spider: Species Identity and Evolution in R

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

AuthorSamuel Brown, Rupert Collins, Stephane Boyer, Marie-Caroline Lefort, Jagoba Malumbres-Olarte, Cor Vink, Rob Cruickshank
Date of publication2013-12-27 07:30:41
MaintainerSamuel Brown <s_d_j_brown@hotmail.com>
LicenseGPL
Version1.3-0

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

Functions

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

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.