spiderDev: Species Identity and Evolution in R--development
Version 0.0-10

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

Browse man pages Browse package API and functions Browse package files

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
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("spiderDev", repos="http://R-Forge.R-project.org")

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 Source code
AICweights Man page Source code
DNAbin2alignment Source code
DNAccf Man page Source code
IDunknown Man page Source code
baseContent Man page Source code
best2nullLRT Man page Source code
branches.per.tip Man page Source code
branchesFromNode Man page Source code
carpo28S Man page
carpoCOI Man page
carpoITS Man page
carpophilus Man page
clustCI.gmyc Man page Source code
clustGMYC Man page Source code
col2string Man page Source code
compList Man page Source code
compVectorDist Man page Source code
correctAlignment Source code
doloGMYC Man page
doloMultGMYC Man page
enzymes Man page
exCon Man page Source code
giveMeThePicture Man page Source code
homoP Man page Source code
inCon Man page Source code
maxLike.gmyc Man page Source code
narrowingWindow Man page Source code
narrowingWindow2 Man page Source code
nodeDesc Man page Source code
nodeRect Man page Source code
nucDiagExptl Man page Source code
permDNA Man page Source code
phylo2MRP Man page Source code
pindel Man page Source code
plot.simRFLP Man page Source code
salticidae Man page
satPlot Man page Source code
satPlot2 Man page Source code
screeline Man page Source code
search.GB Man page Source code
seeSegSites Man page Source code
simRFLP Man page Source code
sing2multLRT Man page Source code
sisterMatrix Source code
sppEdge Man page Source code
tclust2sppVector Man page Source code
termBL Source code
termBalance Source code
tipToRootDist Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/AICgmyc.R
R/AICweights.R
R/DNAbin2alignment.R
R/DNAccf.R
R/IDunknown.R
R/baseContent.R
R/best2nullLRT.R
R/branches.per.tip.R
R/branchesFromNode.R
R/clustCI.gmyc.R
R/clustGMYC.R
R/col2string.R
R/compList.R
R/compVectorDist.R
R/correctAlignment.R
R/exCon.R
R/homoP.R
R/inCon.R
R/maxLike.gmyc.R
R/narrowingWindow.R
R/nodeDesc.R
R/nodeRect.R
R/nucDiagExptl.R
R/permDNA.R
R/phylo2MRP.R
R/pindel.R
R/plot.simRFLP.R
R/satPlot.R
R/satPlot2.R
R/screeline.R
R/search.GB.R
R/seeSegSites.R
R/simRFLP.R
R/sing2multLRT.R
R/sisterMatrix.R
R/sppEdge.R
R/tclust2sppVector.R
R/termBL.R
R/termBalance.R
R/tipToRootDist.R
data
data/carpophilus.rda
data/doloGMYC.rda
data/doloMultGMYC.rda
data/enzymes.csv.gz
data/salticidae.rda
inst
inst/CITATION
man
man/AICgmyc.Rd
man/DNAccf.Rd
man/IDunknown.Rd
man/baseContent.Rd
man/best2nullLRT.Rd
man/branches.per.tip.Rd
man/branchesFromNode.Rd
man/carpophilus.Rd
man/clustCI.gmyc.Rd
man/clustGMYC.Rd
man/col2string.Rd
man/compList.Rd
man/compVectorDist.Rd
man/doloGMYC.Rd
man/enzymes.Rd
man/exCon.Rd
man/homoP.Rd
man/narrowingWindow.Rd
man/nodeDesc.Rd
man/nodeRect.Rd
man/nucDiagExptl.Rd
man/permDNA.Rd
man/phylo2MRP.Rd
man/pindel.Rd
man/plot.simRFLP.Rd
man/salticidae.Rd
man/satPlot.Rd
man/screeline.Rd
man/search.GB.Rd
man/seeSegSites.Rd
man/simRFLP.Rd
man/sppEdge.Rd
man/tclust2sppVector.Rd
man/tipToRootDist.Rd
spiderDev documentation built on May 21, 2017, 1:21 a.m.