spider: Species Identity and Evolution in R
Version 1.4-2

Provides functions for the analysis of species limits and DNA barcoding data. Included are functions for generating important summary statistics from DNA barcode data, assessing specimen identification efficacy, testing and optimizing divergence threshold limits, assessment of diagnostic nucleotides, and calculation of the probability of reciprocal monophyly. Additionally, a sliding window function offers opportunities to analyse information across a gene, often used for marker design in degraded DNA studies. Further information on the package has been published in Brown et al (2012) .

AuthorSamuel Brown, Rupert Collins, Stephane Boyer, Marie-Caroline Lefort, Jagoba Malumbres-Olarte, Cor Vink, Rob Cruickshank
Date of publication2017-05-16 03:13:44
MaintainerSamuel Brown <s_d_j_brown@hotmail.com>
LicenseGPL
Version1.4-2
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("spider", repos="http://R-Forge.R-project.org")

Getting started

Package overview

Popular man pages

chaoHaplo: Chao estimator of haplotype number
dolomedes: Cytochrome oxidase I (COI) sequences of New Zealand...
plot.haploAccum: Plotting haplotype accumulation curves
rosenberg: Rosenberg's probability of reciprocal monophyly
sarkar: Dummy sequences illustrating the categories of diagnostic...
sppDist: Intra and inter-specific distances
sppDistMatrix: Mean intra- and inter-specific distance matrix
See all...

All man pages Function index File listing

Man pages

anoteropsis: Cytochrome oxidase I (COI) sequences of New Zealand...
blockAlignment: Make all sequences the same length
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
salticidae: Cytochrome oxidase I (COI) sequences of world-wide species of...
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

Functions

anoteropsis Man page
bestCloseMatch Man page Source code
blockAlignment Man page Source code
cgraph Man page Source code
chaoHaplo Man page Source code
checkDNA Man page Source code
dataStat Man page Source code
dolomedes Man page
haploAccum Man page Source code
heatmapSpp Man page Source code
is.ambig Man page Source code
localMinima Man page Source code
maxInDist Man page Source code
minInDist Man page Source code
monophyly Man page Source code
monophylyBoot Man page Source code
nearNeighbour Man page Source code
nonConDist Man page Source code
nucDiag Man page Source code
ordinDNA Man page Source code
paa Man page Source code
plot.haploAccum Man page Source code
plot.ordinDNA Man page Source code
plot.slidWin Man page Source code
polyBalance Man page Source code
rankSlidWin Man page Source code
read.BOLD Man page Source code
read.GB Man page Source code
rmSingletons Man page Source code
rnucDiag Man page Source code
rosenberg Man page Source code
salticidae Man page
sarkar Man page
search.BOLD Man page Source code
seeBarcode Man page Source code
seqStat Man page Source code
slideAnalyses Man page Source code
slideBoxplots Man page Source code
slideNucDiag Man page Source code
slidingWindow Man page Source code
spider Man page
spider-package Man page
sppDist Man page Source code
sppDistMatrix Man page Source code
sppVector Man page
stats.BOLD Man page Source code
tajima.K Man page Source code
tclust Man page Source code
threshID Man page Source code
threshOpt Man page Source code
tiporder Man page Source code
titv Man page Source code
tree.comp Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/bestCloseMatch.R
R/blockAlignment.R
R/cgraph.R
R/chaoHaplo.R
R/checkDNA.R
R/dataStat.R
R/haploAccum.R
R/heatmapSpp.R
R/is.ambig.R
R/localMinima.R
R/maxInDist.R
R/minInDist.R
R/monophyly.R
R/monophylyBoot.R
R/nearNeighbour.R
R/nonConDist.R
R/nucDiag.R
R/ordinDNA.R
R/paa.R
R/plot.haploAccum.R
R/plot.ordinDNA.R
R/plot.slidWin.R
R/polyBalance.R
R/rankSlidWin.R
R/read.BOLD.R
R/read.GB.R
R/rmSingletons.R
R/rnucDiag.R
R/rosenberg.R
R/search.BOLD.R
R/seeBarcode.R
R/seqStat.R
R/slideAnalyses.R
R/slideBoxplots.R
R/slideNucDiag.R
R/slidingWindow.R
R/sppDist.R
R/sppDistMatrix.R
R/stats.BOLD.R
R/tajima.K.R
R/tclust.R
R/threshID.R
R/threshOpt.R
R/tiporder.R
R/titv.R
R/tree.comp.R
data
data/anoteropsis.rda
data/dolomedes.rda
data/salticidae.rda
data/sarkar.rda
inst
inst/CITATION
man
man/anoteropsis.Rd
man/blockAlignment.Rd
man/cgraph.Rd
man/chaoHaplo.Rd
man/checkDNA.Rd
man/dataStat.Rd
man/dolomedes.Rd
man/haploAccum.Rd
man/heatmapSpp.Rd
man/is.ambig.Rd
man/localMinima.Rd
man/monophyly.Rd
man/nearNeighbour.Rd
man/nonConDist.Rd
man/nucDiag.Rd
man/ordinDNA.Rd
man/paa.Rd
man/plot.haploAccum.Rd
man/plot.ordinDNA.Rd
man/plot.slidWin.Rd
man/polyBalance.Rd
man/rankSlidWin.Rd
man/read.BOLD.Rd
man/read.GB.Rd
man/rmSingletons.Rd
man/rosenberg.Rd
man/salticidae.Rd
man/sarkar.Rd
man/seeBarcode.Rd
man/seqStat.Rd
man/slideAnalyses.Rd
man/slideBoxplots.Rd
man/slideNucDiag.Rd
man/slidingWindow.Rd
man/spider-package.Rd
man/sppDist.Rd
man/sppDistMatrix.Rd
man/sppVector.Rd
man/tajima.K.Rd
man/tclust.Rd
man/threshOpt.Rd
man/tiporder.Rd
man/titv.Rd
man/tree.comp.Rd
spider documentation built on May 21, 2017, 1:07 a.m.

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