Package: serocalculator 1.4.0.9014

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:Kristina Lai [aut, cre], Chris Orwa [aut], Kwan Ho Lee [ctb], Peter Teunis [aut, cph], Kristen Aiemjoy [aut], Douglas Ezra Morrison [aut]

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serocalculator_1.4.0.9014.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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/docs site:https://ucd-serg.github.io

Datasets:

On CRAN:

Conda:

epidemiologyincidence-estimationseroepidemiology

6.18 score 7 stars 1 packages 17 scripts 565 downloads 42 exports 51 dependencies

Last updated from:c2f516953f. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK227
linux-devel-x86_64OK255
source / vignettesOK251
linux-release-arm64OK246
linux-release-x86_64OK231
macos-release-arm64OK181
macos-release-x86_64OK476
macos-oldrel-arm64OK206
macos-oldrel-x86_64OK279
windows-develOK253
windows-releaseOK228
windows-oldrelOK301
wasm-releaseOK153

Exports:analyze_simsas_curve_paramsas_noise_paramsas_pop_dataas_sr_paramsautoplotcheck_pop_datacompare_seroincidencecount_strataest_seroincidenceest_seroincidence_byest.incidenceest.incidence.byexpect_snapshot_dataf_devf_dev0fdevget_biomarker_levelsget_biomarker_namesget_biomarker_names_varget_valuesget_values_vargraph_loglikgraph_seroresponse_model_1graph.curve.paramsidsids_varnamellikload_curve_paramsload_noise_paramsload_pop_dataload_sr_paramslog_likelihoodserocalculator_exampleset_id_varsim_pop_datasim_pop_data_multisim.cssim.cs.multistrat_ests_barplotstrat_ests_scatterplotstrata

Dependencies:andbitbit64clicliprcodetoolscpp11crayondigestdoParalleldplyrfarverforcatsforeachgenericsggplot2gluegtablehavenhmsisobanditeratorslabelinglabelledlifecyclemagrittrpatchworkpillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppreadrrlangrngtoolsS7scalesstringistringrtibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithr

Readme and manuals

Help Manual

Help pageTopics
Analyze simulation resultsanalyze_sims
Load noise parametersas_noise_params
Load a cross-sectional antibody survey data setas_pop_data
Load longitudinal seroresponse parametersas_sr_params
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 simulation results 'autoplot()' method for 'sim_results' objectsautoplot.sim_results
Plot method for 'summary.seroincidence.by' objectsautoplot.summary.seroincidence.by
Check the formatting of a cross-sectional antibody survey dataset.check_pop_data
Compare seroincidence rates between two groupscompare_seroincidence compare_seroincidence.seroincidence compare_seroincidence.seroincidence.by
Find the maximum likelihood estimate of the incidence rate parameterest_seroincidence
Estimate Seroincidenceest_seroincidence_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 curvesgraph.curve.params
Load noise parametersload_noise_params
Load a cross-sectional antibody survey data setload_pop_data
Load longitudinal seroresponse parameter samplesload_sr_params
Calculate log-likelihoodlog_likelihood
Small example cross-sectional data setsees_pop_data_100
Small example cross-sectional data setsees_pop_data_pk_100
Example '"seroincidence.by"' objectsees_typhoid_ests_strat
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' metadata 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