monophyly(spider)
monophyly()所属R语言包：spider
Species monophyly over a tree
种单系树
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Determines if the species given in sppVector form monophyletic groups on a given tree.
确定的物种给sppVector给定的树形成单系群。
用法----------Usage----------
monophyly(phy, sppVector, pp = NA, singletonsMono = TRUE)
monophylyBoot(phy, sppVector, DNAbin, thresh = 0.7, reroot=TRUE,
pp = NA, singletonsMono = TRUE, reps = 1000, block = 3)
参数----------Arguments----------
参数：phy
A tree of class "phylo".
一棵树类的phylo。
参数：sppVector
Species vector. See sppVector </table>
种向量。 sppVector </表>
参数：pp
Object of class "prop.part". Assists in speeding up the function, if it has been called already. Default of NA, calling prop.part internally.
对象类的prop.part“。协助加快的功能，如果它已经被称为。默认的NA，呼吁prop.part内部。
参数：singletonsMono
Logical. Should singletons (i.e. only a single specimen representing that species) be treated as monophyletic? Default of TRUE. Possible values of FALSE and NA.
逻辑。如果单身人士（即只有一个样本代表品种）被视为单系呢？默认值为TRUE。可能的值FALSE和NA。
参数：DNAbin
An object of class 'DNAbin'. Required for calculating bootstrap values.
对象类的DNAbin。 bootstrap值的计算需要。
参数：thresh
Numeric between 0 and 1. Bootstrap threshold under which potentially monophyletic species are negated. Default of 0.7.
数字0和1之间。引导阈下潜在的单系类群的物种被否定。默认为0.7。
参数：reroot
Logical. Should the bootstrap replicates be rerooted on the longest edge? Default of TRUE.
逻辑。如果引导复制rerooted的最长的边缘？默认值为TRUE。
参数：reps
Numeric. Number of bootstrap replications. Default of 1000.
数字。引导复制的数量。默认为1000。
参数：block
The number of nucleotides that will be resampled together. Default of 3 to resample on the codon level.
的核苷酸序列，将一起进行重新采样的数目。 3默认的密码子水平上重新取样。
Details
详细信息----------Details----------
monophyly determines if each species is monophyletic. monophylyBoot incorporates a bootstrap test to determine the support for this monophyly. Species with a bootstrap support lower than "thresh" are recorded as FALSE.
monophyly确定每个物种是单系。 monophylyBoot集成了自举测试，以确定此单系的支持。一类具有一个引导支持下除“"thresh"记录为FALSE。
Rerooting is done on the longest internal edge in the tree returned by nj(dist.dna(DNAbin)).
Rerooting在树中最长的内部边缘返回nj(dist.dna(DNAbin))。
值----------Value----------
monophyly returns a logical vector, stating if each species is monophyletic. Values correspond to the species order given by unique(sppVector).
monophyly返回一个逻辑向量，如果每个物种是单系群。值对应的物种的unique(sppVector)给定的顺序。
monophylyBoot returns a list with the following elements:
monophylyBoot返回一个列表，包含下列元素：
参数：results
A logical vector, stating if each species is monophyletic with a bootstrap support higher than the given threshold.
逻辑向量，说明具有自举支持高于给定的阈值，如果每个物种是单系。
参数：BSvalues
A numeric vector giving the bootstrap proportions for each node of phy.
一个数值向量给引导的比例，每个节点的phy。
（作者）----------Author(s)----------
Samuel Brown <s_d_j_brown@hotmail.com>
参见----------See Also----------
prop.part, root, boot.phylo.
prop.part，root，boot.phylo。
实例----------Examples----------
#Random trees[随机树]
set.seed(16)
tr <- rtree(15)
spp <- rep(LETTERS[1:5], rep(3,5))
monophyly(tr, spp)
tr2 <- tr
spp2 <- c(rep(LETTERS[1:4], rep(3,4)), LETTERS[5:7])
monophyly(tr2, spp2)
#Empirical data[实证数据]
data(anoteropsis)
anoTree <- nj(dist.dna(anoteropsis))
anoSpp <- sapply(strsplit(dimnames(anoteropsis)[[1]], split="_"),
function(x) paste(x[1], x[2], sep="_"))
monophyly(anoTree, anoSpp)
monophyly(anoTree, anoSpp, singletonsMono=FALSE)
unique(anoSpp)
#To get score for each individual[每一个人得分]
anoMono <- monophyly(anoTree, anoSpp)
anoMono[match(anoSpp, unique(anoSpp))]
data(woodmouse)
woodTree <- nj(dist.dna(woodmouse))
woodSpp <- c("D", "C", "C", "A", "A", "E", "A", "F", "C", "F", "E", "D", "A", "A", "E")
unique(woodSpp)
monophyly(woodTree, woodSpp)
woodMono <- monophylyBoot(woodTree, woodSpp, woodmouse)
woodMono$results
woodMono$BSvalues
monophylyBoot(woodTree, woodSpp, woodmouse, reroot = FALSE)
monophylyBoot(woodTree, woodSpp, woodmouse, thresh = 0.9, reroot = 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。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
|
发表于 2012-9-30 15:17:40
