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Useful function to extract all phenotype values as data frame from RITHMS output

get_phenotypes.Rd

The gets functions use the output of holo_simu() to extract the information of interest from a given generation. get_phenotypesextract phenotype for each individuals as the combined effects of microbiota and direct genetic effects, from a generation object.

Usage

get_phenotypes(data)

Arguments

data

List corresponding to one generation, as returned by holo_simu(). Containing simulation output.

Value

A data.frame of phenotype for each individuals of a given generation. Phenotype values are given as the result of the combined effects of the microbiota and direct genetic effects.

See also

get_mean_phenotypes(), get_phenotypes_value(), get_om_beta_g(), get_selected_ind(), get_microbiomes()

Examples

if (FALSE) { # \dontrun{
library(magrittr)
library(purrr)
data("Deru")
ToyData <- Deru
taxa_assign_g <- assign_taxa(founder_object = ToyData)
generations_simu <- holo_simu(h2 = 0.25, b2 = 0.25, founder_object = ToyData,
                              n_clust = taxa_assign_g, n_ind = 500,
                              verbose = FALSE, seed = 1234)
                              
#Extract phenotypes of the G1 generation
G1_phenotypes <- get_phenotypes(generations_simu$G1)
 
#Extract phenotypes for all generations
## Don't forget to substract the metadata
phenotypes <- generations_simu[-1] %>% map(get_phenotypes)
} # }