output_results_HOME: Representing all the results of HOME

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

Representing all the results of HOME

Description

This function outputs all the results of HOME into a HTML file with figures and tables. The results are reported in one separate file for each OTU ("index").

Usage

output_results_HOME(iter,name,name_index,lambda=c(1,2,3,4,5,6,7,8,9,10,12,14,16,18,20,25),
nb_tree=10000,empirical,randomize,raref,nb_random=10,figure=FALSE,...)

Arguments

iter	the number of iteration of a particular index from name_index
name	the name of the run
name_index	a vector with the names of the different symbionts (e.g. name of the OTUs)
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 integer values of number of switches to test during estimations
empirical	a boolean indicating if the run has been done on empirical data or on simulations (in the latter case, the output will be different)
randomize	a boolean indicating wheter the model selection testing independent evolutions has been performed yet.
raref	if TRUE rarefactions on the number of trees have been performed (i.e. to test if nb_tree is large enough) and a separate figure with rarefactions curves will be stored in the folder "figures/"
nb_random	a integer value of the number of randomizations (R) performed during the model selection testing independent evolutions.
figure	indicates whether it automatically outputs figures (default: FALSE).
...	optional - other arguments to be passed.

Details

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

Value

This function sums up all the results for each index in a HTML file (see in folder "figures/").

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, 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.