Package: serofoi 1.0.2

Zulma M. Cucunubá

serofoi: Bayesian Estimation of the Force of Infection from Serological Data

Estimating the force of infection from time varying, age varying, or constant serocatalytic models from population based seroprevalence studies using a bayesian framework, including data simulation functions enabling the generation of serological surveys based on this models. This tool also provides a flexible prior specification syntax for the force of infection and the seroreversion rate, as well as methods to assess model convergence and comparison criteria along with useful visualisation functions.

Authors:Zulma M. Cucunubá [aut, cre], Nicolás T. Domínguez [aut], Ben Lambert [aut], Pierre Nouvellet [aut], Geraldine Gómez [ctb], Jaime A. Pavlich-Mariscal [ctb], Hugo Gruson [ctb], David Santiago Quevedo [ctb], Miguel Gámez [ctb], Sumali Bajaj [ctb], Everlyn Kamau [ctb], Richard Creswell [ctb], International Development Research Center [fnd], Pontificia Universidad Javeriana [cph]

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serofoi.pdf |serofoi.html✨
serofoi/json (API)
NEWS

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

Bug tracker:https://github.com/epiverse-trace/serofoi/issues

Pkgdown site:https://epiverse-trace.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • chagas2012 - Chagas seroprevalence data in serofoi
  • chik2015 - Chikungunya seroprevalence data in serofoi
  • veev2012 - Venezuelan Equine Encephalitis Virus (VEEV) seroprevalence data in serofoi

On CRAN:

antibodiesbayesian-methodsepidemiologyepiverseserological-surveysstan-languagecpp

6.17 score 18 stars 10 scripts 33 exports 67 dependencies

Last updated 3 hours agofrom:19e0a7ff8b. Checks:4 OK, 7 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 19 2025
R-4.5-win-x86_64NOTEFeb 19 2025
R-4.5-mac-x86_64OKFeb 19 2025
R-4.5-mac-aarch64OKFeb 19 2025
R-4.5-linux-x86_64OKFeb 19 2025
R-4.4-win-x86_64NOTEFeb 19 2025
R-4.4-mac-x86_64NOTEFeb 19 2025
R-4.4-mac-aarch64NOTEFeb 19 2025
R-4.3-win-x86_64NOTEFeb 19 2025
R-4.3-mac-x86_64NOTEFeb 19 2025
R-4.3-mac-aarch64NOTEFeb 19 2025

Exports:add_age_group_to_serosurveybuild_stan_dataextract_central_estimatesfit_seromodelget_foi_indexplot_foi_estimatesplot_rhatsplot_seromodelplot_seroprev_estimatesplot_serosurveyplot_summaryprepare_serosurvey_for_plotprob_seroprev_age_by_ageprob_seroprev_age_time_by_ageprob_seroprev_by_ageprob_seroprev_gen_by_ageprob_seroprev_time_by_ageprobability_exact_age_varyingprobability_exact_time_varyingset_foi_initset_stan_data_defaultssf_cauchysf_nonesf_normalsf_uniformsimulate_serosurveysimulate_serosurvey_agesimulate_serosurvey_age_timesimulate_serosurvey_generalsimulate_serosurvey_timesummarise_central_estimatesummarise_loo_estimatesummarise_seromodel

Dependencies:abindbackportsbayesplotBHcallrcheckmateclicolorspaceconfigcowplotcpp11descdistributionaldplyrfansifarvergenericsggplot2ggridgesgluegridExtragtableinlineisobandlabelinglatticelifecycleloomagrittrMASSMatrixmatrixStatsmgcvmunsellnlmenumDerivpillarpkgbuildpkgconfigplyrposteriorprocessxpspurrrQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelreshape2rlangrstanrstantoolsscalesStanHeadersstringistringrtensorAtibbletidyrtidyselectutf8vctrsviridisLitewithryaml

An introduction to serofoi

Rendered fromserofoi.Rmdusingknitr::rmarkdownon Feb 19 2025.

Last update: 2025-02-19
Started: 2023-03-22

Readme and manuals

Help Manual

Help pageTopics
The 'serofoi' package.serofoi-package serofoi
Adds age group marker to serosurveyadd_age_group_to_serosurvey
Builds stan data for sampling depending on the selected modelbuild_stan_data
Chagas seroprevalence data in serofoichagas2012
Chikungunya seroprevalence data in serofoichik2015
Extracts central estimates from stan_fit object for specified parameterextract_central_estimates
Runs specified stan model for the Force-of-Infection (FoI)fit_seromodel
Generates Force-of-Infection indexes for heterogeneous age groupsget_foi_index
Plots Force-of-Infection central estimatesplot_foi_estimates
Plot r-hats convergence criteria for the specified modelplot_rhats
Visualise results of the provided modelplot_seromodel
Plot seroprevalence estimates on top of the serosurveyplot_seroprev_estimates
Plots seroprevalence from the given serosurveyplot_serosurvey
Plots model summaryplot_summary
Prepares serosurvey for plottingprepare_serosurvey_for_plot
Generate probabilities of seropositivity by age based on an age-varying Force-of-Infection (FoI) model.prob_seroprev_age_by_age
Generate probabilities of seropositivity by age based on an age-and-time varying Force-of-Infection (FoI) model.prob_seroprev_age_time_by_age
Generate probabilities of seropositivity by age based on model choice.prob_seroprev_by_age
Generate probabilities of seropositivity by age based on a general Force-of-Infection (FoI) model.prob_seroprev_gen_by_age
Generate probabilities of seropositivity by age based on a time-varying Force-of-Infection (FoI) model.prob_seroprev_time_by_age
Computes the probability of being seropositive when Forces-of-Infection (FoIs) vary by ageprobability_exact_age_varying
Computes the probability of being seropositive when Forces-of-Infection (FoIs) vary by timeprobability_exact_time_varying
Sets initialization function for samplingset_foi_init
Set stan data defaults for samplingset_stan_data_defaults
Sets Cauchy distribution parameters for samplingsf_cauchy
Sets empty prior distributionsf_none
Sets normal distribution parameters for samplingsf_normal
Sets uniform distribution parameters for samplingsf_uniform
Simulate serosurvey data based on various Force-of-Infection (FoI) models.simulate_serosurvey
Simulate serosurvey data based on an age-varying Force-of-Infection (FoI) model.simulate_serosurvey_age
Simulate serosurvey data based on an age-and-time-varying Force-of-Infection (FoI) model.simulate_serosurvey_age_time
Simulate serosurvey data based on general serocatalytic model.simulate_serosurvey_general
Simulate serosurvey data based on a time-varying Force-of-Infection (FoI) model.simulate_serosurvey_time
Summarise central estimatesummarise_central_estimate
Extract specified loo estimatesummarise_loo_estimate
Summarise specified modelsummarise_seromodel
Venezuelan Equine Encephalitis Virus (VEEV) seroprevalence data in serofoiveev2012