popEpi-package: popEpi: Functions for large-scale epidemiological analysis

In WetRobot/popEpi: Functions for Epidemiological Analysis using Population Data

popEpi: Functions for large-scale epidemiological analysis

Description

popEpi is built for the needs of registry-based (large-scale) epidemiological analysis. This is in most part enabled by the efficient data.table package for handling and aggregating large data sets.

popEpi currently supplies some utility functions such as splitMulti and get.yrs for preparing large data sets for epidemiological analysis. Included are also a a few functions that can be used in epidemiological analysis such as sir for estimating standardized incidence/mortality ratios (SIRs/SMRs) and survtab for estimating observed and relative/net survival as well as cumulative incidence functions (CIFs). In particular, survtab implements the Ederer II (Ederer and Heise (1959)) and Pohar Perme estimators (Pohar Perme, Stare, and Esteve (2012) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/j.1541-0420.2011.01640.x")}) and allows for easy age-standardisation.

Since there are many benefits to using data.tables, popEpi returns outputs by default in the data.table format where appropriate. Since data.table objects are usually modified by reference, this may have surprising side effects for users uninitiated in using data.table. To ensure that appropriate outputs are in the data.frame format, set options("popEpi.datatable" = FALSE). However, data.table usage is recommended due to better performance and testing coverage. data.table is used by most functions internally in both cases.

Author(s)

Maintainer: Joonas Miettinen [e-mail] (ORCID)

Authors:

• Matti Rantanen [e-mail]

Other contributors:

• Karri Seppa [e-mail] [contributor]

See Also

Useful links:

• https://github.com/FinnishCancerRegistry/popEpi

• Report bugs at https://github.com/FinnishCancerRegistry/popEpi/issues

WetRobot/popEpi documentation built on Aug. 29, 2023, 3:53 a.m.