fit_HOME: General inference of HOME

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

General inference of HOME

Description

This function infers parameters (substitution rate and number of host-switches) of HOME for one given OTU ("index").

Usage

fit_HOME(index,name,nb_tree=10000,lambda=c(1,2,3,4,5,6,7,8,9,10,12,14,16,18,20,25),
nb_cores=1,tolerance=0.05,raref=FALSE,...)

Arguments

index	the name of the particular index from name_index (e.g. name of one OTU)
name	the name of the run
nb_tree	a number of tree for Monte Carlo estimation of the number of switches (a low value will give inaccurate results whereas a high value will increase the computation time)
lambda	a vector of integer values of number of switches to test during estimations
raref	if TRUE rarefactions on the number of trees are performed (i.e. to test if nb_tree is large enough). thus their results are vizualizable using the function output_results_HOME.
tol	the desired accuracy of the optimize function (to estimate mu). A low value will give a more accurate estimate, but will take more computational time.
nb_cores	a number of cores to run the analyses (ideally, it should be equal to the length of lambda for an optimal speed)
...	optional - other arguments to be passed.

Details

The functions prepare_data_HOME and simul_bank_tree must be run before. See reference for more details.

Value

The function infers the parameters (subtitution rate and number of switches) for one given index. Use the function output_results to interpret them.

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, simul_bank_tree, output_results_HOME, model_selection_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")

#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.