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Innumerable changes to pass R CMD check

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1 parent acbf90a commit 8ce3bc8c0d6fe17cde7b7c77b1d7e365d5bb0c19 Charles R. Hogg III committed Jul 13, 2012
Showing with 1,380 additions and 1,478 deletions.
  1. +2 −0 .Rbuildignore
  2. +2 −1 DESCRIPTION
  3. +22 −11 NAMESPACE
  4. +29 −0 NEWS
  5. +228 −105 R/Covariance.R
  6. +21 −38 R/CovarianceNoise.R
  7. +32 −45 R/CovarianceSE.R
  8. +38 −55 R/CovarianceSEAniso2D.R
  9. +43 −61 R/CovarianceSELocalized.R
  10. +48 −78 R/CovarianceSEVaryingEll.R
  11. +76 −55 R/Dataset.R
  12. +11 −30 R/LazyMatrix.R
  13. +64 −81 R/Model.R
  14. +71 −0 R/generics.R
  15. +8 −5 R/geometry.R
  16. +3 −0 R/gppois.R
  17. +3 −3 R/layout.R
  18. +4 −0 R/poisson.R
  19. +5 −0 R/rgl.R
  20. +3 −2 R/utils.R
  21. +1 −1 demo/00Index
  22. +0 −54 document.R
  23. +0 −1 inst/tests/test-Covariance.R
  24. +2 −1 inst/tests/test-Dataset.R
  25. +1 −0 man/AddCovariance.Model.Rd
  26. +5 −0 man/Anscombe.Rd
  27. +2 −0 man/BubblingRandomMatrix.Rd
  28. +24 −89 man/Covariance.Rd
  29. +17 −73 man/CovarianceNoise.Rd
  30. +24 −79 man/CovarianceSE.Rd
  31. +37 −85 man/CovarianceSEAniso2D.Rd
  32. +39 −87 man/CovarianceSELocalized.Rd
  33. +45 −97 man/CovarianceSEVaryingEll.Rd
  34. +55 −78 man/Dataset.Rd
  35. +1 −0 man/DeleteRows.Dataset.Rd
  36. +7 −2 man/FindGapPoints.Rd
  37. +1 −0 man/FixConstParam.Covariance.Rd
  38. +1 −0 man/Forget.Model.Rd
  39. +1 −0 man/Freeze.Model.Rd
  40. +4 −0 man/K.Covariance.Rd
  41. +20 −0 man/K.specific.Rd
  42. +21 −0 man/KDerivImplementation.Rd
  43. +1 −0 man/L.Model.Rd
  44. +4 −55 man/LazyMatrix.Rd
  45. +1 −0 man/MSR.Dataset.Rd
  46. +39 −145 man/Model.Rd
  47. +1 −0 man/NamedCovariance.Model.Rd
  48. +1 −0 man/NeedToRecalculate.LazyMatrix.Rd
  49. +1 −0 man/Plot2D.Dataset.Rd
  50. +1 −0 man/PlotBubblingSurfaces2D.Model.Rd
  51. +3 −0 man/PlotSurface.Rd
  52. +1 −0 man/PosteriorInterval.Model.Rd
  53. +1 −0 man/PosteriorMean.Model.Rd
  54. +1 −0 man/PosteriorStandardDeviation.Model.Rd
  55. +1 −0 man/PredictionMatrix.Model.Rd
  56. +1 −0 man/RemoveRange.Dataset.Rd
  57. +1 −0 man/Same.Dataset.Rd
  58. +4 −0 man/ScaleY.Rd
  59. +1 −0 man/SetNoiseBounds.Model.Rd
  60. +1 −0 man/StoreMatrix.LazyMatrix.Rd
  61. +1 −0 man/Train.Model.Rd
  62. +1 −0 man/Untransform.Dataset.Rd
  63. +18 −0 man/Variance.Rd
  64. +1 −0 man/ell.CovarianceSEVaryingEll.Rd
  65. +27 −0 man/flameSpeed.Rd
  66. +1 −0 man/getContributionIds.Model.Rd
  67. +20 −0 man/getLogspaceNames.Rd
  68. +2 −1 man/getLower.Model.Rd
  69. +1 −0 man/getParamNames.Covariance.Rd
  70. +22 −20 man/getParams.Covariance.Rd
  71. +2 −3 man/getParams.Model.Rd
  72. +1 −0 man/getSignalIds.Model.Rd
  73. +1 −0 man/getVaryingParamNames.Model.Rd
  74. +27 −0 man/lower.Rd
  75. +33 −0 man/lowerPlain.Rd
  76. +21 −0 man/paramNamesPlain.Rd
  77. +29 −0 man/params.Rd
  78. +3 −3 man/print.Covariance.Rd
  79. +2 −2 man/print.Dataset.Rd
  80. +2 −2 man/print.Model.Rd
  81. +0 −5 man/setLower.Covariance.Rd
  82. +11 −14 man/setParamsPlain.Covariance.Rd
  83. +0 −5 man/setUpper.Covariance.Rd
  84. +1 −0 man/sigma.f.CovarianceSEVaryingEll.Rd
  85. +6 −2 man/steelStrain.Rd
  86. +27 −0 man/upper.Rd
  87. +33 −0 man/upperPlain.Rd
  88. +2 −4 tests/run-all.R
View
@@ -0,0 +1,2 @@
+extras/data/big_steel_dataset.csv
+.git
View
@@ -11,7 +11,7 @@ Description: Analyzes data using Gaussian processes. Supported noise models
License: GPL-3
LazyLoad: yes
Suggests:
- debug,geometry,rgl,Cairo,ggplot2
+ debug,geometry,rgl,Cairo,ggplot2,testthat
Depends:
R.oo
URL: http://www.nist.gov/mml/ceramics/structure_determination/gppois.cfm
@@ -31,3 +31,4 @@ Collate:
'poisson.R'
'rgl.R'
'utils.R'
+ 'generics.R'
View
@@ -93,19 +93,31 @@ S3method(getXformedDpts,Dataset)
S3method(print,Covariance)
S3method(print,Dataset)
S3method(print,Model)
+S3method(setId,Covariance)
+S3method(setId,Dataset)
+S3method(setId,Model)
S3method(setLower,Covariance)
S3method(setLower,Model)
+S3method(setLowerPlain,CovarianceSE)
S3method(setParams,Covariance)
S3method(setParams,Model)
S3method(setParamsPlain,Covariance)
S3method(setQuantity,Dataset)
S3method(setUpper,Covariance)
S3method(setUpper,Model)
+S3method(setUpperPlain,CovarianceSE)
S3method(sigma.f,CovarianceSEVaryingEll)
export(AddCovariance)
export(AddCovariance.Model)
export(Anscombe)
export(BubblingRandomMatrix)
+export(Covariance)
+export(CovarianceNoise)
+export(CovarianceSE)
+export(CovarianceSEAniso2D)
+export(CovarianceSELocalized)
+export(CovarianceSEVaryingEll)
+export(Dataset)
export(DeleteRows)
export(DeleteRows.Dataset)
export(DemoPause)
@@ -144,9 +156,11 @@ export(KOutOut)
export(KOutOut.Covariance)
export(L)
export(L.Model)
+export(LazyMatrix)
export(LogML)
export(MSR)
export(MSR.Dataset)
+export(Model)
export(NamedCovariance)
export(NamedCovariance.Model)
export(NeedToRecalculate)
@@ -258,10 +272,15 @@ export(getX)
export(getX.Dataset)
export(getXformedDpts)
export(getXformedDpts.Dataset)
-export(print.Dataset)
+export(setId)
+export(setId.Covariance)
+export(setId.Dataset)
+export(setId.Model)
export(setLower)
export(setLower.Covariance)
export(setLower.Model)
+export(setLowerPlain)
+export(setLowerPlain.CovarianceSE)
export(setParams)
export(setParams.Covariance)
export(setParams.Model)
@@ -272,16 +291,8 @@ export(setQuantity.Dataset)
export(setUpper)
export(setUpper.Covariance)
export(setUpper.Model)
+export(setUpperPlain)
+export(setUpperPlain.CovarianceSE)
export(sigma.f)
export(sigma.f.CovarianceSEVaryingEll)
import(R.oo)
-
-export(CovarianceNoise)
-export(Covariance)
-export(CovarianceSEAniso2D)
-export(CovarianceSELocalized)
-export(CovarianceSE)
-export(CovarianceSEVaryingEll)
-export(Dataset)
-export(LazyMatrix)
-export(Model)
View
29 NEWS
@@ -0,0 +1,29 @@
+gppois 0.2-0
+===============================================================================
+
+* Upgraded to use the latest version of R (2.15.1).
+
+* All documentation now uses roxygen2 (previously, functions used roxygen2, but
+ classes were documented with Rdoc from R.oo)
+
+DEMOS
+-----
+
+* Made a demo for the steelStrain data, to get a feel for the package. It's
+ somewhat long (training can take upwards of 10 minutes), but the pictures are
+ pretty.
+
+DATASETS
+--------
+
+* steelStrain now includes all three strain columns, as well as a separate
+ data.frame with the "gap" datapoints
+
+* Added flameSpeed dataset
+
+BUG FIXES
+---------
+
+* getLower() and getUpper() now match positionally with getParams(), when
+ for.training is TRUE. Model$Train() had been failing because of a defect in
+ how optim() handles bounds for the L-BFGS-B method.
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