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R/c212.params.R
In c212: Methods for Detecting Safety Signals in Clinical Trials Using Body-Systems (System Organ Classes)
Defines functions
c212.BB.hyper.params
c212.1a.hyper.params
c212.hyper.params
c212.BB.global.sim.params
c212.1a.global.sim.params
c212.global.sim.params
c212.BB.sim.control.params
c212.1a.sim.control.params
c212.sim.control.params
Documented in
c212.global.sim.params
c212.hyper.params
c212.sim.control.params
# c212
# Default params
# R. Carragher
# Date: 20/08/2020
Id <- "$Id: c212.params.R,v 1.4 2020/08/31 10:03:45 clb13102 Exp clb13102 $"
c212.sim.control.params = function(trial.data, model = "1a") {
if (model == "1a") {
sim_param = c212.1a.sim.control.params(trial.data)
}
else {
sim_param = c212.BB.sim.control.params(trial.data)
}
sim_param
}
c212.1a.sim.control.params = function(trial.data) {
if (is.character(trial.data)) {
file = trial.data
trial.data <- read.table(file, header=TRUE, stringsAsFactors = FALSE)
}
trial.data = trial.data[trial.data$Group == 2,]
n = nrow(trial.data)
facs <- sapply(trial.data, is.factor)
trial.data[facs] <- sapply(trial.data[facs], as.character)
if ("Interval" %in% names(trial.data)) {
p_SLICE = "w"
v_SLICE = 1.0
c_SLICE = 6
p_MH = "sigma_MH"
v_MH = 0.2
c_MH = 0.0
sp1 = data.frame(type = "SLICE", variable = "gamma",
Interval = trial.data$Interval,
I_index = trial.data$I_index, B = trial.data$B,
AE = trial.data$AE,
param = p_SLICE, value = v_SLICE, control = c_SLICE,
stringsAsFactors = FALSE)
sp2 = data.frame(type = "SLICE", variable = "theta",
Interval = trial.data$Interval,
I_index = trial.data$I_index, B = trial.data$B,
AE = trial.data$AE,
param = p_SLICE, value = v_SLICE, control = c_SLICE,
stringsAsFactors = FALSE)
sp3 = data.frame(type = "MH", variable = "gamma",
Interval = trial.data$Interval,
I_index = trial.data$I_index, B = trial.data$B,
AE = trial.data$AE,
param = p_MH, value = v_MH, control = c_MH,
stringsAsFactors = FALSE)
sp4 = data.frame(type = "MH", variable = "theta",
Interval = trial.data$Interval,
I_index = trial.data$I_index, B = trial.data$B,
AE = trial.data$AE,
param = p_MH, value = v_MH, control = c_MH,
stringsAsFactors = FALSE)
}
else {
p_SLICE = "w"
v_SLICE = 1.0
c_SLICE = 6
p_MH = "sigma_MH"
v_MH = 0.35
c_MH = 0.0
sp1 = data.frame(type = "SLICE", variable = "gamma",
B = trial.data$B,
AE = trial.data$AE,
param = p_SLICE, value = v_SLICE, control = c_SLICE,
stringsAsFactors = FALSE)
sp2 = data.frame(type = "SLICE", variable = "theta",
B = trial.data$B,
AE = trial.data$AE,
param = p_SLICE, value = v_SLICE, control = c_SLICE,
stringsAsFactors = FALSE)
sp3 = data.frame(type = "MH", variable = "gamma",
B = trial.data$B,
AE = trial.data$AE,
param = p_MH, value = v_MH, control = c_MH,
stringsAsFactors = FALSE)
sp4 = data.frame(type = "MH", variable = "theta",
B = trial.data$B,
AE = trial.data$AE,
param = p_MH, value = v_MH, control = c_MH,
stringsAsFactors = FALSE)
}
sim_params = rbind(sp1, sp2, sp3, sp4)
sim_params
}
c212.BB.sim.control.params = function(trial.data) {
if (is.character(trial.data)) {
file = trial.data
trial.data <- read.table(file, header=TRUE, stringsAsFactors = FALSE)
}
facs <- sapply(trial.data, is.factor)
trial.data[facs] <- sapply(trial.data[facs], as.character)
trial.data = trial.data[trial.data$Group == 2,]
if ("Interval" %in% names(trial.data)) {
v_sigma_MH_gamma = 0.2
v_sigma_MH_theta = 0.15
v_w = 1
v_w_control = 6
v_sigma = 3
sp1 = data.frame(type = "MH", variable = "gamma",
Interval = trial.data$Interval,
I_index = trial.data$I_index,
B = trial.data$B,
AE = trial.data$AE,
param = "sigma_MH_gamma", value = v_sigma_MH_gamma,
control = 0,
stringsAsFactors = FALSE)
sp2 = data.frame(type = "MH", variable = "theta",
Interval = trial.data$Interval,
I_index = trial.data$I_index,
B = trial.data$B,
AE = trial.data$AE,
param = "sigma_MH_theta", value = v_sigma_MH_theta,
control = 0,
stringsAsFactors = FALSE)
sp3 = data.frame(type = "SLICE", variable = "gamma",
Interval = trial.data$Interval,
I_index = trial.data$I_index,
B = trial.data$B,
AE = trial.data$AE,
param = "w_gamma", value = v_w,
control = v_w_control,
stringsAsFactors = FALSE)
sp4 = data.frame(type = "MH", variable = "alpha",
Interval = unique(trial.data$Interval),
I_index = unique(trial.data$I_index),
B = NA,
AE = NA,
param = "sigma_MH_alpha", value = v_sigma,
control = 0,
stringsAsFactors = FALSE)
sp5 = data.frame(type = "SLICE", variable = "alpha",
Interval = unique(trial.data$Interval),
I_index = unique(trial.data$I_index),
B = NA,
AE = NA,
param = "w_alpha", value = v_w,
control = v_w_control,
stringsAsFactors = FALSE)
sp6 = data.frame(type = "MH", variable = "beta",
Interval = unique(trial.data$Interval),
I_index = unique(trial.data$I_index),
B = NA,
AE = NA,
param = "sigma_MH_beta", value = v_sigma,
control = 0,
stringsAsFactors = FALSE)
sp7 = data.frame(type = "SLICE", variable = "beta",
Interval = unique(trial.data$Interval),
I_index = unique(trial.data$I_index),
B = NA,
AE = NA,
param = "w_beta", value = v_w,
control = v_w_control,
stringsAsFactors = FALSE)
sim_params = rbind(sp1, sp2, sp3, sp4, sp5, sp6, sp7)
}
else {
v_sigma_MH_gamma = 0.2
v_sigma_MH_theta = 0.2
v_w_gamma = 1
v_w_gamma_control = 6
sp1 = data.frame(type = "MH", variable = "gamma",
B = trial.data$B,
AE = trial.data$AE,
param = "sigma_MH_gamma", value = v_sigma_MH_gamma,
control = 0,
stringsAsFactors = FALSE)
sp2 = data.frame(type = "MH", variable = "theta",
B = trial.data$B,
AE = trial.data$AE,
param = "sigma_MH_theta", value = v_sigma_MH_theta,
control = 0,
stringsAsFactors = FALSE)
sp3 = data.frame(type = "SLICE", variable = "gamma",
B = trial.data$B,
AE = trial.data$AE,
param = "w_gamma", value = v_w_gamma,
control = v_w_gamma_control,
stringsAsFactors = FALSE)
sim_params = rbind(sp1, sp2, sp3)
}
sim_params
}
c212.global.sim.params <- function(trial.data, model = "BB", hier = 3) {
if (is.null(model)) {
return(NULL)
}
global.sim.params <- NULL
if (model == "1a") {
global.sim.params <- c212.1a.global.sim.params(trial.data, hier)
}
else if (model == "BB") {
global.sim.params <- c212.BB.global.sim.params(trial.data, hier)
}
global.sim.params
}
c212.1a.global.sim.params <- function(trial.data, hier = 3) {
if (is.character(trial.data)) {
file = trial.data
trial.data <- read.table(file, header=TRUE, stringsAsFactors = FALSE)
}
if (is.null(trial.data)) {
return(NULL)
}
global.sim.params <- NULL
if ("Interval" %in% names(trial.data)) {
global.sim.params = data.frame(type = c("MH", "SLICE"),
param = c("sigma_MH", "w"),
value = c(0.2,1),
control = c(0,6), stringsAsFactors = FALSE)
}
else {
#EOT 1a
global.sim.params = data.frame(type = c("MH", "SLICE"),
param = c("sigma_MH", "w"),
value = c(0.35,1),
control = c(0,6), stringsAsFactors = FALSE)
}
global.sim.params
}
c212.BB.global.sim.params <- function(trial.data, hier = 3) {
if (is.character(trial.data)) {
file = trial.data
trial.data <- read.table(file, header=TRUE, stringsAsFactors = FALSE)
}
if (is.null(trial.data)) {
return(NULL)
}
global.sim.params <- NULL
if ("Interval" %in% names(trial.data)) {
if (hier == 3) {
global.sim.params = data.frame(type = c("MH", "MH", "MH", "MH",
"SLICE", "SLICE", "SLICE"),
param = c("sigma_MH_alpha", "sigma_MH_beta",
"sigma_MH_gamma", "sigma_MH_theta",
"w_alpha", "w_beta", "w_gamma"),
value = c(3, 3, 0.2, 0.25, 1, 1, 1),
control = c(0, 0, 0, 0, 6, 6, 6),
stringsAsFactors = FALSE)
}
else if (hier == 2) {
global.sim.params = data.frame(type = c("MH", "MH", "MH", "MH",
"SLICE", "SLICE", "SLICE"),
param = c("sigma_MH_alpha", "sigma_MH_beta",
"sigma_MH_gamma", "sigma_MH_theta",
"w_alpha", "w_beta", "w_gamma"),
value = c(3, 3, 0.2, 0.5, 1, 1, 1),
control = c(0, 0, 0, 0, 6, 6, 6),
stringsAsFactors = FALSE)
}
}
else {
# EOT BB
global.sim.params = data.frame(type = c("MH", "MH", "MH", "MH",
"SLICE", "SLICE", "SLICE"),
param = c("sigma_MH_alpha", "sigma_MH_beta",
"sigma_MH_gamma", "sigma_MH_theta",
"w_alpha", "w_beta", "w_gamma"),
value = c(3, 3, 0.2, 0.2, 1, 1, 1),
control = c(0, 0, 0, 0, 6, 6, 6),
stringsAsFactors = FALSE)
}
global.sim.params
}
c212.hyper.params <- function(trial.data, model = "BB", hier = 3) {
if (is.null(model)) {
return(NULL)
}
hyper_params <- NULL
if (model == "1a") {
hyper_params <- c212.1a.hyper.params(trial.data, hier)
}
else if (model == "BB") {
hyper_params <- c212.BB.hyper.params(trial.data, hier)
}
hyper_params
}
c212.1a.hyper.params <- function(trial.data, hier = 3) {
if (is.character(trial.data)) {
file = trial.data
trial.data <- read.table(file, header=TRUE, stringsAsFactors = FALSE)
}
if (is.null(trial.data)) {
return(NULL)
}
hyper_params <- NULL
if ("Interval" %in% names(trial.data)) {
if (hier == 3) {
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)
}
else if (hier == 2) {
hyper_params = list(mu.gamma.0 = 0, tau2.gamma.0 = 10,
mu.theta.0 = 0, tau2.theta.0 = 10, alpha.gamma = 3,
beta.gamma = 1,
alpha.theta = 3, beta.theta = 1)
}
}
else {
#EOT 1a
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)
}
hyper_params
}
c212.BB.hyper.params <- function(trial.data, hier = 3) {
if (is.character(trial.data)) {
file = trial.data
trial.data <- read.table(file, header=TRUE, stringsAsFactors = FALSE)
}
if (is.null(trial.data)) {
return(NULL)
}
hyper_params <- NULL
if ("Interval" %in% names(trial.data)) {
if (hier == 3) {
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, lambda.alpha = 1.0, lambda.beta = 1.0)
}
else if (hier == 2) {
hyper_params = list(mu.gamma.0 = 0, tau2.gamma.0 = 10,
mu.theta.0 = 0, tau2.theta.0 = 10, alpha.gamma = 3,
beta.gamma = 1, alpha.theta = 3,
beta.theta = 1, alpha.pi = 1.1, beta.pi = 1.1)
}
}
else {
# EOT BB
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, lambda.alpha = 1.0, lambda.beta = 1.0)
}
hyper_params
}
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c212 documentation built on Sept. 8, 2020, 5:07 p.m.
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Defines functions c212.BB.hyper.params c212.1a.hyper.params c212.hyper.params c212.BB.global.sim.params c212.1a.global.sim.params c212.global.sim.params c212.BB.sim.control.params c212.1a.sim.control.params c212.sim.control.params
Documented in c212.global.sim.params c212.hyper.params c212.sim.control.params
# c212
# Default params
# R. Carragher
# Date: 20/08/2020
Id <- "$Id: c212.params.R,v 1.4 2020/08/31 10:03:45 clb13102 Exp clb13102 $"
c212.sim.control.params = function(trial.data, model = "1a") {
if (model == "1a") {
sim_param = c212.1a.sim.control.params(trial.data)
}
else {
sim_param = c212.BB.sim.control.params(trial.data)
}
sim_param
}
c212.1a.sim.control.params = function(trial.data) {
if (is.character(trial.data)) {
file = trial.data
trial.data <- read.table(file, header=TRUE, stringsAsFactors = FALSE)
}
trial.data = trial.data[trial.data$Group == 2,]
n = nrow(trial.data)
facs <- sapply(trial.data, is.factor)
trial.data[facs] <- sapply(trial.data[facs], as.character)
if ("Interval" %in% names(trial.data)) {
p_SLICE = "w"
v_SLICE = 1.0
c_SLICE = 6
p_MH = "sigma_MH"
v_MH = 0.2
c_MH = 0.0
sp1 = data.frame(type = "SLICE", variable = "gamma",
Interval = trial.data$Interval,
I_index = trial.data$I_index, B = trial.data$B,
AE = trial.data$AE,
param = p_SLICE, value = v_SLICE, control = c_SLICE,
stringsAsFactors = FALSE)
sp2 = data.frame(type = "SLICE", variable = "theta",
Interval = trial.data$Interval,
I_index = trial.data$I_index, B = trial.data$B,
AE = trial.data$AE,
param = p_SLICE, value = v_SLICE, control = c_SLICE,
stringsAsFactors = FALSE)
sp3 = data.frame(type = "MH", variable = "gamma",
Interval = trial.data$Interval,
I_index = trial.data$I_index, B = trial.data$B,
AE = trial.data$AE,
param = p_MH, value = v_MH, control = c_MH,
stringsAsFactors = FALSE)
sp4 = data.frame(type = "MH", variable = "theta",
Interval = trial.data$Interval,
I_index = trial.data$I_index, B = trial.data$B,
AE = trial.data$AE,
param = p_MH, value = v_MH, control = c_MH,
stringsAsFactors = FALSE)
}
else {
p_SLICE = "w"
v_SLICE = 1.0
c_SLICE = 6
p_MH = "sigma_MH"
v_MH = 0.35
c_MH = 0.0
sp1 = data.frame(type = "SLICE", variable = "gamma",
B = trial.data$B,
AE = trial.data$AE,
param = p_SLICE, value = v_SLICE, control = c_SLICE,
stringsAsFactors = FALSE)
sp2 = data.frame(type = "SLICE", variable = "theta",
B = trial.data$B,
AE = trial.data$AE,
param = p_SLICE, value = v_SLICE, control = c_SLICE,
stringsAsFactors = FALSE)
sp3 = data.frame(type = "MH", variable = "gamma",
B = trial.data$B,
AE = trial.data$AE,
param = p_MH, value = v_MH, control = c_MH,
stringsAsFactors = FALSE)
sp4 = data.frame(type = "MH", variable = "theta",
B = trial.data$B,
AE = trial.data$AE,
param = p_MH, value = v_MH, control = c_MH,
stringsAsFactors = FALSE)
}
sim_params = rbind(sp1, sp2, sp3, sp4)
sim_params
}
c212.BB.sim.control.params = function(trial.data) {
if (is.character(trial.data)) {
file = trial.data
trial.data <- read.table(file, header=TRUE, stringsAsFactors = FALSE)
}
facs <- sapply(trial.data, is.factor)
trial.data[facs] <- sapply(trial.data[facs], as.character)
trial.data = trial.data[trial.data$Group == 2,]
if ("Interval" %in% names(trial.data)) {
v_sigma_MH_gamma = 0.2
v_sigma_MH_theta = 0.15
v_w = 1
v_w_control = 6
v_sigma = 3
sp1 = data.frame(type = "MH", variable = "gamma",
Interval = trial.data$Interval,
I_index = trial.data$I_index,
B = trial.data$B,
AE = trial.data$AE,
param = "sigma_MH_gamma", value = v_sigma_MH_gamma,
control = 0,
stringsAsFactors = FALSE)
sp2 = data.frame(type = "MH", variable = "theta",
Interval = trial.data$Interval,
I_index = trial.data$I_index,
B = trial.data$B,
AE = trial.data$AE,
param = "sigma_MH_theta", value = v_sigma_MH_theta,
control = 0,
stringsAsFactors = FALSE)
sp3 = data.frame(type = "SLICE", variable = "gamma",
Interval = trial.data$Interval,
I_index = trial.data$I_index,
B = trial.data$B,
AE = trial.data$AE,
param = "w_gamma", value = v_w,
control = v_w_control,
stringsAsFactors = FALSE)
sp4 = data.frame(type = "MH", variable = "alpha",
Interval = unique(trial.data$Interval),
I_index = unique(trial.data$I_index),
B = NA,
AE = NA,
param = "sigma_MH_alpha", value = v_sigma,
control = 0,
stringsAsFactors = FALSE)
sp5 = data.frame(type = "SLICE", variable = "alpha",
Interval = unique(trial.data$Interval),
I_index = unique(trial.data$I_index),
B = NA,
AE = NA,
param = "w_alpha", value = v_w,
control = v_w_control,
stringsAsFactors = FALSE)
sp6 = data.frame(type = "MH", variable = "beta",
Interval = unique(trial.data$Interval),
I_index = unique(trial.data$I_index),
B = NA,
AE = NA,
param = "sigma_MH_beta", value = v_sigma,
control = 0,
stringsAsFactors = FALSE)
sp7 = data.frame(type = "SLICE", variable = "beta",
Interval = unique(trial.data$Interval),
I_index = unique(trial.data$I_index),
B = NA,
AE = NA,
param = "w_beta", value = v_w,
control = v_w_control,
stringsAsFactors = FALSE)
sim_params = rbind(sp1, sp2, sp3, sp4, sp5, sp6, sp7)
}
else {
v_sigma_MH_gamma = 0.2
v_sigma_MH_theta = 0.2
v_w_gamma = 1
v_w_gamma_control = 6
sp1 = data.frame(type = "MH", variable = "gamma",
B = trial.data$B,
AE = trial.data$AE,
param = "sigma_MH_gamma", value = v_sigma_MH_gamma,
control = 0,
stringsAsFactors = FALSE)
sp2 = data.frame(type = "MH", variable = "theta",
B = trial.data$B,
AE = trial.data$AE,
param = "sigma_MH_theta", value = v_sigma_MH_theta,
control = 0,
stringsAsFactors = FALSE)
sp3 = data.frame(type = "SLICE", variable = "gamma",
B = trial.data$B,
AE = trial.data$AE,
param = "w_gamma", value = v_w_gamma,
control = v_w_gamma_control,
stringsAsFactors = FALSE)
sim_params = rbind(sp1, sp2, sp3)
}
sim_params
}
c212.global.sim.params <- function(trial.data, model = "BB", hier = 3) {
if (is.null(model)) {
return(NULL)
}
global.sim.params <- NULL
if (model == "1a") {
global.sim.params <- c212.1a.global.sim.params(trial.data, hier)
}
else if (model == "BB") {
global.sim.params <- c212.BB.global.sim.params(trial.data, hier)
}
global.sim.params
}
c212.1a.global.sim.params <- function(trial.data, hier = 3) {
if (is.character(trial.data)) {
file = trial.data
trial.data <- read.table(file, header=TRUE, stringsAsFactors = FALSE)
}
if (is.null(trial.data)) {
return(NULL)
}
global.sim.params <- NULL
if ("Interval" %in% names(trial.data)) {
global.sim.params = data.frame(type = c("MH", "SLICE"),
param = c("sigma_MH", "w"),
value = c(0.2,1),
control = c(0,6), stringsAsFactors = FALSE)
}
else {
#EOT 1a
global.sim.params = data.frame(type = c("MH", "SLICE"),
param = c("sigma_MH", "w"),
value = c(0.35,1),
control = c(0,6), stringsAsFactors = FALSE)
}
global.sim.params
}
c212.BB.global.sim.params <- function(trial.data, hier = 3) {
if (is.character(trial.data)) {
file = trial.data
trial.data <- read.table(file, header=TRUE, stringsAsFactors = FALSE)
}
if (is.null(trial.data)) {
return(NULL)
}
global.sim.params <- NULL
if ("Interval" %in% names(trial.data)) {
if (hier == 3) {
global.sim.params = data.frame(type = c("MH", "MH", "MH", "MH",
"SLICE", "SLICE", "SLICE"),
param = c("sigma_MH_alpha", "sigma_MH_beta",
"sigma_MH_gamma", "sigma_MH_theta",
"w_alpha", "w_beta", "w_gamma"),
value = c(3, 3, 0.2, 0.25, 1, 1, 1),
control = c(0, 0, 0, 0, 6, 6, 6),
stringsAsFactors = FALSE)
}
else if (hier == 2) {
global.sim.params = data.frame(type = c("MH", "MH", "MH", "MH",
"SLICE", "SLICE", "SLICE"),
param = c("sigma_MH_alpha", "sigma_MH_beta",
"sigma_MH_gamma", "sigma_MH_theta",
"w_alpha", "w_beta", "w_gamma"),
value = c(3, 3, 0.2, 0.5, 1, 1, 1),
control = c(0, 0, 0, 0, 6, 6, 6),
stringsAsFactors = FALSE)
}
}
else {
# EOT BB
global.sim.params = data.frame(type = c("MH", "MH", "MH", "MH",
"SLICE", "SLICE", "SLICE"),
param = c("sigma_MH_alpha", "sigma_MH_beta",
"sigma_MH_gamma", "sigma_MH_theta",
"w_alpha", "w_beta", "w_gamma"),
value = c(3, 3, 0.2, 0.2, 1, 1, 1),
control = c(0, 0, 0, 0, 6, 6, 6),
stringsAsFactors = FALSE)
}
global.sim.params
}
c212.hyper.params <- function(trial.data, model = "BB", hier = 3) {
if (is.null(model)) {
return(NULL)
}
hyper_params <- NULL
if (model == "1a") {
hyper_params <- c212.1a.hyper.params(trial.data, hier)
}
else if (model == "BB") {
hyper_params <- c212.BB.hyper.params(trial.data, hier)
}
hyper_params
}
c212.1a.hyper.params <- function(trial.data, hier = 3) {
if (is.character(trial.data)) {
file = trial.data
trial.data <- read.table(file, header=TRUE, stringsAsFactors = FALSE)
}
if (is.null(trial.data)) {
return(NULL)
}
hyper_params <- NULL
if ("Interval" %in% names(trial.data)) {
if (hier == 3) {
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)
}
else if (hier == 2) {
hyper_params = list(mu.gamma.0 = 0, tau2.gamma.0 = 10,
mu.theta.0 = 0, tau2.theta.0 = 10, alpha.gamma = 3,
beta.gamma = 1,
alpha.theta = 3, beta.theta = 1)
}
}
else {
#EOT 1a
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)
}
hyper_params
}
c212.BB.hyper.params <- function(trial.data, hier = 3) {
if (is.character(trial.data)) {
file = trial.data
trial.data <- read.table(file, header=TRUE, stringsAsFactors = FALSE)
}
if (is.null(trial.data)) {
return(NULL)
}
hyper_params <- NULL
if ("Interval" %in% names(trial.data)) {
if (hier == 3) {
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, lambda.alpha = 1.0, lambda.beta = 1.0)
}
else if (hier == 2) {
hyper_params = list(mu.gamma.0 = 0, tau2.gamma.0 = 10,
mu.theta.0 = 0, tau2.theta.0 = 10, alpha.gamma = 3,
beta.gamma = 1, alpha.theta = 3,
beta.theta = 1, alpha.pi = 1.1, beta.pi = 1.1)
}
}
else {
# EOT BB
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, lambda.alpha = 1.0, lambda.beta = 1.0)
}
hyper_params
}
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