Man pages for boopsboops/spider
Species Identity and Evolution in R

anoteropsisCytochrome oxidase I (COI) sequences of New Zealand...
bestCloseMatchMeasures of identification accuracy
blockAlignmentMake all sequences the same length
cgraphComplete graph
chaoHaploChao estimator of haplotype number
checkDNACheck a DNA alignment for missing data
dataStatTaxa statistics
dolomedesCytochrome oxidase I (COI) sequences of New Zealand...
haploAccumHaplotype accumulation curves
heatmapSppVisualise a distance matrix using a heatmap
is.ambigMissing bases in alignments
localMinimaDetermine thresholds from a density plot
maxInDistNearest non-conspecific and maximum intra-specific distances
minInDistNearest non-conspecific and maximum intra-specific distances
monophylySpecies monophyly over a tree
monophylyBootSpecies monophyly over a tree
nearNeighbourMeasures of identification accuracy
nonConDistNearest non-conspecific and maximum intra-specific distances
nucDiagNucleotide diagnostics for species alignments
ordinDNACalculates a Principal Components Ordination of genetic...
paaPopulation Aggregate Analysis
plot.haploAccumPlotting haplotype accumulation curves
plot.ordinDNAPlot an 'ordinDNA' object
plot.slidWinPlot a 'slidWin' object
polyBalanceBalance of a phylogenetic tree with polytomies
rankSlidWinRank a 'slidWin' object.
read.BOLDDownloads DNA sequences from the Barcode of Life Database...
read.GBDownload sequences from Genbank with metadata.
rmSingletonsDetect and remove singletons
rnucDiagNucleotide diagnostics for species alignments
rosenbergRosenberg's probability of reciprocal monophyly
salticidaeCytochrome oxidase I (COI) sequences of world-wide species of...
sarkarDummy sequences illustrating the categories of diagnostic...
search.BOLDDownloads DNA sequences from the Barcode of Life Database...
seeBarcodeCreate illustrative barcodes
seqStatSequence statistics
slideAnalysesSliding window analyses
slideBoxplotsBoxplots across windows
slideNucDiagSliding nucleotide diagnostics
slidingWindowCreate windows along an alignment
spider-packageSpecies Identity and Evolution in R
sppDistIntra and inter-specific distances
sppDistMatrixMean intra- and inter-specific distance matrix
sppVectorSpecies Vectors
stats.BOLDDownloads DNA sequences from the Barcode of Life Database...
tajima.KCalculate Tajima's K index of divergence
tclustClustering by a threshold
threshIDMeasures of identification accuracy
threshOptThreshold optimisation
tiporderOrders tip labels by their position on the tree.
titvNumber of pairwise transitions and transversions in an...
tree.compTree comparisons
woodmouseCytochrome b Gene Sequences of Woodmice
boopsboops/spider documentation built on Feb. 19, 2018, 12:04 p.m.