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Character or list specifying the tree model under which the trees
should be generated as well as their parameters. Available are:
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"yule" - Yule model.
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"pda" - PDA model.
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"etm" - ETM.
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list("aldous", BETA) - Aldous' beta splitting model with parameter
BETA >= -2.
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list("ford", ALPHA) - Ford's alpha model with parameter
ALPHA >= 0 and <= 1.
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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.
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list("density", BIRTHRATE, EQUILIB) or
list("density", BIRTHRATE, EQUILIB, TRIES, TIMEperTRY) -
Density dependent model with parameters BIRTHRATE >0 and
EQULIB>= 1.
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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).
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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).
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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).
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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).
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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).
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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).
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list("biased", ZETA) or
list("biased", ZETA, STARTING_RATE) - Biased speciation
with parameter ZETA >=0 and <=1 and optionally
STARTING_RATE > 0 (default = 1).
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list("ASB", ZETA) or
list("ASB", ZETA, STARTING_RATE) - Age-step-based fertility
with parameter ZETA > 0 and optionally STARTING_RATE > 0
(default = 1).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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.
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