spider: Species Identity and Evolution in R

CRAN: http://cran.r-project.org/web/packages/spider/index.html

> library(spider)

Loading required package: pegas
Loading required package: adegenet
Loading required package: ade4

   /// adegenet 2.0.0 is loaded ////////////

   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature resquests: adegenetIssues()



Attaching package: 'pegas'

The following object is masked from 'package:ade4':

    amova

The following object is masked from 'package:ape':

    mst

> data("dolomedes")

バージョン: 1.3.0

関数名	概略
`anoteropsis`	Cytochrome oxidase I (COI) sequences of New Zealand Anoteropsis species
`cgraph`	Complete graph
`chaoHaplo`	Chao estimator of haplotype number
`checkDNA`	Check a DNA alignment for missing data
`dataStat`	Taxa statistics
`dolomedes`	Cytochrome oxidase I (COI) sequences of New Zealand Dolomedes species
`haploAccum`	Haplotype accumulation curves
`heatmapSpp`	Visualise a distance matrix using a heatmap
`is.ambig`	Missing bases in alignments
`localMinima`	Determine thresholds from a density plot
`monophyly`	Species monophyly over a tree
`nearNeighbour`	Measures of identification accuracy
`nonConDist`	Nearest non-conspecific and maximum intra-specific distances
`nucDiag`	Nucleotide diagnostics for species alignments
`ordinDNA`	Calculates a Principal Components Ordination of genetic distances
`paa`	Population Aggregate Analysis
`plot.haploAccum`	Plotting haplotype accumulation curves
`plot.ordinDNA`	Plot an 'ordinDNA' object
`plot.slidWin`	Plot a 'slidWin' object
`polyBalance`	Balance of a phylogenetic tree with polytomies
`rankSlidWin`	Rank a 'slidWin' object.
`read.BOLD`	Downloads DNA sequences from the Barcode of Life Database (BOLD)
`read.GB`	Download sequences from Genbank with metadata.
`rmSingletons`	Detect and remove singletons
`rosenberg`	Rosenberg's probability of reciprocal monophyly
`sarkar`	Dummy sequences illustrating the categories of diagnostic nucleotides
`seeBarcode`	Create illustrative barcodes
`seqStat`	Sequence statistics
`slideAnalyses`	Sliding window analyses
`slideBoxplots`	Boxplots across windows
`slideNucDiag`	Sliding nucleotide diagnostics
`slidingWindow`	Create windows along an alignment
`spider-package`	Species Identity and Evolution in R
`sppDist`	Intra and inter-specific distances
`sppDistMatrix`	Mean intra- and inter-specific distance matrix
`sppVector`	Species Vectors
`tajima.K`	Calculate Tajima's K index of divergence
`tclust`	Clustering by a threshold
`threshOpt`	Threshold optimisation
`tiporder`	Orders tip labels by their position on the tree.
`titv`	Number of pairwise transitions and transversions in an alignment.
`tree.comp`	Tree comparisons

dolomedes

> data("dolomedes")
> dolomedes %>% class()

[1] "DNAbin"

haploAccum