pedne: Calculate Effective Population Size

In visPedigree: Tidying, Analysis, and Fast Visualization of Animal and Plant Pedigrees

Calculate Effective Population Size

Description

Calculates the effective population size (Ne) based on the rate of coancestry, the rate of inbreeding, or demographic parent numbers.

Usage

pedne(
  ped,
  method = c("coancestry", "inbreeding", "demographic"),
  by = NULL,
  reference = NULL,
  nsamples = 1000,
  ncores = 1,
  seed = NULL
)

Arguments

ped	A tidyped object.
method	Character. The method to compute Ne. One of "coancestry" (default), "inbreeding", or "demographic".
by	Character. The name of the column used to group cohorts (e.g., "Year", "BirthYear"). If NULL, calculates overall Ne for all individuals.
reference	Character vector. Optional subset of individual IDs defining the reference cohort. If NULL, uses all individuals in the pedigree.
nsamples	Integer. Number of individuals to randomly sample per cohort when using the "coancestry" method. Very large cohorts will be sampled down to this size to save memory and time (default: 1000).
ncores	Integer. Number of cores for parallel processing. Currently only effective for method = "coancestry" (default: 1).
seed	Integer or NULL. Random seed passed to set.seed() before sampling in the coancestry method, ensuring reproducible N_e estimates. Default is NULL (no fixed seed).

Details

The effective population size can be calculated using one of three methods:

• "coancestry" (Default): Based on the rate of coancestry (f_{ij}) between pairs of individuals. In this context, f_{ij} is the probability that two alleles randomly sampled from individuals $i$ and $j$ are identical by descent, which is equivalent to half the additive genetic relationship (f_{ij} = a_{ij} / 2). This method is generally more robust as it accounts for full genetic drift and bottlenecks (Cervantes et al., 2011).

  \Delta c_{ij} = 1 - (1 - c_{ij})^{1/(\frac{ECG_i + ECG_j}{2})}

  N_e = \frac{1}{2 \overline{\Delta c}}

  To handle large populations, this method samples nsamples individuals per cohort and computes the mean rate of coancestry among them.

• "inbreeding": Based on the individual rate of inbreeding ($F_i$) (Gutiérrez et al., 2008, 2009).

  \Delta F_i = 1 - (1 - F_i)^{1/(ECG_i - 1)}

  N_e = \frac{1}{2 \overline{\Delta F}}

• "demographic": Based on the demographic census of breeding males and females (Wright, 1931).

  N_e = \frac{4 N_m N_f}{N_m + N_f}

  Where N_m and N_f are the number of unique male and female parents contributing to the cohort.

Value

A data.table with columns:

• Cohort: Cohort or grouping variable value.

• N: Number of individuals in the cohort.

• Ne: Calculated effective population size.

• ...: Additional columns depending on the selected method (e.g., NSampled, DeltaC, MeanF, DeltaF, Nm, Nf).

References

Cervantes, I., Goyache, F., Molina, A., Valera, M., & Gutiérrez, J. P. (2011). Estimation of effective population size from the rate of coancestry in pedigreed populations. Journal of Animal Breeding and Genetics, 128(1), 56-63.

Gutiérrez, J. P., Cervantes, I., Molina, A., Valera, M., & Goyache, F. (2008). Individual increase in inbreeding allows estimating effective sizes from pedigrees. Genetics Selection Evolution, 40(4), 359-370.

Gutiérrez, J. P., Cervantes, I., & Goyache, F. (2009). Improving the estimation of realized effective population sizes in farm animals. Journal of Animal Breeding and Genetics, 126(4), 327-332.

Wright, S. (1931). Evolution in Mendelian populations. Genetics, 16(2), 97-159.

Examples

# Coancestry-based Ne (default) using a simple pedigree grouped by year
tp_simple <- tidyped(simple_ped)
tp_simple$BirthYear <- 2000 + tp_simple$Gen
ne_coan <- suppressMessages(pedne(tp_simple, by = "BirthYear", seed = 42L))
ne_coan

# Inbreeding-based Ne using an inbred pedigree
tp_inbred <- tidyped(inbred_ped)
ne_inb <- suppressMessages(pedne(tp_inbred, method = "inbreeding", by = "Gen"))
ne_inb

# Demographic Ne from the number of contributing sires and dams
ne_demo <- suppressMessages(pedne(tp_simple, method = "demographic", by = "BirthYear"))
ne_demo

visPedigree documentation built on March 30, 2026, 9:07 a.m.