Nothing
# c212.interim
# Case 2/12: Interim Analysis wrapper
# R. Carragher
# Date: 28/04/2015
Md <- new.env()
Md$Id <- "$Id: c212.interim.1a.hier3.lev2.R,v 1.9 2018/10/03 15:40:55 clb13102 Exp clb13102 $"
c212.interim.1a.dep.lev2 <- function(trial.data, sim_type = "SLICE", burnin = 10000, iter = 40000, nchains = 3,
global.sim.params = data.frame(type = c("MH", "SLICE"), param = c("sigma_MH", "w"), value = c(0.2,1),
control = c(0,6)),
sim.params = NULL,
monitor = data.frame(variable = c("theta", "gamma", "mu.gamma", "mu.theta",
"sigma2.theta", "sigma2.gamma",
"mu.theta.0", "mu.gamma.0", "tau2.theta.0", "tau2.gamma.0"),
monitor = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
stringsAsFactors = FALSE),
initial_values = NULL,
hyper_params = list(mu.gamma.0.0 = 0, tau2.gamma.0.0 = 10,
mu.theta.0.0 = 0, tau2.theta.0.0 = 10, alpha.gamma.0.0 = 3, beta.gamma.0.0 = 1, alpha.theta.0.0 = 3,
beta.theta.0.0 = 1, alpha.gamma = 3, beta.gamma = 1, alpha.theta = 3, beta.theta = 1), memory_model = "HIGH")
{
interim = M_global$INTERIMdata(Md, trial.data, iter, nchains, burnin, initial_values)
if (is.null(interim)) {
return(NULL)
}
trial.data = interim$trial.data
cntrl.data = interim$cntrl.data
Md$sim_type <- sim_type
if (nrow(global.sim.params[global.sim.params$type == sim_type,]) != 1) {
print("Missing simulation parametetrs");
return(NULL)
}
Md$global.sim.param <- global.sim.params[global.sim.params$type == sim_type,]$value
Md$global.sim.param_ctrl <- global.sim.params[global.sim.params$type == sim_type,]$control
if (Md$global.sim.param <= 0) {
print("Invalid simulation parametetr value");
return(NULL)
}
Md$level = 2
sim.params = M_global$INTERIM_sim_params1a(Md, sim.params, sim_type, trial.data, cntrl.data)
monitor = M_global$INTERIM_monitor_1a_3(monitor)
# Initialise the hyper-parameters
Md$mu.gamma.0.0 <- hyper_params$mu.gamma.0.0
Md$tau2.gamma.0.0 <- hyper_params$tau2.gamma.0.0
Md$alpha.gamma <- hyper_params$alpha.gamma
Md$beta.gamma <- hyper_params$beta.gamma
Md$alpha.gamma.0.0 <- hyper_params$alpha.gamma.0.0
Md$beta.gamma.0.0 <- hyper_params$beta.gamma.0.0
Md$mu.theta.0.0 <- hyper_params$mu.theta.0.0
Md$tau2.theta.0.0 <- hyper_params$tau2.theta.0.0
Md$alpha.theta <- hyper_params$alpha.theta
Md$beta.theta <- hyper_params$beta.theta
Md$alpha.theta.0.0 <- hyper_params$alpha.theta.0.0
Md$beta.theta.0.0 <- hyper_params$beta.theta.0.0
Ret2 = .Call("c2121a_poisson_mc_exec", as.integer(nchains), as.integer(burnin),
as.integer(iter), Md$sim_type,
memory_model,
as.numeric(Md$global.sim.param),
as.numeric(Md$global.sim.param_ctrl),
sim.params,
monitor,
as.integer(Md$numIntervals), as.integer(Md$level),
Md$maxBs, as.integer(Md$numB), as.integer(Md$maxAEs),
as.integer(t(Md$nAE)), as.integer(aperm(Md$x)), as.integer(aperm(Md$y)),
as.numeric(aperm(Md$C)),
as.numeric(aperm(Md$T)),
as.numeric(aperm(Md$theta)),
as.numeric(aperm(Md$gamma)),
as.numeric(Md$mu.gamma.0.0),
as.numeric(Md$tau2.gamma.0.0),
as.numeric(Md$mu.theta.0.0),
as.numeric(Md$tau2.theta.0.0),
as.numeric(Md$alpha.gamma.0.0),
as.numeric(Md$beta.gamma.0.0),
as.numeric(Md$alpha.theta.0.0),
as.numeric(Md$beta.theta.0.0),
as.numeric(Md$alpha.gamma),
as.numeric(Md$beta.gamma),
as.numeric(Md$alpha.theta),
as.numeric(Md$beta.theta),
as.numeric(Md$mu.gamma.0),
as.numeric(Md$tau2.gamma.0),
as.numeric(Md$mu.theta.0),
as.numeric(Md$tau2.theta.0),
as.numeric(aperm(Md$mu.gamma)),
as.numeric(aperm(Md$mu.theta)),
as.numeric(aperm(Md$sigma2.gamma)),
as.numeric(aperm(Md$sigma2.theta)))
mu.gamma.0_samples = NULL
if (monitor[monitor$variable == "mu.gamma.0", ]$monitor == 1) {
mu.gamma.0_samples <- .Call("getMuGamma0SamplesInterimAll")
mu.gamma.0_samples = aperm(mu.gamma.0_samples)
}
mu.theta.0_samples = NULL
if (monitor[monitor$variable == "mu.theta.0", ]$monitor == 1) {
mu.theta.0_samples <- .Call("getMuTheta0SamplesInterimAll")
mu.theta.0_samples = aperm(mu.theta.0_samples)
}
tau2.gamma.0_samples = NULL
if (monitor[monitor$variable == "tau2.gamma.0", ]$monitor == 1) {
tau2.gamma.0_samples <- .Call("getTau2Gamma0SamplesInterimAll")
tau2.gamma.0_samples = aperm(tau2.gamma.0_samples)
}
tau2.theta.0_samples = NULL
if (monitor[monitor$variable == "tau2.theta.0", ]$monitor == 1) {
tau2.theta.0_samples <- .Call("getTau2Theta0SamplesInterimAll")
tau2.theta.0_samples = aperm(tau2.theta.0_samples)
}
mu.theta_samples = NULL
if (monitor[monitor$variable == "mu.theta", ]$monitor == 1) {
mu.theta_samples <- .Call("getMuThetaSamplesInterimAll")
mu.theta_samples <- aperm(mu.theta_samples)
}
mu.gamma_samples = NULL
if (monitor[monitor$variable == "mu.gamma", ]$monitor == 1) {
mu.gamma_samples <- .Call("getMuGammaSamplesInterimAll")
mu.gamma_samples <- aperm(mu.gamma_samples)
}
sigma2.theta_samples = NULL
if (monitor[monitor$variable == "sigma2.theta", ]$monitor == 1) {
sigma2.theta_samples <- .Call("getSigma2ThetaSamplesInterimAll")
sigma2.theta_samples <- aperm(sigma2.theta_samples)
}
sigma2.gamma_samples = NULL
if (monitor[monitor$variable == "sigma2.gamma", ]$monitor == 1) {
sigma2.gamma_samples <- .Call("getSigma2GammaSamplesInterimAll")
sigma2.gamma_samples <- aperm(sigma2.gamma_samples)
}
gamma_samples = NULL
gamma_acc = NULL
if (monitor[monitor$variable == "gamma", ]$monitor == 1) {
gamma_samples = .Call("getGammaSamplesInterimAll")
gamma_samples = aperm(gamma_samples)
gamma_acc = .Call("getGammaAcceptInterimAll")
gamma_acc <- aperm(gamma_acc)
}
theta_samples = NULL
theta_acc = NULL
if (monitor[monitor$variable == "theta", ]$monitor == 1) {
theta_samples = .Call("getThetaSamplesInterimAll")
theta_samples = aperm(theta_samples)
theta_acc = .Call("getThetaAcceptInterimAll")
theta_acc <- aperm(theta_acc)
}
.C("Release_Interim")
model_fit = list(id = Md$Id, sim_type = Md$sim_type, chains = nchains, nIntervals = Md$numIntervals,
Intervals = Md$Intervals, nBodySys = Md$numB, maxBs = Md$maxBs,
maxAEs = Md$maxAEs, nAE = Md$nAE, AE=Md$AE, B = Md$B,
burnin = burnin, iter = iter,
monitor = monitor,
gamma = gamma_samples,
theta = theta_samples,
mu.gamma = mu.gamma_samples,
mu.theta = mu.theta_samples,
sigma2.gamma = sigma2.gamma_samples,
sigma2.theta = sigma2.theta_samples,
mu.gamma.0 = mu.gamma.0_samples,
mu.theta.0 = mu.theta.0_samples,
tau2.gamma.0 = tau2.gamma.0_samples,
tau2.theta.0 = tau2.theta.0_samples,
gamma_acc = gamma_acc,
theta_acc = theta_acc)
# Model is poisson with BB1a hierarchy and independent intervals
attr(model_fit, "model") = "1a_pois_dep_lev2"
return(model_fit)
}
Md$initVars = function() {
# Data Structure
Md$B <- c()
Md$numB <- NA
Md$numIntervals <- NA
Md$nAE <- c()
Md$maxAEs <- NA
# Trial Event Data
Md$x <- array()
Md$C <- array()
Md$y <- array()
Md$T <- array()
# Hyperparameters
Md$mu.gamma.0.0 <- NA
Md$tau2.gamma.0.0 <- NA
Md$mu.theta.0.0 <- NA
Md$tau2.theta.0.0 <- NA
Md$alpha.gamma.0.0 <- NA
Md$beta.gamma.0.0 <- NA
Md$alpha.theta.0.0 <- NA
Md$beta.theta.0.0 <- NA
Md$alpha.gamma <- NA
Md$beta.gamma <- NA
Md$alpha.theta <- NA
Md$beta.theta <- NA
# Parameters/Simulated values
# Stage 3
Md$mu.gamma.0 <- c()
Md$tau2.gamma.0 <- c()
Md$mu.theta.0 <- c()
Md$tau2.theta.0 <- c()
# Stage 2
Md$mu.gamma <- array()
Md$mu.theta <- array()
Md$sigma2.gamma <- array()
Md$sigma2.theta <- array()
# Stage 1
Md$theta <- array()
Md$gamma <- array()
}
Md$initChains = function(c) {
# Choose random values for gamma and theta
for (i in 1:Md$numIntervals) {
numB = Md$numB[i]
for (b in 1:numB) {
Md$gamma[c, i, b, 1:Md$nAE[i, b]] <- runif(Md$nAE[i, b], -10, 10)
Md$theta[c, i, b, 1:Md$nAE[i, b]] <- runif(Md$nAE[i, b], -10, 10)
Md$theta[c, i, b, ][is.infinite(Md$theta[c, i, b, ])] = -10
Md$gamma[c, i, b, ][is.infinite(Md$gamma[c, i, b, ])] = -10
Md$theta[c, i, b, ][is.nan(Md$theta[c, i, b, ])] = -10 # -1000
Md$gamma[c, i, b, ][is.nan(Md$gamma[c, i, b, ])] = -10 # -1000
}
Md$mu.gamma[c, i, 1:numB] = runif(numB, -10, 10)
Md$mu.theta[c, i, 1:numB] = runif(numB, -10, 10)
Md$sigma2.gamma[c, i, 1:numB] = runif(numB, 5, 20)
Md$sigma2.theta[c, i, 1:numB] = runif(numB, 5, 20)
Md$mu.gamma.0[c] = runif(1, -10, 10)
Md$tau2.gamma.0[c] = runif(1, 5, 20)
Md$mu.theta.0[c] = runif(1, -10, 10)
Md$tau2.theta.0[c] = runif(1, 5, 20)
}
}
Md$initialiseChains = function(initial_values, nchains) {
Md$theta = array(0, dim=c(nchains, Md$numIntervals, Md$maxBs, Md$maxAEs))
Md$gamma = array(0, dim=c(nchains, Md$numIntervals, Md$maxBs, Md$maxAEs))
if (is.null(initial_values)) {
# Initialise the first chain with the data
for (i in 1:Md$numIntervals) {
numB = Md$numB[i]
for (b in 1:numB) {
Md$gamma[1, i, b, ] <- log(Md$x[i, b,]/Md$C[i, b, ])
Md$theta[1, i, b, ] <- log(Md$y[i, b,]/Md$T[i, b, ]) - Md$gamma[1, i, b, ]
Md$theta[1, i, b, ][is.infinite(Md$theta[1, i, b, ])] = -10 # -1000
Md$gamma[1, i, b, ][is.infinite(Md$gamma[1, i, b, ])] = -10 # -1000
Md$theta[1, i, b, ][is.nan(Md$theta[1, i, b, ])] = -10 # -1000
Md$gamma[1, i, b, ][is.nan(Md$gamma[1, i, b, ])] = -10 # -1000
}
}
Md$mu.gamma <- array(0, dim = c(nchains, Md$numIntervals, Md$maxBs))
Md$mu.theta <- array(0, dim = c(nchains, Md$numIntervals, Md$maxBs))
Md$sigma2.gamma <- array(10, dim = c(nchains, Md$numIntervals, Md$maxBs))
Md$sigma2.theta <- array(10, dim = c(nchains, Md$numIntervals, Md$maxBs))
Md$mu.gamma.0 <- rep(0, nchains)
Md$tau2.gamma.0 <- rep(10, nchains)
Md$mu.theta.0 <- rep(0, nchains)
Md$tau2.theta.0 <- rep(10, nchains)
if (nchains > 1) {
for (c in 2:nchains) {
Md$initChains(c)
}
}
}
else {
Md$mu.gamma.0 <- rep(0, nchains)
Md$tau2.gamma.0 <- rep(10, nchains)
Md$mu.theta.0 <- rep(0, nchains)
Md$tau2.theta.0 <- rep(10, nchains)
for (c in 1:nchains) {
Md$mu.gamma.0[c] = initial_values$mu.gamma.0[c]
Md$mu.theta.0[c] = initial_values$mu.theta.0[c]
Md$tau2.gamma.0[c] = initial_values$tau2.gamma.0[c]
Md$tau2.theta.0[c] = initial_values$tau2.theta.0[c]
}
Md$mu.gamma <- array(0, dim = c(nchains, Md$numIntervals, Md$maxBs))
Md$mu.theta <- array(0, dim = c(nchains, Md$numIntervals, Md$maxBs))
Md$sigma2.gamma <- array(0, dim = c(nchains, Md$numIntervals, Md$maxBs))
Md$sigma2.theta <- array(0, dim = c(nchains, Md$numIntervals, Md$maxBs))
for (c in 1:nchains) {
for (i in 1:Md$numIntervals) {
interval = Md$Intervals[i]
for (b in 1:Md$numB[i]) {
data = initial_values$mu.gamma[initial_values$mu.gamma$chain == c &
initial_values$mu.gamma$Interval == interval
& initial_values$mu.gamma$B == Md$B[i, b],]
Md$mu.gamma[c, i, b] = data$value
data = initial_values$mu.theta[initial_values$mu.theta$chain == c &
initial_values$mu.theta$Interval == interval
& initial_values$mu.theta$B == Md$B[i, b],]
Md$mu.theta[c, i, b] = data$value
data = initial_values$sigma2.gamma[initial_values$sigma2.gamma$chain == c &
initial_values$sigma2.gamma$Interval == interval
& initial_values$sigma2.gamma$B == Md$B[i, b],]
Md$sigma2.gamma[c, i, b] = data$value
data = initial_values$sigma2.theta[initial_values$sigma2.theta$chain == c &
initial_values$sigma2.theta$Interval == interval
& initial_values$sigma2.theta$B == Md$B[i, b],]
Md$sigma2.theta[c, i, b] = data$value
}
}
}
for (c in 1:nchains) {
for (i in 1:Md$numIntervals) {
interval = Md$Intervals[i]
for (b in 1:Md$numB[i]) {
for (j in 1:Md$nAE[i, b]) {
ae = Md$AE[i, b, j]
data = initial_values$gamma[initial_values$gamma$chain == c
& initial_values$gamma$Interval == interval
& initial_values$gamma$B == Md$B[i, b]
& initial_values$gamma$AE == ae,]
Md$gamma[c, i, b, j] = data$value
data = initial_values$theta[initial_values$theta$chain == c
& initial_values$theta$Interval == interval
& initial_values$theta$B == Md$B[i, b]
& initial_values$theta$AE == ae,]
Md$theta[c, i, b, j] = data$value
}
}
}
}
}
}
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