Package: serocalculator 1.0.3

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. Methods originally published in Simonsen et al. (2009) <doi:10.1002/sim.3592> and Teunis et al. (2012) <doi:10.1002/sim.5322>, and further developed in subsequent publications by de Graaf et al. (2014) <doi:10.1016/j.epidem.2014.08.002>, Teunis et al. (2016) <doi:10.1016/j.epidem.2016.04.001>, and Teunis et al. (2020) <doi:10.1002/sim.8578>.

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

serocalculator_1.0.3.tar.gz
serocalculator_1.0.3.tar.gz(r-4.5-noble)serocalculator_1.0.3.tar.gz(r-4.4-noble)
serocalculator_1.0.3.tgz(r-4.4-emscripten)serocalculator_1.0.3.tgz(r-4.3-emscripten)
serocalculator.pdf |serocalculator.html✨
serocalculator/json (API)
NEWS

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

Peer review:

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

16 exports 0.09 score 108 dependencies 7 scripts 189 downloads

Last updated 2 months agofrom:ddad74d1e0. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKAug 21 2024
R-4.5-linux-x86_64OKAug 21 2024

Exports:check_pop_dataclean_pop_dataest.incidenceest.incidence.byf_devfdevgraph.curve.paramsgraph.loglikllikload_curve_paramsload_noise_paramsload_pop_datalog_likelihoodplot_curve_params_one_absim.cssim.cs.multi

Dependencies:abindaskpassbackportsbase64encbootbroombslibcachemcarcarDataclicodetoolscolorspacecorrplotcowplotcpp11crosstalkcurldata.tableDerivdigestdoBydoParalleldplyrevaluatefansifarverfastmapfontawesomeforeachfsgenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehighrhtmltoolshtmlwidgetshttrisobanditeratorsjquerylibjsonlitekernlabknitrlabelinglaterlatticelazyevallifecyclelme4magrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamixtoolsmodelrmunsellnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplotlypolynompromisespurrrquantregR6rappdirsRColorBrewerRcppRcppEigenrlangrmarkdownrngtoolsrstatixsassscalessegmentedSparseMstringistringrsurvivalsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml

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
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
Reformat a cross-sectional antibody survey datasetclean_pop_data
Convert a data.frame (or tibble) into a multidimensional arraydf_to_array
Find the maximum likelihood estimate of the incidence rate parameterest.incidence
Estimate Seroincidenceest.incidence.by
Graph estimated antibody decay curvegraph.curve.params
Graph log-likelihood of datagraph.loglik
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
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 a cross-sectional antibody survey data setsummary.pop_data
Summarizing fitted seroincidence modelssummary.seroincidence
Summary Method for '"seroincidence.by"' Objectssummary.seroincidence.by
Warn about missing stratifying variables in a datasetwarn.missing.strata