Package: serocalculator 1.2.0.9022

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'))

Peer review:

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

Datasets:

On CRAN:

5.31 score 4 stars 10 scripts 122 downloads 21 exports 110 dependencies

Last updated 7 days agofrom:84bb2f7f7d. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 16 2024
R-4.5-win-x86_64NOTENov 16 2024
R-4.5-linux-x86_64NOTENov 16 2024
R-4.4-win-x86_64NOTENov 16 2024
R-4.4-mac-x86_64NOTENov 16 2024
R-4.4-mac-aarch64NOTENov 16 2024
R-4.3-win-x86_64NOTENov 16 2024
R-4.3-mac-x86_64NOTENov 16 2024
R-4.3-mac-aarch64NOTENov 16 2024

Exports:as_curve_paramsas_noise_paramsas_pop_dataautoplotcheck_pop_dataest.incidenceest.incidence.byf_devf_dev0fdevget_additional_datagetAdditionalDatagraph_loglikgraph.curve.paramsllikload_curve_paramsload_noise_paramsload_pop_datalog_likelihoodsim.cssim.cs.multi

Dependencies:abindandaskpassbackportsbase64encbootbroombslibcachemcarcarDataclicodetoolscolorspacecorrplotcowplotcpp11crosstalkcurldata.tableDerivdigestdoBydoParalleldplyrevaluatefansifarverfastmapfontawesomeforeachFormulafsgenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehighrhtmltoolshtmlwidgetshttrisobanditeratorsjquerylibjsonlitekernlabknitrlabelinglaterlatticelazyevallifecyclelme4magrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamixtoolsmodelrmunsellnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplotlypolynompromisespurrrquantregR6rappdirsRColorBrewerRcppRcppEigenrlangrmarkdownrngtoolsrstatixsassscalessegmentedSparseMstringistringrsurvivalsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Extract or replace parts of a 'seroincidence.by' object[.seroincidence.by
kinetics of the antibody (ab) response (power function decay)ab
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
Get Additional Dataget_additional_data
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
generate random sample from baseline distributionmk_baseline
Graph an antibody decay curve modelplot_curve_params_one_ab
Print Method for 'seroincidence' Objectprint.seroincidence
Print Method for 'seroincidence.by' Objectprint.seroincidence.by
Print Method for Seroincidence Summary Objectprint.summary.seroincidence.by
extract a row from longitudinal parameter setrow_longitudinal_parameter
Small example cross-sectional data setsees_pop_data_pk_100
Small example cross-sectional data setsees_pop_data_pk_100_old_names
Estimating Infection Rates from Serological Dataserocalculator-package serocalculator
Simulate a cross-sectional serosurvey with noisesim.cs
Simulate multiple data setssim.cs.multi
collect cross-sectional datasimcs.tinf
simulate antibody kinetics of y over a time intervalsimresp.tinf
Extract strata from an objectstrata
Extract the 'Strata' attribute from an object, if presentstrata.seroincidence.by
Summarize cross-sectional antibody survey dataprint.summary.pop_data summary.pop_data
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
Warn about missing stratifying variables in a datasetwarn.missing.strata