Simulation for determining sample size in Repeated Measures ANOVA

powerSampleSize.R

# Simulation study for sample size between/within
# got Treat + Sham between subjects
# got Time within subjects

nPerGroup <- 30
nTime     <- 4
muTreat   <- c(37, 32, 20, 15)
muSham    <- c(37, 32, 25, 22)
stdevs    <- c(12, 10, 8, 6)
stdiff    <- 9
nSim      <- 1000

# set up the indep var data
Subject <- factor(1:(nPerGroup*2))
Time <- factor(1:nTime, labels = c("0min", "15min", "48hrs", "96hrs"))

theData <- expand.grid(Time, Subject)
names(theData) <- c("Time", "Subject")

tmp <- rep(c("Treat", "Sham"), each = nPerGroup * nTime)
theData$Method <- factor(tmp)

# to set up variance-covariance matrix
ones <- rep(1, nTime)
A <- stdevs^2 %o% ones
B <- (A + t(A) + (stdiff^2)*(diag(nTime) - ones %o% ones))/2


# can run it through once to check that it works
library(MASS)
tmp1 <- mvrnorm(nPerGroup, mu = muTreat, Sigma = B)
tmp2 <- mvrnorm(nPerGroup, mu = muSham, Sigma = B)
theData$NDI <- c(as.vector(t(tmp1)), as.vector(t(tmp2)))
aovComp <- aov(NDI ~ Time*Method + Error(Subject/Time), theData)
summary(aovComp)

# some descriptive statistics and graphs
print(model.tables(aovComp, "means"), digits = 3) 
boxplot(NDI ~ Time, data = theData)              
boxplot(NDI ~ Method, data = theData)            
boxplot(NDI ~ Time*Method, data = theData)       
with(theData, interaction.plot(Time, Method, NDI))


###############################################
# for power estimate run the below
# don't forget to set up theData and var-cov
library(MASS)

runTest <- function(){
  tmp1 <- mvrnorm(nPerGroup, mu = muTreat, Sigma = B)
  tmp2 <- mvrnorm(nPerGroup, mu = muSham, Sigma = B)
  theData$NDI <- c(as.vector(t(tmp1)), as.vector(t(tmp2)))
  aovComp <- aov(NDI ~ Time*Method + Error(Subject/Time), theData) 
  b <- summary(aovComp)$'Error: Subject:Time'[[1]][2,5]
  b < 0.05
}

# here is estimate of power for given nPerGroup
mean(replicate(nSim, runTest()))

Hi gjkerns, I first found this ost of yours on R-bloggers and I'm trying to use it, but I can't run the 'stdevs' command in line 25. Is it supposed to be a standard deviation command or is there something special about it - and if the latter, which package does it belong to? I'm an R and git newbie so I hope you don't mind my asking this question here! -Tory.

Hi gjkerns, I first found this ost of yours on R-bloggers and I'm trying to use it, but I can't run the 'stdevs' command in line 25. Is it supposed to be a standard deviation command or is there something special about it - and if the latter, which package does it belong to? I'm an R and git newbie so I hope you don't mind my asking this question here! -Tory.

Hi, Tory
This is a very good example.
'stdevs' is a variable defined in line 9 if you run the code from the beginning. Hope this helps. Good Luck.