enhancer (version 1.1.0)

DT_sleepstudy: Reaction times in a sleep deprivation study

Description

The average reaction time per day for subjects in a sleep deprivation study. On day 0 the subjects had their normal amount of sleep. Starting that night they were restricted to 3 hours of sleep per night. The observations represent the average reaction time on a series of tests given each day to each subject. Data from sleepstudy to see how lme4 models can be translated in sommer.

Usage

data("DT_sleepstudy")

Format

The format is: chr "DT_sleepstudy"

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

Giovanny Covarrubias-Pazaran (2024). lme4breeding: enabling genetic evaluation in the age of genomic data. To be submitted to Bioinformatics.

Douglas Bates, Martin Maechler, Ben Bolker, Steve Walker (2015). Fitting Linear Mixed-Effects Models Using lme4. Journal of Statistical Software, 67(1), 1-48.

Gregory Belenky et al. (2003) Patterns of performance degradation and restoration during sleep restrictions and subsequent recovery: a sleep dose-response study. Journal of Sleep Research 12, 1-12.

Examples

data(DT_sleepstudy)
DT <- DT_sleepstudy
head(DT)

# \donttest{

##############################################
###############  sommer.     #################
##############################################
if(requireNamespace("sommer")){
library(sommer)
##################################
fm2 <- mmes(Reaction ~ Days,
            random= ~ Subject, 
            data=DT, tolParInv = 1e-6, verbose = FALSE)
summary(fm2)$varcomp

##################################
fm2 <- mmes(Reaction ~ Days,
            random= ~ Subject + vsm(ism(Days), ism(Subject)), 
            data=DT, tolParInv = 1e-6, verbose = FALSE)
summary(fm2)$varcomp

##################################
fm2 <- mmes(Reaction ~ Days,
            random= ~ Subject + vsm(ism(Days), ism(Subject)), 
            data=DT, tolParInv = 1e-6, verbose = FALSE)
summary(fm2)$varcomp

##################################
fm2 <- mmes(Reaction ~ Days,
            random= ~ vsm(ism(Days), ism(Subject)), 
            data=DT, tolParInv = 1e-6, verbose = FALSE)
summary(fm2)$varcomp

}

##############################################
############### lme4breeding #################
##############################################
if(requireNamespace("lme4breeding")){
library(lme4breeding)
##################################
fm1 <- lmeb(Reaction ~ Days + (1 | Subject),
                data=DT)
vc <- VarCorr(fm1); print(vc,comp=c("Variance"))
sigma(fm1)^2 # error variance

##################################
fm1 <- lmeb(Reaction ~ Days + (Days || Subject), data=DT)
vc <- VarCorr(fm1); print(vc,comp=c("Variance"))

##################################
fm1 <- lmeb(Reaction ~ Days + (Days | Subject), data=DT)
vc <- VarCorr(fm1); print(vc,comp=c("Variance"))

##################################
fm1 <- lmeb(Reaction ~ Days + (0 + Days | Subject), data=DT)
vc <- VarCorr(fm1); print(vc,comp=c("Variance"))

BLUP <- ranef(fm1, condVar=TRUE)
condVAR <- lapply(BLUP, function(x){attr(x, which="postVar")}) # take sqrt() for SEs

}
# }