check_sim_tral_fun: Check if the function to create a true alignment with (from...

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

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

Description

Will stop if not

Usage

check_sim_tral_fun(sim_tral_fun)

Arguments

sim_tral_fun

function to simulate a true alignment with. This function must have two arguments, called true_phylogeny (which will hold the true phylogeny) and root_sequence (which holds the DNA root sequence). The return type must be DNAbin. Use check_sim_tral_fun to verify if the function has the right signature and output. Some standard functions: Use get_sim_tral_with_std_nsm_fun to get a function (sim_tral_with_std_nsm) the use a standard site model. Use get_sim_tral_with_lns_nsm_fun to get a function (sim_tral_with_lns_nsm) the use a linked node substitution site model. Use get_sim_tral_with_uns_nsm_fun to get a function (sim_tral_with_uns_nsm) the use an unlinked node substitution site model.

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use check_sim_twal_fun to check a function to generate a twin alignment

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