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compute_beta_g()
- Compute product of matrixes based on few parameters
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compute_current_microbiome()
- Compute microbiomes for all individuals of current generation gathering all relevant object already computed.
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compute_mean_microbiome()
- apply mean on rows for each taxa across population
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compute_phenotypes()
- Compute phenotype values based on generated object of current generation
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assign_taxa()
- Assign all taxa to a cluster, eventually under genetic control using hclust
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gen_effect_calibration()
- Calibration of genetic effect from founder population data
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generate_founder()
- Formatting of ped and map files into haplotypes table and filter individuals
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holo_simu()
- Main function to generate transgenerational hologenomic data
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read_input_data()
- Formatting data from file paths to base population object
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replace_zero()
- Replace zero in the matrix by 1e-15 to avoid infinite values when CLR transformation is computed
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richness_from_abundances_gen()
- If selection based on diversity, need to go back to counts using multinomial sampling from abundances.
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root()
- Compute root value for beta matrix construction
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select_individual()
- Obtain id of the parents selected for the next generation based on the criteria chosen by the user