#Here the attributes (or data) and methods (or behaviours) for each object are defined
#Population is defined as an array which will hold the "individuals" objects
class Population < Array
alias_method :old_init, :initialize
def initialize(num = 0, val = nil, &proc)
if block_given?
num.times {|i| self.push (yield i)}
else
old_init(num, val)
end
end
end
#This is the individual
class Individual
#The various attributes for each individual animal are assigned
# they are variables that hold:
# alive (=1) or dead (alive = 0)
# pregnant (mother = 1) or barren (mother = 0)
# the age of the animal (continuous integer, ages)
# disease status (infected = 0 or 1)
attr_writer :sex, :alive, :mother, :ages, :infected
def initialize(sex, alive = 1,mother = 0, ages=0, infected=0)
@sex = sex
@alive = alive
@mother = mother
@ages = ages
@infected = infected
end
#This just tells the computer what to do if I call a "puts" (= print)
def to_s
"Sex: #{@sex} Alive: #{@alive} Pregnant: #{@mother} Age: #{@ages} Infected: #{@infected}\n "
end
# I defined the exp function here
def exp(num)
(2.71828182845904523536)**num
end
# these are accessor functions that allow the main portion of the program
# to access individual object's attributes:
def sex
@sex
end
def alive
@alive
end
def mother
@mother
end
def ages
@ages
end
def infected
@infected
end
#These are the various methods or behaviours that each critter can do:
#Choose sex
def chooseSex
if rand < 0.5
@sex = "M"
else
@sex = "F"
end
end
# Get infected (McCarty infection probability function)
def infect(n,nInfectious)
r = rand
p = 1-(1-1/n)**(nInfectious*2)
if @infected ==0
if r < p
@infected = 1
else
@infected = 0
end
elsif @infected ==1 #These are animals that have been infected, but in a latent state for one year
r1 = rand
if r1 < 0.09
@infected = 2 #Stay latent
elsif (r1 >= 0.09) and (r1 < 0.99)
@infected=3 #Become infectious
else
@infected = 7 #Dead
end
elsif @infected == 2 #These have been latent for one year
if rand < 0.9
@infected = 4 #become infectious
else
@infected=7 #die
end
elsif @infected == 3 #these are infectious
if rand < 0.955
@infected = 7 #these are dead
else
@infected = 5
end
elsif @infected >= 4
@infected = 7
end
end
#Disease status- and age-specific survival curve (Siler model - lx is the survivorship)
def survive
if @sex == "M"
lx1= exp(-0*(1-exp(-9*@ages))-0.329*@ages-0.00017*(exp(2*@ages)-1))
lx2= exp(-0*(1-exp(-9*(@ages+1)))-0.329*(@ages+1)-0.00017*(exp(2*(@ages+1))-1))
sx=lx2/lx1
if @infected ==7
@alive = 0
else
if rand>sx
@alive = 0
else
@alive = 1
end
end
elsif @sex == "F"
lx1= exp(-0.01*(1-exp(-9*@ages))-0.158*@ages-0*(exp(2*@ages)-1))
lx2= exp(-0.01*(1-exp(-9*(@ages+1)))-0.158*(@ages+1)-0.000*(exp(2*(@ages+1))-1))
sx=lx2/lx1
if @infected ==7
@alive = 0
else
if rand>sx
@alive = 0
else
@alive = 1
end
end
end
end
#Reproduction curve (age independent above 2, but a function of pop size)
def reproduce(n)
if @sex == "F"
if @ages > 1
if rand>exp(2.5-0.005*n)/(1+exp(2.5-0.005*n))
@mother = 0
else
@mother = 1
end
else
@mother= 0
end
else
@mother = 0
end
end
#This ages each animal
def age
@ages+=1
end
end
#******************************************************************************
#This is the main portion of the model
# Number of time steps
t = 50
#Initial pop size
males= Population.new(250) {Individual.new("M",1,0,3,0)}
females = Population.new(250) {Individual.new("F",1,0,3,0)}
n = 500.0
population = []
population = males + females
#Here you enter the initial number of infected critters:
4.times {population< 1
mums += 1
end
}
if n < 1000
mult = 2 - 0.0000018*(n**2)
babies = mums*mult
babies = Integer(babies)
end
#A new array is created to hold the new babies
newBabies = Population.new(babies) {Individual.new("N",1,0,0,0)}
#Choose sex
newBabies.each { |member|
member.chooseSex
}
#And then is added to the population array
population = population + newBabies
#Infect critters
population.each { |member|
member.infect(n,nInfectious)
}
#Determine if critters are going to die
population.each { |member|
member.survive
}
#Delete dead critters
population.delete_if{|member|
member.alive ==0}
#Age critters
population.each { |member|
member.age
}
#Count live critters
n = 0.0
population.each { |member|
if member.alive == 1
n= n+1
end
}
#Count infected critters
nInfected = 0.0
population.each { |member|
if member.infected > 1
nInfected = nInfected+1
end
}
#Count infectious critters
nInfectious = 0.0
population.each { |member|
if member.infected >= 3
nInfectious = nInfectious+1
end
}
#Here, the data are put into storage arrays:
popSize[i] = n
numberInfected[i]=nInfected
numberInfectious[i]=nInfectious
#Just prints stuff to the screen:
#puts "Year no. #{i}"
#puts population
puts "Time: #{i} Number infectious: #{nInfectious} Number infected: #{nInfected} Population size: #{n}"
end #here ends the time loop
#Now the data are sent to files
results = File.new("results", "w")
results.puts popSize
results.close
infectedResults = File.new("infectedresults", "w")
infectedResults.puts numberInfected
infectedResults.close
infectiousResults = File.new("infectiousresults", "w")
infectiousResults.puts numberInfectious
infectiousResults.close
finalAge = File.new("finalAge", "w")
finalAge.puts population
finalAge.close
puts "--PRESS ENTER TO CONTINUE--"
fun = gets
#******************************************************************************