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#---------------------------------------------------------------------------
# Simulate partial and full replicate design and scaled ABE power
# using 'widened' limits (EMA)
# But the estimation method via intra-subject contrasts (FDA, HC)
#
# Author: dlabes
#---------------------------------------------------------------------------
# degrees of freedom for the TR/RR analysis:
# Using the intrasubject contrasts T-R and R-R and analyze them
# by sequence groups the df's = n-seq (robust df's).
# 2x3x3 dfRR = n-3
# 2x2x4 dfRR = n-2
# 2x2x3 dfRR = n/2 - 2
power.scABEL2 <- function(alpha=0.05, theta1, theta2, theta0, CV, n,
design=c("2x3x3", "2x2x4", "2x2x3"), regulator,
nsims, details=FALSE, setseed=TRUE)
{
# function is no longer visible via NAMESPACE
# .Deprecated(new="power.scABEL", msg=paste0("'power.scABEL2' is deprecated.",
# " Use 'power.scABEL' instead."))
if (missing(CV)) stop("CV must be given!")
if (missing(n)) stop("Number of subjects n must be given!")
if (missing(theta0)) theta0 <- 0.90
if (length(theta0)>1) {
theta0 <- theta0[2]
warning(paste0("theta0 has to be scalar. theta0 = ",
theta0, " used."), call. = FALSE)
}
if (missing(theta1) & missing(theta2)) theta1 <- 0.8
if (missing(theta2)) theta2 <- 1/theta1
if (missing(theta1)) theta1 <- 1/theta2
ptm <- proc.time()
CVwT <- CV[1]
if (length(CV)==2) CVwR <- CV[2] else CVwR <- CVwT
if (missing(nsims)) { # not given
if (theta0 == scABEL(CVwR)[["lower"]] | theta0 == scABEL(CVwR)[["upper"]]) {
nsims <- 1e6 # simulating TIE
} else {
nsims <- 1e5 # simulating power
}
}
s2wT <- log(1.0 + CVwT^2)
s2wR <- log(1.0 + CVwR^2)
if(missing(regulator)) regulator <- "EMA"
# check regulator and get
# constants acc. to regulatory bodies (function in scABEL.R)
reg <- reg_check(regulator)
CVcap <- reg$CVcap
CVswitch <- reg$CVswitch
r_const <- reg$r_const
pe_constr <- reg$pe_constr
if(is.null(pe_constr)) pe_constr <- TRUE
design <- match.arg(design)
if (design=="2x3x3") {
seqs <- 3
dfe <- parse(text="n-3", srcfile=NULL)
# this is only for testing purposes
dfRRe <- parse(text="n-3", srcfile=NULL)
#sd2 <- s2D + (s2wT + s2wR)/2 # used in v1.1-00 - v1.1-02
# according to McNally et al.
# verified via simulations:
Emse <- s2wT + s2wR/2
}
if (design=="2x2x4") {
seqs <- 2
dfe <- parse(text="n-2", srcfile=NULL)
dfRRe <- parse(text="n-2", srcfile=NULL)
# sd^2 of the differences T-R from their components
Emse <- (s2wT + s2wR)/2
}
if (design=="2x2x3") {
seqs <- 2
dfe <- parse(text="n-2", srcfile=NULL)
dfRRe <- parse(text="n/2-1", srcfile=NULL) # for balanced designs
# sd^2 of the differences T-R from their components
Emse <- 1.5*(s2wT + s2wR)/2 # for balanced design
}
if (length(n)==1){
# then we assume n=ntotal
# for unbalanced designs we divide the ns by ourself
# to have only small imbalance
nv <- nvec(n=n, grps=seqs)
if (nv[1]!=nv[length(nv)]){
message("Unbalanced design. n(i)=", paste(nv, collapse="/"), " assumed.")
}
} else {
# then we assume n = vector of n's in sequences
# check length
if (length(n)!=seqs) stop("n must be a vector of length=",seqs,"!")
nv <- n
}
C3 <- sum(1/nv)/seqs^2
n <- sum(nv)
df <- eval(dfe)
if (design=="2x2x3"){
dfTT <- nv[1]-1
dfRR <- nv[2]-1
# where does this next came from?
Emse <- (dfRR*(s2wT + s2wR/2)+dfTT*(s2wT/2 + s2wR))/(dfRR+dfTT)
# warning in case of unbalanced design and heteroscdasticity
# here not? TODO: check this against subject sims
# if (abs(s2wT - s2wR)>1e-5 & abs(dfRR-dfTT)>2){
# warning(paste("Heteroscedasticity in unbalanced 2x2x3 design may led",
# "to poor accuracy of power!"), call.=FALSE)
# }
} else {
dfRR <- eval(dfRRe)
}
# sd of the mean T-R (point estimate)
sdm <- sqrt(Emse*C3)
# pe in the log domain
mlog <- log(theta0)
if(setseed) set.seed(123456)
p <- .pwr.ABEL.ISC(mlog, sdm, C3, Emse, df, s2wR, dfRR, nsims,
CVswitch=CVswitch, r_const=r_const, CVcap=CVcap,
pe_constr=pe_constr, ln_lBEL=log(theta1),ln_uBEL=log(theta2),
alpha=alpha)
if (details) {
ptm <- summary(proc.time()-ptm)
message(nsims," sims. Time elapsed (sec): ",
formatC(ptm["elapsed"], digits=2), "\n")
#print(ptm)
# return also the components
names(p) <- c("p(BE)", "p(BE-ABEL)", "p(BE-pe)", "p(BE-ABE)")
if (!pe_constr) p <- p[-3] # without pe constraint
p
} else {
# return only the 'power'
as.numeric(p["BE"])
}
}
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