permutations(vegan)
permutations()所属R语言包：vegan
Permutation tests in Vegan
置换试验，素食主义者
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Unless stated otherwise, vegan currently provides for two types of permutation test:
除非另有说明，素食主义者目前提供了两种类型的置换检验：
Free permutation of DATA, also known as randomisation, and
免置换的数据，也被称为随机化，并且
Free permutation of DATA within the levels of a factor variable.
免置换DATA的一个因素变量的水平内。
We use DATA to mean either the observed data themselves or some function of the data, for example the residuals of an ordination model in the presence of covariables.
我们使用DATA意味着无论是观测数据本身或一些功能的数据，例如一个协调的存在下，协变量模型在残差。
The second type of permutation test above is available if the function providing the test accepts an argument strata or passes additional arguments (via ...) to permuted.index.
第二种类型的排列上述测试提供测试的功能是可以的，如果接受的话，strata或通过额外的参数（通过...）permuted.index。
The Null hypothesis for these two types of permutation test assumes free exchangeability of DATA (within the levels of strata if specified). Dependence between observations, such as that which arises due to spatial or temporal autocorrelation, or more-complicated experimental designs, such as split-plot designs, violates this fundamental assumption of the test and requires restricted permutation test designs. The next major version of Vegan will include infrastructure to handle these more complicated permutation designs.
这两种类型的置换检验的零假设不承担任何免费的可交换性数据（strata如果指定的水平）。相关性的观察，如所产生因时间或空间自相关性，或更复杂的实验设计，如裂区设计，违反了这个基本假设的测试，并要求限制排列测试设计。素食主义者的下一个主要版本将包括基础设施来处理这些更复杂的排列设计。
Again, unless otherwise stated in the help pages for specific functions, permutation tests in Vegan all follow the same format/structure:
同样，除非另有说明，在帮助页面上特定的功能，置换试验，素食主义者都遵循相同的格式/结构：
An appropriate test statistic is chosen. Which statistic is chosen should be described on the help pages for individual functions.
选择适当的检验统计量。所选择的统计应个别功能的帮助页面。
The value of the test statistic is evaluate for the observed data and analysis/model and recorded. Denote this value x[0].
的检验统计量的值评价和记录所观察到的数据和分析/模型。表示该值x[0]。
The DATA are randomly permuted according to one of the above two schemes, and the value of the test statistic for this permutation is evaluated and recorded.
随机置换的DATA根据上述两个计划之一，该置换的检验统计量的值进行评估，并记录。
Step 3 is repeated a total of n times, where n is the number of permutations requested. Denote these values as x[i], where {i = 1, …, n}.
重复第3步共n倍，其中n是请求的排列的数目。表示这些值x[i]，其中{i = 1, …, n}.
The values of the test statistic for the n permutations of the DATA are added to the value of the test statistic for the observed data. These n + 1 values represent the Null or randomisation distribution of the test statistic. The observed value for the test statistic is included in the Null distribution because under the Null hypothesis being tested, the observed value is just a typical value of the test statistic, inherently no different from the values obtained via permutation of DATA.
n排列的DATA的检验统计量的值被添加到所观察到的数据的检验统计量的值。这些n + 1的值表示空或随机分布的检验统计量。检验统计量的观测值，因为被测试的零假设下，空分布的观测值就是一个典型的检验统计量的值，本质上没有什么不同的数据通过置换获得的值。
The number of times that a value of the test statistic in the Null distribution is equal to or greater than the value of the test statistic for the observed data is recorded. Note the point mentioned in step 5 above; the Null distribution includes the <STRONG>observed</STRONG> value of the test statistic. Denote this count as N.
的次数，在Null分布的检验统计量的值是等于或大于为所观察到的数据的检验统计量的值被记录下来。上面的第5步中提到的注意点，空分配包括<STRONG>的观察</ STRONG>检验统计量的值。表示这个数N。
The permutation p-value is computed as
置换的p-值被计算为
The above description illustrates why the default number of permutations specified in Vegan functions takes values of 199 or 999 for example. Once the observed value of the test statistic is added to this number of random permutations of DATA, pretty p-values are achievable because n + 1 becomes 200 or 1000, for example.
在上述的说明为什么默认的排列的素食函数中指定的值例如199或999。一旦检验统计量的观测值被添加到这个数目的随机排列的DATA，漂亮的p-值是可以实现的，这是因为n + 1变为200或1000，例如。
The minimum achievable p-value is
可达到的最小p值
A more common definition, in ecological circles, for N would be the number of x[i] greater than or equal to x[0]. The permutation p-value would then be defined as
在生态圈中，更常见的定义，N将是x[i]大于或等于x[0]的的。置换然后将被定义为p-值
The + 1 in the numerator of the above equation represents the observed statistic x[0]. The minimum p-value would then be defined as
上述方程的分子中的“+”1表示所观察到的统计x[0]。的最小，然后将被定义为p-值
However this definition discriminates between the observed statistic and the other x[i]. Under the Null hypothesis there is no such distinction, hence we prefer the definintion used in the numbered steps above.
然而，这定义判别之间的观察到的统计量和其他x[i]。的零假设下，有没有这样的区分，因此我们喜欢definintion的在上述编号的步骤。
One cannot simply increase the number of permutations (n) to achieve a potentially lower p-value unless the number of observations available permits such a number of permutations. This is unlikely to be a problem for all but the smallest data sets when free permutation (randomisation) is valid, but in designs where strata is specified and there are a low number of observations within each level of strata, there may not be as many actual permutations of the data as you might want.
我们不能简单地增加的排列数（n）来实现的若干意见，除非允许这样的排列数可能降低p值。这是不太可能是一个问题，但最小数据集，免费置换（随机）是有效的，但在设计中，strata指定和strata每个级别内有一个低的若干意见，有可能不会像许多实际的数据排列，你可能想。
It is currently the responsibility of the user to determine the total number of possible permutations for their DATA. No checks are made within Vegan functions to ensure a sensible number of permutations is chosen.
这是目前的用户，以确定可能的排列的总数为他们的DATA的责任。没有检查，在素食的功能，以确保一个明智的选择排列。
Limits on the total number of permutations of DATA are more severe in temporally or spatially ordered data or experimental designs with low replication. For example, a time series of n = 100 observations has just 100 possible permutations <STRONG>including</STRONG> the observed ordering.
的DATA的排列的总数限制为更严重的，在时间上或空间排列的数据或实验设计低复制。例如，一个时间序列的n = 100观察所观察到的只是潜在的100个的排列<STRONG>包括</ STRONG>订购。
In situations where only a low number of permutations is possible due to the nature of DATA or the experimental design, enumeration of all permutations becomes important and achievable computationally. Currently, Vegan does not include functions to perform complete enumeration of the set of possible permutations. The next major release of Vegan will include such functionality, however.
在低的排列数的情况下，可能是由于数据的性质和实验设计，枚举所有的排列组合成为重要的和可实现的计算。目前，素食主义者不包括功能执行完全列举的一组可能的排列。素食主义者的下一个主要版本将包括这样的功能，但是。
（作者）----------Author(s)----------
Gavin Simpson
参见----------See Also----------
permutest, permuted.index
permutest，permuted.index
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 15:11:00
