Species Identity and Evolution in R

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Documentation for package ‘spider’ version 1.5.0

• DESCRIPTION file.
• Package NEWS.

Help Pages

spider-package	Species Identity and Evolution in R
anoteropsis	Cytochrome oxidase I (COI) sequences of New Zealand _Anoteropsis_ species
bestCloseMatch	Measures of identification accuracy
blockAlignment	Make all sequences the same length
cgraph	Complete graph
chaoHaplo	Chao estimator of haplotype number
checkDNA	Check a DNA alignment for missing data
dataStat	Taxa statistics
dolomedes	Cytochrome oxidase I (COI) sequences of New Zealand _Dolomedes_ species
haploAccum	Haplotype accumulation curves
heatmapSpp	Visualise a distance matrix using a heatmap
is.ambig	Missing bases in alignments
localMinima	Determine thresholds from a density plot
maxInDist	Nearest non-conspecific and maximum intra-specific distances
minInDist	Nearest non-conspecific and maximum intra-specific distances
monophyly	Species monophyly over a tree
monophylyBoot	Species monophyly over a tree
nearNeighbour	Measures of identification accuracy
nonConDist	Nearest non-conspecific and maximum intra-specific distances
nucDiag	Nucleotide diagnostics for species alignments
ordinDNA	Calculates a Principal Components Ordination of genetic distances
paa	Population Aggregate Analysis
plot.haploAccum	Plotting haplotype accumulation curves
plot.ordinDNA	Plot an 'ordinDNA' object
plot.slidWin	Plot a 'slidWin' object
polyBalance	Balance of a phylogenetic tree with polytomies
rankSlidWin	Rank a 'slidWin' object.
read.BOLD	Downloads DNA sequences from the Barcode of Life Database (BOLD)
read.GB	Download sequences from Genbank with metadata.
rmSingletons	Detect and remove singletons
rnucDiag	Nucleotide diagnostics for species alignments
rosenberg	Rosenberg's probability of reciprocal monophyly
salticidae	Cytochrome oxidase I (COI) sequences of world-wide species of Salticidae
sarkar	Dummy sequences illustrating the categories of diagnostic nucleotides
search.BOLD	Downloads DNA sequences from the Barcode of Life Database (BOLD)
seeBarcode	Create illustrative barcodes
seqStat	Sequence statistics
slideAnalyses	Sliding window analyses
slideBoxplots	Boxplots across windows
slideNucDiag	Sliding nucleotide diagnostics
slidingWindow	Create windows along an alignment
spider	Species Identity and Evolution in R
sppDist	Intra and inter-specific distances
sppDistMatrix	Mean intra- and inter-specific distance matrix
sppVector	Species Vectors
stats.BOLD	Downloads DNA sequences from the Barcode of Life Database (BOLD)
tajima.K	Calculate Tajima's K index of divergence
tclust	Clustering by a threshold
threshID	Measures of identification accuracy
threshOpt	Threshold optimisation
tiporder	Orders tip labels by their position on the tree.
titv	Number of pairwise transitions and transversions in an alignment.
tree.comp	Tree comparisons
woodmouse	Cytochrome b Gene Sequences of Woodmice