R语言 TreeSim包 sim.bd.taxa()函数中文帮助文档(中英文对照)

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sim.bd.taxa(TreeSim)
sim.bd.taxa()所属R语言包：TreeSim

                                        sim.bd.taxa: Simulating birth-death trees on a fixed number of extant taxa
                                         sim.bd.taxa：模拟一个固定数量的现存类群的出生与死亡的树木

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

sim.bd.taxa simulates trees on n species under the constant rate birth-death process. The method allows for incomplete sampling, i.e. (i) only a fixed fraction of all extant tips is included in the sampled tree or (ii) each tip from a big tree is included with a fixed probability. In both cases, the tree is conditioned to have n tips after sampling.
sim.bd.taxa下的恒定速率生灭过程的模拟N种上的树木。该方法允许不完整的采样，即（i）只有一个固定的分数是所有现存的提示中包含的采样树，或（ii）每个从一棵大树的顶端有固定的概率。在这两种情况下，树的条件是具有n个采样后的提示。


用法----------Usage----------


sim.bd.taxa(n, numbsim, lambda, mu, frac = 1, complete = TRUE,
stochsampling = FALSE)



参数----------Arguments----------

参数：n
Number of extant sampled leaves
现存的采样叶数


参数：numbsim
Number of trees to simulate
树木的数量模拟


参数：lambda
Speciation rate
形态率


参数：mu
Extinction rate
消光率


参数：frac
When complete = FALSE: Sampling fraction: If stochsampling=FALSE: The actual number of tips is n/frac, but only n tips are included (incomplete sampling). If stochsampling=TRUE: Each tip is included into the final tree with probability frac. When complete = TRUE: all extinct and non-sampled lineages are included, i.e. the tree has n/frac extant leaves.
完成时= FALSE：抽样比：stochsampling如果= FALSE的秘诀是n /压裂的实际数量，但只有n个技巧（不完全抽样）。如果stochsampling = TRUE：每头进入决赛的概率压裂树。当完成时= TRUE：全部灭绝和非抽样谱系的，即树有n个，/压裂现存叶子。


参数：complete
If TRUE, the tree with the extinct and non-sampled lineages is returned. If FALSE, the extinct lineages are suppressed.
如果返回TRUE，树的灭绝和非抽样谱系的。如果为FALSE，已经灭绝的血统被抑制。


参数：stochsampling
See frac.
请参阅压裂。


值----------Value----------


参数：out[[1]]
List of numbsim simulated trees with n extant sampled leaves
有n个现存的采样叶numbsim模拟树木名单


参数：out[[2]]
Vector of age of trees (time to root plus length of edge above root)
向量的树龄（根际以上的时间来根加边缘的长度）


注意----------Note----------

For stochsampling = TRUE: The algorithm is fast for the critical process, lambda=mu.
对于stochsampling = TRUE：该算法的关键过程是快速，λ=亩。


（作者）----------Author(s)----------


Tanja Stadler



参考文献----------References----------




参见----------See Also----------

sim.bd.age, sim.rateshift.taxa, sim.gsa.taxa, birthdeath.tree
sim.bd.age，sim.rateshift.taxa，sim.gsa.taxa，birthdeath.tree


实例----------Examples----------


n<-10
lambda <- 2.0
mu <- 0.5
frac <-0.6
numbsim<-2

##[＃]
# Simulating numbsim trees with n species under a birth-death process with [N种模拟numbsim树木，下一个生灭过程]
# speciation rate lambda an extinction rate mu:[形态率的lambda的灭绝率万亩：]

sim.bd.taxa(n,numbsim,lambda,mu)

# Each extant species is included in final tree with probability frac [每一个现存的物种被列入最终的概率压裂树]
# (the tree has n species AFTER sampling):[（树有N种采样后）：]

sim.bd.taxa(n,numbsim,lambda,mu,frac,complete=FALSE,stochsampling=TRUE)

# A fraction frac of the extant species is included into the final tree [一小部分压裂现存的物种被纳入到最终的树]
# (the tree has n species AFTER sampling):[（树有N种采样后）：]

sim.bd.taxa(n,numbsim,lambda,mu,frac,complete=FALSE,stochsampling=FALSE)


转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


注：
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