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rprev

rprev estimates disease prevalence at a specified index date from registry data. To improve the estimate accuracy, Monte Carlo simulation techniques are used to simulate incident cases in years for which incidence data is unavailable. Disease survival is modelled with parametric Weibull regression. See the user_guide vignette for more details about the implementation, and the original publication for details of the algorithm, available at http://www.ncbi.nlm.nih.gov/pubmed/24656754.

Installation

To install from CRAN, simply use install.packages('rprev'). The code is currently not available elsewhere.

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Version

Install

install.packages('rprev')

Monthly Downloads

250

Version

0.2.3

License

GPL-2

Maintainer

Stuart Lacy

Last Published

February 13th, 2017

Functions in rprev (0.2.3)

test_prevalence_fit

Test simulated prevalence fit.
UKmortality

General population survival data.
incidence

Summarise disease incidence.
summary.survfit.prev

Obtain N-year survival probability estimates.
yearly_incidence

Disease incidence.
raw_incidence

DEPRECATED: Please use yearly_incidence instead.
prevalence_counted

Count prevalence from registry data.
population_survival_rate

Transform yearly mortality rates to daily.
mean_incidence_rate

Mean disease incidence.
prevsim

Simulated patient dataset.
prevalence_simulated

Estimate prevalence using Monte Carlo simulation.
prevalence

Estimate point prevalence at an index date.
test_incidence_fit

Test homogeneous Poisson assumption of disease incidence.
plot.survfit.prev

Plot bootstrapped survival curves.
functional_form_age

View the suitability of a linear effect of age on hazard.
plot.incidence

Visualise disease incidence.
incidence_age_distribution

Plot the age distribution of incident cases.
rprev

rprev: Estimate disease point prevalence using a combination of registry data and Monte Carlo simulations.
determine_yearly_endpoints

Determine annual event delimiters.
survfit.prevalence

Form bootstrapped survival curves.
determine_registry_years

DEPRECATED: Use determine_yearly_endpoints instead.