vegan-package(vegan)
vegan-package()所属R语言包：vegan
Community Ecology Package: Ordination, Diversity and Dissimilarities
社区生态包装方式：排序，多样性和不同点
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The vegan package provides tools for descriptive community ecology. It has most basic functions of diversity analysis, community ordination and dissimilarity analysis. Most of its
vegan包提供的工具为描述性的社会生态。它最基本的功能多样性分析，社会的协调和差异性分析。它的大部分
Details
详细信息----------Details----------
The functions in the vegan package contain tools for diversity analysis (see vignette vegandocs("diversity")), ordination and analysis of dissimilarities (see vignette vegandocs("intro")). Together with the labdsv package, the vegan package provides most standard tools of descriptive community analysis. Package ade4 provides an alternative comprehensive package, and several other packages complement vegan and provide tools for deeper analysis in specific fields. Package BiodiversityR provides a GUI for a large subset of vegan functionality.
的功能多样性分析vegan包中包含的工具（见vignettevegandocs("diversity")），协调和分析的相异（见vignettevegandocs("intro")）。 labdsv包，vegan工具包提供了最标准的，描述性的社会分析。套件ade4提供了另一种全面的包装，和其他几个包补充vegan在特定领域进行更深入的分析，并提供工具。套件BiodiversityR提供了一个图形用户界面的一个大子vegan功能。
The vegan package is developed at R-Forge (http://vegan.r-forge.r-project.org). The R-Forge provides up-to-date information and mailing lists for help queries and bug reports. Bug reports can also be emailed to the function authors or to the package maintainers.
vegan包开发（R-Forge的http://vegan.r-forge.r-project.org）。 R-Forge提供的最新信息和邮件列表，帮助查询和错误报告。问题的报告，也可以通过电子邮件发送的功能作者或包维护者。
The vegan documents can be read with vegandocs function. In addition to vignettes of basic usage, you can read NEWS on the new features and bug fixes in the release version (vegandocs("NEWS")), and more technical and fine grained ChangeLog (vegandocs("Change")). Several frequently asked questions really are answered in the vegan FAQ (vegandocs("FAQ")). The discussion on design decisions can be read with vegandocs("decision"). A tutorial of the package at http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf provides a more thorough introduction to the package.
vegan文件可以读取与vegandocs功能。除了vignette的基本用法，你可以阅读NEWS的新功能和bug修复版本（vegandocs("NEWS")），和更多的技术和细粒度ChangeLog的（vegandocs("Change")“）。几个常见问题的回答真的是素食主义者常见问题解答（vegandocs("FAQ")）。设计决策的讨论，可以读取vegandocs("decision")。 http://cc.oulu.fi/~jarioksa / opetus / metodi / vegantutor.pdf的教程的包的包提供了一个更深入的介绍。
To see the preferable citation of the package, type citation("vegan").
要看到最好的包，类型citation("vegan")引用。
（作者）----------Author(s)----------
The <span class="pkg">vegan</span> development team is Jari Oksanen,
F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, Peter
R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry
H. Stevens, Helene Wagner. Many other people have contributed to
individual functions: see credits in function help pages.
The maintainers at the R-Forge are Jari Oksanen <jari.oksanen@oulu.fi>
and Gavin Simpson <gavin.simpson@ucl.ac.uk>.
实例----------Examples----------
### Example 1: Unconstrained ordination[＃＃例1：无约束的协调]
## NMDS[＃NMDS]
data(varespec)
data(varechem)
ord <- metaMDS(varespec)
plot(ord, type = "t")
## Fit environmental variables[＃适合的环境变量。]
ef <- envfit(ord, varechem)
ef
plot(ef, p.max = 0.05)
### Example 2: Constrained ordination (RDA)[＃＃例2：约束协调（RDA）]
## The example uses formula interface to define the model[＃示例使用公式接口定义模型]
data(dune)
data(dune.env)
## No constraints: PCA[＃无约束：PCA]
mod0 <- rda(dune ~ 1, dune.env)
mod0
plot(mod0)
## All environmental variables: Full model[＃所有环境变量：全模式]
mod1 <- rda(dune ~ ., dune.env)
mod1
plot(mod1)
## Automatic selection of variables by permutation P-values[＃自动选择的变量排列的P-值]
mod <- ordistep(mod0, scope=formula(mod1))
mod
plot(mod)
## Permutation test for all variables[＃对所有变量的置换检验]
anova(mod)
## Permutation test of "type III" effects, or significance when a term[＃置换检验时，术语的“III型”的影响，或意义]
## is added to the model after all other terms[＃添加到模型后，所有其他条款]
anova(mod, by = "margin")
## Plot only sample plots, use different symbols and draw SD ellipses [＃图只有样地，用不同的符号，绘制SD椭圆形]
## for Managemenet classes[＃Managemenet类]
plot(mod, display = "sites", type = "n")
with(dune.env, points(mod, disp = "si", pch = as.numeric(Management)))
with(dune.env, legend("topleft", levels(Management), pch = 1:4,
title = "Management"))
with(dune.env, ordiellipse(mod, Management, label = TRUE))
## add fitted surface of diversity to the model[＃添加安装面的模型的多样性]
ordisurf(mod, diversity(dune), add = TRUE)
### Example 3: analysis of dissimilarites a.k.a. non-parametric[＃＃又名非参数的dissimilarites实施例3：分析]
### permutational anova[＃＃permutational方差分析]
adonis(dune ~ ., dune.env)
adonis(dune ~ Management + Moisture, dune.env)
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 15:14:53
