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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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Install
install.packages('spider')
Monthly Downloads
365
Version
1.2-0
License
GPL
Maintainer
Samuel Brown
Last Published
December 25th, 2012
Functions in spider (1.2-0)
Search functions
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