Validated variance components, heritabilities and genetic correlation.

var_total = var(y) (PHENOTYPIC; var(yHat) carries no residual and yields a NEGATIVE residual by subtraction). var_resid = var_total - (varG + varE + varGE) h2_entry = varG / (varG + varE/q + varGE/(p*q) + var_resid) varG is retained in the denominator; omitting it produced h2 > 1 even with true inputs (observed 1.025 and 0.983).

Usage

varcomp_summary(
  fit,
  method = c("postmean", "gibbs"),
  y = NULL,
  p = NULL,
  q = NULL,
  digits = 4
)

Arguments

fit

a fitted kernel_model object (or a compatible list carrying variance components).

method

character. "postmean" (default) uses posterior-mean effects; "gibbs" uses the stored Gibbs variance components.

y

numeric. Observed phenotypes used as the total-variance reference. Taken from fit$meta$y when NULL.

p

integer. Number of genotypes. Inferred from fit$meta$gid when NULL.

q

integer. Number of environments. Inferred from fit$meta$env when NULL.

digits

integer. Number of decimal places in the summary table. Default 4.

Value

An object of class "km_varcomp", a list with elements table (a data.frame of variance components with their absolute values and proportions of the phenotypic variance), the individual variances varG, varE, varGE, var_resid and var_total, the heritabilities h2_entry_mean and h2_plot, the genetic correlation rg, the counts p and q, the method used, and the logical flags negative_residual and few_environments. A dedicated print method displays the table and derived quantities.