Package: serocalculator 1.4.1.9046

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]

# 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

Datasets:

example_noise_params_pk - Small example of noise parameters for typhoid
example_noise_params_sees - Small example of noise parameters for typhoid
sees_pop_data_100 - Small example cross-sectional data set
sees_pop_data_pk_100 - Small example cross-sectional data set
sees_typhoid_ests_strat - Example '"seroincidence.by"' object
typhoid_curves_nostrat_100 - Small example of antibody response curve parameters for typhoid

On CRAN:

epidemiology incidence-estimation seroepidemiology

6.52 score 7 stars 1 packages 17 scripts 518 downloads 53 exports 74 dependencies

Last updated from:108f56aab8. Checks:15 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	273
linux-devel-x86_64	OK	308
source / vignettes	OK	258
linux-release-arm64	OK	287
linux-release-x86_64	OK	359
macos-release-arm64	OK	249
macos-release-x86_64	OK	302
macos-oldrel-arm64	OK	230
macos-oldrel-x86_64	OK	341
windows-devel-arm64	OK	589
windows-devel-x86_64	OK	401
windows-release-arm64	OK	543
windows-release-x86_64	OK	351
windows-oldrel-x86_64	OK	346
wasm-release	OK	160

Exports:ab_5p analyze_sims antibody_decay_curve as_curve_params as_noise_params as_pop_data as_sr_params autoplot check_pop_data compare_seroincidence count_strata curve_app est_seroincidence est_seroincidence_by est_seroincidence_by_cached est.incidence est.incidence.by expect_snapshot_data f_dev f_dev0 fdev get_biomarker_levels get_biomarker_names get_biomarker_names_var get_values get_values_var graph_loglik graph_seroresponse_model_1 graph.curve.params ids ids_varname llik load_curve_params load_noise_params load_pop_data load_sr_params log_likelihood pathogen_decay_curve plot_decay_curve refit_strata serocalculator_example set_id_var sim_pop_data sim_pop_data_2 sim_pop_data_multi sim_pop_data_multi_cached sim.cs sim.cs.multi strat_ests_barplot strat_ests_scatterplot strata t1f y1f

Dependencies:and base64enc bit bit64 bslib cachem cli clipr codetools commonmark cpp11 crayon digest doParallel dplyr farver fastmap fontawesome forcats foreach fs generics ggplot2 glue gtable haven hms htmltools httpuv isoband iterators jquerylib jsonlite labeling labelled later lifecycle magrittr memoise mime otel patchwork pillar pkgconfig prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp readr rlang rngtools S7 sass scales shiny sourcetools stringi stringr tibble tidyr tidyselect tzdb units utf8 vctrs viridisLite vroom withr xfun xtable

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Analyze simulation results	analyze_sims
Antibody decay curve with natural parameters	antibody_decay_curve
Load noise parameters	as_noise_params
Load a cross-sectional antibody survey data set	as_pop_data
Load longitudinal seroresponse parameters	as_sr_params
Graph antibody decay curves by antigen isotype	autoplot.curve_params
Plot distribution of antibodies	autoplot.pop_data
Plot the log-likelihood curve for the incidence rate estimate	autoplot.seroincidence
Plot 'seroincidence.by' log-likelihoods	autoplot.seroincidence.by
Plot simulation results 'autoplot()' method for 'sim_results' objects	autoplot.sim_results
Plot method for 'summary.seroincidence.by' objects	autoplot.summary.seroincidence.by
Check the formatting of a cross-sectional antibody survey dataset.	check_pop_data
Compare seroincidence rates between two groups	compare_seroincidence compare_seroincidence.seroincidence compare_seroincidence.seroincidence.by
Launch the interactive Shiny app for the antigen-antibody kinetics model	curve_app
Find the maximum likelihood estimate of the incidence rate parameter	est_seroincidence
Estimate Seroincidence	est_seroincidence_by
Estimate seroincidence by stratum, caching the result on disk	est_seroincidence_by_cached
Small example of noise parameters for typhoid	example_noise_params_pk
Small example of noise parameters for typhoid	example_noise_params_sees
Extract biomarker levels	get_biomarker_levels
Get biomarker variable name	get_biomarker_names_var
Get antibody measurement values	get_values
Extract antibody measurement values	get_values_var
Graph log-likelihood of data	graph_loglik
Graph estimated antibody decay curves	graph.curve.params
Load noise parameters	load_noise_params
Load a cross-sectional antibody survey data set	load_pop_data
Load longitudinal seroresponse parameter samples	load_sr_params
Calculate log-likelihood	log_likelihood
Pathogen decay curve	pathogen_decay_curve
Plot a decay function	plot_decay_curve
Re-fit a subset of strata, with log-likelihood graphs attached	refit_strata
Small example cross-sectional data set	sees_pop_data_100
Small example cross-sectional data set	sees_pop_data_pk_100
Example '"seroincidence.by"' object	sees_typhoid_ests_strat
Get path to an example file	serocalculator_example
Simulate a cross-sectional serosurvey with noise	sim_pop_data
Simulate multiple data sets	sim_pop_data_multi
Simulate multiple data sets, caching the result on disk	sim_pop_data_multi_cached
Extract 'Strata' metadata from an object	strata
Summarizing fitted seroincidence models	summary.seroincidence
Summary Method for '"seroincidence.by"' Objects	summary.seroincidence.by
Small example of antibody response curve parameters for typhoid	typhoid_curves_nostrat_100