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spider (version 1.1-5)

Species Identity and Evolution in R

Description

A package for the analysis of species limits and DNA barcoding data

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Version

Install

install.packages('spider')

Monthly Downloads

311

Version

1.1-5

License

GPL

Maintainer

Samuel Brown

Last Published

November 15th, 2012

Functions in spider (1.1-5)

slideNucDiag

Sliding nucleotide diagnostics

anoteropsis

Cytochrome oxidase I (COI) sequences of New Zealand _Anoteropsis_ species

monophyly

Species monophyly over a tree

titv

Number of pairwise transitions and transversions in an alignment.

tajima.K

Calculate Tajima's K index of divergence

rmSingletons

Detect and remove singletons

read.GB

Download sequences from Genbank with metadata.

rosenberg

Rosenberg's probability of reciprocal monophyly

sarkar

Dummy sequences illustrating the categories of diagnostic nucleotides

polyBalance

Balance of a phylogenetic tree with polytomies

seqStat

Sequence statistics

slidingWindow

Create windows along an alignment

nearNeighbour

Measures of identification accuracy

dataStat

Taxa statistics

seeBarcode

Create illustrative barcodes

sppDist

Intra and inter-specific distances

sppDistMatrix

Mean intra- and inter-specific distance matrix

nucDiag

Nucleotide diagnostics for species alignments

spider-package

Species Identity and Evolution in R

tiporder

Orders tip labels by their position on the tree.

localMinima

Determine thresholds from a density plot

read.BOLD

Downloads DNA sequences from the Barcode of Life Database (BOLD)

plot.slidWin

Plot a 'slidWin' object

rankSlidWin

Rank a 'slidWin' object.

tree.comp

Tree comparisons

threshOpt

Threshold optimisation

plot.haploAccum

Plotting haplotype accumulation curves

slideAnalyses

Sliding window analyses

chaoHaplo

Chao estimator of haplotype number

sppVector

Species Vectors

dolomedes

Cytochrome oxidase I (COI) sequences of New Zealand _Dolomedes_ species

nonConDist

Nearest non-conspecific and maximum intra-specific distances

tclust

Clustering by a threshold

checkDNA

Check a DNA alignment for missing data

slideBoxplots

Boxplots across windows

haploAccum

Haplotype accumulation curves

paa

Population Aggregate Analysis

is.ambig

Missing bases in alignments