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base repository: boopsboops/spider
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base: v1.3.0
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head repository: boopsboops/spider
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compare: master
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Showing with 5,134 additions and 1,775 deletions.
  1. +4 −0 .Rbuildignore
  2. +2 −0 .gitignore
  3. +12 −0 .travis.yml
  4. +8 −10 DESCRIPTION
  5. +2 −21 LICENSE
  6. +0 −92 MD5
  7. +89 −13 NAMESPACE
  8. +40 −0 NEWS
  9. +90 −6 R/bestCloseMatch.R
  10. +59 −0 R/blockAlignment.R
  11. +29 −0 R/cgraph.R
  12. +34 −0 R/chaoHaplo.R
  13. +22 −0 R/checkDNA.R
  14. +29 −0 R/dataStat.R
  15. +124 −76 R/haploAccum.R
  16. +64 −2 R/heatmapSpp.R
  17. +24 −2 R/is.ambig.R
  18. +39 −1 R/localMinima.R
  19. +69 −5 R/maxInDist.R
  20. +77 −0 R/minInDist.R
  21. +78 −0 R/monophyly.R
  22. +89 −0 R/monophylyBoot.R
  23. +82 −0 R/nearNeighbour.R
  24. +62 −0 R/nonConDist.R
  25. +59 −0 R/nucDiag.R
  26. +48 −0 R/ordinDNA.R
  27. +41 −1 R/paa.R
  28. +74 −28 R/plot.haploAccum.R
  29. +104 −12 R/plot.ordinDNA.R
  30. +49 −0 R/plot.slidWin.R
  31. +28 −0 R/polyBalance.R
  32. +58 −1 R/rankSlidWin.R
  33. +68 −34 R/read.BOLD.R
  34. +44 −44 R/read.GB.R
  35. +33 −1 R/rmSingletons.R
  36. +78 −0 R/rnucDiag.R
  37. +45 −0 R/rosenberg.R
  38. +68 −29 R/search.BOLD.R
  39. +31 −1 R/seeBarcode.R
  40. +28 −5 R/seqStat.R
  41. +70 −0 R/slideAnalyses.R
  42. +58 −0 R/slideBoxplots.R
  43. +40 −0 R/slideNucDiag.R
  44. +43 −0 R/slidingWindow.R
  45. +165 −0 R/spider-package.R
  46. +34 −0 R/sppDist.R
  47. +24 −0 R/sppDistMatrix.R
  48. +66 −8 R/stats.BOLD.R
  49. +25 −0 R/tajima.K.R
  50. +33 −1 R/tclust.R
  51. +90 −6 R/threshID.R
  52. +47 −0 R/threshOpt.R
  53. +31 −0 R/tiporder.R
  54. +39 −0 R/titv.R
  55. +59 −0 R/tree.comp.R
  56. +77 −1 README.md
  57. +25 −0 cran-comments.md
  58. BIN data/salticidae.rda
  59. BIN data/woodmouse.rda
  60. +17 −12 man/anoteropsis.Rd
  61. +103 −0 man/bestCloseMatch.Rd
  62. +50 −0 man/blockAlignment.Rd
  63. +24 −27 man/cgraph.Rd
  64. +31 −29 man/chaoHaplo.Rd
  65. +23 −23 man/checkDNA.Rd
  66. +24 −35 man/dataStat.Rd
  67. +15 −11 man/dolomedes.Rd
  68. +46 −35 man/haploAccum.Rd
  69. +40 −23 man/heatmapSpp.Rd
  70. +23 −26 man/is.ambig.Rd
  71. +29 −30 man/localMinima.Rd
  72. +74 −0 man/maxInDist.Rd
  73. +74 −0 man/minInDist.Rd
  74. +42 −52 man/monophyly.Rd
  75. +108 −0 man/monophylyBoot.Rd
  76. +64 −52 man/nearNeighbour.Rd
  77. +37 −43 man/nonConDist.Rd
  78. +48 −28 man/nucDiag.Rd
  79. +38 −30 man/ordinDNA.Rd
  80. +27 −24 man/paa.Rd
  81. +50 −37 man/plot.haploAccum.Rd
  82. +80 −51 man/plot.ordinDNA.Rd
  83. +32 −37 man/plot.slidWin.Rd
  84. +41 −43 man/polyBalance.Rd
  85. +40 −41 man/rankSlidWin.Rd
  86. +57 −53 man/read.BOLD.Rd
  87. +42 −40 man/read.GB.Rd
  88. +22 −21 man/rmSingletons.Rd
  89. +79 −0 man/rnucDiag.Rd
  90. +36 −36 man/rosenberg.Rd
  91. +19 −0 man/salticidae.Rd
  92. +13 −12 man/sarkar.Rd
  93. +89 −0 man/search.BOLD.Rd
  94. +23 −23 man/seeBarcode.Rd
  95. +19 −28 man/seqStat.Rd
  96. +62 −64 man/slideAnalyses.Rd
  97. +52 −52 man/slideBoxplots.Rd
  98. +30 −38 man/slideNucDiag.Rd
  99. +31 −32 man/slidingWindow.Rd
  100. +39 −39 man/spider-package.Rd
  101. +25 −31 man/sppDist.Rd
  102. +18 −23 man/sppDistMatrix.Rd
  103. +86 −0 man/stats.BOLD.Rd
  104. +23 −29 man/tajima.K.Rd
  105. +23 −27 man/tclust.Rd
  106. +103 −0 man/threshID.Rd
  107. +33 −42 man/threshOpt.Rd
  108. +20 −26 man/tiporder.Rd
  109. +18 −25 man/titv.Rd
  110. +48 −45 man/tree.comp.Rd
  111. +22 −0 man/woodmouse.Rd
  112. +5 −0 tests/testthat.R
  113. +7 −0 tests/testthat/test-seqStat.R
4 changes: 4 additions & 0 deletions .Rbuildignore
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temp
.travis.yml
.gitignore
cran-comments.md
2 changes: 2 additions & 0 deletions .gitignore
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temp
LICENCE
12 changes: 12 additions & 0 deletions .travis.yml
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language: r
sudo: required
cache: packages

addons:
apt:
packages:
- libxml2-dev
- libudunits2-dev
- gdal-bin
- libgdal-dev
- libgdal1-dev
18 changes: 8 additions & 10 deletions DESCRIPTION
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@@ -1,15 +1,13 @@
Package: spider
Type: Package
Title: Species Identity and Evolution in R
Version: 1.3-0
Date: 2013-12-25
Version: 1.5.0.9000
Date: 2018-02-15
Author: Samuel Brown, Rupert Collins, Stephane Boyer, Marie-Caroline Lefort, Jagoba Malumbres-Olarte, Cor Vink, Rob Cruickshank
Maintainer: Samuel Brown <s_d_j_brown@hotmail.com>
Description: A package for the analysis of species limits and DNA barcoding data
License: GPL
Maintainer: Rupert A. Collins <rupertcollins@gmail.com>
Description: 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>.
License: MIT + file LICENSE
LazyLoad: yes
Depends: ape, pegas
Packaged: 2013-12-27 04:41:31 UTC; sam
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-12-27 07:30:41
Imports: ape, pegas, graphics, stats, utils
RoxygenNote: 6.1.1
Suggests: testthat
23 changes: 2 additions & 21 deletions LICENSE
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@@ -1,21 +1,2 @@
MIT License

Copyright (c) 2018 Rupert A. Collins

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
YEAR: 2018
COPYRIGHT HOLDER: Rupert A. Collins
92 changes: 0 additions & 92 deletions MD5

This file was deleted.

102 changes: 89 additions & 13 deletions NAMESPACE
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@@ -1,14 +1,90 @@
# Remove the previous line if you edit this file
# Generated by roxygen2: do not edit by hand

# Export all names
exportPattern("^[^\\.]")

# Import all packages listed as Imports or Depends
importFrom(ape, dist.dna, base.freq, seg.sites)
importFrom(pegas, haplotype)
importFrom(graphics, plot)


#S3 methods
S3method(plot, slidWin)
S3method(plot, haploAccum)
S3method(plot,haploAccum)
S3method(plot,ordinDNA)
S3method(plot,slidWin)
export(bestCloseMatch)
export(blockAlignment)
export(cgraph)
export(chaoHaplo)
export(checkDNA)
export(dataStat)
export(haploAccum)
export(heatmapSpp)
export(is.ambig)
export(localMinima)
export(maxInDist)
export(minInDist)
export(monophyly)
export(monophylyBoot)
export(nearNeighbour)
export(nonConDist)
export(nucDiag)
export(ordinDNA)
export(paa)
export(polyBalance)
export(rankSlidWin)
export(read.BOLD)
export(read.GB)
export(rmSingletons)
export(rnucDiag)
export(rosenberg)
export(search.BOLD)
export(seeBarcode)
export(seqStat)
export(slideAnalyses)
export(slideBoxplots)
export(slideNucDiag)
export(slidingWindow)
export(sppDist)
export(sppDistMatrix)
export(stats.BOLD)
export(tajima.K)
export(tclust)
export(threshID)
export(threshOpt)
export(tiporder)
export(titv)
export(tree.comp)
importFrom(ape,as.DNAbin)
importFrom(ape,boot.phylo)
importFrom(ape,di2multi)
importFrom(ape,dist.dna)
importFrom(ape,ladderize)
importFrom(ape,nj)
importFrom(ape,node.depth)
importFrom(ape,prop.part)
importFrom(ape,root)
importFrom(ape,rtree)
importFrom(ape,seg.sites)
importFrom(ape,unroot)
importFrom(ape,write.dna)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,barplot)
importFrom(graphics,boxplot)
importFrom(graphics,bxp)
importFrom(graphics,hist)
importFrom(graphics,image)
importFrom(graphics,layout)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,matlines)
importFrom(graphics,matplot)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,polygon)
importFrom(graphics,segments)
importFrom(graphics,symbols)
importFrom(graphics,text)
importFrom(pegas,haplotype)
importFrom(stats,aggregate)
importFrom(stats,cmdscale)
importFrom(stats,density)
importFrom(stats,dist)
importFrom(stats,median)
importFrom(stats,sd)
importFrom(utils,as.roman)
importFrom(utils,combn)
importFrom(utils,head)
40 changes: 40 additions & 0 deletions NEWS
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@@ -1,3 +1,43 @@
############################################
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
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