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NEWS
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############################################
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
############################################