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0 parents commit e45945cecdebf3d20c4cfaac121b8eebea72a66c @pmidford pmidford committed Feb 17, 2015
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  1. +1 −0 README.md
  2. BIN Resources/.DS_Store
  3. +137 −0 Resources/Tests/45LBR70.PDI
  4. +383 −0 Resources/Tests/45LBR70.STA
  5. BIN Resources/Tests/45LBR70.STA.doc
  6. +149 −0 Resources/Tests/49LBR.PDI
  7. +341 −0 Resources/Tests/49LBR.PDI.nex
  8. +388 −0 Resources/Tests/49LBR.STA
  9. +149 −0 Resources/Tests/49LBR70.PDI
  10. +399 −0 Resources/Tests/49LBR70.PDI_Missing_4.nex
  11. +387 −0 Resources/Tests/49LBR70.STA
  12. BIN Resources/Tests/49LBR70.STA.doc
  13. +149 −0 Resources/Tests/49P1.PDI
  14. +388 −0 Resources/Tests/49P1.STA
  15. +149 −0 Resources/Tests/49P2.PDI
  16. +350 −0 Resources/Tests/49P2.PDI.nex
  17. +388 −0 Resources/Tests/49P2.STA
  18. +149 −0 Resources/Tests/49P3.PDI
  19. +350 −0 Resources/Tests/49P3.PDI.nex
  20. +388 −0 Resources/Tests/49P3.STA
  21. +353 −0 Resources/Tests/49poly.nex
  22. +182 −0 Resources/Tests/60LBR70T.PDI
  23. +398 −0 Resources/Tests/60LBR70T.STA
  24. BIN Resources/Tests/60LBR70T.STA.doc
  25. +253 −0 Resources/Tests/DATA.FIC
  26. +568 −0 Resources/Tests/DATA.STA
  27. +1 −0 Resources/Tests/Data.pdi.nex
  28. +1,148 −0 Resources/Tests/Lavin/Lavin_Tree.nex
  29. +1,233 −0 Resources/Tests/Lavin/Lavin_Tree_new.pdi.nex
  30. +1,481 −0 Resources/Tests/Lavin/Lavin_tree.pdi
  31. +1,481 −0 Resources/Tests/Lavin/NewLavin.pdi
  32. +1,233 −0 Resources/Tests/Lavin/NewLavin.pdi.nex
  33. BIN Resources/Tests/Midford_OU.zip
  34. +50 −0 Resources/Tests/Midford_OU/49.tip
  35. BIN Resources/Tests/Midford_OU/49.tip.xls
  36. +49 −0 Resources/Tests/Midford_OU/49LBR70.DSC
  37. +149 −0 Resources/Tests/Midford_OU/49LBR70.PDI
  38. +49 −0 Resources/Tests/Midford_OU/49LBR_tip_names.txt
  39. +49 −0 Resources/Tests/Midford_OU/OUtransformedV_LBW1.txt
  40. +1 −0 Resources/Tests/Midford_OU/TREE.BRK
  41. +203 −0 Resources/Tests/Midford_OU/TREE.BRK.nex
  42. +426 −0 Resources/Tests/Midford_OU/treeconv5.lsp
  43. +17 −0 Resources/Tests/POLYTEST.PDI
  44. +257 −0 Resources/Tests/POLYTEST.PDI.nex
  45. +164 −0 Resources/Tests/Simple8.nex
  46. BIN Resources/Tests/Tests_with_TG_Aug_7_2009.doc
  47. +225 −0 Resources/Tests/bino.pdi.nex
  48. +45 −0 Resources/Tests/multitree.nex
  49. +409 −0 Resources/Tests/pagelPoly.nex
  50. +35 −0 Resources/Tests/pagelPoly.pdi
  51. +262 −0 Resources/Tests/pagelPoly.pdi.nex
  52. +245 −0 Resources/Tests/polytest.nex
  53. +126 −0 Resources/Tests/smallpoly.nex
  54. +37 −0 Resources/notices/install.xml
  55. +127 −0 Resources/notices/notices.xml
  56. BIN Resources/pdap_examples/.DS_Store
  57. BIN Resources/pdap_examples/Guided Tour.zip
  58. +445 −0 Resources/pdap_examples/Guided Tour/Part1.nex
  59. +442 −0 Resources/pdap_examples/Guided Tour/Part2.nex
  60. +434 −0 Resources/pdap_examples/Guided Tour/Part3.nex
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  65. +373 −0 Resources/pdap_examples/Guided Tour/Part8.nex
  66. +291 −0 Resources/pdap_examples/Guided Tour/Part9.nex
  67. +362 −0 Resources/pdap_examples/Old Guided Tour/Part1.nex
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  75. +291 −0 Resources/pdap_examples/Old Guided Tour/Part9.nex
  76. BIN Resources/pdap_examples/guided_tour.tgz
  77. +149 −0 Resources/pdap_examples/misc examples/49LBR.PDI
  78. +1 −0 Resources/pdap_examples/misc examples/APPAMG91.PDI
  79. +317 −0 Resources/pdap_examples/misc examples/IndependentContrastsExample.nex
  80. +202 −0 buildfiles/build.xml
  81. +1 −0 src/mesquite/pdap/Alog10TransformChar/Alog10TransformChar.java
  82. +1 −0 src/mesquite/pdap/CIReport/CIReport.java
  83. +1 −0 src/mesquite/pdap/ContrastResiduals/ContrastResiduals.java
  84. +1 −0 src/mesquite/pdap/DivideChars/DivideChars.java
  85. +1 −0 src/mesquite/pdap/ExpTransform/ExpTransform.java
  86. +1 −0 src/mesquite/pdap/ExpTransformChar/ExpTransformChar.java
  87. +1 −0 src/mesquite/pdap/FICReport/FICReport.java
  88. +1 −0 src/mesquite/pdap/FelsContrWithChar/FelsContrWithChar.java
  89. +1 −0 src/mesquite/pdap/FelsensteinContrasts/FelsensteinContrasts.java
  90. +1 −0 src/mesquite/pdap/FelsensteinCorrelation/FelsensteinCorrelation.java
  91. +1 −0 src/mesquite/pdap/GrafenTransform/GrafenTransform.java
  92. +1 −0 src/mesquite/pdap/GrafensRhoTransform/GrafensRhoTransform.java
  93. +1 −0 src/mesquite/pdap/IndepContrastsVariance/IndepContrastsVariance.java
  94. +293 −0 src/mesquite/pdap/InterpretPDDIST/InterpretPDDIST.java
  95. +1 −0 src/mesquite/pdap/InterpretPDI/InterpretPDI.java
  96. +1 −0 src/mesquite/pdap/Log10TransformChar/Log10TransformChar.java
  97. +1 −0 src/mesquite/pdap/LogTransform/LogTransform.java
  98. +1 −0 src/mesquite/pdap/NeeTransform/NeeTransform.java
  99. +282 −0 src/mesquite/pdap/NodeValueNodeHeightCorrelation/NodeValueNodeHeightCorrelation.java
  100. +1 −0 src/mesquite/pdap/PDAPDiagnosticChart/PDAPDiagnosticChart.java
  101. +263 −0 src/mesquite/pdap/PDAPReRootingSet/PDAPReRootingSet.java
  102. +1 −0 src/mesquite/pdap/PagelTransform/PagelTransform.java
  103. +1 −0 src/mesquite/pdap/RaiseStatesToPowerChar/RaiseStatesToPowerChar.java
  104. +239 −0 src/mesquite/pdap/RootReconstructionCIs/RootReconstructionCIs.java
  105. +1 −0 src/mesquite/pdap/RootReconstructions/RootReconstructions.java
  106. +1 −0 src/mesquite/pdap/RootedRegression/RootedRegression.java
  107. +1 −0 src/mesquite/pdap/SPOriDiagnostics/SPOriDiagnostics.java
  108. +1 −0 src/mesquite/pdap/SPRegDiagnostics/SPRegDiagnostics.java
  109. +1 −0 src/mesquite/pdap/SPRootReconstruction/SPRootReconstruction.java
  110. +386 −0 src/mesquite/pdap/SPRootRegression/SPRootRegression.java
  111. +1 −0 src/mesquite/pdap/ScatterDiagnostics/ScatterDiagnostics.java
  112. +1 −0 src/mesquite/pdap/ScatterOriDiagnostics/ScatterOriDiagnostics.java
  113. +1 −0 src/mesquite/pdap/ScatterRegDiagnostics/ScatterRegDiagnostics.java
  114. +1 −0 src/mesquite/pdap/ScatterResXDiagnostics/ScatterResXDiagnostics.java
  115. +1 −0 src/mesquite/pdap/ScatterRootCIPI/ScatterRootCIPI.java
  116. +1 −0 src/mesquite/pdap/ScatterRootRegCIPI/ScatterRootRegCIPI.java
  117. +1 −0 src/mesquite/pdap/aPDAPIntro/aPDAPIntro.java
  118. +1 −0 src/mesquite/pdap/aPDAPIntro/index.html
  119. +701 −0 src/mesquite/pdap/aPDAPIntro/splash
  120. +701 −0 src/mesquite/pdap/aPDAPIntro/splash.ai
  121. BIN src/mesquite/pdap/aPDAPIntro/splash.gif
  122. +1 −0 src/mesquite/pdap/lib/BivariateContrastCalculator.java
  123. +1 −0 src/mesquite/pdap/lib/ContrastCalculator.java
  124. +1 −0 src/mesquite/pdap/lib/ContrastCoordinator.java
  125. +1 −0 src/mesquite/pdap/lib/ContrastForChar.java
  126. +96 −0 src/mesquite/pdap/lib/FICDialog.java
  127. +1 −0 src/mesquite/pdap/lib/NoPolyTree.java
  128. +229 −0 src/mesquite/pdap/lib/PDAP2CTStatPak.java
  129. +24 −0 src/mesquite/pdap/lib/PDAP2CTStatPakSource.java
  130. +1 −0 src/mesquite/pdap/lib/PDAPFileReporter.java
  131. +1 −0 src/mesquite/pdap/lib/PDAPReporterDialog.java
  132. +21 −0 src/mesquite/pdap/lib/PDAPRootReconStatPak.java
  133. +99 −0 src/mesquite/pdap/lib/PDAPRootRegStatPak.java
  134. +455 −0 src/mesquite/pdap/lib/PDAPRootStatPak.java
  135. +1 −0 src/mesquite/pdap/lib/PDAPScatterAsst.java
  136. +1 −0 src/mesquite/pdap/lib/PDAPStatPak.java
  137. +1 −0 src/mesquite/pdap/lib/PDAPTreeWinAsstC.java
  138. +1 −0 src/mesquite/pdap/lib/ResidualsCalculator.java
  139. +1 −0 src/mesquite/pdap/lib/RootRegressionCalculator.java
  140. +1 −0 src/mesquite/pdap/lib/ScatterRegisterableAsst.java
  141. +68 −0 src/mesquite/pdap/lib/SignTest.java
  142. +1 −0 src/mesquite/pdap/lib/StatPakSource.java
  143. +1 −0 src/mesquite/pdap/lib/UnivariateContrastCalculator.java
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