contribdiv(vegan)
contribdiv()所属R语言包：vegan
Contribution Diversity Approach
贡献分集方法
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The contribution diversity approach is based in the differentiation of within-unit and among-unit diversity by using additive diversity partitioning and unit distinctiveness.
的贡献多样性的方法是基于在单位内的分化和间单位通过使用添加剂多样性分区和单位的独特性，多样性。
用法----------Usage----------
contribdiv(comm, index = c("richness", "simpson"),
relative = FALSE, scaled = TRUE, drop.zero = FALSE)
## S3 method for class 'contribdiv'
plot(x, sub, xlab, ylab, ylim, col, ...)
参数----------Arguments----------
参数：comm
The community data matrix with samples as rows and species as column.
社区矩阵的行和列物种的样本数据。
参数：index
Character, the diversity index to be calculated.
字符，多样性指数来计算的。
参数：relative
Logical, if TRUE then contribution diversity values are expressed as their signed deviation from their mean. See details.
逻辑，如果TRUE然后签署偏离其平均贡献多样性值表示为。查看详细信息。
参数：scaled
Logical, if TRUE then relative contribution diversity values are scaled by the sum of gamma values (if index = "richness") or by sum of gamma values times the number of rows in comm (if index = "simpson"). See details.
逻辑，如果TRUE然后的相对贡献多样性值调整伽玛值的总和（如果如果index = "richness"）或的总和的伽玛值的行数在comm（index = "simpson"）。查看详细信息。
参数：drop.zero
Logical, should empty rows dropped from the result? If empty rows are not dropped, their corresponding results will be NAs.
逻辑，空行下降的结果吗？如果空行不下降，其相应的结果将是NA的。
参数：x
An object of class "contribdiv".
对象的类"contribdiv"。
参数：sub, xlab, ylab, ylim, col
Graphical arguments passed to plot.
图形参数传递给图。
参数：...
Other arguments passed to plot.
其他参数传递给绘制。
Details
详细信息----------Details----------
This approach was proposed by Lu et al. (2007). Additive diversity partitioning (see adipart for more references) deals with the relation of mean alpha and the total (gamma) diversity. Although alpha diversity values often vary considerably. Thus, contributions of the sites to the total diversity are uneven. This site specific contribution is measured by contribution diversity components. A unit that has e.g. many unique species will contribute more to the higher level (gamma) diversity than another unit with the same number of species, but all of which common.
Lu等人提出的这种方法。 （2007年）。添加剂多样性分区（见adipart更多的参考文献）交易的平均α和总多样性（γ）的关系。虽然α多样性的价值观往往有很大的不同。因此，网站的总多样性的贡献是不均衡的。本网站的具体贡献衡量的贡献多样性组成部分。有例如A股许多独特的物种，将有助于更多的更高的水平（γ）与相同数量的物种多样性比另一个单位，但所有这一切都常见。
Distinctiveness of species j can be defined as the number of sites where it occurs (n_j), or the sum of its relative frequencies (p_j). Relative frequencies are computed sitewise and sum_j{p_ij}s at site i sum up to 1.
可以被定义为显着性的物种j的站点数量出现的（n_j），或它的相对频率的总和（p_j）。相对频率的计算sitewise和sum_j{p_ij}的在现场i总结1。
The contribution of site i to the total diversity is given by alpha_i = sum_j(1 / n_ij) when dealing with richness and alpha_i = sum(p_{ij} * (1 - p_{ij})) for the Simpson index.
现场的贡献i的总多样性alpha_i = sum_j(1 / n_ij)处理的丰富性和alpha_i = sum(p_{ij} * (1 - p_{ij}))Simpson指数。
The unit distinctiveness of site i is the average of the species distinctiveness, averaging only those species which occur at site i. For species richness: alpha_i = mean(n_i) (in the paper, the second equation contains a typo, n is without index). For the Simpson index: alpha_i = mean(n_i).
单位的独特性的网站i是平均的，平均每场只出现在现场i这些物种的物种的独特性。物种丰富度：alpha_i = mean(n_i)（在本文中，第二个方程包含一个错字，n是没有索引）。 Simpson指数：alpha_i = mean(n_i)。
The Lu et al. (2007) gives an in-depth description of the different indices.
路等。 （2007）给出了一个深入的描述，不同的指数。
值----------Value----------
An object of class "contribdiv" in heriting from data frame.
对象的类"contribdiv"从数据框中heriting。
Returned values are alpha, beta and gamma components for each sites (rows) of the community matrix. The "diff.coef" attribute gives the differentiation coefficient (see Examples).
返回的值是每个网站（行）的社区矩阵的α，β和γ组件。 "diff.coef"属性提供了分化系数（见例）。
（作者）----------Author(s)----------
P茅ter S贸lymos, <a href="mailto:solymos@ualberta.ca">solymos@ualberta.ca</a>
参考文献----------References----------
approach to evaluate species diversity. Basic and Applied Ecology, 8, 1–12.
参见----------See Also----------
adipart, diversity
adipart，diversity
实例----------Examples----------
## Artificial example given in[＃人工给出的例子]
## Table 2 in Lu et al. 2007[表2中鲁等。 2007]
x <- matrix(c(
1/3,1/3,1/3,0,0,0,
0,0,1/3,1/3,1/3,0,
0,0,0,1/3,1/3,1/3),
3, 6, byrow = TRUE,
dimnames = list(LETTERS[1:3],letters[1:6]))
x
## Compare results with Table 2[＃结果与表2]
contribdiv(x, "richness")
contribdiv(x, "simpson")
## Relative contribution (C values), compare with Table 2[＃相对贡献（C值），与表2的比较]
(cd1 <- contribdiv(x, "richness", relative = TRUE, scaled = FALSE))
(cd2 <- contribdiv(x, "simpson", relative = TRUE, scaled = FALSE))
## Differentiation coefficients[＃分化系数]
attr(cd1, "diff.coef") # D_ST[D_ST]
attr(cd2, "diff.coef") # D_DT[D_DT]
## BCI data set[＃BCI数据集]
data(BCI)
opar <- par(mfrow=c(2,2))
plot(contribdiv(BCI, "richness"), main = "Absolute")
plot(contribdiv(BCI, "richness", relative = TRUE), main = "Relative")
plot(contribdiv(BCI, "simpson"))
plot(contribdiv(BCI, "simpson", relative = TRUE))
par(opar)
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。
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发表于 2012-10-1 15:04:59
