Author: R. Mark Sharp, Ph.D.
Date: 2026-06-25

# Gene-Drop Iteration Convergence

### nprcgenekeepr: an R Package for the Genetic Management of Colonies

#### R. Mark Sharp, Ph.D.

#### 2026-06-25

## How many gene-drop iterations does a pedigree need?

The Genetic Value Analysis ranks animals by mean kinship and genome uniqueness. Mean kinship is deterministic, but genome uniqueness (`gu`) is estimated by a gene-drop simulation: alleles are dropped down the pedigree a chosen number of times, and `gu` is the average result. Like any estimate from a finite number of draws, it carries sampling noise, so the precision of `gu` – and, more importantly, the selection order it produces – depends on how many iterations you run.

There is no single iteration count that is right for every colony. A pedigree with many animals whose true genome uniqueness sits near a ranking boundary needs more iterations before the chosen set of animals stops changing run to run; a pedigree whose ranked animals are well separated settles almost immediately. `gvaConvergence()` answers the question for the pedigree in hand: it reports how reproducible the selection order is at a range of iteration counts, and the smallest count at which it has settled.

### What it measures

Because the gene-drop iteration columns are independent replicates, the whole convergence picture is recoverable from a single gene drop. `gvaConvergence()` runs one gene drop at a budget `nMax`, then for each candidate iteration count `N` it splits the columns into two disjoint halves of `N` columns each – two genuinely independent `N`-iteration runs – ranks each half through the same ordering pipeline the report uses, and compares the two orderings on two criteria:

- top-`k` overlap – do the two runs choose the same top animals? (default `k = 20`, threshold `oMin = 0.90`)
- Kendall rank agreement – do the chosen animals come out in the same order? (threshold `rhoMin = 0.95`)

The run is reproducible at `N` when both hold, and the recommended iteration count is the smallest `N` meeting both. The “Undetermined” animals (both parents unknown, no recorded origin) are a policy constant with rank `NA`; they are excluded from the order and reported separately as `nUndetermined`.

This is distinct from seed reproducibility. A fixed seed already makes `gu` bit-identical run to run – that is reproducibility of the process. `gvaConvergence()` reports the sampling reproducibility of the estimate: would a fresh, independent run lead to the same animals being chosen, in the same order?

## A pedigree where the iteration count matters

No bundled pedigree exercises the diagnostic well – after the `gu = 0` de-inflation the shipped pedigrees have no `gu` signal left to rank on, so their selection order is settled at the smallest iteration count. To show a pedigree where the count does matter, we build a small half-sib web in which the founders (the sources of the private alleles) are excluded from the analyzed population, so their alleles survive among the offspring only through descendants. Overlapping sire/dam mating windows give the offspring distinct true genome-uniqueness values that straddle the ranking boundary, so at low iteration counts the gene-drop estimate randomly crosses the boundary and the selection order churns.

    ## A deterministic dense-mid-range pedigree: 14 founder sires, each mated to a
    ## wrapping window of 5 of 15 founder dams (one offspring per pair). Windows
    ## overlap, so dam fan sizes vary and the 70 offspring get distinct genome
    ## uniqueness straddling the 10% ranking cutoff. Founders are excluded from the
    ## analyzed population (`pop`); the offspring are the probands.
    makeConvergenceFixture <- function() {
      w <- rep(5L, 14L)          # sire window widths
      b <- 15L                   # number of founder dams
      a <- length(w)
      sids <- sprintf("S%03d", seq_len(a))
      dids <- sprintf("D%03d", seq_len(b))
      id <- c(sids, dids)
      sire <- rep(NA_character_, a + b)
      dam <- rep(NA_character_, a + b)
      sex <- c(rep("M", a), rep("F", b))
      off <- character(0L)
      ocount <- 0L
      start <- 1L
      for (i in seq_len(a)) {
        for (j in seq_len(w[i])) {
          dj <- ((start + j - 2L) %% b) + 1L
          ocount <- ocount + 1L
          o <- sprintf("O%04d", ocount)
          id <- c(id, o)
          sire <- c(sire, sids[i])
          dam <- c(dam, dids[dj])
          sex <- c(sex, if (ocount %% 2L == 0L) "F" else "M")
          off <- c(off, o)
        }
        start <- start + max(1L, w[i] - 1L)
      }
      ped <- data.frame(id = id, sire = sire, dam = dam, sex = sex,
                        stringsAsFactors = FALSE)
      ped$gen <- findGeneration(ped$id, ped$sire, ped$dam)
      list(ped = ped, pop = off)
    }

    fx <- makeConvergenceFixture()
    nrow(fx$ped)      # total animals (founders + offspring)
    #> [1] 99
    length(fx$pop)    # offspring (the analyzed population)
    #> [1] 70

We assess iteration counts from 25 up to 800 (a fixed `seed` makes the curve reproducible):

    conv <- gvaConvergence(
      fx$ped, pop = fx$pop, nMax = 1600L,
      grid = c(25L, 50L, 100L, 200L, 400L, 800L), seed = 11L
    )

    kable(
      conv$convergence,
      digits = c(0L, 3L, 3L),
      col.names = c("Iterations (N)", "Top-20 overlap", "Kendall agreement"),
      caption = "Selection-order reproducibility vs. iteration count (half-sib web)."
    ) |>
      kable_styling(bootstrap_options = c("striped", "hover"), full_width = FALSE)

Selection-order reproducibility vs. iteration count (half-sib web).
Iterations (N) | Top-20 overlap | Kendall agreement
--- | --- | ---
25 | 0.80 | 0.790
50 | 0.80 | 0.766
100 | 1.00 | 0.945
200 | 0.95 | 0.901
400 | 1.00 | 0.925
800 | 1.00 | 0.952

    conv$recommendedIter   # smallest N meeting both criteria
    #> [1] 800
    conv$converged
    #> [1] TRUE
    conv$nRankable
    #> [1] 70
    conv$nUndetermined
    #> [1] 0

At the smallest counts the two independent half-runs disagree on both which animals are chosen and their order; both measures climb as `N` grows, and the selection order has settled by the higher counts and stays settled there. `recommendedIter` (printed below the table) reports the smallest count meeting both criteria. For this pedigree the default of 1000 iterations is in the right range, and `gvaConvergence()` is how you would confirm that rather than guess it.

## A pedigree that converges immediately

Contrast the bundled `qcPed`. After the `gu = 0` de-inflation none of its ranked animals carry a non-zero genome uniqueness, so the selection order is driven by deterministic mean kinship and does not move with the iteration count.

    convQc <- gvaConvergence(
      nprcgenekeepr::qcPed, nMax = 400L,
      grid = c(25L, 50L, 100L, 200L), seed = 11L
    )

    kable(
      convQc$convergence,
      digits = c(0L, 3L, 3L),
      col.names = c("Iterations (N)", "Top-20 overlap", "Kendall agreement"),
      caption = "Selection-order reproducibility vs. iteration count (qcPed)."
    ) |>
      kable_styling(bootstrap_options = c("striped", "hover"), full_width = FALSE)

Selection-order reproducibility vs. iteration count (qcPed).
Iterations (N) | Top-20 overlap | Kendall agreement
--- | --- | ---
25 | 1 | 1
50 | 1 | 1
100 | 1 | 1
200 | 1 | 1

    convQc$recommendedIter   # converges at the grid floor
    #> [1] 25
    convQc$nRankable
    #> [1] 156
    convQc$nUndetermined     # the excluded Undetermined set
    #> [1] 124

Overlap and agreement are at their maximum from the smallest count, so the recommended count is the floor of the grid: this pedigree needs almost no iterations for the order to be reproducible. The `nUndetermined` count reports how many animals were set aside without a rank.

## Choosing an iteration count

Run `gvaConvergence()` on your own pedigree and read `recommendedIter`. If `converged` is `FALSE`, no count in the grid settled the order – raise `nMax` and extend the `grid` (each candidate `N` needs `2 * N <= nMax`), or accept that this pedigree is intrinsically near a ranking boundary and interpret the ranking with care. The thresholds `k`, `oMin`, and `rhoMin` are arguments, so you can make the definition of “reproducible” stricter or looser for your purpose.

Keep two ideas separate. The per-animal sampling standard error (`guSE`, reported beside `gu` in `reportGV()`) tells you how precise the genome uniqueness number is; it shrinks like one over the square root of the iteration count. The selection order – what `gvaConvergence()` measures – is what actually decides which animals are chosen for breeding. A small `guSE` does not by itself mean the order has settled, which is exactly why the convergence check exists.

See also `reportGV()` (the analysis whose iterations this advises on), `calcGUSE()` (the per-animal standard error), and the Colony Manager Tutorial vignette.