Useful function to extract microbiomes from RITHMS output

The gets functions use the output of holo_simu() to extract the information of interest from a given generation. get_microbiomes extract the microbiome abundance matrix from a generation object, with or without CLR transformation or transposition.

Usage

get_microbiomes(data, transpose = F, CLR = F)

Arguments

data

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

transpose

Logical; if TRUE, transpose the microbiome matrix (OTUs in rows, individuals in columns).

CLR

Logical; if TRUE, applies a CLR transformation to the abundance data. This transformation requires transpose = TRUE.

Value

A data.framecontaining the microbiome abundances of individuals. Default, individuals are in rows and OTUs in columns. Change transposeparameter if needed.

See also

get_mean_phenotypes(), get_phenotypes_value(), get_om_beta_g(), get_selected_ind(), get_phenotypes()

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 microbiome matrix for G1 generation
G1_microbiome <- get_microbiomes(generations_simu$G1)

# Extract with transposition
G1_t_microbiome <- get_microbiomes(generations_simu$G1, transpose = TRUE)

# Extract with CLR transformation
G1_CLR_microbiome <- get_microbiomes(generations_simu$G1, transpose = TRUE, CLR = TRUE)

# Extract all microbiome matrices of all generations
# substract metadata
microbiomes <- generations_simu[-1] %>% map(get_microbiomes)
} # }