simul_bank_tree: Simulate a bank of trees for running HOME.

In BPerezLamarque/HOME: Phylogenetic Models of HOst-Microbiota Evolution

Simulate a bank of trees for running HOME.

Description

This function simulates the bank of symbiont trees, used for running HOME, for a given number of host-switches.

Usage

simul_bank_tree(nb_ksi,name,
provided_tree=NULL,nb_tree=10000,
lambda=c(1,2,3,4,5,6,7,8,9,10,12,14,16,18,20,25),
seed=1)

Arguments

nb_ksi	a positive integer which represents the given number of host-switches to simulate on the host tree
name	the name of the run
provided_tree	optional - the host tree of your study. It can also be provided as saved in the working directory
nb_tree	a number of trees to simulate
lambda	a vector of integer values of number of switches to test during estimations
seed	a seed to assure the reproducibility

Details

The function prepare_data_HOME must be run before. See reference for more details.

Value

The function outputs trees in the folder simulated_trees/ for each value of number of switches. Then, use the function fit_HOME to infer the results.

Author(s)

Benoit Perez-Lamarque

References

Perez-Lamarque B, Morlon H (2019). Characterizing symbiont inheritance during host-microbiota evolution: Application to the great apes gut microbiota. Molecular Ecology Resources 19:1659-1671.

See Also

sim_microbiota, prepare_data_HOME, output_results_HOME, model_selection_HOME, fit_HOME, HOME_model

Examples

# Some examples may take a little bit of time. Be patient!

# Simulate 3 microbial alignments on a host tree
# (1 is vertically transmitted, 1 is transmitted with 5 host-switches,
#  and 1 is environmentally acquired)

name="example_simulation"
name_index=c("Simul_1","Simul_2","Simul_3")
path=getwd()

#sim_microbiota(name, name_index, simul=c(0,5,"indep"), n=10, mu=1, N=300, proportion_variant=0.1)

# Inference

# Prepare the data (format, substitution model...)
#for (i in 1:3){prepare_data_HOME(iter=i,name,name_index)}

# Simulate the bank of trees
#for (ksi in 1:length(seq(1,25))){simul_bank_tree(ksi,name,nb_tree=1000,
#lambda=seq(1,15),seed=1)}

# Infer the parameters
#for (i in 1:3){fit_HOME(index=name_index[i],name,nb_tree=1000,lambda=seq(1,25),nb_cores=1)}

# Plot the first outputs
#for (i in 1:3){output_results_HOME(iter=i,name,name_index,lambda=seq(1,25),
#nb_tree=1000,empirical=FALSE,randomize=FALSE,raref=FALSE)}

# Perform the model selection
#for (i in 1:3){model_selection_HOME(index=name_index[i],name,nb_tree=1000,
#lambda=seq(1,25),nb_cores=1,seed=1)}

# Plot the final outputs
#for (i in 1:3){output_results_HOME(iter=i,name,name_index,lambda=seq(1,25),nb_tree=1000,
#empirical=FALSE,randomize=TRUE,raref=FALSE)}

BPerezLamarque/HOME documentation built on May 17, 2023, 7:02 a.m.