Package: serocalculator 1.3.0.9029

Kristina Lai

serocalculator: Estimating Infection Rates from Serological Data

Translates antibody levels measured in cross-sectional population samples into estimates of the frequency with which seroconversions (infections) occur in the sampled populations. Replaces the previous `seroincidence` package.

Authors:Peter Teunis [aut, cph], Kristina Lai [aut, cre], Chris Orwa [aut], Kristen Aiemjoy [aut], Douglas Ezra Morrison [aut]

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

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

Bug tracker:https://github.com/ucd-serg/serocalculator/issues

Pkgdown site:https://ucd-serg.github.io

Datasets:

On CRAN:

epidemiologyincidence-estimationseroepidemiology

5.55 score 5 stars 14 scripts 358 downloads 31 exports 113 dependencies

Last updated 18 hours agofrom:0d75631b61. Checks:11 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 18 2025
R-4.5-win-x86_64OKFeb 18 2025
R-4.5-mac-x86_64OKFeb 18 2025
R-4.5-mac-aarch64OKFeb 18 2025
R-4.5-linux-x86_64OKFeb 18 2025
R-4.4-win-x86_64OKFeb 18 2025
R-4.4-mac-x86_64OKFeb 18 2025
R-4.4-mac-aarch64OKFeb 18 2025
R-4.3-win-x86_64OKFeb 18 2025
R-4.3-mac-x86_64OKFeb 18 2025
R-4.3-mac-aarch64OKFeb 18 2025

Exports:as_curve_paramsas_noise_paramsas_pop_dataautoplotcheck_pop_dataest.incidenceest.incidence.byf_devf_dev0fdevget_biomarker_levelsget_biomarker_namesget_biomarker_names_varget_valuesget_values_vargraph_loglikgraph.curve.paramsidsids_varnamellikload_curve_paramsload_noise_paramsload_pop_datalog_likelihoodserocalculator_exampleset_id_varsim_pop_datasim_pop_data_multisim.cssim.cs.multistrata

Dependencies:abindandaskpassbackportsbase64encbootbroombslibcachemcarcarDataclicodetoolscolorspacecorrplotcowplotcpp11crosstalkcurldata.tableDerivdigestdoBydoParalleldplyrevaluatefansifarverfastmapfontawesomeforeachFormulafsgenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehighrhtmltoolshtmlwidgetshttrisobanditeratorsjquerylibjsonlitekernlabknitrlabelinglaterlatticelazyevallifecyclelme4magrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamixtoolsmodelrmunsellnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplotlypolynompromisespurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRdpackreformulasrlangrmarkdownrngtoolsrstatixsassscalessegmentedSparseMstringistringrsurvivalsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Load antibody decay curve parameteras_curve_params
Load noise parametersas_noise_params
Load a cross-sectional antibody survey data setas_pop_data
graph antibody decay curves by antigen isotypeautoplot.curve_params
Plot distribution of antibodiesautoplot.pop_data
Plot the log-likelihood curve for the incidence rate estimateautoplot.seroincidence
Plot 'seroincidence.by' log-likelihoodsautoplot.seroincidence.by
Plot method for 'summary.seroincidence.by' objectsautoplot.summary.seroincidence.by
Check the formatting of a cross-sectional antibody survey dataset.check_pop_data
Find the maximum likelihood estimate of the incidence rate parameterest.incidence
Estimate Seroincidenceest.incidence.by
Small example of noise parameters for typhoidexample_noise_params_pk
Small example of noise parameters for typhoidexample_noise_params_sees
Extract biomarker levelsget_biomarker_levels
Get biomarker variable nameget_biomarker_names_var
Get antibody measurement valuesget_values
Extract antibody measurement valuesget_values_var
Graph log-likelihood of datagraph_loglik
Graph estimated antibody decay curvegraph.curve.params
Load antibody decay curve parameter samplesload_curve_params
Load noise parametersload_noise_params
Load a cross-sectional antibody survey data setload_pop_data
Calculate log-likelihoodlog_likelihood
Small example cross-sectional data setsees_pop_data_100
Small example cross-sectional data setsees_pop_data_pk_100
Get path to an example fileserocalculator_example
Simulate a cross-sectional serosurvey with noisesim_pop_data
Simulate multiple data setssim_pop_data_multi
Extract strata from an objectstrata
Summarizing fitted seroincidence modelssummary.seroincidence
Summary Method for '"seroincidence.by"' Objectssummary.seroincidence.by
Small example of antibody response curve parameters for typhoidtyphoid_curves_nostrat_100