Package: serofoi 0.1.0

Zulma M. Cucunubá

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

Estimate time-varying Force-of-Infection of a given pathogen 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:

On CRAN:

antibodiesbayesian-methodsepidemiologyepiverseserological-surveysstan-language

6.76 score 17 stars 12 scripts 19 exports 95 dependencies

Last updated 3 months agofrom:a608a0ddd2. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 05 2024
R-4.5-win-x86_64NOTENov 05 2024
R-4.5-linux-x86_64NOTENov 05 2024
R-4.4-win-x86_64NOTENov 05 2024
R-4.4-mac-x86_64NOTENov 05 2024
R-4.4-mac-aarch64NOTENov 05 2024
R-4.3-win-x86_64NOTENov 05 2024
R-4.3-mac-x86_64NOTENov 05 2024
R-4.3-mac-aarch64NOTENov 05 2024

Exports:extract_seromodel_summaryfit_seromodelgenerate_sim_dataget_chunk_structureget_cohort_agesget_foi_central_estimatesget_prev_expandedget_sim_n_seropositiveget_sim_probabilityget_table_rhatsgroup_sim_dataplot_foiplot_info_tableplot_rhatsplot_seromodelplot_seroprevplot_seroprev_fittedprepare_serodatarun_seromodel

Dependencies:abindbackportsbase64encbayesplotBHbslibcachemcallrcheckmatecliclustercolorspacecowplotdata.tabledescdigestdistributionaldplyrevaluatefansifarverfastmapfontawesomeforeignFormulafsgenericsggplot2ggridgesgluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetsinlineisobandjquerylibjsonliteknitrlabelinglatticelifecycleloomagrittrMASSMatrixmatrixStatsmemoisemgcvmimemunsellnlmennetnumDerivpillarpkgbuildpkgconfigplyrposteriorprocessxpspurrrQuickJSRR6rappdirsRColorBrewerRcppRcppEigenRcppParallelreshape2rlangrmarkdownrpartrstanrstantoolsrstudioapisassscalesStanHeadersstringistringrtensorAtibbletidyselecttinytexutf8vctrsviridisviridisLitewithrxfunyaml

An introduction to Force-of-Infection (FoI) Models

Rendered fromfoi_models.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2024-04-30
Started: 2023-04-04

An introduction to serofoi

Rendered fromserofoi.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2024-04-30
Started: 2023-03-22

Real-life use cases for serofoi

Rendered fromuse_cases.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2024-04-30
Started: 2023-03-22

Readme and manuals

Help Manual

Help pageTopics
The 'serofoi' package.serofoi-package serofoi
Seroprevalence data on serofoichagas2012
Seroprevalence data on serofoichik2015
Function to extract a summary of the specified serological model objectextract_seromodel_summary
Fit selected model to the specified seroprevalence survey datafit_seromodel
Generate simulated serosurvey according to the specified FoIgenerate_sim_data
Construct age-group variable from age columnget_age_group
Generate list containing the chunk structure to be used in the retrospective estimation of the force of infection.get_chunk_structure
Generate data frame containing the age of each cohort corresponding to each birth year excluding the year of the survey.get_cohort_ages
Extract central estimates for the fitted forced FoIget_foi_central_estimates
Generate data frame containing the confidence interval based on a force-of-infection fittingget_prev_expanded
Generate sample of counts of seropositive individuals by sampling from a binomial distributionget_sim_n_seropositive
Generate probabilities of being previously exposed to a pathogen given a historical force-of-infection.get_sim_probability
Build dataframe containing the R-hat estimates for a given serological modelget_table_rhats
Group simulated serological dataset by agegroup_sim_data
Generate force-of-infection plot corresponding to the specified fitted serological modelplot_foi
Generate plot summarizing a given tableplot_info_table
Generate plot of the R-hat estimates for the specified fitted serological modelplot_rhats
Generate vertical arrangement of plots showing a summary of a model, the estimated seroprevalence, the force-of-infection fit and the R-hat estimates plots.plot_seromodel
Generate seropositivity plot from a raw serological survey datasetplot_seroprev
Generate seropositivity plot corresponding to the specified fitted serological modelplot_seroprev_fitted
Prepare data from a serological survey for modellingprepare_serodata
Returns the probability of being seropositive for age-varying force-of-infection including seroreversionprobability_exact_age_varying
Computes the probability of being seropositive for age-varying force-of-infection including seroreversionprobability_exact_time_varying
Run specified stan model for the force-of-infection and estimate the seroprevalence based on the result of the fitrun_seromodel
Constant force-of-infection simulated serosurveysimdata_constant
Large epidemic simulated serosurveysimdata_large_epi
Step-wise decreasing force-of-infection simulated serosurveysimdata_sw_dec
Seroprevalence data on serofoiveev2012