sommer (version 4.3.5)

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

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.

See Also

The core functions of the package mmer

Examples

####=========================================####
#### For CRAN time limitations most lines in the
#### examples are silenced with one '#' mark,
#### remove them and run the examples
####=========================================####
# library(lme4)
data(DT_sleepstudy)
DT <- DT_sleepstudy
head(DT)
##################################
## lme4
# fm1 <- lmer(Reaction ~ Days + (1 | Subject), data=DT)
# vc <- VarCorr(fm1); print(vc,comp=c("Variance"))
## sommer
fm2 <- mmer(Reaction ~ Days,
            random= ~ Subject, 
            data=DT, tolParInv = 1e-6, verbose = FALSE)
summary(fm2)$varcomp

##################################
## lme4
# fm1 <- lmer(Reaction ~ Days + (Days || Subject), data=DT)
# vc <- VarCorr(fm1); print(vc,comp=c("Variance"))
## sommer
fm2 <- mmer(Reaction ~ Days,
            random= ~ Subject + vsr(Days, Subject), 
            data=DT, tolParInv = 1e-6, verbose = FALSE)
summary(fm2)$varcomp

##################################
## lme4
# fm1 <- lmer(Reaction ~ Days + (Days | Subject), data=DT)
# vc <- VarCorr(fm1); print(vc,comp=c("Variance"))
## sommer
## no equivalence in sommer to find the correlation between the 2 vc
## this is the most similar which is equivalent to (intercept || slope)
fm2 <- mmer(Reaction ~ Days,
            random= ~ Subject + vsr(Days, Subject), 
            data=DT, tolParInv = 1e-6, verbose = FALSE)
summary(fm2)$varcomp

##################################
## lme4
# fm1 <- lmer(Reaction ~ Days + (0 + Days | Subject), data=DT)
# vc <- VarCorr(fm1); print(vc,comp=c("Variance"))
## sommer
fm2 <- mmer(Reaction ~ Days,
            random= ~ vsr(Days, Subject), 
            data=DT, tolParInv = 1e-6, verbose = FALSE)
summary(fm2)$varcomp