spider: Species Identity and Evolution in R

> 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':


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

> 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


> data("dolomedes")
> dolomedes %>% class()
[1] "DNAbin"