R语言 spacodiR包 spacodi.by.nodes()函数中文帮助文档(中英文对照)

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spacodi.by.nodes(spacodiR)
spacodi.by.nodes()所属R语言包：spacodiR

                                        conducting randomization tests of turnover in diversity through time
                                         通过时间进行的随机试验的营业额多样性

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

spacodi.by.nodes is a function for testing the null expectation of uniform diversity turnover across nodes of a phylogeny.
spacodi.by.nodes是一个函数，用于测试空期望均匀多样性成交的系统发育跨节点。


用法----------Usage----------


spacodi.by.nodes(sp.plot, phy, sp.parm = "Bst", obs.only = FALSE, return.all = TRUE, n.rep = 10, method = "1s", parm = NULL, dmat = NULL, rand.test = TRUE, r.rep = 10000, ...)



参数----------Arguments----------

参数：sp.plot
a community dataset in spacodiR format (see as.spacodi)
社区spacodiR格式的数据集（见as.spacodi）


参数：phy
a phylogenetic tree of class phylo; see read.tree
类的进化树phylo; read.tree


参数：sp.parm
a parameter of interest (one of "Ist","Pst","Bst","PIst" or analogs for trait data); see <STRONG>Details</STRONG>
利益的参数（一个"Ist","Pst","Bst","PIst"或类似物特征数据）; <STRONG>详情</ STRONG>


参数：obs.only
Boolean; whether only estimated sp.parmss for the empirical data are returned
布尔值;，是否只是估计sp.parms的经验数据返回


参数：return.all
Boolean; whether results for all nodes are returned for the empirical data (regardless NA estimates)
布尔值;结果是否返回所有节点的经验数据（NA估算无论）


参数：n.rep
number of permutations to perform on the dataset
的排列数执行对数据集


参数：method
reshuffling or simulation procedure to perform (see <STRONG>Details</STRONG> for optional methods)
改组或模拟的程序来执行（见<STRONG>详情</ STRONG>可选的方法）


参数：parm
additional parameters, required for methods "1a", "2x", and "3x" (see <STRONG>Details</STRONG>)
额外的参数，需要的方法"1a", "2x", and "3x"（见<STRONG>详情</ STRONG>）


参数：dmat
an optional matrix of spatial distances between plots, for use only with method "3t"
一个可选的矩阵图之间的空间距离，使用的方法"3t"只


参数：rand.test
Boolean; whether a randomization test of observed and expected sp.parms is performed
布尔值;是否随机试验观察到的和预期的sp.parm的执行


参数：r.rep
number of randomization iterations to perform
数量的随机迭代执行


参数：...
additional settings to be set for functions called by spacodi.matrices
额外的设置要设置的功能称为spacodi.matrices


Details

详细信息----------Details----------

spacodi.by.nodes is a function to conduct randomization tests on estimated and observed sp.parmss through time. See spacodi.calc  for further information on the possible estimators to use, whether considering phylogenetic or trait diversity.   
spacodi.by.nodes是通过时间的估计和观察到的sp.parms的一个函数来进行的随机测试。见spacodi.calc的为进一步信息可能使用的估计，是否考虑系统发育性状的多样性。

spacodi.by.nodes computes measures of community structure for nodes of  a phylogeny that subtend greater than two species and where nodes subtend species  that are sampled in multiple plots.
spacodi.by.nodes的亲缘关系，对着大于两个品种，其中的节点对着物种进行采样，在多条曲线的节点计算社会结构的措施。

Note: whether for the empirical data or for permuted datasets, if fewer than two species are sampled in a given plot, the plot will be dynamically  removed from the dataset. This behavior can be controlled directly in spacodi.calc with the prune option.
注：如果少于两物种进行采样，在一个给定的图，无论是经验数据或置换后的数据集，该图将被动态删除的数据集。直接在spacodi.calcprune选项中，可以控制这种行为。

For significance testing, permuted datasets may be generated by one of several methods:
对于显着性检验，置换后的数据集，可能会产生由几个methods之一：

method = "1a" shuffling based on abundance classes of species (see resamp.1a);  requires specification of abund.class.ratio as a parm
method = "1a"洗牌物种的丰富的类的基础上（见resamp.1a）;需要abund.class.ratio作为一个parm规格，

method = "1s" shuffling of abundances across entire dataset (see resamp.1s)
method = "1s"的洗牌的丰度在整个数据集（见resamp.1s）

method = "2s" shuffling of abundances across species but within plots (see resamp.2s)
method = "2s"洗牌的跨物种的丰度，但内图（见resamp.2s）

method = "2x" Gotelli swapping of abundances for pairs of species and within a pair of plots (see resamp.2x);  requires specification of level as a parm
method = "2x"的戈泰利换对物种的丰度和对图内（见resamp.2x）levelparm需要指定

method = "3i" shuffling of abundances within species and among plots (see resamp.3i)
method = "3i"洗牌种内和图之间的丰度（见resamp.3i）

method = "3t" shuffling of abundances to adjacent plots but within species (see resamp.3t); if supplied, dmat  is used to condition abundance shuffling, where closer plots, on average, have higher likelihoods of abundances being swapped
method = "3t"洗牌的丰度，以相邻图，但种内（见resamp.3t），如果提供，dmat是用来的条件丰富洗牌，接近图，平均，具有较高的丰度可能性被交换

method = "3x" Gotelli swapping of abundances for pairs of plots and within a pair of species (see resamp.3x);  requires specification of level as a parm
method = "3x"的戈泰利换对图，并在对物种的丰度（见resamp.3x）;需要指定一个levelparm


值----------Value----------

spacodi.by.nodes returns a list of three elements:
spacodi.by.nodes返回一个列表的三个要素：

observed.sp.parm: estimated sp.parm for nodes of the tree (either all nodes, if return.all=TRUE or for only  those nodes for which sp.parm is non-null)
observed.sp.parm：预计sp.parm树的节点（或者所有的节点，如果return.all=TRUE或只为那些节点sp.parm非空的）

expected.sp.parm: expected sp.parm for all nodes of the emprical data for which sp.parm is calculable; nodes in  this element of the output array are row names
expected.sp.parm：预计sp.parm的所有节点的实证数据的sp.parm计算输出数组元素的节点在此行的名称

randomization.test: results from randomization tests of sp.parm for each node. Note: if randomization test is used,  some randomization iterations may return NA for particular nodes (see details above). The tally of valid expected  sp.parms from permutation is recorded as a column in this element (i.e., randomization.test$valid.comparisons).   Be wary of significant results that are based off few valid comparisons.
randomization.test：sp.parm的每个节点的随机化试验结果。注意：如果使用随机化试验，可能会返回一些随机迭代NA为特定的节点（见上面的详细信息）。从排列相符的有效预期sp.parm的记录中的一列元素（即，randomization.test$valid.comparisons）。警惕的重大成果，是基于一些有效的比较。


（作者）----------Author(s)----------


Jonathan Eastman and Timothy Paine



参考文献----------References----------

phylogenetic structure of communities by an additive partitioning of  phylogenetic diversity. Journal of Ecology 95:493-506.
structure of local communities: statistical performances of  different null models and test statistics on a locally neutral  community. Journal of Ecology 96:914-926.

参见----------See Also----------

spacodi.calc for interpretation of results; resamp.test; randomizeMatrix
spacodi.calc结果的解释，“resamp.testrandomizeMatrix


实例----------Examples----------


# load a species-by-plots matrix, along with a tree[加载一个物种的图的矩阵，沿树]
data(sp.example)
attributes(sp.example)
attach(sp.example)
spl
phy

# generate a plot of observed and expected Bst[产生积的观察和预期的BST]
sp.permut<-spacodi.by.nodes(sp.plot=spl, phy=phy, n.rep=35)
sp.permut$randomization.test

# plot observed and expected Bst[图观察值和期望值BST]
spacodi.permutplot(spacodi.permutations=sp.permut, envelope=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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