beals(vegan)
beals()所属R语言包：vegan
Beals Smoothing and Degree of Absence
比尔斯平滑度缺席
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Beals smoothing replaces each entry in the community data with a probability of a target species occurring in that particular site, based on the joint occurrences of the target species with the species that actually occur in the site. Swan's (1970) degree of absence applies Beals smoothing to zero items so long that all zeros are replaced with smoothed values.
比尔斯平滑替换中的每个条目社会目标物种的概率发生在该特定网站的基础上的共同目标物种的物种出现在该网站出现的数据。天鹅（1970）的适用度的情况下比尔斯平滑零个项目的所有被替换为0，平滑值。
用法----------Usage----------
beals(x, species = NA, reference = x, type = 0, include = TRUE)
swan(x, maxit = Inf)
参数----------Arguments----------
参数：x
Community data frame or matrix.
社区数据框或矩阵。
参数：species
Column index used to compute Beals function for a single species. The default (NA) indicates that the function will be computed for all species.
列索引用于计算比尔斯功能单一品种。默认值（NA）表示该功能将被计算为所有物种。
参数：reference
Community data frame or matrix to be used to compute joint occurrences. By default, x is used as reference to compute the joint occurrences.
要使用的社区数据框或矩阵计算联合出现。默认情况下，x作为参考，计算联合的发生。
参数：type
Numeric. Specifies if and how abundance values have to be used in function beals. See details for more explanation.
数字。指定是否以及如何丰度值，必须使用在功能beals。详情请参阅更多的解释。
参数：include
This logical flag indicates whether the target species has to be included when computing the mean of the conditioned probabilities. The original Beals (1984) definition is equivalent to include=TRUE, while the formulation of M眉nzbergov谩 and Herben is equal to include=FALSE.
此逻辑标志指示是否空调概率计算的平均值时，必须被包括在目标物种。原来比尔斯（1984）的定义是等价于include=TRUE，而制定的是等于include=FALSE的Münzbergová和Herben的。
参数：maxit
Maximum number of iterations. The default Inf means that iterations are continued until there are no zeros or the number of zeros does not change. Probably only maxit = 1 makes sense in addition to the default.
最大迭代次数。默认的Inf意味着继续迭代，直到没有零或零的个数不改变。大概只有maxit = 1是有道理的除了默认的。
Details
详细信息----------Details----------
Beals smoothing is the estimated probability p[ij] that species j occurs at site i. It is defined as p[ij] = 1/S[i] Sum(k) N[jk] I[ik] / N[k], where S[i] is the number of species at site i, N[jk] is the number of joint occurrences of species j and k, N[k] is the number of occurrences of species k, and I is the incidence (0 or 1) of species (this last term is usually omitted from the equation, but it is necessary). As N[jk] can be interpreted as a mean of conditional probability, the beals function can be interpreted as a mean of conditioned probabilities (De C谩ceres & Legendre 2008). The present function is generalized to abundance values (De C谩ceres & Legendre 2008).
比尔斯平滑的概率p[ij]，物种j的出现在现场i，。它被定义为p[ij] = 1/S[i] Sum(k) N[jk] I[ik] / N[k]，S[i]是物种的数量在现场i，N[jk]是联合出现的物种j和<所述>，k是出现的次数物种N[k]，和k是发病率（0或1）的物种（这最后的术语通常是从方程中省略，但这是必要的）。作为I条件概率的平均值可以被解释为，N[jk]函数可以被解释的条件概率（德卡塞雷斯＆雷建德2008）作为一个平均值。本函数是广义的丰度值（德卡塞雷斯2008年和勒让德）。
The type argument specifies if and how abundance values have to be used. type = 0 presence/absence mode. type = 1 abundances in reference (or x) are used to compute conditioned probabilities. type = 2 abundances in x are used to compute weighted averages of conditioned probabilities. type = 3 abundances are used to compute both conditioned probabilities and weighted averages.
type参数指定的丰度值是否以及如何被使用。 type = 0存在/不存在的模式。 type = 1的丰度在reference（或x）来计算空调的概率。 type = 2丰度x被用来计算条件概率的加权平均值。 type = 3丰度被用来计算两个空调的概率和加权平均值。
Beals smoothing was originally suggested as a method of data transformation to remove excessive zeros (Beals 1984, McCune 1994). However, it is not a suitable method for this purpose since it does not maintain the information on species presences: a species may have a higher probability of occurrence at a site where it does not occur than at sites where it occurs. Moreover, it regularizes data too strongly. The method may be useful in identifying species that belong to the species pool (Ewald 2002) or to identify suitable unoccupied patches in metapopulation analysis (M眉nzbergov谩 & Herben 2004). In this case, the function should be called with include = FALSE for cross-validation smoothing for species; argument species can be used if only one species is studied.
比尔斯平滑最初建议作为数据转换的方法，来去除过多的零（比尔斯1984年，麦克卡尼1994）。然而，它不是用于此目的的合适的方法，因为它不保持对物种的存在的信息：一个物种可能有较高的概率发生的，在一个网站，在这里它不会发生比在那里发生的网站。此外，规范数据过于强烈。该方法可用于鉴定物种，属于鱼种池（埃瓦尔德2002年），或物色合适的空置补丁的集合种群的分析（于2004年Münzbergová与Herben）。在这种情况下，该功能应被称为include = FALSE的物种进行交叉验证平滑参数species可以使用，如果只有一个物种，研究。
Swan (1970) suggested replacing zero values with degrees of absence of a species in a community data matrix. Swan expressed the method in terms of a similarity matrix, but it is equivalent to applying Beals smoothing to zero values, at each step shifting the smallest initially non-zero item to value one, and repeating this so many times that there are no zeros left in the data. This is actually very similar to extended dissimilarities (implemented in function stepacross), but very rarely used.
天鹅（1970）建议更换零值的程度没有一个物种在一个社区数据矩阵。天鹅表达方面的相似性矩阵的方法，但它是相当于申请比尔斯平滑到零值，在每一步最小最初非零资料转移到值1，并重复这样多次有无零点离开在数据中。这实际上是扩展的异同（实施stepacross），但很少使用的功能非常相似。
值----------Value----------
The function returns a transformed data matrix or a vector if Beals smoothing is requested for a single species.
该函数返回一个转换后的数据矩阵或向量，如果比尔斯平滑要求一个单一的物种。
（作者）----------Author(s)----------
Miquel De C谩ceres and Jari Oksanen
参考文献----------References----------
analysis of multivariate ecological data. Pp. 1–55 in: MacFadyen, A. & E.D. Ford [eds.] Advances in Ecological Research, 14. Academic Press, London.
revisited. Oecologia 156: 657–669.
from large compositional matrices. J. Veg. Sci. 13: 191–198.
function. Ecoscience 1: 82–86.
suitable unoccupied habitats in metapopulation studies using co-occurrence of species. Oikos 105: 408–414.
simulated vegetational data. Ecology 51: 89–102.
参见----------See Also----------
decostand for proper standardization methods, specpool for an attempt to assess the size of species pool. Function indpower assesses the power of each species
decostand适当的标准化方法，specpool试图评估鱼种池的大小。功能indpower评估每一个物种的力量
实例----------Examples----------
data(dune)
## Default[＃默认]
x <- beals(dune)
## Remove target species[＃删除目标物种]
x <- beals(dune, include = FALSE)
## Smoothed values against presence or absence of species[＃平滑值，对存在或不存在的物种]
pa <- decostand(dune, "pa")
boxplot(as.vector(x) ~ unlist(pa), xlab="Presence", ylab="Beals")
## Remove the bias of tarbet species: Yields lower values.[＃删除的偏见tarbet种产量较低的值。]
beals(dune, type =3, include = FALSE)
## Uses abundance information.[＃使用丰富的信息。]
## Vector with beals smoothing values corresponding to the first species[＃与平滑值对应于第一个物种的比尔斯向量]
## in dune.[＃沙丘。]
beals(dune, species=1, include=TRUE)
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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 15:03:19
