example_great_apes_microbiota: Example of empirical application of HOME

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

Example of empirical application of HOME

Description

This function provides an example of empirical application using HOME for 3 different OTUs from the great apes microbiota. It only downloads the data (alignments and host tree).

Usage

example_great_apes_microbiota(name,path)

Arguments

name	the name of the run
path	optional - the path to the working directory

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

HOME_model, great_apes_microbiota

Examples

# This example may take a little bit of time. Be patient!


example_great_apes_microbiota(name="great_apes")

# Run HOME (parameters estimations and model selections)

#HOME_model(name="great_apes", name_index=c("OTU0001","OTU0002","OTU0003"),
#nb_tree=500, lambda=seq(1,25), nb_random=10)

# NB: this should be run on a larger number of tree!

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