plot.cca(vegan)
plot.cca()所属R语言包：vegan
Plot or Extract Results of Constrained Correspondence Analysis
图或提取结果的约束对应分析
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Functions to plot or extract results of constrained correspondence analysis (cca), redundancy analysis (rda) or constrained analysis of principal coordinates (capscale).
到绘制或提取结果的约束对应分析（cca），冗余分析（rda）或受约束的主坐标分析（capscale），功能。
用法----------Usage----------
## S3 method for class 'cca'
plot(x, choices = c(1, 2), display = c("sp", "wa", "cn"),
scaling = 2, type, xlim, ylim, const, ...)
## S3 method for class 'cca'
text(x, display = "sites", labels, choices = c(1, 2), scaling = 2,
arrow.mul, head.arrow = 0.05, select, const, ...)
## S3 method for class 'cca'
points(x, display = "sites", choices = c(1, 2), scaling = 2,
arrow.mul, head.arrow = 0.05, select, const, ...)
## S3 method for class 'cca'
scores(x, choices=c(1,2), display=c("sp","wa","cn"), scaling=2, ...)
## S3 method for class 'rda'
scores(x, choices=c(1,2), display=c("sp","wa","cn"), scaling=2,
const, ...)
## S3 method for class 'cca'
summary(object, scaling = 2, axes = 6, display = c("sp", "wa",
"lc", "bp", "cn"), digits = max(3, getOption("digits") - 3), ...)
## S3 method for class 'summary.cca'
print(x, digits = x$digits, head = NA, tail = head, ...)
## S3 method for class 'summary.cca'
head(x, n = 6, tail = 0, ...)
## S3 method for class 'summary.cca'
tail(x, n = 6, head = 0, ...)
参数----------Arguments----------
参数：x, object
A cca result object.
Acca的结果对象。
参数：choices
Axes shown.
轴所示。
参数：display
Scores shown. These must include some of the alternatives species or sp for species scores, sites or wa for site scores, lc for linear constraints or “LC scores”, or bp for biplot arrows or cn for centroids of factor constraints instead of an arrow.
成绩显示出来。这些都必须包括一些替代品species或sp种分数，sites或wa现场评分，lc线性约束的或“LC分数的为” ，或bp对双标图箭头或cn因素的制约，而不是一个箭头的质心的。
参数：scaling
Scaling for species and site scores. Either species (2) or site (1) scores are scaled by eigenvalues, and the other set of scores is left unscaled, or with 3 both are scaled symmetrically by square root of eigenvalues. Corresponding negative values can be used in cca to additionally multiply results with √(1/(1-λ)). This scaling is know as Hill scaling (although it has nothing to do with Hill's rescaling of decorana). With corresponding negative values inrda, species scores are divided by standard deviation of each species and multiplied with an equalizing constant. Unscaled raw scores stored in the result can be accessed with scaling = 0.
缩放物种和现场评分。无论哪种物种（2）或网站（1）分数是由特征值进行缩放，并留下未缩放其他组分数，或用3都缩放平方根对称的特征值。可用于cca另外相乘的结果与√(1/(1-λ))相应的负值。这的缩放是知道的山缩放（虽然它有没有与希尔的重新调整decorana）。相应的负值rda，种分数除以标准差，每一个物种的平衡常数乘以。未调整的原始分数可以访问存储在结果scaling = 0。
参数：type
Type of plot: partial match to text for text labels, points for points, and none for setting frames only. If omitted, text is selected for smaller data sets, and points for larger.
图：部分匹配text的文本标签，points点，和none帧类型。如果省略，text选择较小的数据集，并points较大。
参数：xlim, ylim
the x and y limits (min,max) of the plot.
x和y的限制（最小值，最大值）的图。
参数：labels
Optional text to be used instead of row names.
可选使用的文本，而不是行名称。
参数：arrow.mul
Factor to expand arrows in the graph. Arrows will be scaled automatically to fit the graph if this is missing.
因子扩大图中的箭头。箭头会自动缩放到适合的图，如果这是失踪。
参数：head.arrow
Default length of arrow heads.
默认的箭头头的长度。
参数：select
Items to be displayed. This can either be a logical vector which is TRUE for displayed items or a vector of indices of displayed items.
要被显示的资料。这可以是一个逻辑向量TRUE显示的项目或显示项目的矢量的索引。
参数：const
General scaling constant to rda scores. The default is to use a constant that gives biplot scores, that is, scores that approximate original data (see vignette decision-vegan.pdf with vegandocs for details and discussion). If const is a vector of two items, the first is used for species, and the second item for site scores.
一般缩放不变rda分数。默认是使用一个常数，它的双标图分数，也就是分数的近似原始数据（见vignettedecision-vegan.pdfvegandocs的详细信息和讨论）。如果const是一个向量的两个项目，第一个是用于种，第二项为网站评分。
参数：axes
Number of axes in summaries.
摘要中的轴数。
参数：digits
Number of digits in output.
输出中的数字位数。
参数：n, head, tail
Number of rows printed from the head and tail of species and site scores. Default NA prints all.
打印的头部和尾部的物种与本站分数的行数。默认NA打印。
参数：...
Parameters passed to other functions.
参数传递给其他函数。
Details
详细信息----------Details----------
Same plot function will be used for cca and rda. This produces a quick, standard plot with current scaling.
同样的plot函数将用于cca和rda。这就产生了一个快速，标准样地与当前scaling。
The plot function sets colours (col), plotting characters (pch) and character sizes (cex) to certain standard values. For a fuller control of produced plot, it is best to call plot with type="none" first, and then add each plotting item separately using text.cca or points.cca functions. These use the default settings of standard text and points functions and accept all their parameters, allowing a full user control of produced plots.
plot功能设置颜色（col），绘制字符（pch）和字符大小（cex），以一定的标准值。为了更全面地控制生产的图，最好是调用“plottype="none"，然后分别添加每个绘图项目使用text.cca或points.cca函数。这些使用标准的text和points函数，并接受其所有参数的默认设置，让用户可完全控制的生产图。
Environmental variables receive a special treatment. With display="bp", arrows will be drawn. These are labelled with text and unlabelled with points. The basic plot function uses a simple (but not very clever) heuristics for adjusting arrow lengths to plots, but the user can give the expansion factor in mul.arrow. With display="cn" the centroids of levels of factor variables are displayed (these are available only if there were factors and a formula interface was used in cca or rda). With this option continuous variables still are presented as arrows and ordered factors as arrows and centroids.
环境变量收到了特殊的处理。用display="bp"，箭头的绘制。这些都标有text和未标记与points。的基本plot函数使用一个简单的（但不是很聪明）启发式的调整箭头的长度图，但用户可以给膨胀系数mul.arrow。 display="cn"的重心水平factor变量的显示（仅当有因素和公式界面中使用cca或rda）。使用此选项连续变量仍然为箭头，并下令因素，箭头和质心。
If you want to have still a better control of plots, it is better to produce them using primitive plot commands. Function scores helps in extracting the needed components with the selected scaling.
如果你还是希望有一个更好的控制图，它是更好的生产使用原始的plot命令。函数scores帮助中提取所需的组件，与选定的scaling。
Function summary lists all scores and the output can be very long. You can suppress scores by setting axes = 0 or display = NA or display = NULL. You can display some first or last (or both) rows of scores by using head or tail or explicit print command for the summary.
函数summary列出了所有的分数，而输出可以是很长的。您可以取消成绩通过设置axes = 0或display = NA或display = NULL。您可以显示第一个或最后一个（或两个）的成绩排head或tail或明确print命令summary。
Palmer (1993) suggested using linear constraints (“LC scores”) in ordination diagrams, because these gave better results in simulations and site scores (“WA scores”) are a step from constrained to unconstrained analysis. However, McCune (1997) showed that noisy environmental variables (and all environmental measurements are noisy) destroy “LC scores” whereas “WA scores” were little affected. Therefore the plot function uses site scores (“WA scores”) as the default. This is consistent with the usage in statistics and other functions in R (lda, cancor).
帕尔默（1993）提出，在协调图的线性约束（“LC分数”），因为这些提供了更好的结果在模拟与本站分数（“WA分数”）是一个步骤，从约束不受约束的分析。然而，麦克卡尼（1997年）表明，嘈杂的环境变量（和所有嘈杂的环境测量）破坏的“LC分数”，而“WA”得分的影响不大。因此，plot函数使用站点的分数（“WA分数”）作为默认值。这是一致的使用情况统计等功能R（lda，cancor“）。
值----------Value----------
The plot function returns invisibly a plotting structure which can be used by function identify.ordiplot to identify the points or other functions in the ordiplot family.
plot函数返回不可见的绘图结构，可以使用的功能identify.ordiplot，找准穴位或其他职能ordiplot家庭。
注意----------Note----------
Package ade4 has function cca which returns constrained correspondence analysis of the same class as the vegan function. If you have results of ade4 in your working environment, vegan functions may try to handle them and fail with cryptic error messages. However, there is a simple utility function ade2vegancca which tries to translate ade4 cca results to vegan cca results so that some vegan functions may work partially with ade4 objects
套件ade4函数cca返回vegan功能相同的类约束的对应分析。如果你有结果ade4在你的工作环境中，vegan功能可能会尝试处理和失败，神秘的错误消息。然而，有一个简单的工具的功能ade2vegancca试图把ade4cca结果vegancca结果，一些vegan的函数可能部分ade4对象工作
（作者）----------Author(s)----------
Jari Oksanen
参见----------See Also----------
cca, rda and capscale for getting something to plot, ordiplot for an alternative plotting routine and more support functions, and text,
cca，rda和capscale得到的东西绘制，ordiplot的替代绘图程序和更多的支持功能，和text
实例----------Examples----------
data(dune)
data(dune.env)
mod <- cca(dune ~ A1 + Moisture + Management, dune.env)
plot(mod, type="n")
text(mod, dis="cn")
points(mod, pch=21, col="red", bg="yellow", cex=1.2)
text(mod, "species", col="blue", cex=0.8)
## Limited output of 'summary'[＃有限的输出“总结”]
head(summary(mod), tail=2)
## Read description of scaling in RDA in vegan:[＃读取缩放RDA全素的描述：]
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 15:11:15
