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Package: serofoi 1.0.3

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]

serofoi_1.0.3.tar.gz
serofoi_1.0.3.zip(r-4.7-x86_64)serofoi_1.0.3.zip(r-4.7-arm64)serofoi_1.0.3.zip(r-4.6-x86_64)serofoi_1.0.3.zip(r-4.6-arm64)
serofoi_1.0.3.tar.gz(r-4.7-arm64)serofoi_1.0.3.tar.gz(r-4.7-x86_64)serofoi_1.0.3.tar.gz(r-4.6-arm64)serofoi_1.0.3.tar.gz(r-4.6-x86_64)
serofoi_1.0.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
serofoi/json (API)

# Install 'serofoi' in R:

install.packages('serofoi', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

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

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

Uses libs:

onetbb– Parallelism library for C++
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:

onetbb cpp

3.29 score 39 scripts 220 downloads 33 exports 66 dependencies

Last updated from:beb5bc6ffe. Checks:10 OK. Indexed: no.

Target	Result	Time
linux-devel-arm64	OK	464
linux-devel-x86_64	OK	498
source / vignettes	OK	909
linux-release-arm64	OK	482
linux-release-x86_64	OK	412
windows-devel-arm64	OK	620
windows-devel-x86_64	OK	544
windows-release-arm64	OK	577
windows-release-x86_64	OK	760
wasm-release	OK	308

Exports:add_age_group_to_serosurvey build_stan_data extract_central_estimates fit_seromodel get_foi_index plot_foi_estimates plot_rhats plot_seromodel plot_seroprev_estimates plot_serosurvey plot_summary prepare_serosurvey_for_plot prob_seroprev_age_by_age prob_seroprev_age_time_by_age prob_seroprev_by_age prob_seroprev_gen_by_age prob_seroprev_time_by_age probability_exact_age_varying probability_exact_time_varying set_foi_init set_stan_data_defaults sf_cauchy sf_none sf_normal sf_uniform simulate_serosurvey simulate_serosurvey_age simulate_serosurvey_age_time simulate_serosurvey_general simulate_serosurvey_time summarise_central_estimate summarise_loo_estimate summarise_seromodel

Dependencies:abind backports bayesplot BH callr checkmate cli config cowplot cpp11 desc distributional dplyr expm farver generics ggdist ggplot2 ggridges glue gridExtra gtable inline isoband labeling lattice lifecycle loo magrittr Matrix matrixStats numDeriv otel pillar pkgbuild pkgconfig plyr posterior processx ps purrr quadprog QuickJSR R6 RColorBrewer Rcpp RcppEigen RcppParallel reshape2 rlang rstan rstantools S7 scales StanHeaders stringi stringr tensorA tibble tidyr tidyselect utf8 vctrs viridisLite withr yaml

An introduction to serofoi

Rendered fromserofoi.Rmdusingknitr::rmarkdown

Last update: 2025-03-31
Started: 2025-03-31

Help page	Topics
The 'serofoi' package.	serofoi-package serofoi
Adds age group marker to serosurvey	add_age_group_to_serosurvey
Builds stan data for sampling depending on the selected model	build_stan_data
Chagas seroprevalence data in serofoi	chagas2012
Chikungunya seroprevalence data in serofoi	chik2015
Extracts central estimates from stan_fit object for specified parameter	extract_central_estimates
Runs specified stan model for the Force-of-Infection (FoI)	fit_seromodel
Generates Force-of-Infection indexes for heterogeneous age groups	get_foi_index
Plots Force-of-Infection central estimates	plot_foi_estimates
Plot r-hats convergence criteria for the specified model	plot_rhats
Visualise results of the provided model	plot_seromodel
Plot seroprevalence estimates on top of the serosurvey	plot_seroprev_estimates
Plots seroprevalence from the given serosurvey	plot_serosurvey
Plots model summary	plot_summary
Prepares serosurvey for plotting	prepare_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 age	probability_exact_age_varying
Computes the probability of being seropositive when Forces-of-Infection (FoIs) vary by time	probability_exact_time_varying
Sets initialization function for sampling	set_foi_init
Set stan data defaults for sampling	set_stan_data_defaults
Sets Cauchy distribution parameters for sampling	sf_cauchy
Sets empty prior distribution	sf_none
Sets normal distribution parameters for sampling	sf_normal
Sets uniform distribution parameters for sampling	sf_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 estimate	summarise_central_estimate
Extract specified loo estimate	summarise_loo_estimate
Summarise specified model	summarise_seromodel
Venezuelan Equine Encephalitis Virus (VEEV) seroprevalence data in serofoi	veev2012

Package: serofoi 1.0.3

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

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)