prc(vegan)
prc()所属R语言包：vegan
Principal Response Curves for Treatments with Repeated Observations
主要处理的重复观测的响应曲线
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Principal Response Curves (PRC) are a special case of Redundancy Analysis (rda) for multivariate responses in repeated observation design. They were originally suggested for ecological communities. They should be easier to interpret than traditional constrained ordination. They can also be used to study how the effects of a factor A depend on the levels of a factor B, that is A + A:B, in a multivariate response experiment.
主要响应曲线（中国）是一个特殊的情况下，冗余分析（rda）在反复观察设计的多元反应。他们最初提出的生态社区。他们应该更容易解释比传统的约束协调。它们也可以被用来研究的效应如何的一个因素A依赖于水平的一个因素B，是A + A:B，在一个多元的反应实验。
用法----------Usage----------
prc(response, treatment, time, ...)
## S3 method for class 'prc'
summary(object, axis = 1, scaling = 3, digits = 4, ...)
## S3 method for class 'prc'
plot(x, species = TRUE, select, scaling = 3, axis = 1, type = "l",
xlab, ylab, ylim, lty = 1:5, col = 1:6, pch, legpos, cex = 0.8,
...)
参数----------Arguments----------
参数：response
Multivariate response data. Typically these are community (species) data. If the data are counts, they probably should be log transformed prior to the analysis.
多元响应数据。通常情况下，这些社区（种）的数据。如果数据计算得出的，他们很可能是对数转换之前的分析。
参数：treatment
A factor for treatments.
治疗的一个因素。
参数：time
An unordered factor defining the observations times in the repeated design.
无序因素的反复设计中定义的观测时间。
参数：object, x
An prc result object.
prc的结果对象。
参数：axis
Axis shown (only one axis can be selected).
轴（可多选）只有一个轴。
参数：scaling
Scaling of species scores, identical to the scaling in scores.rda.
缩放物种分数，相同的scaling中scores.rda的。
参数：digits
Number of significant digits displayed.
的显著位数显示。
参数：species
Display species scores.
显示物种的成绩。
参数：select
Vector to select displayed species. This can be a vector of indices or a logical vector which is TRUE for the selected species
矢量选择显示的物种。这可以是一个矢量的指数或逻辑向量是TRUE选定物种
参数：type
Type of plot: "l" for lines, "p" for points or "b" for both.
图类型："l"行"p"为点或"b"为。
参数：xlab, ylab
Text to replace default axis labels.
文本，以取代默认的坐标轴的标签。
参数：ylim
Limits for the vertical axis.
垂直轴的限制。
参数：lty, col, pch
Line type, colour and plotting characters (defaults supplied).
线的类型，颜色和标识字符（默认提供）。
参数：legpos
The position of the legend. A guess is made if this is not supplied, and NA will suppress legend.
位置的legend。如果没有提供，这是一个猜测是，和NA将抑制传说。
参数：cex
Character expansion for symbols and species labels.
字符扩展的符号和种类的标签。
参数：...
Other parameters passed to functions.
其他参数传递给函数。
Details
详细信息----------Details----------
PRC is a special case of rda with a single factor for treatment and a single factor for time points in repeated observations. In vegan, the corresponding rda model is defined as rda(response ~ treatment * time + Condition(time)). Since the time appears twice in the model formula, its main effects will be aliased, and only the main effect of treatment and interaction terms are available, and will be used in PRC. Instead of usual multivariate ordination diagrams, PRC uses canonical (regression) coefficients and species scores for a single axis. All that the current functions do is to provide a special summary and plot methods that display the rda results in the PRC fashion. The current version only works with default contrasts (contr.treatment) in which the coefficients are contrasts against the first level, and the levels must be arranged so that the first level is the control (or a baseline). If necessary, you must change the baseline level with function relevel.
中国是一个特殊的情况下rda一个单一的因素treatment和一个单一的因素time点重复观测。在vegan，相应的rda模型被定义为rda(response ~ treatment * time + Condition(time))。因为time中出现两次的模型公式，它的主要作用是别名，治疗和互动方面的主要作用是，将用于在中国。而不是通常的多元协调图，中国使用规范（回归）系数和物种的分数为一个单一的轴。 ，目前的功能是提供一个特殊的summary和plot方法rda结果显示，在中国时尚。当前的版本只适用于默认对比（contr.treatment），其中的系数是对第一级的对比，并必须被布置成使得所述第一电平时的控制（或基准线）的水平。如果有必要，你必须改变基线水平与功能relevel。
Function summary prints the species scores and the coefficients. Function plot plots coefficients against time using matplot, and has similar defaults. The graph (and PRC) is meaningful only if the first treatment level is the control, as the results are contrasts to the first level when unordered factors are used. The plot also displays species scores on the right vertical axis using function linestack. Typically the number of species is so high that not all can be displayed with the default settings, but users can reduce character size or padding (air) in linestack, or select only a subset of the species. A legend will be displayed unless suppressed with legpos = NA, and the functions tries to guess where to put the legend if legpos is not supplied.
的函数summary打印的物种的分数和系数。功能plot图系数对time使用matplot，也有类似的默认。的曲线图（及中国）是非常有意义的，如果第一treatment电平的控制，因为其结果是到第一电平的对比时使用无序因子。该图还显示了物种的分数，右纵轴使用功能linestack。通常情况下，物种数量是如此之高，并不是所有可以显示的默认设置，但用户可以减少字符大小或填充（air）linestack或select只有一小部分的品种。除非抑制legpos = NA，将显示一个传奇的功能会尝试去猜测把传说legpos如果不提供。
值----------Value----------
The function is a special case of rda and returns its result object (see cca.object). However, a special summary and plot methods display returns differently than in rda.
该函数是一个特殊的情况下，rda和返回的结果对象（见cca.object“）。然而，一个特殊的summary和plot方法以不同的方式显示回报比rda。
警告----------Warning ----------
The first level of treatment must be the control: use function relevel to guarantee the correct refence level. The current version will ignore user setting of contrasts and always use treatment contrasts (contr.treatment). The time must be an unordered
第一级的treatment必须控制：使用功能relevel保证正确refence的水平。目前的版本会忽略用户设置的contrasts和一直使用治疗对比（contr.treatment）。 time必须是一个无序
（作者）----------Author(s)----------
Jari Oksanen and Cajo ter Braak
参考文献----------References----------
curves: Analysis of time-dependent multivariate responses of biological community to stress. Environmental Toxicology and Chemistry, 18, 138–148.
参见----------See Also----------
rda, anova.cca.
rda，anova.cca。
实例----------Examples----------
# Chlorpyrifos experiment and experimental design[毒死刻度线实验和实验设计]
data(pyrifos)
week <- gl(11, 12, labels=c(-4, -1, 0.1, 1, 2, 4, 8, 12, 15, 19, 24))
dose <- factor(rep(c(0.1, 0, 0, 0.9, 0, 44, 6, 0.1, 44, 0.9, 0, 6), 11))
# PRC[中国]
mod <- prc(pyrifos, dose, week)
mod # RDA[RDA]
summary(mod) # PRC[中国]
logabu <- colSums(pyrifos)
plot(mod, select = logabu > 100)
# Permutations should be done only within one week, and we only[排列，应仅在一周内完成，我们只]
# are interested on the first axis[在第一轴线感兴趣]
anova(mod, strata = week, first=TRUE, perm.max = 100)
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 15:11:23
