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###            Ft. McCoy Population & Initial Conditions           ###
###     Code by Paul Gastanaduy, Prabasaj Paul, Nina Masters       ###
###                     Updated September 2, 2022                  ###
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# Specify population size in each age group: bring in population files (appx sizes for Ft. McCoy, n = 12883) ----------------------
pop1 = 244  #under six months
pop2 = 192  #six months - 12 months
pop3 = 4838 #12 months - 12 years
pop4 = 7327 #12+ years, non pregnant
pop5 = 232  #12+ years, pregnant

N = pop1 + pop2 + pop3 + pop4 + pop5
N_eligible_vax = pop2 + pop3 + pop4

# Specify initial conditions
prop.suscept1=.3333
prop.suscept2=.4021
prop.suscept3=.2247
prop.suscept4=.1335
prop.suscept5=.1335

prop_pop1 = pop1/N
prop_pop2 = pop2/N
prop_pop3 = pop3/N
prop_pop4 = pop4/N
prop_pop5 = pop5/N

S1=floor(pop1*prop.suscept1)
S2=floor(pop2*prop.suscept2)
S3=floor(pop3*prop.suscept3)
S4=floor(pop4*prop.suscept4)   
S5=floor(pop5*prop.suscept5)
total_S = S1+S2+S3+S4+S5
total_S/N


#no incubating cases at the start, all E = 0
E1=E2=E3=E4=E5=0

#no infections at beginning, all 0
I1=I2=I3=I4=I5=0

#no Cases at beginning, all 0
Cases1=Cases2=Cases3=Cases4=Cases5=0

#Set recovered populations 
R1=ceiling(pop1*(1-prop.suscept1))
R2=ceiling(pop2*(1-prop.suscept2))
R3=ceiling(pop3*(1-prop.suscept3))
R4=ceiling(pop4*(1-prop.suscept4))
R5=ceiling(pop5*(1-prop.suscept5))

#For vaccination simulations
Sv2 = Sv3 = Sv4 = 0

#number of importations
nimport = 1