check_sim_twal_fun: Check if the function to create a twin alignment with (from a...

In richelbilderbeek/pirouette: Create a Bayesian Posterior from a Phylogeny

Check if the function to create a twin alignment with (from a true phylogeny and a true alignment) is valid.

Description

Will stop if not

Usage

check_sim_twal_fun(sim_twal_fun)

Arguments

sim_twal_fun

function to simulate a twin alignment with. This function must have two arguments called twin_phylogeny (which will hold the twin phylogeny) and true_alignment (which will hold the alignment simulated from the true phylogeny). The return type must be DNAbin. Use check_sim_twal_fun to verify if the function has the right signature and output. Some standard functions: Use get_copy_tral_fun to get a function (copy_true_alignment) that copies a true to alignment to create a twin alignment Use get_sim_twal_with_std_nsm_fun to get a function (sim_twal_with_std_nsm) that simulates a twin alignment using a standard site model Use get_sim_twal_same_n_muts_fun to get a function (sim_twal_with_same_n_mutation) that simulates -using a standard model- a twin alignment with as much mutations compared to the root sequence as the true alignment has Use sim_twal_with_lns_nsm that simulates a twin alignment using a linked node substitution model Use sim_twal_with_uns_nsm that simulates a twin alignment using an unlinked node substitution model

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use check_sim_tral_fun to check a function to generate a true alignment. Use check_sim_twin_tree_fun to check a function to generate a twin phylogeny.

richelbilderbeek/pirouette documentation built on Oct. 18, 2023, 3:09 p.m.