readme and manuals

Help Manual

Help pageTopics
Adds Pointer Structure to R objectsadd_pointer_struct
A Function to Apply Multiple Aggregations to Model Outputaggregate_model
An Internal Function to Aggregate Model Output Using other Idmodelr functions.aggregate_model_internal
Reduces the Dimensionality of a Stratified Modelcombine_strat_model_output
Combine an Infectious Disease Model To a Demographic Modelcombine_to_age_model
A Function to Estimate a Normal Distribution from Credible or Confidence Intervalsestimate_norm_dist_from_ci
A Function to Gather Multiple Stratified Variables into a Tidy Formatgather_strat_multi_variable
A Function to Gather a Stratified Variable into a Tidy Formatgather_strat_variable
A Function to Generate Parameter Permutationsgenerate_parameter_permutations
Model Detailsmodel_details
Extracts a Single Column, Summarises if from Simulationmodel_df_to_vector
Parameter Detailsparameter_details
Plot Compartment Populations over Time for a Model Simulationplot_model
Lookup the Details of Parameters Required by a Modelrequired_parameters
A Function to Perform Scenario Analysis for a Generic Model Object.scenario_analysis
Susceptible-Exposed-Infected Model with Simple DemographicsSEI_demographics_ode
Susceptible-Exposed-Infected ModelSEI_ode
Susceptible-Exposed-Infected-Recovered Model with Simple DemographicsSEIR_demographics_ode
Susceptible-Exposed-Infected-Recovered ModelSEIR_ode
Susceptible-Exposed-Infected-Recovered-Susceptible Model with Simple DemographicsSEIRS_demographics_ode
Susceptible-Exposed-Infected-Recovered-Susceptible ModelSEIRS_ode
Susceptible-Exposed-Infected-Susceptible Model with Simple DemographicsSEIS_demographics_ode
Susceptible-Exposed-Infected-Susceptible ModelSEIS_ode
Susceptible-High-risk-latent-Low-risk-latent-Infected-Recovered Model with Simple DemographicsSHLIR_demographics_ode
Susceptible-High-risk-latent-Low-risk-latent-Infected-Recovered ModelSHLIR_ode
Susceptible-High-risk-latent-Low-risk-latent-Infected-Treated-Recovered Model with Simple DemographicsSHLITR_demographics_ode
Susceptible-High-risk-latent-Low-risk-latent-Infected-Treated-Recovered ModelSHLITR_ode
Susceptible-High-risk-latent-Low-risk-latent-Infected-Treated-Recovered Model with Demographics, Stratified by RiskSHLITR_risk_demographics_ode
Susceptible-High-risk-latent-Low-risk-latent-Infected-Treated-Recovered Model, Stratified by RiskSHLITR_risk_ode
Susceptible-Infected Model with Simple DemographicsSI_demographics_ode
Susceptible-Infected ModelSI_ode
A Function to Simulate a Model from a Generic Simulation Function, with Pre and Post Processingsimulate_model
Susceptible-Infected-Recovered Model with Simple DemographicsSIR_demographics_ode
Susceptible-Infected-Recovered ModelSIR_ode
Susceptible-Infected-Recovered Model with Simple Demographics and VaccinationSIR_vaccination_demographics_ode
Susceptible-Infected-Recovered Model with VaccinationSIR_vaccination_ode
Susceptible-Infected-Recovered-Susceptible Model with Simple DemographicsSIRS_demographics_ode
Susceptible-Infected-Recovered-Susceptible ModelSIRS_ode
Susceptible-Infected-Recovered-Susceptible Model with Simple Demographics and VaccinationSIRS_vaccination_demographics_ode
Susceptible-Infected-Recovered-Susceptible Model with VaccinationSIRS_vaccination_ode
Susceptible-Infected-Susceptible Model with Simple DemographicsSIS_demographics_ode
Susceptible-Infected-Susceptible ModelSIS_ode
A Simple Wrapper for lsodasolve_ode
Summarise a Model Simulationsummarise_model
Sum a Stratified Variablesummarise_strat_var
Sum a Stratified Variable by Stratification Levelsummarise_var_by_strat