d(vegetarian)
d()所属R语言包：vegetarian
'Numbers Equivalents' for Alpha, Beta and Gamma Diversity Indices
α，β和γ多样性指数的数字等价物“
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The d function calculates the numbers equivalent or effective numbers of species for alpha, beta or gamma diversity as described by Jost (2006, 2007). These are sometimes referred to as 'Hill numbers' (Hill 1973). Jost's interpretation of these number equivalents are more general than Hill's because as the order (q) changes, the sensitivity of the diversity to rare and common species changes. According to Jost (2007), for alpha diversity d calculates Equation 11a for the general case for q and Equation 11b for the Shannon case where q = 1. See Jost (2006) for more on the history and theory behind diversity indices and numbers equivalents.
d函数计算数字相当于或有效的α，β或γ多样性，物种数量，约斯特（2006年，2007年）所描述的。这些有时被称为为山号码“（希尔1973年）。乔斯特的解释都比较一般比山的，因为这些数字等值的顺序（Q）的变化，常见与罕见的物种变化的敏感性的多样性。据约斯特（2007），用于α多样性d计算方程11a的香农的情况下，其中q = 1为q和方程11b的对于一般情况。约斯特（2006），物种多样性指数和数字等值的历史和背后的理论。
用法----------Usage----------
d(abundances, lev = "alpha", wts = FALSE, q = 1, boot = FALSE, boot.arg = list(s.sizes = NULL, num.iter = 100))
参数----------Arguments----------
参数：abundances
Community data as a matrix where columns are individual species and rows are sites. Matrix elements are abundance data (e.g. counts, percent cover estimates).
社区数据列是一个矩阵，其中个别品种和行的网站。矩阵元素丰度数据（如计数，百分比盖的估计）。
参数：lev
Level of diversity to be calculated. Will accept: 'alpha,' 'beta,' or 'gamma.'
多样性水平来计算的。接受：“阿尔法”，“测试”，或“γ”。
参数：wts
A vector of community weights whose length equals the number of communities being compared. See details below for examples of when community weights might be treated as equal or unequal. Defaults to wts=FALSE where all communities are equally weighted.
社区的权重，其长度等于所比较的社区的数量的向量。查看详细资料社会的权重时，可能会被视为相等或者不相等的例子。默认WTS = FALSE，所有社区都同样加权。
参数：q
Order of the diversity measure. Defaults to the Shannon case where q = 1.
订购的多样性的措施。默认的Shannon情况下，q = 1时。
参数：boot
Logical indicating whether to use bootstrapping to estimate uncertainty.
逻辑指示是否使用自举到估计不确定性。
参数：boot.arg
(optional) List of arguments to pass bootstrapping function: list(s.sizes=number you specify, num.iter=number you specify)
（可选）的参数列表，通过自举功能：列表（s.sizes =您指定的号码，num.iter =您指定的号码）
Details
详细信息----------Details----------
Orders higher than one are more sensitive to common species, and orders less than one are more sensitive to rare species. Species richness are diversity measures of q = 0. Shannon diversity measures are first order or q =1. Simpson diversity measures are second order or q = 2.
订单高于常见的品种更敏感，订单不到一个稀有物种更敏感。物种丰富度，多样性措施的q = 0。多样性的措施是一阶或q = 1。辛普森多样性的措施是二阶或q = 2。
Determining how to set community weights depends on the types of comparisons about communities that a researcher wants to make. For instance, Jost (2007) suggests that if species frequencies, but not the actual sizes of the communities are the topic of interest then communities should all be weighed equally. In contrast, community weights are usually unequal when the sizes of the communities has a large influence on the comparisons being made. For instance, when comparing the alpha and beta diversities of a landscape, using unequal community weights makes more sense.
确定如何设置社区的权重取决于类型的比较，研究人员希望的社区。例如，约斯特（2007）认为，如果物种的频率，而不是实际的尺寸的社区感兴趣的主题，然后社区都应该加以权衡同样。与此相反，社区权重通常不平等的社区的大小时，有很大的影响作出比较。例如，当α和β多样性的一道风景线，不平等的社会权重，更有意义。
值----------Value----------
<table summary="R valueblock"> <tr valign="top"><td>D.Value </td> <td> A scalar that gives the numbers equivalent of alpha, beta, or gamma diversity for the specified 'order' (q) and community weights.</td></tr> <tr valign="top"><td>StdErr</td> <td> (optional) Standard error of value estimated through bootstrapping.</td></tr>
<table summary="R valueblock"> <tr valign="top"> <TD> D.Value </ TD> <td>一个指定的标量，给出了数字相当于α，β，γ多样性秩序（q）和社会权重。</ TD> </ TR> <tr valign="top"> <TD> StdErr</ TD> <TD>（可选）的标准误差估计值通过引导。</ TD> </ TR>
</table>
</ TABLE>
（作者）----------Author(s)----------
Noah Charney, Sydne Record
参考文献----------References----------
Jost, L. 2006. Entropy and diversity. Oikos 113(2): 363-375.
Jost, L. 2007. Partitioning diversity into independent alpha and beta components. Ecology 88(10): 2427-2439.
Hill, M. 1973. Diversity and evenness: A unifying notation and its consequences. Ecology 54: 427-432.
参见----------See Also----------
bootstrap,H
bootstrap，H
实例----------Examples----------
data(simesants)
d(simesants[,-1]) #remove column with site names; calculates alpha diversity of entire data-set[删除列与站点名称;计算整个数据集的α多样性]
hemlock<-subset(simesants,Habitat=="Hemlock")
d(hemlock[-1])#alpha diversity of just hemlock site[α多样性的只是铁杉网站]
d(simesants[,-1],lev="gamma", q=0)#species richness for entire data set[整个数据集的物种丰富度]
d(simesants[,-1],q=2,boot=TRUE)
d(simesants[,-1],q=2,boot=TRUE,boot.arg=list(num.iter=1000))
simesants_freq<-normalize.rows(simesants[,-1])#not a necessary step, but just to show what you would do if your data were in the form of frequencies, not counts[不是一个必要的步骤，但只是为了显示你会做什么，如果你的数据在频率的形式，而不是计算]
d(simesants_freq,q=2,boot=TRUE,boot.arg=list(s.sizes=c(198,186,102,108,187)))
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 15:18:49
