summarizePedigrees: Summarize Pedigree Data

In R-Computing-Lab/BGMisc: An R Package for Extended Behavior Genetics Analysis

Summarize Pedigree Data

Description

This function summarizes pedigree data, by computing key summary statistics for all numeric variables and identifying the originating member (founder) for each family, maternal, and paternal lineage.

Usage

summarizePedigrees(
  ped,
  famID = "famID",
  personID = "ID",
  momID = "momID",
  dadID = "dadID",
  matID = "matID",
  patID = "patID",
  type = c("fathers", "mothers", "families"),
  byr = NULL,
  include_founder = FALSE,
  founder_sort_var = NULL,
  nbiggest = 5,
  noldest = 5,
  skip_var = NULL,
  five_num_summary = FALSE,
  network_checks = FALSE,
  verbose = FALSE
)

Arguments

ped	a pedigree dataset. Needs ID, momID, and dadID columns
famID	character. Name of the column to be created in ped for the family ID variable
personID	character. Name of the column in ped for the person ID variable
momID	character. Name of the column in ped for the mother ID variable
dadID	character. Name of the column in ped for the father ID variable
matID	Character. Maternal line ID variable to be created and added to the pedigree
patID	Character. Paternal line ID variable to be created and added to the pedigree
type	Character vector. Specifies which summaries to compute. Options: '"fathers"', '"mothers"', '"families"'. Default includes all three.
byr	Character. Optional column name for birth year. Used to determine the oldest lineages.
include_founder	Logical. If 'TRUE', includes the founder (originating member) of each lineage in the output.
founder_sort_var	Character. Column used to determine the founder of each lineage. Defaults to 'byr' (if available) or 'personID' otherwise.
nbiggest	Integer. Number of largest lineages to return (sorted by count).
noldest	Integer. Number of oldest lineages to return (sorted by birth year).
skip_var	Character vector. Variables to exclude from summary calculations.
five_num_summary	Logical. If 'TRUE', includes the first quartile (Q1) and third quartile (Q3) in addition to the minimum, median, and maximum values.
network_checks	Logical. If 'TRUE', performs network checks on the pedigree data.
verbose	Logical, if TRUE, print progress messages.

Details

The function calculates standard descriptive statistics, including the count of individuals in each lineage, means, medians, minimum and maximum values, and standard deviations. Additionally, if 'five_num_summary = TRUE', the function includes the first and third quartiles (Q1, Q3) to provide a more detailed distributional summary. Users can also specify variables to exclude from the analysis via 'skip_var'.

Beyond summary statistics, the function identifies the founding member of each lineage based on the specified sorting variable ('founder_sort_var'), defaulting to birth year ('byr') when available or 'personID' otherwise. Users can retrieve the largest and oldest lineages by setting 'nbiggest' and 'noldest', respectively.

Value

A data.frame (or list) containing summary statistics for family, maternal, and paternal lines, as well as the 5 oldest and biggest lines.

R-Computing-Lab/BGMisc documentation built on April 3, 2025, 3:12 p.m.