sim.yo(simba)
sim.yo()所属R语言包：simba
Calculate a binary similarity index you define.
计算你定义一个二进制的相似性指数。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Enables the calculation of any binary similarity index via the provision of a formula.
允许任何二进制相似性指数的计算通过提供一个公式。
用法----------Usage----------
sim.yo(x, coord = NULL, method = "(2*a)/((2*a) + b + c)", dn = NULL,
normalize = FALSE, listin = FALSE, listout = FALSE, ...)
参数----------Arguments----------
参数：x
Vegetation data, either as matrix with rows = plots and columns = species (similarities are calculated between rows!), or as data.frame with first three columns representing plots, species and occurence information respectively. All further columns are dumped before calculation. Occurence is only considered as binary. If your list or matrix contains abundances or frequencies they are transformed automatically.
植被数据，无论是作为矩阵的行=图和列=物种（相似之处行与行之间的计算），或data.frame与第一三列分别表示图，的物种和发生信息。所有其他的列倾倒之前计算。发生只考虑为二进制。如果您的列表或矩阵中的丰度或频率的自动转换。
参数：coord
A data.frame with two columns containing the coordinate values of the sampling units. If given, it triggers the simultaneous calculation of the geographical distances between the sampling units, the coordinates of virtual centre-points between all possible pairs of plots, and the geographical distances in either x- or y-direction. If coord is given, output is always in database format (no matrix).
Adata.frame两列抽样单位的坐标值。如果给出，它触发采样单元之间的GEO距离，同时计算的虚拟的中心点的坐标之间的所有可能的对图，和在任一x-或y-方向的GEO距离。 coord如果，输出始终处于database格式（没有矩阵）。
参数：method
Give the formula for a binary similarity index. Defaults to the formula of S酶rensen index. See sim for more examples and general explanations.
让一个二进制的相似性指数的公式。默认Sorensen指数的公式。见sim更多的例子和一般的解释。
参数：dn
Neighbor definition. A geographic distance represented by a numeric or a two value vector defining a ring around each plot. Only takes effect when coord != NULL. If specified, the output does only contain similarities between neighboring plots. A plot is a neighbour to any given plot if it is within the range of the neighbor definition. See details.
邻居的定义。一个GEO上的距离，代表一个数字或两个值向量定义每个小区周围环。只有生效时coord！= NULL。如果指定，输出中只包含相邻图的相似性。有一个图是一个任何给定的图，如果是邻居的邻居定义的范围内。查看详细信息。
参数：normalize
Logical value indicating whether the values for a, b and c which are calculated in the process should be normalized to 100% (per row, which means per plot comparison). If normalize = TRUE an asymmetric index must be chosen (see details in sim).
逻辑值，该值指示是否值a，b和c计算的过程中，应该被标准化为100％（每行，这意味着每图比较）。如果标准化= TRUE，必须选择不对称指数（详情请参阅sim）。
参数：listin
if x is given in database (list) format this must be set to TRUE (there is no automatic detection of the format)
如果x数据库（名单）格式必须设置为TRUE（有没有自动检测到的格式）
参数：listout
If output is wanted in database format rather than as a dist-object set this to TRUE. Output is automatically given in database-format, when coord is specified.
如果输出是想在数据库格式，而不是一个dist对象设置为TRUE。会自动在数据库格式输出，当coord指定。
参数：...
Arguments to other functions
其他函数的参数
Details
详细信息----------Details----------
Presumably this function will rarely be used because sim already allows for the calculation of a large variety of binary similarity coefficients. But just in case you found or thought of an alternative this function is provided. For details regarding similarity indices see sim. You have to give your formula in quotation marks like this: "(2*a)/((2*a) + b + c)".
据推测，这功能很少被使用，因为sim已经允许种类繁多的二进制相似系数的计算。但是为了以防万一，你发现或想提供此功能的替代。有关相似性指数看sim。你必须给你的公式引号这样的：“（2 *）/（（2 *）+ B + C）”。
值----------Value----------
If listout = FALSE a distance matrix of class dist is returned. If listout = TRUE, a data.frame is returned with 7 columns giving the names of the compared plots in the first two and the calculated similarity measure in the third column. The rest of the columns give the values for a, b, c, and d (in this order). Naming of the first three columns can be changed but defaults to NBX (one of the compared plots), NBY (the other one), used index (the values of the calculated index). If coord != NULL, the following columns are given in addition and the columns a:d shift to the end of the data.frame.
如果listout = FALSE的一个距离矩阵类dist，则返回。如果listout = TRUE，data.frame返回与7列给出的名称，在头两个与被比较的图，并在第三列中的计算出的相似性度量。其余的列给a, b, c,和d（按照这个顺序）的值。前三列的命名是可以改变的，但默认为NBX的比较图（一），NBY（1），used index（计算出的指数值）。如果coord！= NULL，除了给出的下面的列和列a:d移位的数据框的末尾。
参数：distance
Geographical distance between compared plots
之间的GEO距离比较图
参数：X
For plotting purposes, the x-coordinate of the virtual position of the calculated similarity value in the center between the two compared plots
用于绘图的目的，所计算出的相似度值的比较的两个图之间的中心的虚拟位置的x坐标的
参数：Y
For plotting purposes, the y-coordinate of the virtual position of the calculated similarity value in the center between the two compared plots
用于绘图的目的，所计算出的相似度值的比较的两个图之间的中心的虚拟位置的y坐标的
参数：xdist
Geographical distance between compared plots, on the x-axis only
GEO距离之间的比较的图，只在x-轴
参数：ydist
Geographical distance between compared plots, on the y-axis only
GEO距离之间的比较的图，只在y-轴
注意----------Note----------
In general, concepts of data-handling are taken from vegdist and the calculation of a, b, c and d is taken from dist.binary. Thanks to Jari Oksanen for his vegan package and the idea to provide a custom build distance formula.
一般情况下，数据处理的概念，从vegdist和计算a，，b，c和d取自dist.binary， 。感谢杰瑞奥克萨宁他的vegan包和想法提供一个自定义的距离公式。
（作者）----------Author(s)----------
Gerald Jurasinski <a href="mailto:gerald.jurasinski@uni-rostock.de">gerald.jurasinski@uni-rostock.de</a>
参考文献----------References----------
参见----------See Also----------
vegdist, designdist, dist.binary, dsvdis, dist for other dissimilarity coefficients, and sim for a variety of formulae for similarity coefficients.
vegdist，designdist，dist.binary，dsvdis，dist其他的相异系数，和sim的各种公式的相似性系数。
实例----------Examples----------
data(abis)
##calculate the default S酶rensen index[＃默认的Sorensen指数计算]
abis.soer <- sim.yo(abis.spec)
##calculate a custom similarity index[＃计算自定义的相似性指数]
abis.sim <- sim.yo(abis.spec, method="(2*a)/((a) + b + c)")
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 2012-9-30 02:30:30
