prepare_data_HOME: Prepare the data for running HOME

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

Prepare the data for running HOME

Description

This function prepares the data for the inference of HOME (format data, run the model of nucleotidic evolution...).

Usage

prepare_data_HOME(iter,name,name_index,provided_tree=NULL,...)

Arguments

name	the name of the run
iter	the number of iteration of a particular index from name_index
name_index	a vector with the names of the different symbionts (e.g. name of the OTUs)
provided_tree	optional - the host tree of your study. It can also be provided in the working directory (see details).
...	optional - other arguments to be passed.

Details

Please provide the binary rooted ultrametric host tree (Newick format .tre) in the working directory. Its name must be weel-formated "host_tree_NAME.tre" (match the name of the run). A folder (“path_alignment” or "path" by default") must contain all the alignments with the filenames "alignment_NAME_OTU.fas" (FASTA format). See reference for more details.

Value

The function creates files to run the following functions simul_bank_tree, fit_HOME...

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, simul_bank_tree, 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(1,25),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.