pcnm(vegan)
pcnm()所属R语言包：vegan
Principal Coordinates of Neighbourhood Matrix
邻里矩阵的主坐标
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function computed classical PCNM by the principal coordinate analysis of a truncated distance matrix. These are commonly used to transform (spatial) distances to rectangular data that suitable for constrained ordination or regression.
此功能计算古典PCNM由主坐标分析的截断距离矩阵。这些都是常用变换（空间）的距离，合适的约束协调或回归的矩形数据。
用法----------Usage----------
pcnm(dis, threshold, w, dist.ret = FALSE)
参数----------Arguments----------
参数：dis
A distance matrix.
距离矩阵。
参数：threshold
A threshold value or truncation distance. If missing, minimum distance giving connected network will be used. This is found as the longest distance in the minimum spanning tree of dis.
阈值或截断距离。如果丢失，给所连接的网络的最小距离将被使用。这是发现的最远的距离最小生成树的dis。
参数：w
Prior weights for rows.
之前行的权重。
参数：dist.ret
Return the distances used to calculate the PCNMs.
返回用于计算PCNMs的距离。
Details
详细信息----------Details----------
Principal Coordinates of Neighbourhood Matrix (PCNM) map distances between rows onto rectangular matrix on rows using a truncation threshold for long distances (Borcard & Legendre 2002). If original distances were Euclidean distances in two dimensions (like normal spatial distances), they could be mapped onto two dimensions if there is no truncation of distances. Because of truncation, there will be a higher number of principal coordinates. The selection of truncation distance has a huge influence on the PCNM vectors. The default is to use the longest distance to keep data connected. The distances above truncation threshold are given an arbitrary value of 4 times threshold. For regular data, the first PCNM vectorsshow a wide scale variation and later PCNM vectors show smaller scale variation (Borcard & Legendre 2002), but for irregular data the intepretation is not as clear.
主要坐标邻里的矩阵（PCNM）图距离到矩形矩阵的行之间的行截断很长的距离阈值（Borcard勒让德2002年）。如果原来的距离是在两维（类似正常空间距离）的欧几里德距离，它们就可以被映射到两个维度上，如果不存在距离截断。由于截断，会有较高数目的主坐标系。的PCNM向量的选择截断距离有着巨大的影响。默认是使用时间最长的距离，以保持数据连接。截断阈值以上的距离是给定的阈值的4倍的任意值。对于常规数据，第一PCNM vectorsshow一个广泛的规模变化和PCNM的的矢量规模较小的变化（Borcard 2002年和勒让德），但，旅游解说不规则的数据是不明确的。
The PCNM functions are used to express distances in rectangular form that is similar to normal explanatory variables used in, e.g., constrained ordination (rda, cca and capscale) or univariate regression (lm) together with environmental variables (row weights should be supplied with cca; see Examples). This is regarded as a more powerful method than forcing rectangular environmental data into distances and using them in partial mantel analysis (mantel.partial) together with geographic distances (Legendre et al. 2008, but see Tuomisto & Ruokolainen 2008).
的PCNM功能是用来表示距离在直角坐标形式是类似正常使用的解释变量，例如，约束协调（rda，cca和capscale）或单变量回归（<所述>）以及环境变量（行权重应提供的lm，见示例）。这被看作是一个更有效的方法不是强迫矩形距离和环境数据，他们在部分壁炉分析的使用（cca）与GEO距离（勒让德等人。2008年，但看到2008年Tuomisto和Ruokolainen）。
The function is based on pcnm function in Dray's unreleased spacemakeR package. The differences are that the current function usesr spantree as an internal support function. The current function also can use prior weights for rows by using weighted metric scaling of wcmdscale. The use of row weights allows finding orthonormal PCNMs also for correspondence analysis (e.g., cca).
该功能是基于pcnm功能板车的未发行spacemakeR包。不同之处在于，当前的的功能usesr spantree内部的支持功能。目前的功能还可以使用前行的权重，通过加权度量尺度的wcmdscale。使用行权重也可以发现正交的PCNMs，对应分析（例如，cca）。
值----------Value----------
A list of the following elements:
下面的列表元素：
参数：values
Eigenvalues obtained by the principal coordinates analysis.
特征值的主坐标分析得到的。
参数：vectors
Eigenvectors obtained by the principal coordinates analysis. They are scaled to unit norm. The vectors can be extracted with scores function. The default is to return all PCNM vectors, but argument choices selects the given vectors.
特征向量的主坐标分析得到的。它们扩展到单位规范。这些向量可以提取scores函数。默认是到返回所有PCNM的向量，但参数choices的选择给定的向量。
参数：threshold
Truncation distance.
截断距离。
参数：dist
The distance matrix where values above threshold are replaced with arbitrary value of four times the threshold. String "pcnm" is added to the method attribute, and new attribute threshold is added to the distances. This is returned only when dist.ret = TRUE.
的距离矩阵，其中上述的threshold值所取代与任意阈值的四倍。字符串"pcnm"被添加到method属性，和新的属性threshold被添加到的距离。这是只返回dist.ret = TRUE。
（作者）----------Author(s)----------
Jari Oksanen, based on the code of Stephane Dray.
参考文献----------References----------
ecological data by means of principal coordinates of neighbour matrices. Ecological Modelling 153, 51–68.
explaining beta diversity? Comment. Ecology 89, 3238–3244.
diversity? A reply. Ecology 89, 3244–3256.
参见----------See Also----------
spantree.
spantree。
实例----------Examples----------
## Example from Borcard & Legendre (2002)[＃示例从Borcard勒让德（2002年）]
data(mite.xy)
pcnm1 <- pcnm(dist(mite.xy))
op <- par(mfrow=c(1,3))
## Map of PCNMs in the sample plot[＃图PCNMs样地]
ordisurf(mite.xy, scores(pcnm1, choi=1), bubble = 4, main = "PCNM 1")
ordisurf(mite.xy, scores(pcnm1, choi=2), bubble = 4, main = "PCNM 2")
ordisurf(mite.xy, scores(pcnm1, choi=3), bubble = 4, main = "PCNM 3")
par(op)
## Plot first PCNMs against each other[＃图对对方的第一PCNMs]
ordisplom(pcnm1, choices=1:4)
## Weighted PCNM for CCA[＃的加权PCNM为CCA]
data(mite)
rs <- rowSums(mite)/sum(mite)
pcnmw <- pcnm(dist(mite.xy), w = rs)
ord <- cca(mite ~ scores(pcnmw))
## Multiscale ordination: residual variance should have no distance[＃多尺度协调：剩余方差应该没有距离]
## trend[＃趋势]
msoplot(mso(ord, mite.xy))
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 15:10:44
