spiderDev: Species Identity and Evolution in R--development

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

Author
Samuel Brown, Rupert Collins, Stephane Boyer, Marie-Caroline Lefort, Jagoba Malumbres-Olarte, Cor Vink, Rob Cruickshank
Date of publication
2016-04-01 10:18:47
Maintainer
Samuel Brown <s_d_j_brown@hotmail.com>
License
GPL
Version
0.0-10

View on R-Forge

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