ChewC 0.0.7

Description:

ChewC 0.0.7

ChewC

In short, this will be a GPU-enabled stochastic simulation for breeding
programs with an emphasis on cost-benefit-analysis for novel breeding
tools and creating a suitable interface for RL agents.

We will also incorporate an emphasis on budget and costs associated with
each action to manage long-term breeding budgets. As well as model
theoretical tools in the plant breeder’s toolbox. e.g.

a treatment which increases crossover rates


a treatment which reduces flowering time


a treatment which enables gene drive at select loci

Each treatment will cost $$ ultimately helping guide the
implementation in real-world breeding programs.
Install
pip install chewc

How to use
First, define the genome of your crop
import torch

ploidy = 2
n_chr = 10
n_loci = 100
n_Ind = 333
g = Genome(ploidy, n_chr, n_loci)
population = Population()
population.create_random_founder_population(g, n_founders=n_Ind)
init_pop = population.get_dosages().float() # gets allele dosage for calculating trait values

# multi_traits
target_means = torch.tensor([0, 5, 20])
target_vars = torch.tensor([1, 1, 0.5]) # Note: I'm assuming you want a variance of 1 for the second trait
correlation_matrix = [
[1.0, 0.2, 0.58],
[0.2, 1.0, -0.37],
[0.58, -0.37, 1.0],
]
correlation_matrix = torch.tensor(correlation_matrix)

ta = TraitModule(g, population, target_means, target_vars, correlation_matrix,100)
ta(population.get_dosages()).shape

Created genetic map

torch.Size([333, 3])