# NOT RUN {
####=========================================####
#### For CRAN time limitations most lines in the
#### examples are silenced with one '#' mark,
#### remove them and run the examples
####=========================================####
data(DT_mohring)
DT <- DT_mohring
head(DT)
DT2 <- add.diallel.vars(DT,par1="Par1", par2="Par2")
head(DT2)
# GRIFFING MODEL 2 with reciprocal effects ###########################
mod1h <- mmer(Ftime ~ 1, data=DT2,
random = ~ Block
# GCA male & female overlayed
+ overlay(Par1, Par2)
# SCA effects (includes cross and selfs)
+ cross.id
# SCAR reciprocal effects (if zero there's no reciprocal effects)
+ cross.id:cross.type)
summary(mod1h)$varcomp
## VarComp VarCompSE Zratio
## Block.Ftime-Ftime 0.00000 9.32181 0.000000
## overlay(Par1, Par2).Ftime-Ftime 1276.73089 750.17269 1.701916
## cross.id.Ftime-Ftime 1110.99090 330.16921 3.364914
## cross.id:cross.type.Ftime-Ftime 66.02295 49.26876 1.340057
## units.Ftime-Ftime 418.47949 74.56442 5.612321
##
# GRIFFING MODEL 2, no reciprocal effects ##############################
mod1h <- mmer(Ftime ~ Block + is.cross, data=DT2,
random = ~
# GCA for all (female and male)
overlay(Par1, Par2)
# GCA (only for hybrids)
+ overlay(Par1, Par2):is.cross
# SCA (hybrids only)
+ cross.id:is.cross)
summary(mod1h)$varcomp
## VarComp VarCompSE Zratio
## overlay(Par1, Par2).Ftime-Ftime 2304.1781 1261.63193 1.826347
## overlay(Par1, Par2):is.cross.Ftime-Ftime 613.6040 402.74347 1.523560
## cross.id:is.cross.Ftime-Ftime 340.7030 148.56225 2.293335
## units.Ftime-Ftime 501.6275 74.36075 6.745864
##
# GRIFFING MODEL 3, no reciprocal effects ###############################
mod1h <- mmer(Ftime ~ Block + is.cross, data=DT2,
random = ~
# GCAC (only for hybrids)
overlay(Par1, Par2):is.cross
# male GCA (only for inbreds)
+ Par1:is.self
# SCA (for hybrids only)
+ cross.id:is.cross)
summary(mod1h)$varcomp
## VarComp VarCompSE Zratio
## overlay(Par1, Par2):is.cross.Ftime-Ftime 927.7895 537.91218 1.724797
## Par1:is.self.Ftime-Ftime 9960.9247 5456.58188 1.825488
## cross.id:is.cross.Ftime-Ftime 341.4567 148.53667 2.298804
## units.Ftime-Ftime 498.5974 73.92066 6.745035
##
# GRIFFING MODEL 2, with reciprocal effects #############################
# In Mohring: mixed model 3 reduced
mod1h <- mmer(Ftime ~ Block + is.cross, data=DT2,
random = ~
# GCAC (for hybrids only)
overlay(Par1, Par2):is.cross
# male GCA (for selfs only)
+ Par1:is.self
# SCA (for hybrids only)
+ cross.id:is.cross
# SCAR reciprocal effects
+ cross.id:cross.type)
summary(mod1h)$varcomp
## VarComp VarCompSE Zratio
## overlay(Par1, Par2):is.cross.Ftime-Ftime 927.78742 537.89981 1.724833
## Par1:is.self.Ftime-Ftime 10001.78854 5456.47578 1.833013
## cross.id:is.cross.Ftime-Ftime 361.89712 148.54264 2.436318
## cross.id:cross.type.Ftime-Ftime 66.43695 49.24492 1.349113
## units.Ftime-Ftime 416.82960 74.27202 5.612203
##
# GRIFFING MODEL 3, with RGCA + RSCA ####################################
# In Mohring: mixed model 3
mod1h <- mmer(Ftime ~ Block + is.cross, data=DT2,
random = ~
# GCAC (for hybrids only)
overlay(Par1,Par2):is.cross
# RGCA: exclude selfs (to identify reciprocal effects)
+ overlay(Par1,Par2):cross.type
# male GCA (for selfs only)
+ Par1:is.self
# SCA (for hybrids only)
+ cross.id:is.cross
# SCAR: exclude selfs (if zero there's no reciprocal effects)
+ cross.id:cross.type)
summary(mod1h)$varcomp
## VarComp VarCompSE Zratio
## overlay(Par1, Par2):is.cross.Ftime-Ftime 927.7843 537.88164 1.7248857
## Par1:is.self.Ftime-Ftime 10001.7570 5456.30125 1.8330654
## cross.id:is.cross.Ftime-Ftime 361.8958 148.53670 2.4364068
## overlay(Par1, Par2):cross.type.Ftime-Ftime 17.9799 19.92428 0.9024114
## cross.id:cross.type.Ftime-Ftime 30.9519 46.43908 0.6665054
## units.Ftime-Ftime
# }
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