goodness.metaMDS(vegan)
goodness.metaMDS()所属R语言包：vegan
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
善良的非度量多维标度的配合和Shepard图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Function goodness.metaMDS find goodness of fit measure for points in nonmetric multidimensional scaling, and function stressplot makes a Shepard diagram.
功能goodness.metaMDS找到善良的合适的测量点在非度量多维标度和功能stressplot使一个Shepard图。
用法----------Usage----------
## S3 method for class 'metaMDS'
goodness(object, dis, ...)
## Default S3 method:[默认方法]
stressplot(object, dis, pch, p.col = "blue", l.col = "red",
lwd = 2, ...)
参数----------Arguments----------
参数：object
A result object from metaMDS, monoMDS or isoMDS.
一个结果对象metaMDS，monoMDS或isoMDS。
参数：dis
Dissimilarities. This should not be used with metaMDS or monoMDS, but must be used with isoMDS.
不同之处。这不应该用metaMDS或monoMDS，但必须使用isoMDS。
参数：pch
Plotting character for points. Default is dependent on the number of points.
绘制字符的点。默认值是依赖于点的数量。
参数：p.col, l.col
Point and line colours.
点和线的颜色。
参数：lwd
Line width. For monoMDS the default is lwd = 1 if more than two lines are drawn, and lwd = 2 otherwise.
线条宽度。对于monoMDS默认的是lwd = 1，如果两个以上的画线，lwd = 2否则。
参数：...
Other parameters to functions, e.g. graphical parameters.
其他参数的功能，例如图形参数。
Details
详细信息----------Details----------
Function goodness.metaMDS finds a goodness of fit statistic for observations (points). This is defined so that sum of squared values is equal to squared stress. Large values indicate poor fit. The absolute values of the goodness statistic depend on the definition of the stress: isoMDS expresses stress in percents, and therefore its goodness values are 100 times higher than those of monoMDS which expresses the stress as a proportion.
函数goodness.metaMDS找到一个善良的观测值的拟合统计量（点）。这是定义，以便平方值之和等于平方压力。大值表示很不适应。的善良统计量的绝对值的依赖于应力的定义：isoMDS表示百分数的应力，并因此它的善良值是那些monoMDS表示的应力作为比例的100倍以上。
Function stressplot draws a Shepard diagram which is a plot of ordination distances and monotone or linear fit line against original dissimilarities. In addition, it displays two correlation-like statistics on the goodness of fit in the graph. The nonmetric fit is based on stress S and defined as R2 = 1-S*S. The “linear fit” is the squared correlation between fitted values and ordination distances. For monoMDS, the “linear fit” and R2 from “stress type 2” are equal.
函数stressplot绘制一个的谢泼德图，这是一个图的协调距离与的单调线性拟合线对原来的异同。此外，它会显示两个相关统计数据的拟合优度在图中。非度量拟合根据压力S，定义为R2 = 1-S*S。 “线性拟合”是拟合值和协调的距离的平方之间的相关性。对于monoMDS，“线性拟合”，R2从“压力型2”是相等的。
Both functions can be used with metaMDS, monoMDS and isoMDS. The original dissimilarities should not be given for monoMDS or metaMDS results (the latter tries to reconstruct the dissimilarities using metaMDSredist if isoMDS was used as its engine). With isoMDS the dissimilarities must be given. In either case, the functions inspect that dissimilarities are consistent with current ordination, and refuse to analyse inconsistent dissimilarities. Function goodness.metaMDS is generic in vegan, but you must spell its name completely with isoMDS which has no class.
这两个函数都可以使用metaMDS，monoMDS和isoMDS。 monoMDS或metaMDS结果（后者试图重建的异同使用原来的异同不应给予metaMDSredist如果isoMDS作为它的发动机）。随着isoMDS的异同必须提供。在这两种情况下，功能检查与当前的协调，不同点是一致的，并拒绝不一致的异同进行分析。函数goodness.metaMDS是通用的vegan的，但你必须清楚它的名字完全与isoMDS没有类。
值----------Value----------
Function goodness returns a vector of values. Function stressplot returns invisibly an object with itmes for
功能goodness返回值的向量。功能stressplot返回不可见的对象itmes
（作者）----------Author(s)----------
Jari Oksanen.
----------See Also----------
metaMDS, monoMDS,
metaMDS，monoMDS，
实例----------Examples----------
data(varespec)
mod <- metaMDS(varespec)
stressplot(mod)
gof <- goodness(mod)
gof
plot(mod, display = "sites", type = "n")
points(mod, display = "sites", cex = 2*gof/mean(gof))
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。
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发表于 2012-10-1 15:06:45
