ordihull(vegan)
ordihull()所属R语言包：vegan
Display Groups or Factor Levels in Ordination Diagrams
显示组或因子水平的排序图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Functions to add convex hulls, "spider" graphs, ellipses or cluster dendrogram to ordination diagrams. The ordination diagrams can be produced by vegan plot.cca,
凸壳，蜘蛛的图形，椭圆形或丛集树状图，统筹图的函数。统筹图，可以通过veganplot.cca的，
用法----------Usage----------
ordihull(ord, groups, display = "sites", draw = c("lines","polygon", "none"),
col = NULL, alpha = 127, show.groups, label = FALSE, ...)
ordiellipse(ord, groups, display="sites", kind = c("sd","se"), conf,
draw = c("lines","polygon", "none"), w = weights(ord, display),
col = NULL, alpha = 127, show.groups, label = FALSE, ...)
ordispider(ord, groups, display="sites", w = weights(ord, display),
show.groups, label = FALSE, ...)
ordicluster(ord, cluster, prune = 0, display = "sites",
w = weights(ord, display), ...)
## S3 method for class 'ordihull'
summary(object, ...)
## S3 method for class 'ordiellipse'
summary(object, ...)
参数----------Arguments----------
参数：ord
An ordination object or an ordiplot object.
协调对象或ordiplot对象。
参数：groups
Factor giving the groups for which the graphical item is drawn.
因素给组的图形绘制。
参数：display
Item to displayed.
项目显示。
参数：draw
Use either lines or polygon to draw the lines. Graphical parameters are passed to both. The main difference is that polygons may be filled and non-transparent. With none nothing is drawn, but the function returns the invisible plotting data.
是lines或polygon画的线条。图形参数传递给双方。主要的区别是，polygons可以被填充和非透明的。 none什么也不绘制，但该函数返回的invisible绘制数据。
参数：col
Colour of hull or ellipse lines (if draw = "lines") or their fills (if draw = "polygon") in ordihull and ordiellipse. When draw = "polygon", the colour of bordering lines can be set with argument border of the polygon function. For other functions the effect depends on the underlining functions this argument is passed to.
船体或椭圆形，线的颜色（如果draw = "lines"）或填充（如果：draw = "polygon"）ordihull和ordiellipse。当draw = "polygon"，接壤线的颜色可以设置参数border的polygon功能。对于其它功能的效果取决于此参数被传递给在强调功能。
参数：alpha
Transparency of the fill colour with draw = "polygon" in ordihull and ordiellipse. The argument takes precedence over possible transparency definitions of the colour. The value must be in range 0...255, and low values are more transparent. Transparency is not available in all graphics devices or file formats.
透明填充col用draw = "polygon"中ordihull和ordiellipse。的参数的优先级高于可能的透明度定义的颜色。该值必须在范围0...255值和最低值，更透明的。在所有的图形设备或文件格式不提供透明度。
参数：show.groups
Show only given groups. This can be a vector, or TRUE if you want to show items for which condition is TRUE. This argument makes it possible to use different colours and line types for groups. The default is to show all groups.
只显示组。这可能是一个向量，或TRUE如果你想显示项目的条件是TRUE。这个论点的群体，使人们有可能使用不同的颜色和线型。默认是显示所有的组。
参数：label
Label the groups by their names in the centroid of the object. ordiellipse and ordihull use standard text, and others use ordilabel.
标签groups他们的名字对象的质心。 ordiellipse和ordihull使用标准的text，和其他人使用ordilabel。
参数：w
Weights used to find the average within group. Weights are used automatically for cca and decorana results, unless undone by the user. w=NULL sets equal weights to all points.
采用的权数，以找到在组内的平均。权重用于自动cca和decorana结果，除非用户撤消。 w=NULL的所有点设置相同的权重。
参数：kind
Whether standard deviations of points (sd) or standard deviations of their (weighted) averages (se) are used.
无论是点（sd）或标准差（加权）平均值（se）用于标准差。
参数：conf
Confidence limit for ellipses, e.g. 0.95. If given, the corresponding sd or se is multiplied with the corresponding value found from the Chi-squared distribution with 2df.
置信限为椭圆形，例如0.95。如果给出，对应的sd或se乘以相应的值的卡方分布2DF。
参数：cluster
Result of hierarchic cluster analysis, such as hclust or agnes.
分层聚类分析，如hclust或agnes的结果。
参数：prune
Number of upper level hierarchies removed from the dendrogram. If prune >0, dendrogram will be disconnected.
数上从树状图的层次结构。如果prune>0，聚类分析将被断开。
参数：object
A result object from ordihull or ordiellipse. The result is invisible, but it can be saved, and used for summaries (areas etc. of hulls and ellipses).
一个结果对象从ordihull或ordiellipse。其结果是invisible，但它可以被保存，用于摘要（等区域的船体和椭圆形）。
参数：...
Parameters passed to graphical functions or to scores to select axes and scaling etc.
参数传递给图形函数或scores选择轴和缩放等。
Details
详细信息----------Details----------
Function ordihull draws lines or polygons for the convex hulls found by function chull encircling the items in the groups.
功能ordihull吸引lines或polygon的凸壳的功能chull包围的群体中的项目。
Function ordiellipse draws lines or polygons for dispersion ellipses using either standard deviation of point scores or standard error of the (weighted) average of scores, and the (weighted) correlation defines the direction of the principal axis of the ellipse. An ellipsoid hull can be drawn with function ellipsoidhull of package cluster.
功能ordiellipse绘制lines或polygon的分散椭圆形，使用标准偏差的分数或标准错误（加权）平均分数（加权）相关定义的方向椭圆的主轴。椭球的船体，可以得出与功能ellipsoidhull包cluster。
Function ordispider draws a "spider" diagram where each point is connected to the group centroid with segments. Weighted centroids are used in the correspondence analysis methods cca and decorana or if the user gives the weights in the call. If ordispider is called with cca or rda result without groups argument, the function connects each "WA" scores to the corresponding "LC" score. If the argument is a (invisible) ordihull object, the function will connect the points of the hull to their centroid.
函数ordispider绘制一个蜘蛛图，其中每个点连接到该组的质心与segments。的对应分析方法中使用的加权的质心cca和decorana或如果用户给出的权重，在该呼叫。如果ordispidercca或rda没有groups参数，调用该函数连接每个WA分数相应的“LC”得分“。如果该参数是（invisible）ordihull对象，该函数将连接点的船体，他们的重心。
Function ordicluster overlays a cluster dendrogram onto ordination. It needs the result from a hierarchic clustering such as hclust or agnes, or other with a similar structure. Function ordicluster connects cluster centroids to each other with line segments. Function uses centroids of all points in the clusters, and is therefore similar to average linkage methods.
函数ordicluster覆盖协调一个聚类树状图上。它需要从一个层次聚类的结果如hclust或agnes，或其他具有类似结构。函数ordicluster彼此连接聚类重心与行segments。函数使用在聚类中的所有点的质心，并因此平均连锁方法类似。
值----------Value----------
Functions ordihull, ordiellipse and ordispider return the invisible plotting structure.
功能ordihull，ordiellipse和ordispider返回invisible绘制结构。
Function ordispider return the coordinates to which each point is connected (centroids or "LC" scores).
功能ordispider返回的坐标，每个点连接（质心或“LC”的分数）。
Function ordihull returns a list of coordinates of the hulls (which can be extracted with scores), and ordiellipse returns a list of covariance matrices and scales used in drawing the ellipses. These result objects have a summary method that returns the coordinates of the centres of the ellipses or hulls and their surface areas in user units. With draw = "none" only the result object is returned and nothing is drawn.
功能ordihull返回一个列表，船舶的船体（可提取的坐标scores），和ordiellipse返回一个列表，用于绘制的椭圆的协方差矩阵和规模。这些结果对象有一个summary方法返回椭圆形或船体和用户单位表面积的中心坐标。随着draw = "none"结果对象被返回，并没有什么画。
注意----------Note----------
These functions add graphical items to ordination graph: You must draw a graph first. To draw line segments, grids or arrows, see ordisegments, ordigrid
这些功能添加图形的项目协调图形：您必须先画一个图。要绘制线段，网格或箭头，ordisegments，ordigrid
（作者）----------Author(s)----------
Jari Oksanen
参见----------See Also----------
The functions pass parameters to basic graphical functions, and you may wish to change the default values in lines, segments and polygon. You can pass parameters to scores as well. Underlying function for
函数传递参数基本的图形功能，您可能希望更改默认值lines，segments和polygon。您可以传递参数给scores以及。相关的功能
实例----------Examples----------
data(dune)
data(dune.env)
mod <- cca(dune ~ Management, dune.env)
attach(dune.env)
## pass non-graphical arguments without warnings[＃通过非图形化的参数，而无需警告]
plot(mod, type="n", scaling = 3)
## Catch the invisible result of ordihull...[＃捕捉的无形的ordihull ...。]
pl <- ordihull(mod, Management, scaling = 3, label = TRUE)
## ... and find centres and areas of the hulls[＃...中心和船舶的船体]
summary(pl)
## use ordispider to label and mark the hull[＃使用ordispider的标签和标记的船体]
plot(mod, type = "n")
pl <- ordihull(mod, Management, scaling = 3)
ordispider(pl, col="red", lty=3, label = TRUE )
## ordispider to connect WA and LC scores[，＃ordispider WA和LC连接分数]
plot(mod, dis=c("wa","lc"), type="p")
ordispider(mod)
## Other types of plots[＃其他类型的图]
plot(mod, type = "p", display="sites")
ordicluster(mod, hclust(vegdist(dune)), prune=3, col = "blue")
plot(mod, type="n", display = "sites")
text(mod, display="sites", labels = as.character(Management))
pl <- ordiellipse(mod, Management, kind="se", conf=0.95, lwd=2, draw = "polygon",
col="skyblue", border = "blue")
summary(pl)
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 2012-10-1 15:09:21
