Model Infectious Disease Parameters from Serosurveys

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Documentation for package ‘serosv’ version 1.1.0

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serosv-package serosv: model infectious disease parameters
compare_models Compare models
compute_ci Compute confidence interval
compute_ci.fp_model Compute confidence interval for fractional polynomial 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 Bayesian estimation
estimate_from_mixture Estimate seroprevalence and foi by combining mixture model and regression
est_foi Estimate force of infection
farrington_model The Farrington (1990) model.
find_best_fp_powers Returns the powers of the GLM fitted 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
mseir_model MSEIR model
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.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.mseir_model plot() overloading for MSEIR model
plot.penalized_spline_model plot() overloading for penalized spline
plot.polynomial_model plot() overloading for polynomial model
plot.sir_basic_model plot() overloading for SIR model
plot.sir_static_model plot() overloading for SIR static model
plot.sir_subpops_model plot() overloading for SIR sub populations model
plot.weibull_model plot() overloading for Weibull model
plot_gcv Plotting GCV values with respect to different nn-s and h-s parameters.
polynomial_model Polynomial models
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
sir_basic_model Basic SIR model
sir_static_model SIR static model (age-heterogeneous, endemic equilibrium)
sir_subpops_model SIR Model with Interacting Subpopulations
tb_nl_1966_1973 Tuberculosis serological data from the Netherlands 1966-1973 (aggregated)
transform_data Generate a dataframe with 't', 'pos' and 'tot' columns from 't' and 'seropositive' vectors.
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.