sommer (version 3.8)

fcm: fixed effect constraint indication matrix

Description

fcm creates a matrix with the correct number of columns to specify a constraint in the fixed effects using the Gtc argument of the vs function.

Usage

fcm(x)

Arguments

x

vector of 1's and 0's corresponding to the traits for which this fixed effect should be fitted. For example, for a trivariate model if the fixed effect "x" wants to be fitted only for trait 1 and 2 but not for the 3rd trait then you would use fcm(c(1,1,0)) in the Gtc argument of the vs() function.

Value

$res

a list with the provided vector and the variance covariance structure expected for the levels of the random effect.

References

Covarrubias-Pazaran G (2016) Genome assisted prediction of quantitative traits using the R package sommer. PLoS ONE 11(6): doi:10.1371/journal.pone.0156744

See Also

The function vs to know how to use fcm in the mmer solver.

Examples

# NOT RUN {
fcm(c(1,1,0))
fcm(c(0,1,1))
fcm(c(1,1,1))

# ## model with Env estimated for both traits
# ans4 <- mmer(cbind(Yield, Weight) ~ Env,
#               random= ~ vs(Name) + vs(Env:Name),
#               rcov= ~ vs(units),
#               data=DT)
# summary(ans4)$betas
# ## model with Env only estimated for Yield
# ans4b <- mmer(cbind(Yield, Weight) ~ vs(Env, Gtc=fcm(c(1,0))),
#              random= ~ vs(Name) + vs(Env:Name),
#              rcov= ~ vs(units),
#              data=DT)
# summary(ans4b)$betas

# }