### 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
)