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