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Set the exit date when no exit column exists

Source: R/setExit.R
setExit.Rd

Part of Pedigree Curation

Usage

setExit(ped, timeOrigin = as.Date("1970-01-01"))

Arguments

ped

dataframe of pedigree and demographic information potentially containing columns indicating the birth and death dates of an individual. The table may also contain dates of sale (departure). Optional columns are birth, death, and departure.

timeOrigin

date object used by as.Date to set origin.

Value

A dataframe with an updated pedigree with exit dates specified based on date information that was available.

Details

An exit column is added only when the pedigree has a birth column and no exit column. When both death and departure are present the exit is the earlier of the two; it is NA if neither column exists. The column names are matched without regard to case (Death is read as death), and the new column is named exit. A pedigree without a birth column, or with no rows, is returned unchanged.

Examples

library(lubridate)
library(nprcgenekeepr)
death <- mdy(paste0(
  sample(1:12, 10, replace = TRUE), "-",
  sample(1:28, 10, replace = TRUE), "-",
  sample(seq(0, 15, by = 3), 10, replace = TRUE) + 2000
))
departure <- as.Date(rep(NA, 10), origin = as.Date("1970-01-01"))
departure[c(1, 3, 6)] <- as.Date(death[c(1, 3, 6)],
  origin = as.Date("1970-01-01")
)
death[c(1, 3, 5)] <- NA
death[6] <- death[6] + days(1)
ped <- data.frame(
  id = paste0(100 + 1:10),
  birth = mdy(paste0(
    sample(1:12, 10, replace = TRUE), "-",
    sample(1:28, 10, replace = TRUE), "-",
    sample(seq(0, 20, by = 3), 10, replace = TRUE) + 1980
  )),
  death = death,
  departure = departure,
  stringsAsFactors = FALSE
)
pedWithExit <- setExit(ped)