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) .


Build Status rstudio mirror cran version

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

News

############################################ SPIDER VERSION 1.5.0 Released 15 February 2018

-- Moved from R-Forge (https://r-forge.r-project.org/projects/spider/). -- Now at Github (https://github.com/boopsboops/spider). -- Package maintainer now Rupert A. Collins. -- Now using Roxygen documentation (Rd source now in R functions). -- Fixes to broken man pages. -- Imported package functions now explicitly called using 'importFrom' and automatically added to namespace. -- Added the testthat infrastructure. -- Functions read.BOLD, search.BOLD, and stats.BOLD have been deprecated in favour of using the better functions in the rOpenSci 'bold' package. -- Function read.GB has been deprecated in favour of using the better functions in the 'rentrez', 'traits', and 'ape' packages.

############################################ SPIDER VERSION 1.4-2 Released 13 May 2017

-- Extra options added to heatmapSpp. Option of showing the data on the heatmap now available. -- Bug fix for seqStat

############################################ SPIDER VERSION 1.4-1 Released 5 July 2016

-- External functions imported in NAMESPACE -- Minor change to nucDiag help file

############################################ SPIDER VERSION 1.4-0 Released 20 June 2016

-- Bugs in heatmapSpp and plot.ordinDNA fixed -- New option "names" added for bestCloseMatch and threshID -- New functions: rnucDiag, blockAlignment, and minInDist

############################################ SPIDER VERSION 1.3-0 Released 25 December 2013

-- read.GB: Space removed from around the pipe in the default naming scheme. -- chaoHaplo: 95% confidence interval calculated around the estimated number of haplotypes. -- New functions: cgraph, ordinDNA and plot.ordinDNA -- namespace issues resolved

############################################ SPIDER VERSION 1.2-0 Released 17 November 2012

-- Functions added: heatmapSpp -- read.BOLD: Function completely rewritten to compensate for BOLD deprecating their eFetch system

############################################ SPIDER VERSION 1.1-5 Released 11 October 2012

-- monophyly: Code changed from calling the ape C routine "bipartition" directly, to using prop.part() -- monophylyBoot: Code changed from calling the ape C routine "bipartition" directly, to using prop.part() -- tree.comp: Code changed from calling the ape C routine "bipartition" directly, to using prop.part()

############################################ SPIDER VERSION 1.1-4 Released 17 June 2012

-- sarkar: The addition of a dataset containing the dummy sequences published in Sarkar et al to illustrate the different categories of diagnostic nucleotides.

############################################ SPIDER VERSION 1.1-3 Released 29 March 2012

-- rankSlidWin: bug fixed that caused an error when multiple names were given to "criteria"

############################################ SPIDER VERSION 1.1-2 Released 10 March 2012

-- read.GB: modified to work with eFetch version 2.0 (http://www.ncbi.nlm.nih.gov/books/NBK25499/) -- read.BOLD: help file updated -- search.BOLD: Modified to work with BOLDsystems v 3.0 -- Functions added: stats.BOLD

############################################ SPIDER VERSION 1.1-1 Released 27 November 2011

-- tiporder: "labels" option added to toggle between returning the labels (when "labels"=TRUE), or returning the indices (when "labels"=FALSE).

############################################ SPIDER VERSION 1.1-0 Released 6 November 2011

-- Initial release onto CRAN -- No known issues

############################################

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("spider")

1.5.0 by Rupert A. Collins, a year ago


Browse source code at https://github.com/cran/spider


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


Documentation:   PDF Manual  


Task views:


MIT + file LICENSE license


Imports ape, pegas, graphics, stats, utils

Suggests testthat


Suggested by quiddich.


See at CRAN