screeplot.cca(vegan)
screeplot.cca()所属R语言包：vegan
Screeplots for Ordination Results and Broken Stick Distributions
排序结果和碎棒分布Screeplots
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Screeplot methods for plotting variances of ordination axes/components and overlaying broken stick distributions. Also, provides alternative screeplot methods for princomp and prcomp.
Screeplot方法绘制协调的轴/组件的差异，覆盖碎棒的分布。此外，为princomp和prcomp的替代screeplot方法。
用法----------Usage----------
## S3 method for class 'cca'
screeplot(x, bstick = FALSE, type = c("barplot", "lines"),
npcs = min(10, if (is.null(x$CCA) || x$CCA$rank == 0) x$CA$rank else x$CCA$rank),
ptype = "o", bst.col = "red", bst.lty = "solid",
xlab = "Component", ylab = "Inertia",
main = deparse(substitute(x)), legend = bstick,
...)
## S3 method for class 'decorana'
screeplot(x, bstick = FALSE, type = c("barplot", "lines"),
npcs = 4,
ptype = "o", bst.col = "red", bst.lty = "solid",
xlab = "Component", ylab = "Inertia",
main = deparse(substitute(x)),
...)
## S3 method for class 'prcomp'
screeplot(x, bstick = FALSE, type = c("barplot", "lines"),
npcs = min(10, length(x$sdev)),
ptype = "o", bst.col = "red", bst.lty = "solid",
xlab = "Component", ylab = "Inertia",
main = deparse(substitute(x)), legend = bstick,
...)
## S3 method for class 'princomp'
screeplot(x, bstick = FALSE, type = c("barplot", "lines"),
npcs = min(10, length(x$sdev)),
ptype = "o", bst.col = "red", bst.lty = "solid",
xlab = "Component", ylab = "Inertia",
main = deparse(substitute(x)), legend = bstick,
...)
bstick(n, ...)
## Default S3 method:[默认方法]
bstick(n, tot.var = 1, ...)
## S3 method for class 'cca'
bstick(n, ...)
## S3 method for class 'prcomp'
bstick(n, ...)
## S3 method for class 'princomp'
bstick(n, ...)
## S3 method for class 'decorana'
bstick(n, ...)
参数----------Arguments----------
参数：x
an object from which the component variances can be determined.
一个对象，从中可确定组件方差。
参数：bstick
logical; should the broken stick distribution be drawn?
逻辑，碎棒分布划分？
参数：npcs
the number of components to be plotted.
组件的数量要绘制。
参数：type
the type of plot.
图的类型。
参数：ptype
if type == "lines" or bstick = TRUE, a character indicating the type of plotting used for the lines; actually any of the types as in plot.default.
如果type == "lines"或bstick = TRUE，其实在type的plot.default的字符类型的图诡计的线条;。
参数：bst.col, bst.lty
the colour and line type used to draw the broken stick distribution.
所使用的颜色和线型绘制碎棒分布。
参数：xlab, ylab, main
graphics parameters.
图形参数。
参数：legend
logical; draw a legend?
逻辑，画一个传说吗？
参数：n
an object from which the variances can be extracted or the number of variances (components) in the case of bstick.default.
一个对象，从中可以提取的方差或（组件）在箱子bstick.default的数量差异。
参数：tot.var
the total variance to be split.
总方差进行分割。
参数：...
arguments passed to other methods.
参数传递给其他方法。
Details
详细信息----------Details----------
The functions provide screeplots for most ordination methods in vegan and enhanced versions with broken stick for prcomp and princomp.
功能提供了最协调的方法vegan和增强版本的screeplots断棒prcomp和princomp。
Function bstick gives the brokenstick values which are ordered random proportions, defined as p[i] = tot/n sum(from x=i to n) 1/x (Legendre & Legendre 1998), where tot is the total and n is the number of brokenstick components (cf. radfit). Broken stick has been recommended as a stopping rule in principal component analysis (Jackson 1993): principal components should be retained as long as observed eigenvalues are higher than corresponding random broken stick components.
的函数bstick给出了brokenstick值是有序的随机比例，定义为p[i] = tot/n sum(from x=i to n) 1/x（勒让德勒让德1998年），其中tot总n是多少brokenstick组件（参见radfit）。碎棒已被推荐为在主成分分析（杰克逊1993年）停止规则：只要观察到的特征值高于相应的随机碎棒成分，主要成分应该保留。
The bstick function is generic. The default needs the number of components and the total, and specific methods extract this information from ordination results. There also is a bstick method for cca. However, the broken stick model is not strictly valid for correspondence analysis (CA), because eigenvalues of CA are defined to be <=1, whereas brokenstick components have no such restrictions. The brokenstick components are not available for decorana where the sum of eigenvalues (total inertia) is unknown, and the eigenvalues of single axes are not additive in detrended analysis.
bstick功能是通用的。默认情况下需要的部件数量和总数，和具体的方法，提取此信息从协调结果。此外，还有一个bstick方法cca。然而，碎棒模型是没有严格有效的对应分析（CA），，因为CA特征值被定义为<=1，而brokenstick部件有没有这样的限制。 brokenstick组件不能用于decorana特征值的总和（总惯量）是未知的，单一轴的特征值是不是去趋势分析的添加剂。
值----------Value----------
Function screeplot draws a plot on the currently active device, and returns invisibly the xy.coords of the points or bars for the eigenvalues.
功能screeplot绘制一个图在当前的活动设备，并返回看不见的xy.coords点或条形的特征值。
Function bstick returns a numeric vector of broken stick components.
功能bstick返回一个数字矢量碎棒组件。
注意----------Note----------
Function screeplot is generic from R version 2.5.0. In these versions you can use plain screeplot command without suffices cca, prcomp etc.
功能screeplot从R2.5.0版是通用的。在这些版本中，您可以使用纯screeplot没有就足够了cca，prcomp等命令
（作者）----------Author(s)----------
Gavin L. Simpson
参考文献----------References----------
analysis: a comparison of heuristical and statistical approaches. Ecology 74, 2204–2214.
ed. Elsevier.
参见----------See Also----------
cca, decorana, princomp and prcomp for the ordination functions, and
cca，decorana，princomp和prcomp的协调功能，并
实例----------Examples----------
data(varespec)
vare.pca <- rda(varespec, scale = TRUE)
bstick(vare.pca)
screeplot(vare.pca, bstick = TRUE, type = "lines")
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 15:12:57
