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Obfuscate a pedigree by aliasing IDs and shifting dates

Source: R/obfuscatePed.R
obfuscatePed.Rd

User provides a pedigree object (ped), the number of characters to be used for alias IDs (size), and the maximum number of days that the birthdate can be shifted (maxDelta).

Usage

obfuscatePed(
  ped,
  size = 6L,
  maxDelta = 30L,
  existingIds = character(0L),
  map = FALSE,
  linkedDateShift = TRUE
)

Arguments

ped

The pedigree information in data.frame format

size

integer value indicating number of characters in alias IDs

maxDelta

integer value indicating maximum number of days that the birthdate can be shifted

existingIds

character vector of existing aliases to avoid duplication.

map

logical if TRUE a list object is returned with the new pedigree and a named character vector with the names being the original IDs and the values being the new alias values. Defaults to FALSE.

linkedDateShift

logical, defaults to TRUE. When TRUE, every Date column of one individual is shifted by the same, single random offset (drawn once per individual), so the gaps between an individual's own dates (e.g. birth, exit, death) are preserved exactly – avoiding a defect where independently-shifted date columns can invert an individual's recorded date order (e.g. an obfuscated exit preceding an obfuscated birth), producing a negative recomputed age (issue #150 D3). When FALSE, each Date column is shifted independently via obfuscateDate (the original, pre-#150 behavior).

Value

An obfuscated pedigree

See also

Other obfuscation: mapIdsToObfuscated(), obfuscateDate(), obfuscateGenomicROH(), obfuscateGenotypeMatrix(), obfuscateId(), obfuscateLdBlocks(), obfuscateTwinRelations()

Examples

library(nprcgenekeepr)
ped <- qcStudbook(nprcgenekeepr::pedGood)
obfuscatedPed <- obfuscatePed(ped)
ped
#>   id sire  dam sex gen      birth exit  age recordStatus
#> 1 d1 <NA> <NA>   F   0 2003-04-13 <NA> 23.4     original
#> 2 d2 <NA> <NA>   F   0 2002-06-22 <NA> 24.2     original
#> 3 s1 <NA> <NA>   M   0 2000-07-18 <NA> 26.1     original
#> 4 s2 <NA> <NA>   M   0 2005-06-19 <NA> 21.2     original
#> 5 o1   s1   d1   F   1 2015-02-04 <NA> 11.6     original
#> 6 o2   s1   d2   F   1 2009-03-17 <NA> 17.4     original
#> 7 o3   s2   d2   F   1 2012-04-11 <NA> 14.4     original
#> 8 o4   s2   d2   M   1 2008-04-13 <NA> 18.4     original
obfuscatedPed
#>       id   sire    dam sex gen      birth exit  age recordStatus
#> 1 SN7TLJ   <NA>   <NA>   F   0 2003-05-12 <NA> 23.3     original
#> 2 2ZFC1W   <NA>   <NA>   F   0 2002-06-02 <NA> 24.2     original
#> 3 FCDNFK   <NA>   <NA>   M   0 2000-08-05 <NA> 26.1     original
#> 4 GJGR1A   <NA>   <NA>   M   0 2005-05-24 <NA> 21.3     original
#> 5 T5NBEL FCDNFK SN7TLJ   F   1 2015-01-29 <NA> 11.6     original
#> 6 FEHHE9 FCDNFK 2ZFC1W   F   1 2009-02-23 <NA> 17.5     original
#> 7 LSYDEB GJGR1A 2ZFC1W   F   1 2012-03-23 <NA> 14.4     original
#> 8 7YDSRN GJGR1A 2ZFC1W   M   1 2008-05-03 <NA> 18.3     original