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

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

Functions

AICgmyc Man page
AICweights Man page
baseContent Man page
best2nullLRT Man page
branchesFromNode Man page
branches.per.tip Man page
carpo28S Man page
carpoCOI Man page
carpoITS Man page
carpophilus Man page
clustCI.gmyc Man page
clustGMYC Man page
col2string Man page
compList Man page
compVectorDist Man page
DNAccf Man page
doloGMYC Man page
doloMultGMYC Man page
enzymes Man page
exCon Man page
giveMeThePicture Man page
homoP Man page
IDunknown Man page
inCon Man page
maxLike.gmyc Man page
narrowingWindow Man page
narrowingWindow2 Man page
nodeDesc Man page
nodeRect Man page
nucDiagExptl Man page
permDNA Man page
phylo2MRP Man page
pindel Man page
plot.simRFLP Man page
salticidae Man page
satPlot Man page
satPlot2 Man page
screeline Man page
search.GB Man page
seeSegSites Man page
simRFLP Man page
sing2multLRT Man page
sppEdge Man page
tclust2sppVector Man page
tipToRootDist Man page

Files

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

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.