def get_from_parent_and_environment(self): # parental inheritance and environmental acquisition
parental_contribution = []
for i in range(self.number_of_host_in_population): # select parent for next generation
rnd = random.randint(0, self.number_of_environmental_species - 1)
parental_contribution.append(
self.composition_of_individual[rnd].microbiome / float(self.number_of_microbes_in_host))
self.composition_of_individual[rnd].microbiome *= 2
environmental_contribution = addition_of_arrays(
self.percentage_of_pooled_environmental_component,
1 - self.percentage_of_pooled_environmental_component,
self.microbiome_sum, self.environment) # mix pooled and fixed env
for i in range(self.number_of_host_in_population): # mix environmental and parental contribution
mixed_contribution = addition_of_arrays(
1 - self.percentage_of_environmental_acquisition,
self.percentage_of_environmental_acquisition,
parental_contribution[i], environmental_contribution)
self.composition_of_individual[i].microbiome = numpy.random.multinomial(
self.number_of_microbes_in_host, mixed_contribution / sum(mixed_contribution))
def sum_species(self):
self.microbiome_sum = numpy.array([])
for individual in self.composition_of_individual:
self.microbiome_sum = addition_of_arrays(1, 1, self.microbiome_sum, individual.microbiome)
self.microbiome_sum = self.microbiome_sum / float(sum(self.microbiome_sum)) # composition of the microbiomes within the population in terms of genome
self.species_community = self.microbiome_sum # composition of the microbiomes within the population in terms of species marker
