Description Usage Arguments Value See Also Examples
Computes the pooled within-group covariance matrix. The effect of sexual dimorphism can be removed by using, for each group, the average of the covariance matrix of males and the covariance matrix of females.
1 |
X |
a data matrix with variables in columns and group names as row names |
groups |
a character / factor vector containing grouping variable |
sex |
NULL (default). A character / factor vector containing sex variable, to remove sexual dimorphism by averaging males and females in each group |
weighted |
logical. If FALSE (default), the average of all the within-group covariance matrices is used. If TRUE, the within-group covariance matrices are weighted by their sample size. |
The pooled within-group covariance matrix
1 2 3 4 5 6 7 8 9 10 11 12 13 | # Data matrix of 2D landmark coordinates
data("Tropheus.IK.coord")
coords <- which(names(Tropheus.IK.coord) == "X1"):which(names(Tropheus.IK.coord) == "Y19")
proc.coord <- as.matrix(Tropheus.IK.coord[coords])
# Pooled within-group covariance matrix for all populations (weighted by sample size)
W <- cov.W(proc.coord, groups = Tropheus.IK.coord$POP.ID, weighted = TRUE)
# Pooled within-group covariance matrix for all populations (unweighted)
W <- cov.W(proc.coord, groups = Tropheus.IK.coord$POP.ID)
# Within-group covariance matrix for all populations, pooled by sex
W.mf <- cov.W(proc.coord, groups = Tropheus.IK.coord$POP.ID, sex = Tropheus.IK.coord$Sex)
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