splitLexisDT: Split case-level observations

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

Split case-level observations

Description

Split a Lexis object along one time scale (as splitLexis) with speed

Usage

splitLexisDT(lex, breaks, timeScale, merge = TRUE, drop = TRUE)

Arguments

lex	a Lexis object, split or not
breaks	a vector of [a,b) breaks to split data by
timeScale	a character string; name of the time scale to split by
merge	logical; if TRUE, retains all variables from the original data - i.e. original variables are repeated for all the rows by original subject
drop	logical; if TRUE, drops all resulting rows after expansion that reside outside the time window defined by the given breaks

Details

splitLexisDT is in essence a data.table version of splitLexis or survSplit for splitting along a single time scale. It requires a Lexis object as input, which may have already been split along some time scale.

Unlike splitLexis, splitLexisDT drops observed time outside the roof and floor of breaks by default - with drop = FALSE the functions have identical behaviour.

The Lexis time scale variables can be of any arbitrary format, e.g. Date, fractional years (see cal.yr) and get.yrs, or other. However, using date variables (from package date) are not recommended, as date variables are always stored as integers, whereas Date variables (see ?as.Date) are typically stored in double ("numeric") format. This allows for breaking days into fractions as well, when using e.g. hypothetical years of 365.25 days.

Value

A data.table or data.frame (depending on options("popEpi.datatable"); see ?popEpi) object expanded to accommodate split observations.

Author(s)

Joonas Miettinen

See Also

Other splitting functions: lexpand(), splitMulti()

Examples

library(Epi)
data("sire", package = "popEpi")
x <- Lexis(data=sire[1000:1100, ], 
           entry = list(fot=0, per=get.yrs(dg_date), age=dg_age), 
           exit=list(per=get.yrs(ex_date)), exit.status=status)
BL <- list(fot=seq(0, 5, by = 3/12), per=c(2008, 2013))

x2 <- splitMulti(x, breaks = BL, drop = FALSE)

x3 <- splitLexisDT(x, breaks = BL$fot, timeScale = "fot", drop = FALSE)
x3 <- splitLexisDT(x3, breaks = BL$per, timeScale = "per", drop = FALSE)

x4 <- splitLexis(x,  breaks = BL$fot, time.scale = "fot")
x4 <- splitLexis(x4, breaks = BL$per, time.scale = "per")
## all produce identical results

## using Date variables
x <- Lexis(data=sire[1000:1100, ], 
           entry = list(fot=0, per=dg_date, age=dg_date-bi_date), 
           exit=list(per=ex_date), exit.status=status)
BL <- list(fot = 0:5*365.25, per = as.Date(c("2008-01-01", "2013-01-01")))

x2 <- splitMulti(x, breaks = BL, drop = FALSE)

x3 <- splitLexisDT(x, breaks = BL$fot, timeScale = "fot", drop = FALSE)
x3 <- splitLexisDT(x3, breaks = BL$per, timeScale = "per", drop = FALSE)

## splitLexis may not work when using Dates

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