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Øystein Olav Skaar
Øystein Olav Skaar committed Jun 14, 2018
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  1. +38 −0 DESCRIPTION
  2. +2 −0 LICENSE
  3. +114 −0 NAMESPACE
  4. +15 −0 NEWS.md
  5. +685 −0 R/basic_functions.R
  6. +12 −0 R/data_cats.R
  7. +355 −0 R/mcmc.R
  8. +128 −0 R/mcmc_diag.R
  9. +444 −0 R/mcmc_misc.R
  10. +62 −0 R/mcmc_summary.R
  11. +471 −0 R/plotdata.R
  12. +286 −0 R/settings.R
  13. +125 −0 R/stats_bernoulli.R
  14. +185 −0 R/stats_covariate.R
  15. +229 −0 R/stats_fit.R
  16. +104 −0 R/stats_kappa.R
  17. +159 −0 R/stats_mean.R
  18. +144 −0 R/stats_metric.R
  19. +177 −0 R/stats_nominal.R
  20. +93 −0 R/stats_regression.R
  21. +135 −0 R/stats_softmax.R
  22. +262 −0 README.md
  23. +14 −0 TODO.md
  24. +17 −0 bfw.Rproj
  25. BIN data/Cats.rda
  26. +87 −0 inst/extdata/Data/Cats.R
  27. +6 −0 inst/extdata/Models/stats_bernoulli.txt
  28. +38 −0 inst/extdata/Models/stats_covariate.txt
  29. +40 −0 inst/extdata/Models/stats_covariate_robust.txt
  30. +39 −0 inst/extdata/Models/stats_fit_latent.txt
  31. +41 −0 inst/extdata/Models/stats_fit_latent_robust.txt
  32. +77 −0 inst/extdata/Models/stats_fit_observed.txt
  33. +81 −0 inst/extdata/Models/stats_fit_observed_robust.txt
  34. +16 −0 inst/extdata/Models/stats_kappa.txt
  35. +13 −0 inst/extdata/Models/stats_mean.txt
  36. +15 −0 inst/extdata/Models/stats_mean_robust.txt
  37. +31 −0 inst/extdata/Models/stats_metric.txt
  38. +49 −0 inst/extdata/Models/stats_metric2.txt
  39. +51 −0 inst/extdata/Models/stats_metric2_robust.txt
  40. +89 −0 inst/extdata/Models/stats_metric3.txt
  41. +91 −0 inst/extdata/Models/stats_metric3_robust.txt
  42. +183 −0 inst/extdata/Models/stats_metric4.txt
  43. +185 −0 inst/extdata/Models/stats_metric4_robust.txt
  44. +33 −0 inst/extdata/Models/stats_metric_robust.txt
  45. +31 −0 inst/extdata/Models/stats_nominal.txt
  46. +54 −0 inst/extdata/Models/stats_nominal2.txt
  47. +94 −0 inst/extdata/Models/stats_nominal3.txt
  48. +189 −0 inst/extdata/Models/stats_nominal4.txt
  49. +45 −0 inst/extdata/Models/stats_regression.txt
  50. +47 −0 inst/extdata/Models/stats_regression_robust.txt
  51. +38 −0 inst/extdata/Models/stats_softmax.txt
  52. +42 −0 inst/extdata/Models/stats_softmax_robust.txt
  53. +39 −0 man/AddNames.Rd
  54. +29 −0 man/CapWords.Rd
  55. +23 −0 man/Cats.Rd
  56. +22 −0 man/ComputeHDI.Rd
  57. +18 −0 man/ContrastNames.Rd
  58. +71 −0 man/DiagMCMC.Rd
  59. +27 −0 man/DistinctColors.Rd
  60. +20 −0 man/FlattenList.Rd
  61. +27 −0 man/GammaDist.Rd
  62. +38 −0 man/GetRange.Rd
  63. +29 −0 man/Interleave.Rd
  64. +17 −0 man/IsString.Rd
  65. +14 −0 man/JavaGarbage.Rd
  66. +22 −0 man/MatrixCombn.Rd
  67. +28 −0 man/MergeMCMC.Rd
  68. +23 −0 man/Normalize.Rd
  69. +22 −0 man/PadVector.Rd
  70. +25 −0 man/PaperSize.Rd
  71. +25 −0 man/ParseNumber.Rd
  72. +78 −0 man/PlotData.Rd
  73. +30 −0 man/ReadFile.Rd
  74. +22 −0 man/RemoveEmpty.Rd
  75. +22 −0 man/RemoveSpaces.Rd
  76. +28 −0 man/RunContrasts.Rd
  77. +92 −0 man/RunMCMC.Rd
  78. +33 −0 man/SaveName.Rd
  79. +50 −0 man/SavePlot.Rd
  80. +88 −0 man/StatsBernoulli.Rd
  81. +121 −0 man/StatsCovariate.Rd
  82. +50 −0 man/StatsFit.Rd
  83. +56 −0 man/StatsKappa.Rd
  84. +31 −0 man/StatsMean.Rd
  85. +41 −0 man/StatsMetric.Rd
  86. +73 −0 man/StatsNominal.Rd
  87. +41 −0 man/StatsRegression.Rd
  88. +77 −0 man/StatsSoftmax.Rd
  89. +32 −0 man/SumMCMC.Rd
  90. +29 −0 man/SumToZero.Rd
  91. +26 −0 man/Trim.Rd
  92. +33 −0 man/TrimSplit.Rd
  93. +35 −0 man/VectorSub.Rd
  94. +139 −0 man/bfw.Rd
  95. +2 −0 vignettes/.gitignore
  96. BIN vignettes/ProjectAllData-Mean-StagesOfCheese-Plot01-1528465133.png
  97. BIN vignettes/ProjectAllData-Mean-StagesOfCheese-Plot01-1528466639.png
  98. BIN vignettes/ProjectAllData-Mean-StagesOfCheese-Plot01-1528467502.png
  99. +181 −0 vignettes/fit_data.md
  100. +287 −0 vignettes/metric.md
  101. +119 −0 vignettes/plot_data.md
  102. +138 −0 vignettes/regression.md
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Package: bfw
Version: 0.0.1
Date: 2018-06-09
Title: Bayesian Framework for Computational Modelling
Authors@R: person( "Øystein Olav","Skaar", email="bayesianfw@gmail.com", role=c("aut","cre"))
Maintainer: Øystein Olav Skaar <bayesianfw@gmail.com>
URL: https://github.com/oeysan/bfw/
BugReports: https://github.com/oeysan/bfw/issues/
Description: Derived from the work of Kruschke (2015), the present package aim
to provide a framework for conducting Bayesian analysis using
Markov chain Monte Carlo (MCMC) sampling utilizing the Just Another
Gibbs Sampler ("JAGS", Plummer, 2003). The initial version include
several modules for conducting Bayesian equivalents of chi-squared tests,
analysis of variance (ANOVA), multiple (hierarchical) regression,
and for fitting data (e.g., structural equation modeling).
SystemRequirements: JAGS >=4.3.0 <http://mcmc-jags.sourceforge.net/>,
Java JDK >=1.4 <https://www.java.com/en/download/manual.jsp>
Depends: R (>= 3.4.0),
Imports: plyr (>= 1.8.4),
methods (>= 3.5.0),
MASS (>= 7.3-47),
pbapply (>= 1.3-4),
ReporteRs (>= 0.8.9),
coda (>= 0.19-1),
psych (>= 1.7.8),
rJava (>= 0.9-9),
runjags (>= 2.0.4-2),
ggplot2 (>= 2.2.1),
scales (>= 0.5.0),
truncnorm (>= 1.0-8),
robust (>= 0.4-18),
lavaan (>= 0.6-1)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
@@ -0,0 +1,2 @@
YEAR: 2018
COPYRIGHT HOLDER: �ystein Olav Skaar
114 NAMESPACE
@@ -0,0 +1,114 @@
# Generated by roxygen2: do not edit by hand

export(AddNames)
export(CapWords)
export(ComputeHDI)
export(ContrastNames)
export(DiagMCMC)
export(DistinctColors)
export(FlattenList)
export(GammaDist)
export(GetRange)
export(Interleave)
export(IsString)
export(JavaGarbage)
export(MatrixCombn)
export(MergeMCMC)
export(Normalize)
export(PadVector)
export(PaperSize)
export(ParseNumber)
export(PlotData)
export(ReadFile)
export(RemoveEmpty)
export(RemoveSpaces)
export(RunContrasts)
export(RunMCMC)
export(SaveName)
export(SavePlot)
export(StatsBernoulli)
export(StatsCovariate)
export(StatsFit)
export(StatsKappa)
export(StatsMean)
export(StatsMetric)
export(StatsNominal)
export(StatsRegression)
export(StatsSoftmax)
export(SumMCMC)
export(SumToZero)
export(Trim)
export(TrimSplit)
export(VectorSub)
export(bfw)
importFrom(MASS,mvrnorm)
importFrom(ReporteRs,addPlot)
importFrom(ReporteRs,addSlide)
importFrom(ReporteRs,pptx)
importFrom(ReporteRs,writeDoc)
importFrom(coda,as.mcmc.list)
importFrom(coda,effectiveSize)
importFrom(coda,gelman.plot)
importFrom(coda,traceplot)
importFrom(coda,varnames)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_errorbar)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_ribbon)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggproto)
importFrom(ggplot2,labs)
importFrom(ggplot2,layer)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,theme)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.list)
importFrom(grDevices,dev.new)
importFrom(grDevices,dev.off)
importFrom(grDevices,graphics.off)
importFrom(grDevices,recordPlot)
importFrom(grDevices,setEPS)
importFrom(graphics,abline)
importFrom(graphics,layout)
importFrom(graphics,matplot)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot.new)
importFrom(graphics,points)
importFrom(graphics,text)
importFrom(grid,grobName)
importFrom(grid,grobTree)
importFrom(grid,unit)
importFrom(methods,formalArgs)
importFrom(parallel,detectCores)
importFrom(pbapply,pblapply)
importFrom(plyr,arrange)
importFrom(rJava,.jcall)
importFrom(robust,covRob)
importFrom(runjags,combine.mcmc)
importFrom(runjags,run.jags)
importFrom(runjags,runjags.options)
importFrom(scales,zero_range)
importFrom(stats,acf)
importFrom(stats,aggregate)
importFrom(stats,approxfun)
importFrom(stats,complete.cases)
importFrom(stats,cor)
importFrom(stats,cov)
importFrom(stats,density)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,sd)
importFrom(utils,capture.output)
importFrom(utils,combn)
importFrom(utils,modifyList)
importFrom(utils,read.csv)
importFrom(utils,tail)
importFrom(utils,write.table)
15 NEWS.md
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# bfw 0.0.1

* Initial launch with the following modules:
** Bernoulli trials
** Covariate estimations (including correlelation and Cronbach's alpha)
** Fit data (e.g., SEM, CFA, mediation models)
** Bayesian equivalent of Cohen's kappa
** Mean and standard deviation estimations
** Predict metric values (cf., ANOVA)
** Predict nominal values (c.f., chi-square test)
** Simple, multiple and hierarchical regression
** Softmax regression (i.e., multinomial logistic regression)
* Added a `NEWS.md` file to track changes to the package.
* Added a `TODO.md` file to track future work on the package.
* Added a `README.md` file as an introduction to the package.
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