Nothing
## ----echo=F-------------------------------------------------------------------
### get knitr just the way we like it
knitr::opts_chunk$set(
message = FALSE,
warning = FALSE,
error = FALSE,
tidy = FALSE,
cache = FALSE
)
## -----------------------------------------------------------------------------
library(ASSISTant)
##Fix randomization vector N, errors, eps
trialParameters <- list(N = c(200, 340, 476), type1Error = 0.025,
eps = 1/2, type2Error = 0.1)
## -----------------------------------------------------------------------------
designParameters <- list(
nul0 = list(prevalence = rep(1/6, 6), mean = matrix(0, 2, 6),
sd = matrix(1, 2, 6)),
alt1 = list(prevalence = rep(1/6, 6), mean = rbind(rep(0, 6),
c(0.5, 0.4, 0.3, 0, 0, 0)),
sd = matrix(1, 2, 6)),
alt2 = list(prevalence = rep(1/6, 6), mean = rbind(rep(0, 6),
c(0.5, 0.5, 0, 0, 0, 0)),
sd = matrix(1,2, 6)),
alt3 = list(prevalence = rep(1/6, 6), mean = rbind(rep(0, 6), rep(0.36, 6)),
sd = matrix(1,2, 6)),
alt4 = list(prevalence = rep(1/6, 6), mean = rbind(rep(0, 6), rep(0.30, 6)),
sd = matrix(1,2, 6)),
alt5 = list(prevalence = rep(1/6, 6), mean = rbind(rep(0, 6),
c(0.4, 0.3, 0.2, 0, 0, 0)),
sd = matrix(1,2, 6)),
alt6 = list(prevalence = rep(1/6, 6), mean = rbind(rep(0, 6),
c(0.5, 0.5, 0.3, 0.3, 0.1, 0.1)),
sd = matrix(1,2, 6))
)
## -----------------------------------------------------------------------------
defuse3 <- DEFUSE3Design$new(trialParameters = trialParameters,
numberOfSimulations = 500,
designParameters = designParameters$nul0,
showProgress = FALSE)
print(defuse3)
## -----------------------------------------------------------------------------
result <- defuse3$explore(numberOfSimulations = 500,
showProgress = FALSE,
rngSeed = 28912)
analysis <- defuse3$analyze(result)
print(defuse3$summary(analysis))
## -----------------------------------------------------------------------------
result1 <- defuse3$explore(numberOfSimulations = 500,
trueParameters = designParameters$alt1,
showProgress = FALSE,
rngSeed = 737218)
analysis1 <- defuse3$analyze(result1)
print(defuse3$summary(analysis1))
## -----------------------------------------------------------------------------
result2 <- defuse3$explore(numberOfSimulations = 500,
trueParameters = designParameters$alt2,
showProgress = FALSE,
rngSeed = 928812)
analysis2 <- defuse3$analyze(result2)
print(defuse3$summary(analysis2))
## -----------------------------------------------------------------------------
null.uniform <- rep(1, 7L) ## uniform on 7 support points
hourglass <- c(1, 2, 2, 1, 2, 2, 1)
inverted.hourglass <- c(2, 1, 1, 2, 1, 1, 2)
bottom.heavy <- c(2, 2, 2, 1, 1, 1, 1)
bottom.heavier <- c(3, 3, 2, 2, 1, 1, 1)
bottom.loaded <- c(4, 4, 3, 3, 2, 1, 1)
top.heavy <- c(1, 1, 1, 1, 2, 2, 2)
top.heavier <- c(1, 1, 1, 2, 2, 3, 3)
top.loaded <- c(1, 1, 2, 3, 3, 4, 4)
## -----------------------------------------------------------------------------
## -----------------------------------------------------------------------------
knitr::kable(
sapply(list(null = null.uniform,
hourglass = hourglass,
inv.hourglass = inverted.hourglass,
bot.heavy = bottom.heavy,
bot.heavier = bottom.heavier,
bot.loaded = bottom.loaded,
top.heavy = top.heavy,
top.heavier = top.heavier,
top.loaded = top.loaded),
computeMeanAndSD)
)
## -----------------------------------------------------------------------------
designParameters <- list(
nul0 = list(prevalence = rep(1, 2),
ctlDist = null.uniform,
trtDist = cbind(null.uniform,
null.uniform)),
alt1 = list(prevalence = rep(1, 2),
ctlDist = null.uniform,
trtDist = cbind(top.loaded,
null.uniform)),
alt2 = list(prevalence = rep(1, 2),
ctlDist = null.uniform,
trtDist = cbind(null.uniform,
top.loaded))
)
## -----------------------------------------------------------------------------
discDefuse3 <- DEFUSE3Design$new(trialParameters = trialParameters,
numberOfSimulations = 5000,
discreteData = TRUE,
designParameters = designParameters$nul0,
showProgress = FALSE)
print(discDefuse3)
## -----------------------------------------------------------------------------
result <- discDefuse3$explore(numberOfSimulations = 50,
showProgress = FALSE,
rngSeed = 3783)
analysis <- discDefuse3$analyze(result)
print(discDefuse3$summary(analysis))
## -----------------------------------------------------------------------------
result1 <- discDefuse3$explore(numberOfSimulations = 50,
trueParameters = designParameters$alt1,
showProgress = FALSE,
rngSeed = 28912)
analysis1 <- discDefuse3$analyze(result1)
print(discDefuse3$summary(analysis1))
## -----------------------------------------------------------------------------
result2 <- discDefuse3$explore(numberOfSimulations = 50,
trueParameters = designParameters$alt2,
showProgress = FALSE,
rngSeed = 931)
analysis2 <- discDefuse3$analyze(result2)
print(discDefuse3$summary(analysis2))
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