Learn R Programming
⚠️There's a newer version (1.5.1) of this package.Take me there.

spider (version 1.1-0)

Species Identity and Evolution in R

Description

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

Copy Link

Version

Install

install.packages('spider')

Monthly Downloads

311

Version

1.1-0

License

GPL

Maintainer

Samuel Brown

Last Published

November 12th, 2011

Functions in spider (1.1-0)

plot.slidWin

Plot a 'slidWin' object
slideBoxplots

Boxplots across windows
monophyly

Species monophyly over a tree
checkDNA

Check a DNA alignment for missing data
nearNeighbour

Measures of identification accuracy
dolomedes

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

Orders tip labels by their position on the tree.
is.ambig

Missing bases in alignments
dataStat

Taxa statistics
tclust

Clustering by a threshold
rankSlidWin

Rank a 'slidWin' object.
spider-package

Species Identity and Evolution in R
read.BOLD

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

Threshold optimisation
paa

Population Aggregate Analysis
nonConDist

Nearest non-conspecific and maximum intra-specific distances
read.GB

Download sequences from Genbank with metadata.
sppVector

Species Vectors
seqStat

Sequence statistics
sppDist

Intra and inter-specific distances
polyBalance

Balance of a phylogenetic tree with polytomies
rmSingletons

Detect and remove singletons
rosenberg

Rosenberg's probability of reciprocal monophyly
slideNucDiag

Sliding nucleotide diagnostics
chaoHaplo

Chao estimator of haplotype number
tajima.K

Calculate Tajima's K index of divergence
slidingWindow

Create windows along an alignment
tree.comp

Tree comparisons
sppDistMatrix

Mean intra- and inter-specific distance matrix
nucDiag

Nucleotide diagnostics for species alignments
localMinima

Determine thresholds from a density plot
seeBarcode

Create illustrative barcodes
titv

Number of pairwise transitions and transversions in an alignment.
slideAnalyses

Sliding window analyses
haploAccum

Haplotype accumulation curves
plot.haploAccum

Plotting haplotype accumulation curves
anoteropsis

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