spider: Species Identity and Evolution in R

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

Author
Samuel Brown, Rupert Collins, Stephane Boyer, Marie-Caroline Lefort, Jagoba Malumbres-Olarte, Cor Vink, Rob Cruickshank
Date of publication
2013-12-27 07:30:41
Maintainer
Samuel Brown <s_d_j_brown@hotmail.com>
License
GPL
Version
1.3-0

View on CRAN

Man pages

anoteropsis
Cytochrome oxidase I (COI) sequences of New Zealand...
cgraph
Complete graph
chaoHaplo
Chao estimator of haplotype number
checkDNA
Check a DNA alignment for missing data
dataStat
Taxa statistics
dolomedes
Cytochrome oxidase I (COI) sequences of New Zealand...
haploAccum
Haplotype accumulation curves
heatmapSpp
Visualise a distance matrix using a heatmap
is.ambig
Missing bases in alignments
localMinima
Determine thresholds from a density plot
monophyly
Species monophyly over a tree
nearNeighbour
Measures of identification accuracy
nonConDist
Nearest non-conspecific and maximum intra-specific distances
nucDiag
Nucleotide diagnostics for species alignments
ordinDNA
Calculates a Principal Components Ordination of genetic...
paa
Population Aggregate Analysis
plot.haploAccum
Plotting haplotype accumulation curves
plot.ordinDNA
Plot an 'ordinDNA' object
plot.slidWin
Plot a 'slidWin' object
polyBalance
Balance of a phylogenetic tree with polytomies
rankSlidWin
Rank a 'slidWin' object.
read.BOLD
Downloads DNA sequences from the Barcode of Life Database...
read.GB
Download sequences from Genbank with metadata.
rmSingletons
Detect and remove singletons
rosenberg
Rosenberg's probability of reciprocal monophyly
sarkar
Dummy sequences illustrating the categories of diagnostic...
seeBarcode
Create illustrative barcodes
seqStat
Sequence statistics
slideAnalyses
Sliding window analyses
slideBoxplots
Boxplots across windows
slideNucDiag
Sliding nucleotide diagnostics
slidingWindow
Create windows along an alignment
spider-package
Species Identity and Evolution in R
sppDist
Intra and inter-specific distances
sppDistMatrix
Mean intra- and inter-specific distance matrix
sppVector
Species Vectors
tajima.K
Calculate Tajima's K index of divergence
tclust
Clustering by a threshold
threshOpt
Threshold optimisation
tiporder
Orders tip labels by their position on the tree.
titv
Number of pairwise transitions and transversions in an...
tree.comp
Tree comparisons

Files in this package

spider
spider/inst
spider/inst/CITATION
spider/NAMESPACE
spider/NEWS
spider/data
spider/data/dolomedes.rda
spider/data/anoteropsis.rda
spider/data/sarkar.rda
spider/R
spider/R/plot.slidWin.R
spider/R/haploAccum.R
spider/R/threshID.R
spider/R/nucDiag.R
spider/R/read.GB.R
spider/R/nearNeighbour.R
spider/R/slideBoxplots.R
spider/R/tajima.K.R
spider/R/tclust.R
spider/R/is.ambig.R
spider/R/heatmapSpp.R
spider/R/monophylyBoot.R
spider/R/maxInDist.R
spider/R/tiporder.R
spider/R/seeBarcode.R
spider/R/slideAnalyses.R
spider/R/nonConDist.R
spider/R/seqStat.R
spider/R/cgraph.R
spider/R/ordinDNA.R
spider/R/read.BOLD.R
spider/R/tree.comp.R
spider/R/rosenberg.R
spider/R/dataStat.R
spider/R/localMinima.R
spider/R/sppDistMatrix.R
spider/R/monophyly.R
spider/R/stats.BOLD.R
spider/R/plot.haploAccum.R
spider/R/threshOpt.R
spider/R/rmSingletons.R
spider/R/bestCloseMatch.R
spider/R/titv.R
spider/R/slideNucDiag.R
spider/R/paa.R
spider/R/chaoHaplo.R
spider/R/checkDNA.R
spider/R/rankSlidWin.R
spider/R/slidingWindow.R
spider/R/polyBalance.R
spider/R/plot.ordinDNA.R
spider/R/search.BOLD.R
spider/R/sppDist.R
spider/MD5
spider/DESCRIPTION
spider/man
spider/man/ordinDNA.Rd
spider/man/cgraph.Rd
spider/man/slideNucDiag.Rd
spider/man/anoteropsis.Rd
spider/man/tree.comp.Rd
spider/man/sarkar.Rd
spider/man/sppDist.Rd
spider/man/titv.Rd
spider/man/plot.haploAccum.Rd
spider/man/rmSingletons.Rd
spider/man/read.GB.Rd
spider/man/read.BOLD.Rd
spider/man/rosenberg.Rd
spider/man/nearNeighbour.Rd
spider/man/threshOpt.Rd
spider/man/plot.ordinDNA.Rd
spider/man/polyBalance.Rd
spider/man/plot.slidWin.Rd
spider/man/sppDistMatrix.Rd
spider/man/paa.Rd
spider/man/localMinima.Rd
spider/man/checkDNA.Rd
spider/man/seeBarcode.Rd
spider/man/rankSlidWin.Rd
spider/man/haploAccum.Rd
spider/man/nonConDist.Rd
spider/man/is.ambig.Rd
spider/man/heatmapSpp.Rd
spider/man/nucDiag.Rd
spider/man/tiporder.Rd
spider/man/monophyly.Rd
spider/man/dataStat.Rd
spider/man/slidingWindow.Rd
spider/man/tajima.K.Rd
spider/man/sppVector.Rd
spider/man/tclust.Rd
spider/man/dolomedes.Rd
spider/man/spider-package.Rd
spider/man/slideAnalyses.Rd
spider/man/slideBoxplots.Rd
spider/man/chaoHaplo.Rd
spider/man/seqStat.Rd