View source: R/sim_twal_with_same_n_mutation.R
sim_twal_with_same_n_mutation | R Documentation |
This is an adapter function
(see https://en.wikipedia.org/wiki/Adapter_pattern),
with the purpose of passing check_sim_twal_fun,
by being a function with the function arguments twin_phylogeny
and true_alignment
.
sim_twal_with_same_n_mutation(
twin_phylogeny,
true_alignment,
root_sequence,
mutation_rate = 1,
site_model = beautier::create_jc69_site_model(),
max_n_tries = 1000,
verbose = FALSE
)
twin_phylogeny |
a phylogeny of class phylo |
true_alignment |
a DNA alignment, of class DNAbin |
root_sequence |
the DNA sequence at the root of the phylogeny. By default, this will consist out of an equal amount of each letter Use check_root_sequence to check if a root sequence is valid. |
mutation_rate |
the mutation rate per base pair per time unit. Use check_mutation_rate to check if a mutation rate is valid. |
site_model |
a nucleotide substitution model, which can be:
|
max_n_tries |
maximum number of tries before giving up |
verbose |
if TRUE, show more output |
an alignment
Richèl J.C. Bilderbeek
Use sim_twin_alignment to use this function to create a twin alignment
# This adapter function must be a sim_twin_alignment function
check_sim_twal_fun(
sim_twal_with_std_nsm
)
# Simulate a twin DNA alignment
alignment <- sim_twal_with_std_nsm(
twin_phylogeny = ape::read.tree(text = "((A:1, B:1):2, C:3);"),
root_sequence = "aaaa",
mutation_rate = 0.1
)
check_alignment(alignment)
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