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spider (version 1.1-0)
Species Identity and Evolution in R
Description
A package for the analysis of species limits and DNA barcoding data
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Install
install.packages('spider')
Monthly Downloads
365
Version
1.1-0
License
GPL
Maintainer
Samuel Brown
Last Published
November 12th, 2011
Functions in spider (1.1-0)
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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