stepacross(vegan)
stepacross()所属R语言包：vegan
Stepacross as Flexible Shortest Paths or Extended Dissimilarities
Stepacross灵活的最短路径或扩展四不像
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Function stepacross tries to replace dissimilarities with shortest paths stepping across intermediate sites while regarding dissimilarities above a threshold as missing data (NA). With path = "shortest" this is the flexible shortest path (Williamson 1978, Bradfield & Kenkel 1987), and with path = "extended" an approximation known as extended dissimilarities (De'ath 1999). The use of stepacross should improve the ordination with high beta diversity, when there are many sites with no species in common.
函数stepacross尝试更换不同点，加强中间站点之间的最短路径，而丢失的数据（NA）高于阈值相异。 path = "shortest"“”这是灵活的最短路径（威廉姆森1978年，布拉德菲尔德与肯克尔1987），并用path = "extended"扩展的异同（Death 1999）被称为近似。的使用stepacross的应该改善的协调与高β多样性的时候，有很多网站没有种常见的。
用法----------Usage----------
stepacross(dis, path = "shortest", toolong = 1, trace = TRUE, ...)
参数----------Arguments----------
参数：dis
Dissimilarity data inheriting from class dist or a an object, such as a matrix, that can be converted to a dissimilarity matrix. Functions vegdist and dist are some functions producing suitable dissimilarity data.
相异数据从类继承dist或一个对象，如为一个矩阵，可以转换到一个相异矩阵。功能vegdist和dist是合适的相异数据的一些功能。
参数：path
The method of stepping across (partial match) Alternative "shortest" finds the shortest paths, and "extended" their approximation known as extended dissimilarities.
的方法，跨出（部分匹配）替代"shortest"找到的最短路径，并"extended"近似被称为扩展的异同。
参数：toolong
Shortest dissimilarity regarded as NA. The function uses a fuzz factor, so that dissimilarities close to the limit will be made NA, too.
最短相异视为NA。该函数使用一个模糊的因素，所以，接近极限的异同，将NA，太。
参数：trace
Trace the calculations.
跟踪计算。
参数：...
Other parameters (ignored).
其他参数（忽略）。
Details
详细信息----------Details----------
Williamson (1978) suggested using flexible shortest paths to estimate dissimilarities between sites which have nothing in common, or no shared species. With path = "shortest" function stepacross replaces dissimilarities that are toolong or longer with NA, and tries to find shortest paths between all sites using remaining dissimilarities. Several dissimilarity indices are semi-metric which means that they do not obey the triangle inequality d[ij] <= d[ik] + d[kj], and shortest path algorithm can replace these dissimilarities as well, even when they are shorter than toolong.
威廉姆森（1978）建议采用灵活的最短路径估算网站有什么共通之处，或没有共享的物种之间的异同。 path = "shortest"函数stepacross替换不同点是toolong，并试图找到最短的路径所有网站使用剩余的异同之间NA或更长的时间。几个的相异指数是半度量，这意味着他们不服从三角不等式d[ij] <= d[ik] + d[kj]，及最短路径算法可以取代这些差异，即使他们是小于toolong。
De'ath (1999) suggested a simplified method known as extended dissimilarities, which are calculated with path = "extended". In this method, dissimilarities that are toolong or longer are first made NA, and then the function tries to replace these NA dissimilarities with a path through single stepping stone points. If not all NA could be replaced with one pass, the function will make new passes with updated dissimilarities as long as all NA are replaced with extended dissimilarities. This mean that in the second and further passes, the remaining NA dissimilarities are allowed to have more than one stepping stone site, but previously replaced dissimilarities are not updated. Further, the function does not consider dissimilarities shorter than toolong, although some of these could be replaced with a shorter path in semi-metric indices, and used as a part of other paths. In optimal cases, the extended dissimilarities are equal to shortest paths, but they may be longer.
Death（1999）提出了一个简化的方法被称为扩展的异同，这是计算path = "extended"。在这种方法中，不同点是toolong或更长的时间第一次NA，然后该函数尝试通过单一的踏脚石点以取代这些NA的的不同点与路径。如果不是所有的NA可以取代一通，该功能将更新的异同作出新的通行证，只要所有NA被替换为扩展的异同。这意味着，在第二和进一步的通行证，剩下的NA相异允许有一个以上的踏脚石网站，但没有更新之前更换不同点。此外，功能不考虑异同小于toolong，虽然其中一些可以具有较短的路径在半度量指数取代，和使用作为其他的路径的一部分。在最佳的情况下，扩展的不同点是等于最短路径，但它们可能会更长。
As an alternative to defining too long dissimilarities with parameter toolong, the input dissimilarities can contain NAs. If toolong is zero or negative, the function does not make any dissimilarities into NA. If there are no NAs in the input and toolong = 0, path = "shortest" will find shorter paths for semi-metric indices, and path = "extended" will do nothing. Function no.shared can be used to set dissimilarities to NA.
作为一种替代方法来定义参数toolong，输入的异同可以包含NA的太长异同。 toolong如果是零或负数，则该函数不作任何相异到NA。如果没有NA的输入和toolong = 0，path = "shortest"会找到更短的路径半度量指标，并path = "extended"不会做任何事情。功能no.shared可以用来设置不同点NA。
If the data are disconnected or there is no path between all points, the result will contain NAs and a warning is issued. Several methods cannot handle NA dissimilarities, and this warning should be taken seriously. Function distconnected can be used to find connected groups and remove rare outlier observations or groups of observations.
如果数据被切断或不存在路径之间的所有点，结果将包含NA的，并会发出一个警告。几种方法无法处理NA相异，应该认真对待这个警告。功能distconnected可以用来发现和删除连接的组罕见的异常值观测或观测组。
Alternative path = "shortest" uses Dijkstra's method for finding flexible shortest paths, implemented as priority-first search for dense graphs (Sedgewick 1990). Alternative path = "extended" follows De'ath (1999), but implementation is simpler than in his code.
替代path = "shortest"使用Dijkstra的方法，寻找灵活的最短路径，实现为第一优先级的搜索稠密图（Sedgewick 1990年）。替代path = "extended"如下Death（1999年），但实施比在他的代码是简单的。
值----------Value----------
Function returns an object of class dist with extended dissimilarities (see functions vegdist and dist). The value of path is appended to the method attribute.
函数返回一个对象类dist扩展的异同（见功能vegdist和dist）。 path被追加到method属性。
注意----------Note----------
The function changes the original dissimilarities, and not all like this. It may be best to use the function only when you really must: extremely high beta diversity where a large proportion of dissimilarities are at their upper limit (no species in common).
该函数改变了原来的异同，而不是都这样。这可能是最好使用的功能只有当你真的必须非常高β多样性的一个大比例的不同点是在他们的上限（没有种常见的）。
Semi-metric indices vary in their degree of violating the triangle inequality. Morisita and Horn–Morisita indices of vegdist may be very strongly semi-metric, and shortest paths can change these indices very much. Mountford index violates basic rules of dissimilarities: non-identical sites have zero dissimilarity if species composition of the poorer site is a subset of the richer. With Mountford index, you can find three sites i, j, k so that d[ik] = 0 and d[jk] = 0, but d[ij] > 0. The results of stepacross on Mountford index can be very weird. If stepacross is needed, it is best to try to use it with more metric indices only.
半度量指标不同程度的违反三角不等式。的Morisita和喇叭Morisita指数vegdist可能是非常强烈的半度量，和最短路径可以更改这些指标非常多。芒福德指数违反基本规则的异同：相同的网站有零的差异性，如果物种组成的贫穷网站的一个子集，更丰富的。芒福德指数，你可以找到三个地点i, j, k所以这d[ik] = 0和d[jk] = 0，但d[ij] > 0。的结果stepacross芒福德指数是非常奇怪的。如果stepacross是必要的，最好是尝试使用它的多公吨指数。
（作者）----------Author(s)----------
Jari Oksanen
参考文献----------References----------
flexible shortest path adjustment of ecological distances. Ecology 68, 750–753.
estimation of ecological distances from high beta diversity data. Plant Ecol. 144, 191–199.
data. J. Ecol. 66, 911-920.
参见----------See Also----------
Function distconnected can find connected groups in disconnected data, and function no.shared can be used to set dissimilarities as NA. See swan for an alternative approach. Function stepacross is an essential component in isomap and cophenetic.spantree.
功能distconnected可以找到在断开数据连接的组，函数no.shared可以用来设置不同点NA。见swan另一种方法。功能stepacross在isomap和cophenetic.spantree是一个必不可少的组成部分。
实例----------Examples----------
# There are no data sets with high beta diversity in vegan, but this[有没有数据集的与高β多样性的素食主义者，但是这]
# should give an idea.[应该给一个想法。]
data(dune)
dis <- vegdist(dune)
edis <- stepacross(dis)
plot(edis, dis, xlab = "Shortest path", ylab = "Original")
## Manhattan distance have no fixed upper limit.[＃曼哈顿距离没有固定的上限。]
dis <- vegdist(dune, "manhattan")
is.na(dis) <- no.shared(dune)
dis <- stepacross(dis, toolong=0)
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
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发表于 2012-10-1 15:13:56
