# configuration file for program src/newAge.py
# Configuration saved at at  Fri Jul 23 13:14:55 2010

# label:	Replicates
# description:
#	Number of replicates to run the simulation. Between 2 and 1000
reps = '10'

# label:	Generations
# description:
#	Time units (generations) of evolution. Max: 1000
time = '40'

# label:	Burn-in
# description:
#	Lenght of burn-in stage. Between 2 and 1000.
burnin = '20'

# label:	Save stats
# description:
#	Save stats for posterior analysis of distribution
saveDecays = 'False'

# label:	Years to save
# description:
#	List of years to save population in a genepop-format file
saveGens = '[0, 1, 2, 3, 6]'

# label:	Calculate F/pedigree
# description:
#	Calculate F from pedigree. This calculation is expensive.
doFPed = 'False'

# label:	number of Microsats
# description:
#	Number of microsatellite-type loci (multi-allelic). Max: 200
nMSats = '10'

# label:	maximum of alleles
# description:
#	Maximum number of alleles in microsatellite loci. max:100
maxAllele = '20'

# label:	Frequencies initalization
# description:
#	Choose model for intialization of allelic frequencies in microsat loci.
initFreq = 'DIRICHLET'

# label:	Frequencies datafile
# description:
#	File name for user-defined frequencies. Used only if initFreq = FILE.
fileFreq = ''

# label:	Number of SNPs
# description:
#	Number of SNP-type loci (bi-allelic). Max: 200
nSNPs = '0'

# label:	Demographic model
# description:
#	Single pop, Island or Stepping-Stone
demoModel = 'SINGLE'

# label:	Initial N
# description:
#	Initial population size (per deme). Max: 100000
initialN = '430'

# label:	Number of Demes
# description:
#	Number of demes. Max:100
demes = '5'

# label:	Migration rate
# description:
#	Migration rate
migration = '0.001'

# label:	Maximum age (max 25)
# description:
#	Maximum age of individuals. Note that 0 is the age of newborns
maxAge = '20'

# label:	Adult age
# description:
#	age of individuals when they become adults
adultAge = '2'

# label:	Initial Age Structure
# description:
#	List of probability of age of individuals. Relative (no need to sum up to 100/1)
ASinit = '[25.445, 13.679, 10.162, 8.839, 8.208, 7.142, 6.003, 5.339, 4.543, 3.374, 2.712, 2.042, 1.058, 0.6, 0.322, 0.201, 0.112, 0.082, 0.06, 0.077]'

# label:	Mating mode
# description:
#	Mode of mating: RANDOM: random mating with replacement; MONOGFEMS1: monogamic females with one offspring per female; MONOG: monogamy
matingMode = 'MONOGFEMS1'

# label:	Constant born size
# description:
#	Force population with constant born size over time
constSize = 'False'

# label:	Cohort size N0
# description:
#	Cohort size. Number of newborns generated if constant born size
cohortN = '100'

# label:	Male survivorship
# description:
#	List of age-specific survivorship in males. Last value must be 0
sMales = '[0.55, 0.76, 0.89, 0.95, 0.89, 0.86, 0.91, 0.87, 0.76, 0.82, 0.77, 0.54, 0.57, 0.55, 0.64, 0.57, 0.75, 0.75, 0.75, 0.0]'

# label:	Female survivorship
# description:
#	List of age-specific survivorship in females. Last value must be 0.
sFemales = '[0.55, 0.76, 0.89, 0.95, 0.89, 0.86, 0.91, 0.87, 0.76, 0.82, 0.77, 0.54, 0.57, 0.55, 0.64, 0.57, 0.75, 0.75, 0.75, 0.0]'

# label:	Male probability of mating
# description:
#	List of age-specific probability of mates in males. They are relative, there is no need to sum up to 1.
bMales = '[0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]'

# label:	Female fecundity (b)
# description:
#	List of age-specific fecundity in females. If the population has not constant born size then mean the average number of offspring per indivdual or each age.
bFemales = '[0, 0, 0.7, 0.7, 0.95, 0.93, 0.93, 0.93, 0.93, 0.92, 0.92, 0.92, 0.92, 0.92, 0.8, 0.8, 0.572485695, 0.460581969, 0.336261303, 0.218573287]'

# label:	Alpha males
# description:
#	Enable the alpha males mating system
alphaMating = 'False'

# label:	Prop. offspring by alphas
# description:
#	Proportion of offspring sired by alphas
alphaOff = '0.0'

# label:	Minimum age of alphas
# description:
#	Minimum age of an individual who can become an alpha
alphaMinAge = '0'

# label:	Maximum age of alphas
# description:
#	Maximum age of an individual who can become an alpha
alphaMaxAge = '0'

# label:	Duration of alpha
# description:
#	Duration of alpha trait
alphaDuration = '0'

# label:	Prop. of alphas
# description:
#	Proportion of males being alphas
alphaProp = '0.0'

# label:	Has Carrying capacity?
# description:
#	Environment imposes a population limit
hasCarrying = 'False'

# label:	Carrying capacity
# description:
#	Population limit
capacity = '100'

# label:	Culling
# description:
#	Allow culling
culling = 'True'

# label:	Culling objective
# description:
#	Population size after culling
cullObjective = '400'

# label:	Culling target
# description:
#	Target for culling: ALL: random culling; YOUNG: Random culling of non-adult individuals; ADULTS: random culling of adult individuals
cullTarget = 'ALL'

# label:	Culling mode
# description:
#	Mode for culling: INTERVAL: culling occurs every x years; THRESHOLD: culling occurs when population size is larger than a threshold
cullMode = 'INTERVAL'

# label:	Culling threshold
# description:
#	Population size threshold to do culling if mode = THRESHOLD
cullLevel = '700'

# label:	Culling Interval
# description:
#	Interval of time between culling events if mode = INTERVAL
cullInterval = '0'


#The same options can be given by command line options (subject to minor changes)
#    --gui=False  --reps='10' --time='40' --burnin='20' \
#    --saveGens='[0, 1, 2, 3, 6]' --nMSats='10' --maxAllele='20' \
#    --initFreq='DIRICHLET' --fileFreq='' --nSNPs='0' --demoModel='SINGLE' \
#    --initialN='430' --demes='5' --migration='0.001' --maxAge='20' \
#    --adultAge='2' --ASinit='[25.445, 13.679, 10.162, 8.839, 8.208, 7.142, \
#    6.003, 5.339, 4.543, 3.374, 2.712, 2.042, 1.058, 0.6, 0.322, 0.201, \
#    0.112, 0.082, 0.06, 0.077]' --matingMode='MONOGFEMS1' --cohortN='100' \
#    --sMales='[0.55, 0.76, 0.89, 0.95, 0.89, 0.86, 0.91, 0.87, 0.76, 0.82, \
#    0.77, 0.54, 0.57, 0.55, 0.64, 0.57, 0.75, 0.75, 0.75, 0.0]' \
#    --sFemales='[0.55, 0.76, 0.89, 0.95, 0.89, 0.86, 0.91, 0.87, 0.76, \
#    0.82, 0.77, 0.54, 0.57, 0.55, 0.64, 0.57, 0.75, 0.75, 0.75, 0.0]' \
#    --bMales='[0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, \
#    1]' --bFemales='[0, 0, 0.7, 0.7, 0.95, 0.93, 0.93, 0.93, 0.93, 0.92, \
#    0.92, 0.92, 0.92, 0.92, 0.8, 0.8, 0.572485695, 0.460581969, \
#    0.336261303, 0.218573287]' --alphaOff='0.0' --alphaMinAge='0' \
#    --alphaMaxAge='0' --alphaDuration='0' --alphaProp='0.0' \
#    --capacity='100' --culling --cullObjective='400' --cullTarget='ALL' \
#    --cullMode='INTERVAL' --cullLevel='700' --cullInterval='0'


#Or a shorter version if default arguments are ignored
#    --gui=False  --reps='10' --time='40' --burnin='20' \
#    --saveGens='[0, 1, 2, 3, 6]' --nMSats='10' --maxAllele='20' \
#    --initFreq='DIRICHLET' --fileFreq='' --nSNPs='0' --demoModel='SINGLE' \
#    --initialN='430' --demes='5' --migration='0.001' --maxAge='20' \
#    --adultAge='2' --ASinit='[25.445, 13.679, 10.162, 8.839, 8.208, 7.142, \
#    6.003, 5.339, 4.543, 3.374, 2.712, 2.042, 1.058, 0.6, 0.322, 0.201, \
#    0.112, 0.082, 0.06, 0.077]' --matingMode='MONOGFEMS1' --cohortN='100' \
#    --sMales='[0.55, 0.76, 0.89, 0.95, 0.89, 0.86, 0.91, 0.87, 0.76, 0.82, \
#    0.77, 0.54, 0.57, 0.55, 0.64, 0.57, 0.75, 0.75, 0.75, 0.0]' \
#    --sFemales='[0.55, 0.76, 0.89, 0.95, 0.89, 0.86, 0.91, 0.87, 0.76, \
#    0.82, 0.77, 0.54, 0.57, 0.55, 0.64, 0.57, 0.75, 0.75, 0.75, 0.0]' \
#    --bMales='[0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, \
#    1]' --bFemales='[0, 0, 0.7, 0.7, 0.95, 0.93, 0.93, 0.93, 0.93, 0.92, \
#    0.92, 0.92, 0.92, 0.92, 0.8, 0.8, 0.572485695, 0.460581969, \
#    0.336261303, 0.218573287]' --alphaOff='0.0' --alphaMinAge='0' \
#    --alphaMaxAge='0' --alphaDuration='0' --alphaProp='0.0' \
#    --capacity='100' --culling --cullObjective='400' --cullTarget='ALL' \
#    --cullMode='INTERVAL' --cullLevel='700' --cullInterval='0'