perspqrrvglm(VGAM)
perspqrrvglm()所属R语言包：VGAM
Perspective plot for QRR-VGLMs
QRR-VGLMs的的透视图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Produces a perspective plot for a CQO model (QRR-VGLM). It is only applicable for rank-1 or rank-2 models with argument Norrr = ~ 1.
产生一个，CQO模型（QRR VGLM）为透视图。这是只适用于等级1或等级2模型参数Norrr = ~ 1。
用法----------Usage----------
perspqrrvglm(x, varlvI = FALSE, reference = NULL, plot.it = TRUE,
xlim = NULL, ylim = NULL, zlim = NULL,
gridlength = if (Rank == 1) 301 else c(51,51),
whichSpecies = NULL,
xlab = if (Rank == 1) "Latent Variable" else "Latent Variable 1",
ylab = if (Rank == 1) "Expected Value" else "Latent Variable 2",
zlab = "Expected value", labelSpecies = FALSE,
stretch = 1.05, main = "", ticktype = "detailed",
col = if (Rank == 1) par()$col else "white",
llty = par()$lty, llwd = par()$lwd,
add1 = FALSE, ...)
参数----------Arguments----------
参数：x
Object of class "qrrvglm", i.e., a constrained quadratic ordination (CQO) object.
类"qrrvglm"，即受约束的二次协调（CQO）对象的对象。
参数：varlvI
Logical that is fed into Coef.qrrvglm.
逻辑被送入Coef.qrrvglm。
参数：reference
Integer or character that is fed into Coef.qrrvglm.
整数或字符，被送入Coef.qrrvglm。
参数：plot.it
Logical. Plot it?
逻辑。图呢？
参数：xlim, ylim
Limits of the x- and y-axis. Both are numeric of length 2. See par.
的x-和y-轴的界限。两者都是长度为2的数字。见par。
参数：zlim
Limits of the z-axis. Numeric of length 2. Ignored if rank is 1. See par.
界限的z-轴。数字的长度为2。如果忽略秩为1。见par。
参数：gridlength
Numeric. The fitted values are evaluated on a grid, and this argument regulates the fineness of the grid. If Rank = 2 then the argument is recycled to length 2, and the two numbers are the number of grid points on the x- and y-axes respectively.
数字。在网格上的拟合值进行评估，参数调节细度的网格。如果Rank = 2然后再循环到该参数，则长度为2，和两个数字的网格点的数目，在x-轴和y轴分别。
参数：whichSpecies
Numeric or character vector. Indicates which species are to be plotted. The default is to plot all of them. If numeric, it should contain values in the set {1,2,...,S} where S is the number of species.
数字或字符向量。表示要绘制的物种。默认值是绘制所有的人。如果数字，它应该包含值的集合{1,2，...，S}S是物种的数量。
参数：xlab, ylab
Character caption for the x-axis and y-axis. By default, a suitable caption is found. See the xlab argument in plot or title.
的x-轴和y-轴的字符标题。默认情况下，找到一个合适的标题。 xlabplot或title参数。
参数：zlab
Character caption for the z-axis. Used only if Rank = 2. By default, a suitable caption is found. See the xlab argument in plot or title.
z轴的字符标题。用只有Rank = 2。默认情况下，找到一个合适的标题。 xlabplot或title参数。
参数：labelSpecies
Logical. Whether the species should be labelled with their names. Used for Rank = 1 only. The position of the label is just above the species' maximum.
逻辑。这个物种是否应该被贴上自己的名字。用于Rank = 1只。物种的最大的标签位置的正上方。
参数：stretch
Numeric. A value slightly more than 1, this argument adjusts the height of the y-axis. Used for Rank = 1 only.
数字。略超过1的值，这个参数调整的y-轴的高度。用于Rank = 1只。
参数：main
Character, giving the title of the plot. See the main argument in plot or title.
人物，图的标题。 mainplot或title参数。
参数：ticktype
Tick type. Used only if Rank = 2. See persp for more information.
勾选类型。用只有Rank = 2。见persp更多信息。
参数：col
Color. See persp for more information.
颜色。见persp更多信息。
参数：llty
Line type. Rank-1 models only. See the lty argument of par.
线路类型。等级1机型。请参阅ltypar参数。
参数：llwd
Line width. Rank-1 models only. See the lwd argument of par.
线条宽度。等级1机型。请参阅lwdpar参数。
参数：add1
Logical. Add to an existing plot? Used only for rank-1 models.
逻辑。添加到现有图？仅用于排名1款。
参数：...
Arguments passed into persp. Useful arguments here include theta and phi, which control the position of the eye.
传递参数到persp。有用的参数包括theta和phi，控制仓位的眼睛。
Details
详细信息----------Details----------
For a rank-1 model, a perspective plot is similar to lvplot.qrrvglm but plots the curves along a fine grid and there is no rugplot to show the site scores.
对于一个等级1的模型，透视图是类似的lvplot.qrrvglm“可是细网格，绘制的曲线，有没有rugplot，显示网站分数。
For a rank-2 model, a perspective plot has the first latent variable as the x-axis, the second latent variable as the y-axis, and the expected value (fitted value) as the z-axis. The result of a CQO is that each species has a response surface with elliptical contours. This function will, at each grid point, work out the maximum fitted value over all the species. The resulting response surface is plotted. Thus rare species will be obscured and abundant species will dominate the plot. To view rare species, use the whichSpecies argument to select a subset of the species.
对于秩2模型的立体图的x-轴，y-轴的第二潜变量作为，作为z轴的预期值（拟合值）具有第一潜变量。一个CQO的结果是，每个物种的响应面椭圆形的轮廓。此功能将在每个网格点，工作的最大拟合值在所有的物种。产生的响应表面绘制。因此，珍稀物种将被遮盖和丰富的物种将主导图。要查看稀有品种，使用whichSpecies参数的品种选择的一个子集。
A perspective plot will be performed if Norrr = ~ 1, and Rank = 1 or 2. Also, all the tolerance matrices of those species to be plotted must be positive-definite.
透视图如果Norrr = ~ 1，Rank = 1或2。此外，所有这些物种的公差矩阵以绘制必须是正定的。
值----------Value----------
For a rank-2 model, a list with the following components.
对于秩2模型中，与以下组件的列表。
参数：fitted
A (G1*G2) by M matrix of fitted values on the grid. Here, G1 and G2 are the two values of gridlength.
A(G1*G2)M矩阵对电网的拟合值。在这里，G1和G2的两个值gridlength。
参数：lv1grid, lv2grid
The grid points for the x-axis and y-axis.
的网格点的x-轴和y-轴。
参数：maxfitted
A G1 by G2 matrix of maximum of the fitted values over all species. These are the values that are plotted on the z-axis.
AG1G2矩阵的所有物种的拟合值超过最大。这些值被绘制在z轴。
For a rank-1 model, the components lv2grid and maxfitted are NULL.
对于一个等级-1型，组件lv2grid，和maxfitted是NULL。
注意----------Note----------
Yee (2004) does not refer to perspective plots. Instead, contour plots via lvplot.qrrvglm are used.
议（2004年）并不是指透视图。相反，通过lvplot.qrrvglm的等高线图。
For rank-1 models, a similar function to this one is lvplot.qrrvglm. It plots the fitted values at the actual site score values rather than on a fine grid here. The result has the advantage that the user sees the curves as a direct result from a model fitted to data whereas here, it is easy to think that the smooth bell-shaped curves are the truth because the data is more of a distance away.
对于排名-1型号，一个类似的功能，这一个是lvplot.qrrvglm。它绘制在工地的实际得分值的拟合值，而不是细网格，在这里。结果具有优势，用户可以看到曲线的直接结果从模型拟合数据，而在这里，很容易让人联想到平滑的钟形曲线是真理，因为数据的距离。
（作者）----------Author(s)----------
Thomas W. Yee
参考文献----------References----------
A new technique for maximum-likelihood canonical Gaussian ordination. Ecological Monographs, 74, 685–701.
参见----------See Also----------
persp, cqo, Coef.qrrvglm, lvplot.qrrvglm, par, title.
persp，cqo，Coef.qrrvglm，lvplot.qrrvglm，par，title。
实例----------Examples----------
hspider[,1:6] = scale(hspider[,1:6]) # Good idea when ITolerances = TRUE[好主意，当ITolerances = TRUE]
set.seed(111)
r1 = cqo(cbind(Alopacce, Alopcune, Alopfabr, Arctlute, Arctperi,
Auloalbi, Pardmont, Pardnigr, Pardpull, Trocterr) ~
WaterCon + BareSand + FallTwig + CoveMoss + CoveHerb + ReflLux,
poissonff, hspider, trace = FALSE, ITolerances = TRUE)
set.seed(111) # r2 below is an ill-conditioned model[R2下面是一个病态的模型]
r2 = cqo(cbind(Alopacce, Alopcune, Alopfabr, Arctlute, Arctperi,
Auloalbi, Pardmont, Pardnigr, Pardpull, Trocterr) ~
WaterCon + BareSand + FallTwig + CoveMoss + CoveHerb + ReflLux,
isdlv = c(2.4,1.0), Muxfactor = 3.0, trace = FALSE,
poissonff, hspider, Rank = 2, EqualTolerances = TRUE)
sort(r1@misc$deviance.Bestof) # A history of the fits[一个历史的拟合]
sort(r2@misc$deviance.Bestof) # A history of the fits[一个历史的拟合]
if (deviance(r2) > 857) stop("suboptimal fit obtained")
persp(r1, xlim = c(-6,5), col = 1:4, label = TRUE)
# Involves all species [涉及到的所有物种]
persp(r2, xlim = c(-6,5), ylim = c(-4,5), theta = 10, phi = 20, zlim = c(0,220))
# Omit the two dominant species to see what's behind them[省略的优势种，在他们身后，看看有什么]
persp(r2, xlim = c(-6,5), ylim = c(-4,5), theta = 10, phi = 20, zlim = c(0,220),
which = (1:10)[-c(8,10)]) # Use zlim to retain the original z-scale[使用zlim保留了原有的规模Z-]
## End(Not run)[＃（不执行）]
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 15:46:46
