R: Model Infectious Disease Parameters from Serosurveys

# Model Infectious Disease Parameters from Serosurveys

## Documentation for package ‘serosv’ version 1.3.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

serosv-package | serosv: model infectious disease parameters
add_thresholds | Visualize positive threshold at different dilution factors
age_time_model | Age-time varying seroprevalence
compare_models | Generate table of metrics for model comparison
compute_ci.age_time_model | Compute confidence interval for time age model
compute_ci.default | Compute confidence interval for a model of serosv
compute_ci.fp_model | Compute confidence interval for fractional polynomial model
compute_ci.hierarchical_bayesian_model | Compute 95% credible interval for hierarchical Bayesian model
compute_ci.lp_model | Compute confidence interval for local polynomial model
compute_ci.mixture_model | Compute confidence interval for mixture model
compute_ci.penalized_spline_model | Compute confidence interval for penalized_spline_model
compute_ci.weibull_model | Compute confidence interval for Weibull model
correct_prevalence | Estimate the true sero prevalence using Frequentist/Bayesian estimation
estimate_from_mixture | Estimate seroprevalence and FOI from a fixed mixture model
est_foi | Estimate force of infection
farrington_model | The Farrington (1990) model.
find_best_fp_powers | Returns the powers of the fractional polynomial model which has the lowest deviance score.
fp_model | A fractional polynomial model.
hav_be_1993_1994 | Hepatitis A serological data from Belgium in 1993 and 1994 (aggregated)
hav_be_2002 | Hepatitis A serological data from Belgium in 2002 (line listing)
hav_bg_1964 | Hepatitis A serological data from Bulgaria in 1964 (aggregated)
hbv_ru_1999 | Hepatitis B serological data from Russia in 1999 (aggregated)
hcv_be_2006 | Hepatitis C serological data from Belgium in 2006 (line listing)
hierarchical_bayesian_model | Hierarchical Bayesian Model
lp_model | A local polynomial model.
mixture_model | Fit a mixture model to classify serostatus
mumps_uk_1986_1987 | Mumps serological data from the UK in 1986 and 1987 (aggregated)
parvob19_be_2001_2003 | Parvo B19 serological data from Belgium from 2001-2003 (line listing)
parvob19_ew_1996 | Parvo B19 serological data from England and Wales in 1996 (line listing)
parvob19_fi_1997_1998 | Parvo B19 serological data from Finland from 1997-1998 (line listing)
parvob19_it_2003_2004 | Parvo B19 serological data from Italy from 2003-2004 (line listing)
parvob19_pl_1995_2004 | Parvo B19 serological data from Poland from 1995-2004 (line listing)
pava | Monotonize seroprevalence
penalized_spline_model | Penalized Spline model
plot.age_time_model | Plot output for age_time_model
plot.estimate_from_mixture | plot() overloading for result of estimate_from_mixture
plot.farrington_model | plot() overloading for Farrington model
plot.fp_model | plot() overloading for fractional polynomial model
plot.hierarchical_bayesian_model | plot() overloading for hierarchical_bayesian_model
plot.lp_model | plot() overloading for local polynomial model
plot.mixture_model | plot() overloading for mixture model
plot.penalized_spline_model | plot() overloading for penalized spline
plot.polynomial_model | plot() overloading for polynomial model
plot.weibull_model | plot() overloading for Weibull model
plot_corrected_prev | Plot output for corrected_prevalence
plot_gcv | Plotting GCV values with respect to different nn-s and h-s parameters.
plot_standard_curve | Visualize standard curves for each plate
plot_titer_qc | Quality control plot
polynomial_model | Polynomial models
predict.age_time_model | Predict from the age_time_mdoel
predict.farrington_model | Prediction for serosv Farrington model
predict.fp_model | Prediction for serosv fractional polynomial model
predict.hierarchical_bayesian_model | Predict from an hierarchical bayesian model
predict.lp_model | Prediction for serosv local polynomial model
predict.penalized_spline_model | Prediction for serosv penalized spline model
predict.polynomial_model | Prediction for serosv polynomial model
predict.weibull_model | Prediction for serosv Weibull model
rubella_mumps_uk | Rubella - Mumps data from the UK (aggregated)
rubella_uk_1986_1987 | Rubella serological data from the UK in 1986 and 1987 (aggregated)
serosv | serosv: model infectious disease parameters
set_plot_style | Helper to adjust styling of a plot
standardize_data | Standardize raw serological test data for titer conversion
tb_nl_1966_1973 | Tuberculosis serological data from the Netherlands 1966-1973 (aggregated)
to_titer | Convert assay readings to titers
transform_data | Aggregate data
vzv_be_1999_2000 | VZV serological data from Belgium (Flanders) from 1999-2000 (aggregated)
vzv_be_2001_2003 | VZV serological data from Belgium from 2001-2003 (line listing)
vzv_parvo_be | VZV and Parvovirus B19 serological data in Belgium (line listing)
weibull_model | The Weibull model.