rprev: Estimating Disease Prevalence from Registry Data

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Estimates disease prevalence for a given index date, using existing registry data extended with Monte Carlo simulations.

Author
Simon Crouch [aut], Stephanie Lax [aut], Stuart Lacy [cre, aut]
Date of publication
2016-09-02 22:45:26
Maintainer
Stuart Lacy <stuart.lacy@york.ac.uk>
License
GPL-2
Version
0.2.2
URLs

View on CRAN

Man pages

determine_registry_years
Calculate yearly dates.
functional_form_age
View the suitability of a linear effect of age on hazard.
incidence
Summarise disease incidence.
incidence_age_distribution
Plot the age distribution of incident cases.
mean_incidence_rate
Mean disease incidence.
plot.incidence
Visualise disease incidence.
plot.survfit.prev
Plot bootstrapped survival curves.
population_survival_rate
Transform yearly mortality rates to daily.
prevalence
Estimate point prevalence at an index date.
prevalence_counted
Count prevalence from registry data.
prevalence_simulated
Estimate prevalence using Monte Carlo simulation.
prevsim
Simulated patient dataset.
raw_incidence
Disease incidence.
rprev
rprev: Estimate disease point prevalence using a combination...
summary.survfit.prev
Obtain N-year survival probability estimates.
survfit.prevalence
Form bootstrapped survival curves.
test_incidence_fit
Test homogeneous Poisson assumption of disease incidence.
test_prevalence_fit
Test simulated prevalence fit.
UKmortality
General population survival data.

Files in this package

rprev
rprev/inst
rprev/inst/doc
rprev/inst/doc/user_guide.html
rprev/inst/doc/user_guide.Rmd
rprev/inst/doc/user_guide.R
rprev/tests
rprev/tests/testthat.R
rprev/tests/testthat
rprev/tests/testthat/cache
rprev/tests/testthat/cache/survival
rprev/tests/testthat/cache/survival/transform_registry_data_4.rds
rprev/tests/testthat/cache/survival/calculate_bootstrapped_coefficients_6.rds
rprev/tests/testthat/cache/survival/population_survival_rate_4.rds
rprev/tests/testthat/cache/survival/calculate_coefficients_2.rds
rprev/tests/testthat/cache/survival/registry_survival_bootstrapped_9.rds
rprev/tests/testthat/cache/survival/population_survival_rate_1.rds
rprev/tests/testthat/cache/survival/fit_weibull_4.rds
rprev/tests/testthat/cache/survival/registry_survival_bootstrapped_1.rds
rprev/tests/testthat/cache/survival/prob_alive_4.rds
rprev/tests/testthat/cache/survival/fit_weibull_6.rds
rprev/tests/testthat/cache/survival/calculate_bootstrapped_coefficients_2.rds
rprev/tests/testthat/cache/survival/calculate_coefficients_1.rds
rprev/tests/testthat/cache/survival/calculate_coefficients_3.rds
rprev/tests/testthat/cache/survival/registry_survival_bootstrapped_8.rds
rprev/tests/testthat/cache/survival/prob_alive_2.rds
rprev/tests/testthat/cache/survival/prob_alive_1.rds
rprev/tests/testthat/cache/survival/fit_weibull_1.rds
rprev/tests/testthat/cache/survival/transform_registry_data_1.rds
rprev/tests/testthat/cache/survival/population_survival_rate_5.rds
rprev/tests/testthat/cache/survival/registry_survival_bootstrapped_4.rds
rprev/tests/testthat/cache/survival/population_survival_rate_2.rds
rprev/tests/testthat/cache/survival/calculate_coefficients_4.rds
rprev/tests/testthat/cache/survival/prob_alive_5.rds
rprev/tests/testthat/cache/survival/fit_weibull_5.rds
rprev/tests/testthat/cache/survival/registry_survival_bootstrapped_7.rds
rprev/tests/testthat/cache/survival/transform_registry_data_3.rds
rprev/tests/testthat/cache/survival/registry_survival_bootstrapped_1000_3.rds
rprev/tests/testthat/cache/survival/registry_survival_bootstrapped_2.rds
rprev/tests/testthat/cache/survival/registry_survival_bootstrapped_5.rds
rprev/tests/testthat/cache/survival/registry_survival_bootstrapped_1000_2.rds
rprev/tests/testthat/cache/survival/calculate_bootstrapped_coefficients_1.rds
rprev/tests/testthat/cache/survival/population_survival_rate_3.rds
rprev/tests/testthat/cache/survival/population_survival_rate_6.rds
rprev/tests/testthat/cache/survival/calculate_bootstrapped_coefficients_4.rds
rprev/tests/testthat/cache/survival/transform_registry_data_2.rds
rprev/tests/testthat/cache/survival/fit_weibull_3.rds
rprev/tests/testthat/cache/survival/registry_survival_bootstrapped_3.rds
rprev/tests/testthat/cache/survival/prob_alive_3.rds
rprev/tests/testthat/cache/survival/fit_weibull_2.rds
rprev/tests/testthat/cache/survival/calculate_bootstrapped_coefficients_5.rds
rprev/tests/testthat/cache/survival/registry_survival_bootstrapped_6.rds
rprev/tests/testthat/cache/survival/registry_survival_bootstrapped_1000_1.rds
rprev/tests/testthat/cache/survival/calculate_bootstrapped_coefficients_3.rds
rprev/tests/testthat/cache/prevalence
rprev/tests/testthat/cache/prevalence/countedprevalence_newparam_3.rds
rprev/tests/testthat/cache/prevalence/countedprevalence_newparam_1.rds
rprev/tests/testthat/cache/prevalence/countedprevalence_1.rds
rprev/tests/testthat/cache/prevalence/countedprevalence_2.rds
rprev/tests/testthat/cache/prevalence/countedprevalence_newparam_4.rds
rprev/tests/testthat/cache/prevalence/countedprevalence_newparam_2.rds
rprev/tests/testthat/cache/diagnostics
rprev/tests/testthat/cache/diagnostics/prev_chisq.rds
rprev/tests/testthat/cache/diagnostics/sim_check_100000.rds
rprev/tests/testthat/cache/diagnostics/functional_form_age.rds
rprev/tests/testthat/cache/diagnostics/sim_check.rds
rprev/tests/testthat/cache/diagnostics/poisson_incidence_sim.rds
rprev/tests/testthat/cache/diagnostics/inspect_incidence.rds
rprev/tests/testthat/cache/incidence
rprev/tests/testthat/cache/incidence/incidence_3.rds
rprev/tests/testthat/cache/incidence/incidence_1.rds
rprev/tests/testthat/cache/incidence/meanir_3.rds
rprev/tests/testthat/cache/incidence/meanir_2.rds
rprev/tests/testthat/cache/incidence/meanir_1.rds
rprev/tests/testthat/cache/incidence/incidence_2.rds
rprev/tests/testthat/test_survival.R
rprev/tests/testthat/test_prevalence.R
rprev/tests/testthat/test_incidence.R
rprev/tests/testthat/test_diagnostics.R
rprev/NAMESPACE
rprev/NEWS.md
rprev/data
rprev/data/prevsim.rda
rprev/data/UKmortality.rda
rprev/R
rprev/R/rprev.R
rprev/R/utils.R
rprev/R/survfit.prev.R
rprev/R/diagnostics.R
rprev/R/data.R
rprev/R/prevalence.R
rprev/R/survival.R
rprev/R/incidence.R
rprev/vignettes
rprev/vignettes/bibliography.bib
rprev/vignettes/user_guide.Rmd
rprev/vignettes/diagram.png
rprev/README.md
rprev/MD5
rprev/build
rprev/build/vignette.rds
rprev/DESCRIPTION
rprev/man
rprev/man/incidence_age_distribution.Rd
rprev/man/prevsim.Rd
rprev/man/plot.survfit.prev.Rd
rprev/man/test_prevalence_fit.Rd
rprev/man/rprev.Rd
rprev/man/prevalence_counted.Rd
rprev/man/test_incidence_fit.Rd
rprev/man/plot.incidence.Rd
rprev/man/prevalence_simulated.Rd
rprev/man/raw_incidence.Rd
rprev/man/mean_incidence_rate.Rd
rprev/man/prevalence.Rd
rprev/man/determine_registry_years.Rd
rprev/man/summary.survfit.prev.Rd
rprev/man/functional_form_age.Rd
rprev/man/population_survival_rate.Rd
rprev/man/incidence.Rd
rprev/man/UKmortality.Rd
rprev/man/survfit.prevalence.Rd