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Define residual covariance entries for observed phenotypes

Source: R/define_residual_cov.R
define_residual_cov.Rd

Writes rows to phenotype_var_comp (with effect_name = "residual") representing the residual (co)variance matrix for one or more phenotypes, optionally conditioned on a group variable (e.g. farm, sex). Both (i,j) and (j,i) pairs are stored.

Three typical call patterns:

  1. Called by define_phenotype() internally when residual_var is supplied (scalar diagonal, unconditional).

  2. Called by define_effect_cov_matrix() when effect_name = "residual" to store a full multi-trait unconditional R matrix.

  3. Called directly to add group-specific (heterogeneous) residual rows after define_phenotype() has written the unconditional default.

Usage

define_residual_cov(
  pop,
  phenotype_names,
  cov_matrix,
  condition_column = NULL,
  condition_table = "ind_meta",
  condition_level = NULL
)

Arguments

pop

A tidybreed_pop object.

phenotype_names

Character vector of phenotype names (must match rownames(cov_matrix) and colnames(cov_matrix)). For a single phenotype, a scalar is accepted.

cov_matrix

Numeric matrix. Must be symmetric with dimnames(cov_matrix) matching phenotype_names. For a single phenotype the matrix is 1×1.

condition_column

Character or NULL. Column in condition_table used to look up group membership at phenotype time. NULL (default) stores an unconditional default row (the fallback when no group-specific row exists).

condition_table

Character. Table containing condition_column. Default "ind_meta".

condition_level

Character or NULL. Specific level of condition_column this row applies to. NULL (default) = unconditional fallback row.

Value

The modified tidybreed_pop (invisibly).

See also

define_phenotype(), define_effect_cov_matrix()

Examples

if (FALSE) { # \dontrun{
# Heterogeneous residual by sex for turkey BW
pop <- pop |>
  define_phenotype("BW_turkey",
    type         = "continuous",
    mean         = 8000,
    residual_var = 600) |>   # unconditional default
  define_residual_cov("BW_turkey",
    cov_matrix       = matrix(900, 1, 1, dimnames = list("BW_turkey","BW_turkey")),
    condition_column = "sex",
    condition_level  = "M") |>
  define_residual_cov("BW_turkey",
    cov_matrix       = matrix(400, 1, 1, dimnames = list("BW_turkey","BW_turkey")),
    condition_column = "sex",
    condition_level  = "F")
} # }