genTrees: Generation of rooted binary trees under a given tree model

Description

genTrees - Is a wrapper function that generates Ntrees-many rooted binary trees with the given number of n leaves under any tree model tm contained in this package (more details on the available models are given in the parameter information for tm).

Usage

genTrees(n, Ntrees = 1L, tm)

Value

genTrees If Ntrees is 1, then a single tree of class phylo is returned. If Ntrees is larger than 1, a list of class multiPhylo containing the trees of class phylo is returned.

Arguments

n

Integer value that specifies the desired number of leaves, i.e., vertices with in-degree 1 and out-degree 0.
Due to the restrictions of the phylo or multiPhylo format, the number of leaves must be at least 2 since there must be at least one edge.

Ntrees

Integer value (default = 1) that specifies the desired number of generated trees.

tm

Character or list specifying the tree model under which the trees should be generated as well as their parameters. Available are:

"yule" - Yule model.
"pda" - PDA model.
"etm" - ETM.
list("aldous", BETA) - Aldous' beta splitting model with parameter BETA >= -2.
list("ford", ALPHA) - Ford's alpha model with parameter ALPHA >= 0 and <= 1.
list("alt-birth-death", BIRTHRATE, DEATHRATE) or
list("alt-birth-death", BIRTHRATE, DEATHRATE, TRIES) - Alternative birth-death model with parameters BIRTHRATE >0 and DEATHRATE>= 0.
list("density", BIRTHRATE, EQUILIB) or
list("density", BIRTHRATE, EQUILIB, TRIES, TIMEperTRY) - Density dependent model with parameters BIRTHRATE >0 and EQULIB>= 1.
list("BiSSE", BIRTHRATES, DEATHRATES, TRANSRATES) or
list("BiSSE", BIRTHRATES, DEATHRATES, TRANSRATES, TRIES, TIMEperTRY) - BiSSE model with parameters BIRTHRATES (vector with 2 values >=0, one value >0), DEATHRATES (vector with 2 values >=0), and TRANSRATES (vector with 2 values >=0, one value >0).
list("DCO_sym", ZETA) or
list("DCO_sym", ZETA, STARTING_RATE) - Symmetric direct-children-only with parameter ZETA > 0 and optionally STARTING_RATE > 0 (default = 1).
list("DCO_asym", ZETA) or
list("DCO_asym", ZETA, STARTING_RATE) - Asymmetric direct-children-only with parameter ZETA > 0 and optionally STARTING_RATE > 0 (default = 1).
list("IF_sym", ZETA) or
list("IF_sym", ZETA, STARTING_RATE) - Symmetric inherited fertility with parameter ZETA > 0 and optionally STARTING_RATE > 0 (default = 1).
list("IF_asym", ZETA) or
list("IF_asym", ZETA, STARTING_RATE) - Asymmetric inherited fertility with parameter ZETA > 0 and optionally STARTING_RATE > 0 (default = 1).
list("IF-diff", ZETA) or
list("IF-diff", ZETA, STARTING_RATE) - Unequal fertility inheritance with parameter ZETA >= 1 and optionally STARTING_RATE > 0 (default = 1).
list("biased", ZETA) or
list("biased", ZETA, STARTING_RATE) - Biased speciation with parameter ZETA >=0 and <=1 and optionally STARTING_RATE > 0 (default = 1).
list("ASB", ZETA) or
list("ASB", ZETA, STARTING_RATE) - Age-step-based fertility with parameter ZETA > 0 and optionally STARTING_RATE > 0 (default = 1).
list("simpleBrown_sym", SIGMA) or
list("simpleBrown_sym", SIGMA, STARTING_RATE) - Symmetric simple Brownian with parameter SIGMA >= 0 and optionally STARTING_RATE > 0 (default = 1).
list("simpleBrown_asym", SIGMA) or
list("simpleBrown_asym", SIGMA, STARTING_RATE) - Asymmetric simple Brownian with parameter SIGMA >= 0 and optionally STARTING_RATE > 0 (default = 1).
list("lin-Brown_sym", SIGMA) or
list("lin-Brown_sym", SIGMA, STARTING_RATE, STARTING_TRAIT) - Sym. punctuated(-intermittent) linear-Brownian with parameter SIGMA (vector with 2 values >=0) and optionally STARTING_RATE > 0 (default = 1) and STARTING_TRAIT (default = 10).
list("lin-Brown_asym", SIGMA) or
list("lin-Brown_asym", SIGMA, STARTING_RATE, STARTING_TRAIT) - Asym. punctuated(-intermittent) linear-Brownian with parameter SIGMA (vector with 2 values >=0) and optionally STARTING_RATE > 0 (default = 1) and STARTING_TRAIT (default = 10).
list("lin-Brown-bounded_sym", SIGMA) or
list("lin-Brown-bounded_sym", SIGMA, STARTING_RATE, STARTING_TRAIT) - Bounded sym. punctuated(-intermittent) linear-Brownian with parameter SIGMA (vector with 2 values >=0) and optionally STARTING_RATE > 0 (default = 1) and STARTING_TRAIT (default = 10).
list("lin-Brown-bounded_asym", SIGMA) or
list("lin-Brown-bounded_asym", SIGMA, STARTING_RATE, STARTING_TRAIT) - Bounded asym. punctuated(-intermittent) linear-Brownian with parameter SIGMA (vector with 2 values >=0) and optionally STARTING_RATE > 0 (default = 1) and STARTING_TRAIT (default = 10).
list("log-Brown_sym", SIGMA) or
list("log-Brown_sym", SIGMA, STARTING_RATE, STARTING_TRAIT) - Sym. punctuated(-intermittent) log-Brownian with parameter SIGMA (vector with 2 values >=0) and optionally STARTING_RATE > 0 (default = 1) and STARTING_TRAIT (default = 10).
list("log-Brown_asym", SIGMA) or
list("log-Brown_asym", SIGMA, STARTING_RATE, STARTING_TRAIT) - Asym. punctuated(-intermittent) log-Brownian with parameter SIGMA (vector with 2 values >=0) and optionally STARTING_RATE > 0 (default = 1) and STARTING_TRAIT (default = 10).

More information on each model and their parameters can be found in the description of each model, accessible with ?genYuleTree, ?genPDATree, ?genETMTree, ?genAldousBetaTree, ?genFordsAlphaTree,
?genBirthDeathTree, ?genAltBirthDeathTree, ?genGrowTree.

References

S. J. Kersting, K. Wicke, and M. Fischer. Tree balance in phylogenetic models. arXiv:2406.05185, 2024.
S. J. Kersting, K. Wicke, and M. Fischer. Tree balance in phylogenetic models: Supplementary material. https://tinyurl.com/278cwdh8, 2024.

Examples

Run this code

genTrees(n = 5, Ntrees = 2, tm = list("aldous", 1))
genTrees(n = 5, tm = "pda")

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