raupcrick(vegan)
raupcrick()所属R语言包：vegan
Raup-Crick Dissimilarity with Unequal Sampling Densities of Species
劳普克里克相异的物种不等的采样密度
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Function finds the Raup-Crick dissimilarity which is a probability of number of co-occurring species with species
函数查找劳普-Crick的相异是共同存在的物种与物种的概率数
用法----------Usage----------
raupcrick(comm, null = "r1", nsimul = 999, chase = FALSE)
参数----------Arguments----------
参数：comm
Community data which will be treated as presence/absence data.
社区数据将被视为存在/不存在的数据。
参数：null
Null model used as the method in oecosimu.
空模型的methodoecosimu。
参数：nsimul
Number of null communities for assessing the dissimilarity index.
空社区评估的相异指数数。
参数：chase
Use the Chase et al. (2011) method of tie handling (not recommended except for comparing the results against the Chase script).
使用Chase等人。 （2011）的领带的处理方法（不推荐，但比较的结果对大通脚本）。
Details
详细信息----------Details----------
Raup-Crick index is the probability that compared sampling units have non-identical species composition. This probability can be regarded as a dissimilarity, although it is not metric: identical sampling units can have dissimilarity slightly above 0, the dissimilarity can be nearly zero over a range of shared species, and sampling units with no shared species can have dissimilarity slightly below 1. Moreover, communities sharing rare species appear as more similar (lower probability of finding rare species together), than communities sharing the same number of common species.
劳普克里克指数的概率相比，抽样单位有不相同的物种组成。该概率可以被视为作为相异，虽然它不是度量：相同的抽样单位可以有相异略高于0，相异度可以是在一个范围内的共享物种，和采样单元几乎为零而没有共享的物种可以有相异略低于1。此外，社区共享稀有物种出现更多类似的（找到稀有物种的概率较低），比常见的品种相同数量的社区共享。
The function will always treat the data as binary (presence/ absence).
该函数将始终把为二进制数据（有/无）。
The probability is assessed using simulation with oecosimu where the test statistic is the observed number of shared species between sampling units evaluated against a community null model (see Examples). The default null model is "r1" where the probability of selecting species is proportional to the species frequencies.
的可能性进行评估使用oecosimu的模拟检验统计量是共享的物种抽样单位之间的对社区空模型评估所观察到的数量（见例）。默认的空模型是"r1"的概率选择物种物种频率成正比。
The vegdist function implements a variant of the Raup-Crick index with equal sampling probabilities for species using exact analytic equations without simulation. This corresponds to null model "r0" which also can be used with the current function. All other null model methods of oecosimu can be used with the current function, but
vegdist函数实现的一个变种劳普克里克指数的物种的情况下使用精确的分析方程，模拟与平等的机率。这对应于null模型"r0"还可以被用于与当前函数。所有其他空模型的方法oecosimu可以使用目前的功能，但
值----------Value----------
The function returns an object inheriting from dist which can be interpreted as a dissimilarity
该函数返回一个对象继承自dist这可以被解释为一个相异
注意----------Note----------
The test statistic is the number of shared species, and this is typically tied with a large number of simulation results. The tied values are handled differently in the current function and in the function published with Chase et al. (2011). In vegan, the index is the number of simulated values that are smaller or equal than the observed value, but smaller than observed value is used by Chase et al. (2011) with option split = FALSE in their script; this can be achieved with chase = TRUE in vegan. Chase et al. (2011) script with split = TRUE uses half of tied simulation values to calculate a distance measure, and that choice cannot be directly reproduced in vegan (it is the average of vegan raupcrick results with chase =
的检验统计量是共享的种数，这通常是并列具有大量的模拟结果。在当前的功能，在功能上与大通等出版，并列值的处理方式不同。 （2011年）。在vegan，该指数的模拟值小于或等于比实测值，但小于观测值大通等。 （2011）的选项“split = FALSE在自己的剧本，这可以实现chase = TRUEvegan。 Chase等人。 （2011）脚本split = TRUE使用捆绑的模拟值的一半来计算距离的措施，并不能直接复制，可以选择素食主义者（这是veganraupcrick结果与平均<代码>追=
（作者）----------Author(s)----------
The function was developed after Brian Inouye contacted us and
informed us about the method in Chase et al. (2011), and the
function takes its idea from the code that was published with their
paper. The current function was written by Jari Oksanen.
参考文献----------References----------
B.D. (2011). Using null models to disentangle variation in community dissimilarity from variation in <code>alpha</code>-diversity. Ecosphere 2:art24 [doi:10.1890/ES10-00117.1]
参见----------See Also----------
The function is based on oecosimu. Function vegdist with method = "raup" implements a related index but with equal sampling densities of species, and
该功能是基于oecosimu。函数vegdist方法=“劳普”实现一个相关的指标，但等于物种采样密度，并
实例----------Examples----------
## data set with variable species richness[＃变量物种丰富度的数据集，]
data(sipoo)
## default raupcrick[＃默认raupcrick]
dr1 <- raupcrick(sipoo)
## use null model "r0" of oecosimu[＃使用空模型“R0”的oecosimu]
dr0 <- raupcrick(sipoo, null = "r0")
## vegdist(..., method = "raup") corresponds to 'null = "r0"'[：＃vegdist（...，方法=“劳普”）对应的空=“r0的”]
d <- vegdist(sipoo, "raup")
op <- par(mfrow=c(2,1), mar=c(4,4,1,1)+.1)
plot(dr1 ~ d, xlab = "Raup-Crick with Null R1", ylab="vegdist")
plot(dr0 ~ d, xlab = "Raup-Crick with Null R0", ylab="vegdist")
par(op)
## The calculation is essentially as in the following oecosimu() call,[＃计算本质上是如下面的oecosimu的（）调用，]
## except that designdist() is replaced with faster code[＃除了designdist（）将被替换为更快的代码]
## Not run: [＃不运行：]
oecosimu(sipoo, function(x) designdist(x, "J", "binary"), method = "r1")
## End(Not run)[＃（不执行）]
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 15:12:08
