R语言 spider包 nearNeighbour()函数中文帮助文档(中英文对照)

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nearNeighbour(spider)
nearNeighbour()所属R语言包：spider

                                        Measures of identification accuracy
                                         识别准确率的措施

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Tests of barcoding efficacy using distance-based methods.
测试的条码效率，采用基于距离的方法。


用法----------Usage----------


bestCloseMatch(distobj, sppVector, threshold = 0.01)
nearNeighbour(distobj, sppVector, names = FALSE)



参数----------Arguments----------

参数：distobj
A distance object (usually from dist.dna).
的距离对象（通常从dist.dna）。


参数：sppVector
Vector of species names. See sppVector.
向量的种类名称。见sppVector。


参数：threshold
Distance cutoff for identifications. Default of 0.01 (1%).
距离截止标识。默认的0.01（1％）。


参数：names
Logical. Should the names of the nearest match be shown? Default of FALSE.
逻辑。的最接近的匹配的名称应显示吗？默认值false。


Details

详细信息----------Details----------

These functions test barcoding efficacy and are not identification tools. All sequences must be identified prior to testing. Each sequence is considered an unknown while the remaining sequences in the dataset constitute the DNA barcoding database that is used for identification. If the identification from the test is the same as the pre-considered identification, a correct result is returned.
这些功能测试条码技术的有效性和识别工具。测试之前，必须确定所有序列。每个序列都可以被认为是一个未知的，而其余的在数据集序列构成的DNA条码技术用于识别的数据库。如果从测试的识别是考虑预先识别的相同，一个正确的结果被返回。

bestCloseMatch conducts the "best close match" analysis of Meier et al. (2006), considering the closest individual unless it is further than the given threshold, which results in no identification. More than one species tied for closest match results in an assignment of "ambiguous". When the threshold is large, this analysis will return essentially the same result as nearNeighbour.
bestCloseMatch举办的“最佳势均力敌的比赛，”分析Meier等人。 （2006年），考虑到最近的个体，除非它是进一步大于给定的阈值，这将导致在没有识别。一个以上的种系最近的比赛结果分配中的“暧昧”。当该阈值是大的，这将返回分析基本上是相同的结果nearNeighbour。

nearNeighbour finds the closest individual and returns if their names are the same (TRUE) or different (FALSE). If names = TRUE, the name of the closest individual is returned. Ties are decided by majority rule.
nearNeighbour找出最接近的个人和回报，如果他们的名字是相同的（TRUE）或不同（FALSE）。如果names = TRUE，最接近的个体的名称被返回。关系是决定多数人的统治。

threshID conducts a threshold-based analysis, similar to that conducted by the "Identify Specimen" tool provided by the Barcode of Life Database (http://www.boldsystems.org/views/idrequest.php). It is more inclusive than bestCloseMatch, considering ALL sequences within the given threshold.
threshID进行基于阈值的分析，类似“确定标本”工具所提供的条码的的生命数据库（http://www.boldsystems.org/views/idrequest.php）进行的。这是更具包容性的bestCloseMatch，考虑所有序列在给定的阈值。


值----------Value----------

bestCloseMatch and threshID return a character vector giving the identification status of each individual.
bestCloseMatch和threshID返回的字符向量，给每一个人识别状态。


参数："correct"
The name of the closest match is the same
最接近的匹配的名字是相同的


参数："incorrect"
The name of the closest match is different
最接近的匹配的名称是不同的


参数："ambiguous"
More than one species is the closest match (bestCloseMatch), or is within the given threshold (threshID)
一种以上的物种是最接近的匹配（bestCloseMatch），或者是在给定的阈值之内（threshID）


参数："no id"
No species are within the threshold distance
无物种内的阈值距离

nearNeighbour returns a logical vector or (if names = TRUE) the name for the nearest individual.
nearNeighbour返回一个逻辑向量或（如names = TRUE）最近的个体的名称。


（作者）----------Author(s)----------



Samuel Brown <s_d_j_brown@hotmail.com>




参考文献----------References----------

*55* (5) 715-728.

参见----------See Also----------

dist.dna,  sppVector
dist.dna，sppVector


实例----------Examples----------



data(anoteropsis)
anoDist <- dist.dna(anoteropsis)
anoSpp <- sapply(strsplit(dimnames(anoteropsis)[[1]], split = "_"),
    function(x) paste(x[1], x[2], sep = "_"))

bestCloseMatch(anoDist, anoSpp)
bestCloseMatch(anoDist, anoSpp, threshold = 0.005)
nearNeighbour(anoDist, anoSpp)
nearNeighbour(anoDist, anoSpp, names = TRUE)
threshID(anoDist, anoSpp)
threshID(anoDist, anoSpp, threshold = 0.003)

data(dolomedes)
doloDist <- dist.dna(dolomedes)
doloSpp <- substr(dimnames(dolomedes)[[1]], 1, 5)

bestCloseMatch(doloDist, doloSpp)
bestCloseMatch(doloDist, doloSpp, threshold = 0.005)
nearNeighbour(doloDist, doloSpp)
nearNeighbour(doloDist, doloSpp, names=TRUE)
threshID(doloDist, doloSpp)
threshID(doloDist, doloSpp, threshold = 0.003)

转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


注：
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