Package: spider 1.5.0.9000

spider: Species Identity and Evolution in R

Analysis of species limits and DNA barcoding data. Included are functions for generating important summary statistics from DNA barcode data, assessing specimen identification efficacy, testing and optimizing divergence threshold limits, assessment of diagnostic nucleotides, and calculation of the probability of reciprocal monophyly. Additionally, a sliding window function offers opportunities to analyse information across a gene, often used for marker design in degraded DNA studies. Further information on the package has been published in Brown et al (2012) <doi:10.1111/j.1755-0998.2011.03108.x>.

Authors:Samuel Brown, Rupert Collins, Stephane Boyer, Marie-Caroline Lefort, Jagoba Malumbres-Olarte, Cor Vink, Rob Cruickshank

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spider/json (API)
NEWS

# Install 'spider' in R:
install.packages('spider', repos = c('https://boopsboops.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/boopsboops/spider/issues

Datasets:
  • anoteropsis - Cytochrome oxidase I (COI) sequences of New Zealand _Anoteropsis_ species
  • dolomedes - Cytochrome oxidase I (COI) sequences of New Zealand _Dolomedes_ species
  • salticidae - Cytochrome oxidase I (COI) sequences of world-wide species of Salticidae
  • sarkar - Dummy sequences illustrating the categories of diagnostic nucleotides
  • woodmouse - Cytochrome b Gene Sequences of Woodmice

On CRAN:

dna-barcodeednaevolutionspecies-delimitationspecies-identity

43 exports 2 stars 2.39 score 6 dependencies 1 dependents 8 mentions 66 scripts 265 downloads

Last updated 6 years agofrom:e93c5b4bc7. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 12 2024
R-4.5-winNOTESep 12 2024
R-4.5-linuxNOTESep 12 2024
R-4.4-winOKSep 12 2024
R-4.4-macOKSep 12 2024
R-4.3-winOKSep 12 2024
R-4.3-macOKSep 12 2024

Exports:bestCloseMatchblockAlignmentcgraphchaoHaplocheckDNAdataStathaploAccumheatmapSppis.ambiglocalMinimamaxInDistminInDistmonophylymonophylyBootnearNeighbournonConDistnucDiagordinDNApaapolyBalancerankSlidWinread.BOLDread.GBrmSingletonsrnucDiagrosenbergsearch.BOLDseeBarcodeseqStatslideAnalysesslideBoxplotsslideNucDiagslidingWindowsppDistsppDistMatrixstats.BOLDtajima.KtclustthreshIDthreshOpttipordertitvtree.comp

Dependencies:apedigestlatticenlmepegasRcpp

Readme and manuals

Help Manual

Help pageTopics
Species Identity and Evolution in Rspider-package spider
Cytochrome oxidase I (COI) sequences of New Zealand _Anoteropsis_ speciesanoteropsis
Measures of identification accuracybestCloseMatch
Make all sequences the same lengthblockAlignment
Complete graphcgraph
Chao estimator of haplotype numberchaoHaplo
Check a DNA alignment for missing datacheckDNA
Taxa statisticsdataStat
Cytochrome oxidase I (COI) sequences of New Zealand _Dolomedes_ speciesdolomedes
Haplotype accumulation curveshaploAccum
Visualise a distance matrix using a heatmapheatmapSpp
Missing bases in alignmentsis.ambig
Determine thresholds from a density plotlocalMinima
Nearest non-conspecific and maximum intra-specific distancesmaxInDist
Nearest non-conspecific and maximum intra-specific distancesminInDist
Species monophyly over a treemonophyly
Species monophyly over a treemonophylyBoot
Measures of identification accuracynearNeighbour
Nearest non-conspecific and maximum intra-specific distancesnonConDist
Nucleotide diagnostics for species alignmentsnucDiag
Calculates a Principal Components Ordination of genetic distancesordinDNA
Population Aggregate Analysispaa
Plotting haplotype accumulation curvesplot.haploAccum
Plot an 'ordinDNA' objectplot.ordinDNA
Plot a 'slidWin' objectplot.slidWin
Balance of a phylogenetic tree with polytomiespolyBalance
Rank a 'slidWin' object.rankSlidWin
Downloads DNA sequences from the Barcode of Life Database (BOLD)read.BOLD
Download sequences from Genbank with metadata.read.GB
Detect and remove singletonsrmSingletons
Nucleotide diagnostics for species alignmentsrnucDiag
Rosenberg's probability of reciprocal monophylyrosenberg
Cytochrome oxidase I (COI) sequences of world-wide species of Salticidaesalticidae
Dummy sequences illustrating the categories of diagnostic nucleotidessarkar
Downloads DNA sequences from the Barcode of Life Database (BOLD)search.BOLD
Create illustrative barcodesseeBarcode
Sequence statisticsseqStat
Sliding window analysesslideAnalyses
Boxplots across windowsslideBoxplots
Sliding nucleotide diagnosticsslideNucDiag
Create windows along an alignmentslidingWindow
Intra and inter-specific distancessppDist
Mean intra- and inter-specific distance matrixsppDistMatrix
Species VectorssppVector
Downloads DNA sequences from the Barcode of Life Database (BOLD)stats.BOLD
Calculate Tajima's K index of divergencetajima.K
Clustering by a thresholdtclust
Measures of identification accuracythreshID
Threshold optimisationthreshOpt
Orders tip labels by their position on the tree.tiporder
Number of pairwise transitions and transversions in an alignment.titv
Tree comparisonstree.comp
Cytochrome b Gene Sequences of Woodmicewoodmouse