spider v1.5.0

0

Monthly downloads

0th

Percentile

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>.

Readme

Build Status rstudio mirror cran version

spider

Overview

The official GitHub repository for the R package "SPecies IDentity and Evolution in R" (spider).

spider provides functions for the 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).

For an introduction to the package, visit our spider tutorial and manual. Over time, the tutorial will be expanded and moved into GitHub vignettes and project pages.

If you are interested in previous versions (before v1.5.0) of the spider source code, check out our old repository hosted at r-forge.

Installation

Stable CRAN version (NOT YET WORKING).

install.packages("spider")

Or development version from GitHub (WORKING).

devtools::install_github("boopsboops/spider")

Examples

Here, we will do a quick "best close match" analysis (Meier et al., 2006) on a Anoteropsis wolf spider dataset (Vink & Paterson, 2003) to see how well DNA barcodes can identify individuals in a simulated identification scenario.

# load up the data
library("spider")
data(anoteropsis)
# make a quick species vector (unique species name for each individual) from the taxon labels
anoSpp <- sapply(strsplit(rownames(anoteropsis), split="_"), function(x) paste(x[1], x[2]))
head(anoSpp, n=4)
#> [1] "Artoria flavimanus" "Artoria separata" "Anoteropsis adumbrata" "Anoteropsis adumbrata"
# get some statistics about the sequence lengths
seqStat(anoteropsis)
#> Min    Max   Mean Median Thresh 
#> 395    409    408    409     33
# make a distance matrix from raw p-distances
anoDist <- ape::dist.dna(anoteropsis, model="raw", pairwise.deletion=TRUE)
# calculate identification success based on a 1% interspecific threshold
table(bestCloseMatch(distobj=anoDist, sppVector=anoSpp, threshold=0.01))
#> correct incorrect     no id 
#>      11         2        20

Current contributors

Meta

Functions in spider

Name Description
chaoHaplo Chao estimator of haplotype number
sarkar Dummy sequences illustrating the categories of diagnostic nucleotides
rnucDiag Nucleotide diagnostics for species alignments
heatmapSpp Visualise a distance matrix using a heatmap
search.BOLD Downloads DNA sequences from the Barcode of Life Database (BOLD)
threshOpt Threshold optimisation
slidingWindow Create windows along an alignment
stats.BOLD Downloads DNA sequences from the Barcode of Life Database (BOLD)
tajima.K Calculate Tajima's K index of divergence
tiporder Orders tip labels by their position on the tree.
slideNucDiag Sliding nucleotide diagnostics
minInDist Nearest non-conspecific and maximum intra-specific distances
paa Population Aggregate Analysis
read.GB Download sequences from Genbank with metadata.
plot.haploAccum Plotting haplotype accumulation curves
nucDiag Nucleotide diagnostics for species alignments
rosenberg Rosenberg's probability of reciprocal monophyly
seeBarcode Create illustrative barcodes
rankSlidWin Rank a 'slidWin' object.
ordinDNA Calculates a Principal Components Ordination of genetic distances
salticidae Cytochrome oxidase I (COI) sequences of world-wide species of Salticidae
polyBalance Balance of a phylogenetic tree with polytomies
slideAnalyses Sliding window analyses
slideBoxplots Boxplots across windows
spider-package Species Identity and Evolution in R
sppDistMatrix Mean intra- and inter-specific distance matrix
titv Number of pairwise transitions and transversions in an alignment.
sppDist Intra and inter-specific distances
seqStat Sequence statistics
sppVector Species Vectors
tree.comp Tree comparisons
tclust Clustering by a threshold
threshID Measures of identification accuracy
woodmouse Cytochrome b Gene Sequences of Woodmice
anoteropsis Cytochrome oxidase I (COI) sequences of New Zealand _Anoteropsis_ species
blockAlignment Make all sequences the same length
dolomedes Cytochrome oxidase I (COI) sequences of New Zealand _Dolomedes_ species
dataStat Taxa statistics
cgraph Complete graph
monophylyBoot Species monophyly over a tree
checkDNA Check a DNA alignment for missing data
monophyly Species monophyly over a tree
nearNeighbour Measures of identification accuracy
nonConDist Nearest non-conspecific and maximum intra-specific distances
bestCloseMatch Measures of identification accuracy
is.ambig Missing bases in alignments
localMinima Determine thresholds from a density plot
maxInDist Nearest non-conspecific and maximum intra-specific distances
plot.ordinDNA Plot an 'ordinDNA' object
plot.slidWin Plot a 'slidWin' object
haploAccum Haplotype accumulation curves
read.BOLD Downloads DNA sequences from the Barcode of Life Database (BOLD)
rmSingletons Detect and remove singletons
No Results!

Last month downloads

Details

Type Package
Date 2018-02-15
License MIT + file LICENSE
LazyLoad yes
RoxygenNote 6.0.1
NeedsCompilation no
Packaged 2018-02-16 19:05:02 UTC; rc16041
Repository CRAN
Date/Publication 2018-02-16 19:33:47 UTC

Include our badge in your README

[![Rdoc](http://www.rdocumentation.org/badges/version/spider)](http://www.rdocumentation.org/packages/spider)