Main function to generate transgenerational hologenomic data
holo_simu.RdMain function to generate transgenerational hologenomic data
Usage
holo_simu(
h2,
b2,
founder_object,
otu_g = 0.05,
qtn_y = NULL,
n_ind = NULL,
n_gen = 5,
n_clust = NULL,
selection = F,
size_selection_F = NULL,
size_selection_M = NULL,
selection_type = "GB",
seed = 1234,
verbose = T,
lambda = 0.5,
correlation = 0.5,
mix.params = c(0.75, 0.25),
mix.params.M = c(0.75, 0.25),
effect.size = 0.1,
noise.microbiome = 0.1,
dir = F,
ao = 25,
thetaX = NULL,
env_gen = NULL,
w.param = c(0.5, 0.5)
)Arguments
- h2
direct heritability value, between 0 and 1
- b2
microbiability value, between 0 and 1
- founder_object
output of generate_founder() function
- otu_g
percentage of taxa under genetic control, between 0 and 1, DEFAULT = 0.05
- qtn_y
number of causal SNPs for the phenotypes
- n_ind
number of individual per generation
- n_gen
number of generation, DEFAULT = 5
- n_clust
vector with taxa assignment, typical output of assign_taxa
- selection
bool, if selection process needed, DEFAULT = FALSE
- size_selection_F
percentage of female to select
- size_selection_M
percentage of male to select
- selection_type
mode of selection to be used, value in ("GB", "B", "G", "diversity", "div.GB"), DEFAULT = "GB"
- seed
seed value for samplings in the function
- verbose
bool, DEFAULT = T
- lambda
proportion of microbiome of offspring coming from vertical transmission, DEFAULT = 0.5
- correlation
Correlation between taxa within the same cluster, value between 0 and 1, DEFAULT = 0.5
- mix.params
Vector of two values giving the weights for the regularisation of the base population microbiome. mix.params1 = weight for raw microbiome and mix.params2 = weight for mean microbiome. DEFAULT = c(0.75,0.25)
- noise.microbiome
sd of microbiome noise, DEFAULT = 0.1
- dir
bool
- ao
for dirichlet sampling parameter
- thetaX
if environmental effect
- env_gen
vector of bool
- w.param
in case div.GB selection mode is chosen