Package index • RITHMS

Formatting data functions

Set of useful functions for preparing input data

read_input_data(): Formatting data from file paths to base population object

rarefied_microbiome(): Rarefaction step within read_input_data

generate_founder(): Formatting of ped/map files or vcf into haplotypes table and add it inside the founder_object list.

Taxa assignation function

Assign all taxa to a cluster

assign_taxa(): Assign all taxa to a cluster, eventually under genetic control using hclust

Calibration of genetic effect

gen_effect_calibration(): Calibration of genetic effect from founder population data

HoloSimu

The main function

holo_simu(): Main function to generate transgenerational hologenomic data

Useful function relative to HoloSimu

Set of functions used within HoloSimu to generate the components of each generation, such as phenotypes and microbiomes.

compute_beta_g(): Compute product of matrixes based on few parameters

compute_current_microbiome(): Compute microbiomes for all individuals of current generation gathering all relevant object already computed.

compute_mean_microbiome(): Compute the mean for each taxa across population

compute_phenotypes(): Compute phenotype values based on generated objects of the current generation

calibrate_params_phenotypes(): Calibration coefficients to compute phenotypes

compute_beta_matrix_cluster(): Generate beta matrix giving genetic effect per SNP on taxa abundances.

Get functions

Useful get functions for accessing the components of each generation from HoloSimu output.

get_microbiomes(): Useful function to extract microbiomes from RITHMS output

get_mean_phenotypes(): Useful function to extract mean phenotype values from RITHMS output

get_phenotypes_value(): Useful function to extract phenotype values from RITHMS output ("gq" by default)

get_phenotypes(): Useful function to extract all phenotype values as data frame from RITHMS output

get_om_beta_g(): Useful function to extract omega beta G values from RITHMS output

get_selected_ind(): Useful function to extract ID of selected individuals from RITHMS output

get_mean_diversity(): Useful function to extract Shannon diversity from RITHMS output

Estimate diversity metrics

richness_from_abundances_gen(): Estimate diversity metrics from relative abundances

Another little useful functions across the HoloSimu process

replace_zero(): Replace zero in the matrix by 1e-15 to avoid infinite values when CLR transformation is computed

root(): Compute root value for beta matrix construction

select_individual(): Obtain id of the parents selected for the next generation based on the criteria chosen by the user

transform_geno_into_vcf(): Convert a 0/1/2 genotype matrix into a VCF-like format

Dataset

Deru: Deru Dataset