Convert status indicators to a standardized code — convertStatusCodes • nprcgenekeepr

Part of Pedigree Curation

Usage

convertStatusCodes(status)

Arguments

status: character vector or NA. Flag indicating an individual's status as alive, dead, sold, etc.

Value

A factor vector of the standardized status codes with levels: ALIVE, DECEASED, SHIPPED, and UNKNOWN. A value that is not recognized becomes NA, not UNKNOWN.

Details

Case is ignored, but spaces are not trimmed. The recognized codes are ALIVE, A, 1 for alive; DECEASED, DEAD, DIED, D, 2 for deceased; SHIPPED, SHIPED, SOLD, SALE, S, 3 for shipped; and UNKNOWN, U, 4 or NA for unknown.

Examples

library(nprcgenekeepr)
original <- c(
  "A", "alive", "Alive", "1", "S", "Sale", "sold", "shipped",
  "D", "d", "dead", "died", "deceased", "2",
  "shiped", "3", "U", "4", "unknown", NA,
  "Unknown", "U", "Unknown", "4"
)
## A value that is not recognized becomes NA
convertStatusCodes("hermaphrodite")
#> [1] <NA>
#> Levels: ALIVE DECEASED SHIPPED UNKNOWN
convertStatusCodes(original)
#>  [1] ALIVE    ALIVE    ALIVE    ALIVE    SHIPPED  SHIPPED  SHIPPED  SHIPPED 
#>  [9] DECEASED DECEASED DECEASED DECEASED DECEASED DECEASED SHIPPED  SHIPPED 
#> [17] UNKNOWN  UNKNOWN  UNKNOWN  UNKNOWN  UNKNOWN  UNKNOWN  UNKNOWN  UNKNOWN 
#> Levels: ALIVE DECEASED SHIPPED UNKNOWN