Model Infectious Disease Parameters from Serosurveys

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Documentation for package ‘serosv’ version 1.3.0

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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.