Package: epidist 0.0.0.9000

Adam Howes

epidist: Estimate Epidemiological Delay Distributions With brms

Understanding and accurately estimating epidemiological delay distributions is important for public health policy. These estimates directly influence epidemic situational awareness, control strategies, and resource allocation. In this package, we provide methods to address the key challenges in estimating these distributions, including truncation, interval censoring, and dynamical biases. Despite their importance, these issues are frequently overlooked, often resulting in biased conclusions.

Authors:Adam Howes [aut, cre], Sang Woo Park [aut], Sam Abbott [aut]

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

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

Peer review:

Bug tracker:https://github.com/epinowcast/epidist/issues

Pkgdown site:https://epidist.epinowcast.org

Datasets:

On CRAN:

6.20 score 13 stars 11 scripts 34 exports 80 dependencies

Last updated 2 months agofrom:dc5779afe5 (on v0.1.0). Checks:1 OK, 6 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 21 2025
R-4.5-winNOTEJan 21 2025
R-4.5-linuxNOTEJan 21 2025
R-4.4-winNOTEJan 21 2025
R-4.4-macNOTEJan 21 2025
R-4.3-winNOTEJan 21 2025
R-4.3-macNOTEJan 21 2025

Exports:add_mean_sdas_epidist_latent_modelas_epidist_linelist_dataas_epidist_naive_modelassert_epidistbfepidistepidist_diagnosticsepidist_familyepidist_family_modelepidist_family_priorepidist_family_reparamepidist_formulaepidist_formula_modelepidist_gen_posterior_epredepidist_gen_posterior_predictepidist_model_priorepidist_priorepidist_stancodeGammais_epidist_latent_modelis_epidist_linelist_datais_epidist_naive_modellognormalnew_epidist_latent_modelnew_epidist_linelist_datanew_epidist_naive_modelpredict_delay_parameterspredict_dparsimulate_exponential_casessimulate_gillespiesimulate_secondarysimulate_uniform_casesweibull

Dependencies:abindbackportsbayesplotBHbridgesamplingbrmsBrobdingnagcallrcheckmateclicodacodetoolscolorspacecpp11descdigestdistributionaldplyrfansifarverfuturefuture.applygenericsggplot2ggridgesglobalsgluegridExtragtableinlineisobandlabelinglatticelifecyclelistenvloolubridatemagrittrMASSMatrixmatrixStatsmgcvmunsellmvtnormnleqslvnlmenumDerivparallellypillarpkgbuildpkgconfigplyrposteriorpracmaprimarycensoredprocessxpspurrrQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelreshape2rlangrstanrstantoolsscalesStanHeadersstringistringrtensorAtibbletidyselecttimechangeutf8vctrsviridisLitewithr

Frequently asked questions and tips

Rendered fromfaq.Rmdusingknitr::rmarkdownon Jan 21 2025.

Last update: 2024-11-21
Started: 2024-07-22

Getting started with epidist

Rendered fromepidist.Rmdusingknitr::rmarkdownon Jan 21 2025.

Last update: 2024-11-21
Started: 2023-12-08

Readme and manuals

Help Manual

Help pageTopics
Add natural scale mean and standard deviation parametersadd_mean_sd
Default method for add natural scale parametersadd_mean_sd.default
Add natural scale mean and standard deviation parameters for a latent gamma modeladd_mean_sd.gamma_samples
Add natural scale mean and standard deviation parameters for a latent lognormal modeladd_mean_sd.lognormal_samples
Convert an object to an 'epidist_latent_model' objectas_epidist_latent_model
The latent model method for 'epidist_linelist_data' objectsas_epidist_latent_model.epidist_linelist_data
Create an epidist_linelist_data objectas_epidist_linelist_data
Create an epidist_linelist_data object from a data frame with event datesas_epidist_linelist_data.data.frame
Create an epidist_linelist_data object from vectors of event timesas_epidist_linelist_data.default
Prepare naive model to pass through to 'brms'as_epidist_naive_model
The naive model method for 'epidist_linelist_data' objectsas_epidist_naive_model.epidist_linelist_data
Validation for epidist objectsassert_epidist
Assert validity of 'epidist_linelist_data' objectsassert_epidist.epidist_linelist_data
Fit epidemiological delay distributions using a 'brms' interfaceepidist
Diagnostics for 'epidist_fit' modelsepidist_diagnostics
Define 'epidist' familyepidist_family
The model-specific parts of an 'epidist_family()' callepidist_family_model epidist_formula_model
Default method for defining a model specific familyepidist_family_model.default
Create the model-specific component of an 'epidist' custom familyepidist_family_model.epidist_latent_model
Family specific prior distributionsepidist_family_prior
Default family specific prior distributionsepidist_family_prior.default
Family specific prior distributions for the lognormal familyepidist_family_prior.lognormal
Reparameterise an 'epidist' family to align 'brms' and Stanepidist_family_reparam
Default method for families which do not require a reparameterisationepidist_family_reparam.default
Reparameterisation for the gamma familyepidist_family_reparam.gamma
Define a model specific formulaepidist_formula
Default method for defining a model specific formulaepidist_formula_model.default
Define the model-specific component of an 'epidist' custom formulaepidist_formula_model.epidist_latent_model
Create a function to calculate the pointwise log likelihood of the latent modelepidist_gen_log_lik_latent
Create a function to draw from the expected value of the posterior predictive distribution for a latent modelepidist_gen_posterior_epred
Create a function to draw from the posterior predictive distribution for a latent modelepidist_gen_posterior_predict
Model specific prior distributionsepidist_model_prior
Default model specific prior distributionsepidist_model_prior.default
Define prior distributions using 'brms' defaults, model specific priors, family specific priors, and user provided priorsepidist_prior
Define model specific Stan codeepidist_stancode
Default method for defining model specific Stan codeepidist_stancode.default
Default method used for interface using 'brms'epidist.default
Check if data has the 'epidist_latent_model' classis_epidist_latent_model
Check if data has the 'epidist_linelist_data' classis_epidist_linelist_data
Check if data has the 'epidist_naive_model' classis_epidist_naive_model
Class constructor for 'epidist_latent_model' objectsnew_epidist_latent_model
Class constructor for 'epidist_linelist_data' objectsnew_epidist_linelist_data
Class constructor for 'epidist_naive_model' objectsnew_epidist_naive_model
Extract samples of the delay distribution parameterspredict_delay_parameters predict_dpar
Ebola linelist data from Fang et al. (2016)sierra_leone_ebola_data
Simulate exponential casessimulate_exponential_cases
Simulate cases from a stochastic SIR modelsimulate_gillespie
Simulate secondary events based on a delay distributionsimulate_secondary
Simulate cases from a uniform distributionsimulate_uniform_cases