### List of parameter initial values for sperm whale analysis of Moore and Barlow
# File edited by Jeff Moore on 2 March 2014

  
##### CHAIN 1 #####
  
list(

  # group size variables
  
    B.cs.0 = 0,
    sig.cs.jt = 0.2,
    b.cs.m = -2,

  # detection function variables
  
    g0 = c(0.8, NA, NA, NA, NA),
    log.g0slope = 0,
    b.df.0 = 1,
  
  # process model parameters
  
    logN0 = 6,
    r = 0,
    sd.pe.n = .4,
    alpha.dirich.sm = c(10,20,20,50), # mean fraction in each stratum, for small groups
    alpha.dirich.lg = c(10,20,10,10), # mean fraction, for large groups
    logit.fsmall = c(0.25,0.5,0.25,0.5,0.5,0.25), # overall fraction of abundance in small groups each year
    mu.fsmall = 0.3,  # mean for the overall fraction in small groups each year
    sd.fsmall = 1,  # random effect variance
    
),

##### CHAIN 2 #####

list(
    
    # group size variables
    
      B.cs.0 = 0.1,
      sig.cs.jt = 0.1,
      b.cs.m = -0.1,
    
    # detection function variables
    
      g0 = c(0.8, NA, NA, NA, NA),
      log.g0slope = -.1,
      b.df.0 = 1,
    
    # process model parameters
    
      logN0 = 5,
      r = 0.03,
      sd.pe.n = .2,
      alpha.dirich.sm = c(10,20,10,50), # mean fraction in each stratum, for small groups
      alpha.dirich.lg = c(10,20,10,50), # mean fraction, for large groups
      logit.fsmall = c(0.5,0.5,0.5,0.5,0.5,0.5), # overall fraction of abundance in small groups each year
      mu.fsmall = 0,  # mean for the overall fraction in small groups each year
      sd.fsmall = 1,  # random effect variance

  )