sim.rateshift.taxa(TreeSim)
sim.rateshift.taxa()所属R语言包：TreeSim
sim.rateshift.taxa: Simulating trees incorporating mass extinction events and rate shifts
sim.rateshift.taxa：模拟树木将大规模灭绝事件和速度的变化
译者：生物统计家园网 机器人LoveR
描述----------Description----------
sim.rateshift.taxa simulates trees on n species under the constant rate birth-death process. At user-specified points in the past, the rates can shift. Further, mass extinction events can be incorporated. The method further allows for incomplete sampling, i.e. only a fixed fraction of all tips is included in the sampled tree. The tree is conditioned to have n tips after sampling.
sim.rateshift.taxa下的恒定速率生灭过程的模拟N种上的树木。在过去，在用户指定的点的汇率可以转移。此外，大规模灭绝事件可以被纳入。该方法还允许对于不完整的采样，即只有一个固定比例的所有的提示的是，包括在采样的树。树的条件是有n个采样后的提示。
用法----------Usage----------
sim.rateshift.taxa(n, numbsim, lambda, mu, frac, times, complete = TRUE, K=0, norm = TRUE)
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
Vector of speciation rates, the rate in entry i is the speciation rate prior to time times[i]
向量的形态率，入学率，我是之前的形态率倍[i]的
参数：mu
Vector of extinction rates, the rate in entry i is the extinction rate prior to time times[i].
向量的物种灭绝率，入学率，我是之前倍[i]的物种灭绝速度。
参数：frac
Vector of proportion of species surviving mass extinction event. Entry i corresponds to the mass extinction at time times[i]. If frac[i]=1, only rate shift but no mass extinction at time times[i].
物种比例媒介生存的生物大灭绝事件。进入i对应于大灭绝倍[I]。如果Frac [I] = 1，只有一倍的变动，但没有大规模灭绝[I]。
参数：times
Vector of mass extinction and rate shift times. Time is 0 today and increasing going backwards in time. Specify the vector as times[i]<times[i+1]. times[1]=0 (today).
向量的质量的灭绝和速度换档时间。时间是0和增加倒退，。指定矢量[]倍[i +1]的。倍[1] = 0（今天）。
参数：complete
If TRUE, the tree with the extinct lineages and non-sampled lineages is returned (so the tree has round(n/frac[1]) extant tips). If FALSE, the extinct lineages and non-sampled lineages are suppressed.
如果返回TRUE，灭绝的血统和非抽样谱系的树（树有圆形（N /压裂[1]）现存的提示）。如果为FALSE，已经灭绝的血统和非抽样谱系被抑制。
参数：K
If K>0, then a density-dependent speciation rate = lambda*(1-numberspecies/K) is used. Only works currently for mu=0.
如果K> 0，那么密度依赖的形态率=与lambda *（1-numberspecies / K）的使用。目前只适用亩= 0。
参数：norm
If norm = TRUE the simulations are exact. If norm = FALSE: see Stadler 2011, p.678, point (7) - tree is always returned when N=0.
如果标准= TRUE模拟是准确的。如果标准= FALSE：施泰德2011，p.678，点（7） - 树总是返回时，N = 0。
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）
（作者）----------Author(s)----------
Tanja Stadler
参考文献----------References----------
参见----------See Also----------
sim.bd.age, sim.bd.taxa, sim.gsa.taxa, birthdeath.tree
sim.bd.age，sim.bd.taxa，sim.gsa.taxa，birthdeath.tree
实例----------Examples----------
n<-10
numbsim<-1
##[＃]
# Simulating trees with a fixed number of species having shifts in rate[具有固定数量的物种具有转变率模拟树]
# and mass extinction events.[大灭绝事件。]
# Between today and time 0.3 in the past, we have speciation rate 2,[今天，在过去的时间0.3之间，我们有形态率2，]
# extinction rate 0. At time 0.3, we have a mass extinction event which[灭绝率0。时间0.3，我们有一个大灭绝事件]
# 10% of the species survive. Prior to 0.3, we have a speciation rate [10％的物种生存。到0.3之前，我们有一个形态率]
# of 1 and an extinction rate of 0.3:[1和物种灭绝速度为0.3：]
sim.rateshift.taxa(n,numbsim,c(2,1),c(0,0.3),
c(1,0.1),c(0,0.3),complete=TRUE)
# The fraction 0.6 of the extant species is included into the final tree[分数0.6的现存物种被纳入到最终的树]
# (the tree has n species AFTER sampling, extinct and[（树N种采样后，灭绝，]
# non-sampled lineages are not included):[非抽样谱系的不包括在内）：]
sim.rateshift.taxa(n,numbsim,c(2,1),c(0,0.3),
c(0.6,0.1),c(0,0.3),complete=FALSE)
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
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发表于 2012-10-1 11:52:53
