Evolutionary terms

Model terms for both geese and flock objects.

Model terms for both geese and flock objects.

rule_limit_changes(p, term_pos, lb, ub, duplication = 1L)

term_gains(p, funs, duplication = 1L)

term_loss(p, funs, duplication = 1L)

term_cogain(p, a, b, duplication = 1L)

term_neofun(p, a, b, duplication = 1L)

term_subfun(p, a, b, duplication = 1L)

term_maxfuns(p, lb, ub, duplication = 1L)

term_overall_changes(p, duplication = 1L)

term_overall_gains(p, duplication = 1L)

term_overall_loss(p, duplication = 1L)

term_kgains(p, funs, k = 1L, duplication = 1L)

term_neofun_a2b(p, a, b, duplication = 1L)

term_genes_changing(p, duplication = 1L)

term_prop_genes_changing(p, duplication = 1L)

term_coopt(p, a, b, duplication = 1L)

term_k_genes_changing(p, k, duplication = 1L)

term_less_than_p_prop_genes_changing(p, prop, duplication = 1L)

term_pairwise_preserving(p, funA, funB, duplication = 1L)

term_gains_from_0(p, fun, duplication = 1L)

term_overall_gains_from_0(p, duplication = 1L)

term_pairwise_first_gain(p, funA, funB, duplication = 1L)

term_preserve_pseudogene(p, funA, funB, duplication = 1L)

term_pairwise_overall_change(p, duplication = 1L)

term_pairwise_neofun_singlefun(p, nfun, duplication = 1L)

Arguments

p

An object of class geese or flock.

lb, ub

Integers, minimum and maximum number of changes.

duplication

Integer. 0 for speciation, 1 for duplication and 2 for either.

funs

Vector of function indices (starting from zero).

a, b

Indices of functions (starting from zero)

Details

In the case of term_neofun_a2b, a represents the origin function from which b is originated.