Calculate Effective Population Size — pedne • visPedigree

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).

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).

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.

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

# \donttest{
# 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
#>    Cohort     N NSampled       DeltaC       Ne
#>     <num> <int>    <int>        <num>    <num>
#> 1:   2001    28       28           NA       NA
#> 2:   2002    16       16 0.0031250000 160.0000
#> 3:   2003     8        8 0.0017708540 282.3496
#> 4:   2004     4        4 0.0009737864 513.4596
#> 5:   2005     2        2 0.0011276950 443.3823
#> 6:   2006     1        1           NA       NA

# Inbreeding-based Ne using an inbred pedigree
tp_inbred <- tidyped(inbred_ped)
ne_inb <- suppressMessages(pedne(tp_inbred, method = "inbreeding", by = "Gen"))
#> Warning: Subsetting removed parent records. Result is a plain data.table, not a tidyped.
#> Use tidyped(tp, cand = ids, trace = "up") to extract a valid sub-pedigree.
ne_inb
#>    Cohort     N  MeanF DeltaF MeanECG    Ne
#>     <int> <int>  <num>  <num>   <num> <num>
#> 1:      3     1 0.2500   0.25       2     2
#> 2:      4     1 0.2500   0.25       2     2
#> 3:      5     1 0.4375   0.25       3     2

# Demographic Ne from the number of contributing sires and dams
ne_demo <- suppressMessages(pedne(tp_simple, method = "demographic", by = "BirthYear"))
ne_demo
#>    Cohort     N    Nm    Nf        Ne
#>     <num> <int> <int> <int>     <num>
#> 1:   2001    28     0     0        NA
#> 2:   2002    16    14    14 28.000000
#> 3:   2003     8     7     8 14.933333
#> 4:   2004     4     4     3  6.857143
#> 5:   2005     2     2     2  4.000000
#> 6:   2006     1     1     1  2.000000
# }