spiderDev: Species Identity and Evolution in R--development

A package for the analysis of species limits and DNA barcoding data. Development area for functions that will eventually be included in spider proper.

AuthorSamuel Brown, Rupert Collins, Stephane Boyer, Marie-Caroline Lefort, Jagoba Malumbres-Olarte, Cor Vink, Rob Cruickshank
Date of publication2016-04-01 10:18:47
MaintainerSamuel Brown <s_d_j_brown@hotmail.com>
LicenseGPL
Version0.0-10

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Man pages

AICgmyc: Calculate AIC values for GMYC objects

baseContent: Base composition analysis of an alignment

best2nullLRT: Calculate likelihood ratio tests on GMYC objects

branchesFromNode: Return the indices of branches descending from a given node

branches.per.tip: Branches leading to each tip

carpophilus: Sequence alignments of _Carpophilus_ species

clustCI.gmyc: Calculate GMYC statistics

clustGMYC: Create a species vector from a GMYC object

col2string: Converts R colous names to RGB strings

compList: Compares two lists

compVectorDist: Calculate composition vector distance

DNAccf: Cross-correlation of DNA sequences

doloGMYC: GMYC results from New Zealand _Dolomedes_ species

enzymes: Data frame of restriction endonuclease enzyme names and...

exCon: Evaluation of sequence contamination

homoP: Homopolymers in DNA sequences

IDunknown: Identifies unknown sequences by comparison against a local...

narrowingWindow: Make all sequences the same length

nodeDesc: Return the descendants of nodes

nodeRect: Plots rectangles on nodes

nucDiagExptl: Experimental nucleotide diagnostic function for species...

permDNA: Permutation of DNA sequences

phylo2MRP: Create a matrix representing a tree

pindel: DNA distance model incorporating alignment gaps

plot.simRFLP: Plot an 'simRFLP' object

salticidae: Cytochrome oxidase I (COI) sequences of world-wide species of...

satPlot: Saturation plots

screeline: Number of clusters over a range of thresholds

search.GB: Searches for and downloads DNA sequences from GenBank

seeSegSites: Visualise the informative sites of an alignment

simRFLP: Simulation of Restriction Fragment Length Polymorphism...

sppEdge: Returns

tclust2sppVector: Creates a species vector from the results of tclust.

tipToRootDist: Distance from root to tip

Files in this package

spiderDev/DESCRIPTION
spiderDev/NAMESPACE
spiderDev/R
spiderDev/R/AICgmyc.R spiderDev/R/AICweights.R spiderDev/R/DNAbin2alignment.R spiderDev/R/DNAccf.R spiderDev/R/IDunknown.R spiderDev/R/baseContent.R spiderDev/R/best2nullLRT.R spiderDev/R/branches.per.tip.R spiderDev/R/branchesFromNode.R spiderDev/R/clustCI.gmyc.R spiderDev/R/clustGMYC.R spiderDev/R/col2string.R spiderDev/R/compList.R spiderDev/R/compVectorDist.R spiderDev/R/correctAlignment.R spiderDev/R/exCon.R spiderDev/R/homoP.R spiderDev/R/inCon.R spiderDev/R/maxLike.gmyc.R spiderDev/R/narrowingWindow.R spiderDev/R/nodeDesc.R spiderDev/R/nodeRect.R spiderDev/R/nucDiagExptl.R spiderDev/R/permDNA.R spiderDev/R/phylo2MRP.R spiderDev/R/pindel.R spiderDev/R/plot.simRFLP.R spiderDev/R/satPlot.R spiderDev/R/satPlot2.R spiderDev/R/screeline.R spiderDev/R/search.GB.R spiderDev/R/seeSegSites.R spiderDev/R/simRFLP.R spiderDev/R/sing2multLRT.R spiderDev/R/sisterMatrix.R spiderDev/R/sppEdge.R spiderDev/R/tclust2sppVector.R spiderDev/R/termBL.R spiderDev/R/termBalance.R spiderDev/R/tipToRootDist.R
spiderDev/data
spiderDev/data/carpophilus.rda
spiderDev/data/doloGMYC.rda
spiderDev/data/doloMultGMYC.rda
spiderDev/data/enzymes.csv.gz
spiderDev/data/salticidae.rda
spiderDev/inst
spiderDev/inst/CITATION
spiderDev/man
spiderDev/man/AICgmyc.Rd spiderDev/man/DNAccf.Rd spiderDev/man/IDunknown.Rd spiderDev/man/baseContent.Rd spiderDev/man/best2nullLRT.Rd spiderDev/man/branches.per.tip.Rd spiderDev/man/branchesFromNode.Rd spiderDev/man/carpophilus.Rd spiderDev/man/clustCI.gmyc.Rd spiderDev/man/clustGMYC.Rd spiderDev/man/col2string.Rd spiderDev/man/compList.Rd spiderDev/man/compVectorDist.Rd spiderDev/man/doloGMYC.Rd spiderDev/man/enzymes.Rd spiderDev/man/exCon.Rd spiderDev/man/homoP.Rd spiderDev/man/narrowingWindow.Rd spiderDev/man/nodeDesc.Rd spiderDev/man/nodeRect.Rd spiderDev/man/nucDiagExptl.Rd spiderDev/man/permDNA.Rd spiderDev/man/phylo2MRP.Rd spiderDev/man/pindel.Rd spiderDev/man/plot.simRFLP.Rd spiderDev/man/salticidae.Rd spiderDev/man/satPlot.Rd spiderDev/man/screeline.Rd spiderDev/man/search.GB.Rd spiderDev/man/seeSegSites.Rd spiderDev/man/simRFLP.Rd spiderDev/man/sppEdge.Rd spiderDev/man/tclust2sppVector.Rd spiderDev/man/tipToRootDist.Rd

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