spider: Species Identity and Evolution in R

Provides functions 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 publication2016-07-04 22:00:55
MaintainerSamuel Brown <s_d_j_brown@hotmail.com>
LicenseGPL
Version1.4-1

View on R-Forge

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

Files in this package

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

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

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