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spider (version 1.2-0)

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

1.2-0

License

GPL

Maintainer

Samuel Brown

Last Published

December 25th, 2012

Functions in spider (1.2-0)

slideNucDiag

Sliding nucleotide diagnostics

sppVector

Species Vectors

titv

Number of pairwise transitions and transversions in an alignment.

monophyly

Species monophyly over a tree

localMinima

Determine thresholds from a density plot

tiporder

Orders tip labels by their position on the tree.

slidingWindow

Create windows along an alignment

rosenberg

Rosenberg's probability of reciprocal monophyly

nonConDist

Nearest non-conspecific and maximum intra-specific distances

slideAnalyses

Sliding window analyses

seqStat

Sequence statistics

tclust

Clustering by a threshold

nucDiag

Nucleotide diagnostics for species alignments

seeBarcode

Create illustrative barcodes

rankSlidWin

Rank a 'slidWin' object.

haploAccum

Haplotype accumulation curves

read.BOLD

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

heatmapSpp

Visualise a distance matrix using a heatmap

nearNeighbour

Measures of identification accuracy

sppDist

Intra and inter-specific distances

anoteropsis

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

plot.slidWin

Plot a 'slidWin' object

plot.haploAccum

Plotting haplotype accumulation curves

polyBalance

Balance of a phylogenetic tree with polytomies

tree.comp

Tree comparisons

threshOpt

Threshold optimisation

tajima.K

Calculate Tajima's K index of divergence

dolomedes

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

spider-package

Species Identity and Evolution in R

rmSingletons

Detect and remove singletons

is.ambig

Missing bases in alignments

slideBoxplots

Boxplots across windows

sppDistMatrix

Mean intra- and inter-specific distance matrix

checkDNA

Check a DNA alignment for missing data

read.GB

Download sequences from Genbank with metadata.

paa

Population Aggregate Analysis

sarkar

Dummy sequences illustrating the categories of diagnostic nucleotides

dataStat

Taxa statistics

chaoHaplo

Chao estimator of haplotype number