### Formating Data for BUGS
library(R2WinBUGS)

#####   Site Confirmation DESIGN  -- Multiple Detection Methods   #####
# Bundle data
data <- list( Y = Y, W = W, R = R, K = K, J = J)
 bugs.data(data, digits = 5, data.file = "data-SiteConf-MM.txt")

# Create initial values for BUGS // here, it's for 2 MCMC chains
inits <- function(){ list ( psi = runif(1, 0.01, 0.99), 
					p10 =  runif(1, 0.01, 0.99), 
					p11 =  runif(1, 0.01, 0.99), 
					r11 =  runif(1, 0.01, 0.99), 
					z = rbinom(R,1,0.5)  ) }
  init1 <- inits()
  init2 <- inits()
bugs.data(init1, digits = 5, data.file = "init1-SiteConf-MM.txt")
bugs.data(init2, digits = 5, data.file = "init2-SiteConf-MM.txt")
##------------------------------------------------------------------------------##


#####   Site Confirmation DESIGN  -- Multiple Detection States   #####
# Bundle data
data <- list( Y = Y, I = R, K = K)
 bugs.data(data, digits = 5, data.file = "data-SiteConf-MS.txt")

# Create initial values for BUGS // here, it's for 2 MCMC chains
inits <- function(){ list ( psi = runif(1, 0.01, 0.99), 
					p10 =  runif(1, 0.01, 0.99), 
					p11 =  runif(1, 0.01, 0.99), 
					b =  runif(1, 0.01, 0.99), 
					z = rbinom(R,1,0.5)  ) }
  init1 <- inits()
  init2 <- inits()
bugs.data(init1, digits = 5, data.file = "init1-SiteConf-MS.txt")
bugs.data(init2, digits = 5, data.file = "init2-SiteConf-MS.txt")
##------------------------------------------------------------------------------##


#####   CALIBRATION DESIGN   #####
# Bundle data
data <- list( Y = Y, w = W, x = X, n1 = n1, n0 = n0, R = R, J = J) 
 bugs.data(data, digits = 5, data.file = "Data-Calibration.txt")

# Create initial values for BUGS // here, it's for 2 MCMC chains
inits <- function(){ list ( psi = runif(1, 0.01, 0.99), 
					p10 =  runif(1, 0.01, 0.99), 
					p11 =  runif(1, 0.01, 0.99), 
					z = rbinom(R,1,0.5)  ) }
  init1 <- inits()
  init2 <- inits()
bugs.data(init1, digits = 5, data.file = "init1-Calibration.txt")
bugs.data(init2, digits = 5, data.file = "init2-Calibration.txt")
##------------------------------------------------------------------------------##


#####   Observation Confirmation DESIGN   #####
# Bundle data
data <- list( Y = Y, V = V, S = K, T = K, I = I, J = J)
 bugs.data(data, digits = 5, data.file = "data-ObsConf.txt")

# Create initial values for BUGS // here, it's for 2 MCMC chains
inits <- function(){ list ( psi = runif(1, 0.01, 0.49), 
					s0 =  runif(1, 0.01, 0.39), 
					s1 =  runif(1, 0.51, 0.99), 
					z1 = rbinom(I,1,0.5),
					z2 = rbinom(J,1,0.5)   ) }
  init1 <- inits()
  init2 <- inits()
bugs.data(init1, digits = 5, data.file = "init1-ObsConf.txt")
bugs.data(init2, digits = 5, data.file = "init2-ObsConf.txt")
##------------------------------------------------------------------------------##