tidyped: Tidy and prepare a pedigree using graph theory

Description

This function takes a pedigree, checks for duplicate and bisexual individuals, detects pedigree loops using graph theory, adds missing founders, assigns generation numbers, sorts the pedigree, and traces the pedigree of specified candidates. If the cand parameter contains individual IDs, only those individuals and their ancestors or descendants are retained. Tracing direction and the number of generations can be specified using the trace and tracegen parameters.

Usage

tidyped(
  ped,
  cand = NULL,
  trace = "up",
  tracegen = NULL,
  addgen = TRUE,
  addnum = TRUE,
  inbreed = FALSE,
  genmethod = "top",
  ...
)

Value

A tidyped object (which inherits from data.table). Individual, sire, and dam ID columns are renamed to Ind, Sire, and Dam. Missing parents are replaced with NA. The Sex column contains "male", "female", or NA. The Cand column is included if cand is not NULL. The Gen column is included if addgen is TRUE. The IndNum, SireNum, and DamNum columns are included if addnum is TRUE. The Family and FamilySize columns identify full-sibling families (e.g., "A x B" for offspring of sire A and dam B). The f column is included if inbreed is TRUE.

Arguments

ped: A data.table or data frame containing the pedigree. The first three columns must be individual, sire, and dam IDs. Additional columns, such as sex or generation, can be included. Column names can be customized, but their order must remain unchanged. Individual IDs should not be coded as "", " ", "0", "*", or "NA"; otherwise, they will be removed. Missing parents should be denoted by "NA", "0", or "*". Spaces and empty strings ("") are also treated as missing parents but are not recommended.
cand: A character vector of individual IDs, or NULL. If provided, only the candidates and their ancestors/descendants are retained.
trace: A character value specifying the tracing direction: "up", "down", or "all". "up" traces ancestors; "down" traces descendants; "all" traces the union of ancestors and descendants. This parameter is only used if cand is not NULL. Default is "up".
tracegen: An integer specifying the number of generations to trace. This parameter is only used if trace is not NULL. If NULL or 0, all available generations are traced.
addgen: A logical value indicating whether to generate generation numbers. Default is TRUE, which adds a Gen column to the output.
addnum: A logical value indicating whether to generate a numeric pedigree. Default is TRUE, which adds IndNum, SireNum, and DamNum columns to the output.
inbreed: A logical value indicating whether to calculate inbreeding coefficients. Default is FALSE. If TRUE, an f column is added to the output. This uses the same optimized engine as pedmat(..., method = "f").
genmethod: A character value specifying the generation assignment method: "top" or "bottom". "top" (top-aligned) assigns generations from parents to offspring, starting founders at Gen 1. "bottom" (bottom-aligned) assigns generations from offspring to parents, aligning terminal nodes at the bottom. Default is "top".
...: Additional arguments passed to inbreed.

Details

Compared to the legacy version, this function handles cyclic pedigrees more robustly by detecting and reporting loops, and it is generally faster for large pedigrees due to the use of sparse graph algorithms from the igraph package. Generation assignment can be performed using either a top-down approach (default, aligning founders at the top) or a bottom-up approach (aligning terminal nodes at the bottom).

Examples

Run this code

library(visPedigree)
library(data.table)

# Tidy a simple pedigree
tidy_ped <- tidyped(simple_ped)
head(tidy_ped)

# Trace ancestors of a specific individual within 2 generations
tidy_ped_tracegen <- tidyped(simple_ped, cand = "J5X804", trace = "up", tracegen = 2)
head(tidy_ped_tracegen)

# Trace both ancestors and descendants for multiple candidates
# This is highly optimized and works quickly even on 100k+ individuals
cand_list <- c("J5X804", "J3Y620")
tidy_ped_all <- tidyped(simple_ped, cand = cand_list, trace = "all")

# Check for loops (will error if loops exist)
try(tidyped(loop_ped))

# Example with a large pedigree: extract 2 generations of ancestors for 2007 candidates
cand_2007 <- big_family_size_ped[Year == 2007, Ind]
# \donttest{
tidy_big <- tidyped(big_family_size_ped, cand = cand_2007, trace = "up", tracegen = 2)
summary(tidy_big)
# }