relltest(scaleboot)
relltest()所属R语言包：scaleboot
RELL Test for Phylogenetic Inference
RELL测试系统发育推理
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Performs the RELL test for finding the largest item. This calculates AU p-values for each item via the multiscale bootstrap resampling. This is particularly useful for testing tree topologies in phylogenetic analysis.
执行RELL测试发现的最大的项目。此计算AU的每个资料的p-值经由多尺度的自举的重采样。这是特别有用的测试树拓扑结构，系统发育分析。
用法----------Usage----------
relltest(dat,nb=10000,sa=9^seq(-1,1,length=13),ass=NULL,
cluster=NULL,nofit=FALSE,models=NULL,seed=100)
参数----------Arguments----------
参数：dat
a matrix. Row vectors are to be resampled. Each column vector gives score values to be evaluated for an item. For the phylogenetic analysis, dat[i,j] is the site-wise log-likelihood value at site-i for tree-j, and we are to find the tree with the largest expected value of sum(dat[,j]).
一个矩阵。行矢量以进行重新采样。每个列向量给出了一个项目进行评价的得分值。的系统发育分析，dat[i,j]是在现场，我的网站上对数似然值树-J，我们要找到树的最大预期值的sum(dat[,j])。
参数：nb
Number of replicates for each scale.
重复为每个规模。
参数：sa
Scales in sigma squared (σ^2).
秤sigma平方（σ^2“）。
参数：ass
A list of association vectors for testing edges as well as trees. If ass=NULL, then only the results for trees are returned.
列表关联向量测试边以及树木。如果ass=NULL，然后将返回的结果树。
参数：cluster
snow cluster object which may be generated by function makeCluster.
snow的聚类对象可能产生的功能makeCluster。
参数：nofit
logical. Passed to sbfit.
逻辑。传递到sbfit。
参数：models
character vectors. Passed to sbfit.
特征向量。传递到sbfit。
参数：seed
If non NULL, then a random seed is set. Specifying a seed is particularly important when cluster is non NULL, in this case seed + seq(along=cluster) are set to cluster nodes.
如果非NULL，然后设置一个随机种子。是特别重要的，当cluster非NULL，在这种情况下，seed + seq(along=cluster)的聚类节点设置为指定的种子。
Details
详细信息----------Details----------
relltest performs the resampling of estimated log-likelihoods (RELL) method of Kishino et al. (1990). For resampling indices stored in a vector i, the resampled log-likelihood for a tree-j is approximately calculated by sum(dat[i,j]). This approximation avoids time-consuming recalculation of the maximum likelihood estimates of tree parameters, which are to be calculated by an external phylogenetic software such as PAML as described in mam15. In the implementation of relltest, the resampled log-likelihood is calculated by sum(dat[i,j])*nrow(dat)/length(i) so that the statistic is comparable to the case when n'=n.
relltest进行重采样的估计数似然法（RELL）木住野等人。 （1990）。用于重新采样存储在一个向量i，经重新采样的对数似然为一个树-j的近似计算的sum(dat[i,j])的指数。此避免了耗时的近似的最大似然估计的树的参数，这是通过以下来计算所述外部系统发育如PAML软件在mam15重新计算。 relltest，重采样数似然的计算方法是在执行sum(dat[i,j])“*nrow(dat)/length(i)这样的统计数据是可比的情况下，当n'=n。
relltest first calls scaleboot internally for multiscale bootstrap resampling, and then scaleboot calls sbfit for fitting models to the bootstrap probabilities. The AU p-values (named "k.3") produced by the summary method are improvements of the third-order p-values calculated by CONSEL software (Shimodaira and Hasegawa 2001). In addition, relltest calls scaleboot with sa=1 for calculating p-values via the Shimodaira-Hasegawa test (SH-test) of Shimodaira and Hasegawa (1999).
relltest第一次调用scaleboot内部的多尺度自举重采样，然后scaleboot调用sbfit拟合模型，以引导概率。的AU p-值（名为“K.3”）summary方法所产生的第三阶数p CONSEL软件（Shimodaira和长谷川2001）计算出的值的改进。此外，relltest调用scalebootsa=1，通过Shimodaira-长谷川试验（SH-检验）Shimodaira和长谷川（1999）的值，用于计算P-。
See mam15 for details through an example.
见mam15的详细信息，通过一个实例。
值----------Value----------
relltest returns an object of class "relltest" that is inherited from the class "scalebootv" by adding two extra components called "stat" and "shtest". "stat" is a vector of the test statistics from the SH-test (i.e., the log-likelihood differences), and "shtest" is a list with two components: "pv", a vector of SH-test p-values, and "pe", a vector of standard errors of the p-values. The results of multiscale bootstrap resampling are stored in the "scalebootv" components returned by a call to sbfit.
relltest返回一个类的对象"relltest"继承自类"scalebootv"添加了两个额外的组件被称为“统计”和“shtest”的。为“stat”是一个向量的检验统计量的SH-测试（即，对数似然的差异），和“shtest”是具有两个组件：“光伏”SH-检验的p-值，一个向量的列表，和“聚乙烯”，一个向量的p值的标准误差。多尺度自举重采样的结果被存储在"scalebootv"组件返回的呼叫sbfit。
（作者）----------Author(s)----------
Hidetoshi Shimodaira
参考文献----------References----------
Kishino, H., Miyata, T. and Hasegawa, M. (1990). Maximum likelihood inference of protein phylogeny and the origin of chloroplasts., J. Mol. Evol., 30, 151-160.
Shimodaira, H. and Hasegawa, M. (1999). Multiple comparisons of log-likelihoods with applications to phylogenetic inference, Molecular Biology and Evolution, 16, 1114-1116.
Shimodaira, H. and Hasegawa, M. (2001). CONSEL: for assessing the confidence of phylogenetic tree selection, Bioinformatics, 17, 1246-1247 (software is available from http://www.is.titech.ac.jp/~shimo/prog/consel/).
Luke Tierney, A. J. Rossini, Na Li and H. Sevcikova. snow: Simple Network of Workstations. R package version 0.2-1.
参见----------See Also----------
sbfit, scaleboot, mam15.
sbfit，scaleboot，mam15。
实例----------Examples----------
## Not run: [＃不运行：]
## An example from data(mam15).[＃例如从的数据（mam15）。]
## It may take 20 mins to run relltest below.[＃这可能需要20分钟以下运行relltest。]
mam15.mt <- read.mt("mam15.mt") # site-wise log-likelihoods[网站上登录似然]
mam15.trees <- relltest(mam15.mt) # resampling and fitting[重采样和装修]
summary(mam15.trees) # AU p-values[AU p-值]
## End(Not run)[＃（不执行）]
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 2012-9-29 22:26:06
