Package: serofoi 1.0.2

Zulma M. Cucunubá

serofoi: Estimates the Force-of-Infection of a Given Pathogen from Population Based Seroprevalence Studies

Estimate time or age varying Force-of-Infection from population based seroprevalence studies using a bayesian framework.

Authors:Zulma M. Cucunubá [aut, cre], Nicolás T. Domínguez [aut], Ben Lambert [aut], Pierre Nouvellet [aut], Miguel Gámez [ctb], Geraldine Gómez [ctb], Jaime A. Pavlich-Mariscal [ctb]

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NEWS

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

Peer review:

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

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

6.11 score 17 stars 10 scripts 24 exports 98 dependencies

Last updated 1 months agofrom:1630c70e2e. Checks:1 OK, 8 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 10 2025
R-4.5-win-x86_64WARNINGJan 10 2025
R-4.5-linux-x86_64WARNINGJan 10 2025
R-4.4-win-x86_64WARNINGJan 10 2025
R-4.4-mac-x86_64WARNINGJan 10 2025
R-4.4-mac-aarch64WARNINGJan 10 2025
R-4.3-win-x86_64WARNINGJan 10 2025
R-4.3-mac-x86_64WARNINGJan 10 2025
R-4.3-mac-aarch64WARNINGJan 10 2025

Exports:build_stan_dataextract_central_estimatesfit_seromodelget_foi_indexplot_foi_estimatesplot_rhatsplot_seromodelplot_seroprevalence_estimatesplot_serosurveyplot_summaryprobability_seropositive_by_ageprobability_seropositive_general_model_by_ageset_foi_initsf_cauchysf_normalsf_uniformsimulate_serosurveysimulate_serosurvey_age_and_time_modelsimulate_serosurvey_age_modelsimulate_serosurvey_general_modelsimulate_serosurvey_time_modelsummarise_central_estimatesummarise_loo_estimatesummarise_seromodel

Dependencies:abindbackportsbase64encbayesplotBHbslibcachemcallrcheckmatecliclustercolorspaceconfigcowplotcpp11data.tabledescdigestdistributionaldplyrevaluatefansifarverfastmapfontawesomeforeignFormulafsgenericsggplot2ggridgesgluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetsinlineisobandjquerylibjsonliteknitrlabelinglatticelifecycleloomagrittrMASSMatrixmatrixStatsmemoisemgcvmimemunsellnlmennetnumDerivpillarpkgbuildpkgconfigplyrposteriorprocessxpspurrrQuickJSRR6rappdirsRColorBrewerRcppRcppEigenRcppParallelreshape2rlangrmarkdownrpartrstanrstantoolsrstudioapisassscalesStanHeadersstringistringrtensorAtibbletidyrtidyselecttinytexutf8vctrsviridisviridisLitewithrxfunyaml

An introduction to serofoi

Rendered fromserofoi.Rmdusingknitr::rmarkdownon Jan 10 2025.

Last update: 2024-12-10
Started: 2023-03-22

Readme and manuals

Help Manual

Help pageTopics
The 'serofoi' package.serofoi-package serofoi
Add bins based on age intervals.add_age_bins
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-infectionfit_seromodel
Generate random sample sizes for each age group.generate_random_sample_sizes
Construct age-group variable from age columnget_age_intervals
Generates force-of-infection indexes for heterogeneous age groupsget_foi_index
Generate random sample sizes using multinomial sampling.multinomial_sampling_group
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_seroprevalence_estimates
Plots seroprevalence from the given serosurveyplot_serosurvey
Plots model summaryplot_summary
Prepares serosurvey for plottingprepare_serosurvey_for_plotting
Computes the probability of being seropositive when FOIs vary by ageprobability_exact_age_varying
Computes the probability of being seropositive when FOIs vary by timeprobability_exact_time_varying
Generate probabilities of seropositivity by age based on an age-and-time varying FOI model.probability_seropositive_age_and_time_model_by_age
Generate probabilities of seropositivity by age based on an age-varying FOI model.probability_seropositive_age_model_by_age
Generate probabilities of seropositivity by age based user's choice of model.probability_seropositive_by_age
Generate probabilities of seropositivity by age based on a general FOI model.probability_seropositive_general_model_by_age
Generate probabilities of seropositivity by age based on a time-varying FOI model.probability_seropositive_time_model_by_age
Generate random sample sizes for each individual age based on survey features.sample_size_by_individual_age_random
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 distributionsf_none
Sets normal distribution parameters for samplingsf_normal
Sets uniform distribution parameters for samplingsf_uniform
Simulate serosurvey data based on various FOI models.simulate_serosurvey
Simulate serosurvey data based on an age-and-time-varying FOI model.simulate_serosurvey_age_and_time_model
Simulate serosurvey data based on an age-varying FOI model.simulate_serosurvey_age_model
Simulate serosurvey data based on general serocatalytic model.simulate_serosurvey_general_model
Simulate serosurvey data based on a time-varying FOI model.simulate_serosurvey_time_model
Summarise central estimatesummarise_central_estimate
Extract specified loo estimatesummarise_loo_estimate
Summarise specified modelsummarise_seromodel
Create a survey dataframe with per individual age information.survey_by_individual_age
Venezuelan Equine Encephalitis Virus (VEEV) seroprevalence data in serofoiveev2012