pedFixBirthYear: pedFixBirthYear.R

In AlphaPart: Partition/Decomposition of Breeding Values by Paths of Information

pedFixBirthYear.R

Description

A function to fix (impute) missing birth years in pedigree.

Usage

pedFixBirthYear(
  x,
  interval,
  down = FALSE,
  na.rm = TRUE,
  sort = TRUE,
  direct = TRUE,
  report = TRUE,
  colId = 1,
  colFid = 2,
  colMid = 3,
  colBY = 4
)

Arguments

x	data.frame , with (at least) the following columns: individual, father, and mother identification, and year of birth; see arguments colId, colFid, colMid, and colBY
interval	Numeric, a value for generation interval in years.
down	Logical, the default is to impute birth years based on the birth year of children starting from the youngest to the oldest individuals, while with down=TRUE birth year is imputed based on the birth year of parents in the opposite order.
na.rm	Logical, remove NA values when searching for the minimal (maximal) year of birth in children (parents); setting this to FALSE can lead to decreased success of imputation
sort	Logical, initially sort x using orderPed() so that children follow parents in order to make imputation as optimal as possible (imputation is performed within a loop from the first to the last unknown birth year); at the end original order is restored.
direct	Logical, insert inferred birth years immediately so they can be used for successive individuals within the loop.
report	Logical, report success.
colId	Numeric or character, position or name of a column holding individual identification.
colFid	Numeric or character, position or name of a column holding father identification.
colMid	Numeric or character, position or name of a column holding mother identification.
colBY	Numeric or character, position or name of a column holding birth year.

Details

Warnings are issued when there is no information to use to impute birth years or missing values (NA) are propagated.

Arguments down and na.rm allow for repeated use of this function, i.e., with down=FALSE and with down=TRUE (both in combination with na.rm=TRUE) in order to propagate information over the pedigree until "convergence".

This function can be very slow on large pedigrees with extensive missingness of birth years.

Value

Object x with imputed birth years based on the birth year of children or parents. If report=TRUE success is printed on the screen as the number of initially, fixed, and left unknown birth years is printed.

See Also

orderPed in pedigree package

Examples

## Example pedigree with missing (unknown) birth year for some individuals
ped0 <- data.frame(     id=c( 1, 2, 3,  4, 5, 6, 7,  8, 9, 10, 11, 12, 13, 14),
                        fid=c( 0, 0, 0,  1, 1, 1, 3,  3, 3,  5,  4,  0,  0, 12),
                        mid=c( 0, 0, 0,  2, 0, 2, 2,  2, 5,  0,  0,  0,  0, 13),
                        birth_dt=c(NA, 0, 1, NA, 3, 3, 3, 3, 4, 4, 5, NA, 6, 6) + 2000)

## First run - using information from children
ped1 <- pedFixBirthYear(x=ped0, interval=1)

## Second run - using information from parents
ped2 <- pedFixBirthYear(x=ped1, interval=1, down=TRUE)

## Third run - using information from children, but with no success
ped3 <- pedFixBirthYear(x=ped2, interval=1)

AlphaPart documentation built on Nov. 16, 2022, 1:09 a.m.