R: Species Identity and Evolution in R

# Species Identity and Evolution in R

## Documentation for package ‘spider’ version 1.5.2

- 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