galaaz 0.4.10 → 2.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (391) hide show
  1. checksums.yaml +4 -4
  2. data/CHANGELOG.md +26 -0
  3. data/LICENSE +0 -0
  4. data/README.md +3123 -882
  5. data/Rakefile +62 -41
  6. data/bin/galaaz-bootstrap +137 -0
  7. data/bin/galaaz-jruby +14 -0
  8. data/bin/galaaz_jruby_env.inc.sh +6 -0
  9. data/bin/gbookdown +64 -0
  10. data/bin/gknit +223 -6
  11. data/bin/gknit-draft +105 -0
  12. data/bin/gknit-draft.rb +28 -0
  13. data/bin/gknit_Rscript +127 -0
  14. data/bin/grun +27 -1
  15. data/bin/gstudio +49 -4
  16. data/bin/{gstudio.rb → gstudio_irb.rb} +0 -0
  17. data/bin/gstudio_pry.rb +7 -0
  18. data/bin/install-tinytex +6 -0
  19. data/bin/run_all_rspec +43 -0
  20. data/bin/run_example +14 -0
  21. data/bin/run_old_rspec +19 -0
  22. data/bin/run_rspec +23 -0
  23. data/bin/run_rspec_subset +38 -0
  24. data/bin/run_slow_rspec +19 -0
  25. data/blogs/R-on-Rails-Planning-Document.md +940 -0
  26. data/blogs/README.md +100 -0
  27. data/blogs/galaaz_ggplot/galaaz_ggplot.Rmd +38 -66
  28. data/blogs/galaaz_ggplot/galaaz_ggplot.log +754 -0
  29. data/blogs/galaaz_ggplot/galaaz_ggplot.md +364 -0
  30. data/blogs/galaaz_ggplot/galaaz_ggplot.tex +607 -0
  31. data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-html/midwest_rb.png +0 -0
  32. data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-html/scatter_plot_rb.png +0 -0
  33. data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-markdown_github/midwest_rb.png +0 -0
  34. data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-markdown_github/scatter_plot_rb.png +0 -0
  35. data/blogs/galaaz_ggplot/midwest.Rmd +3 -3
  36. data/blogs/galaaz_ggplot/midwest_external_png +0 -0
  37. data/blogs/gknit/gknit.Rmd +52 -55
  38. data/blogs/gknit/gknit.md +94 -94
  39. data/blogs/gknit/gknit_files/figure-html/bubble-1.png +0 -0
  40. data/blogs/gknit/gknit_files/figure-html/diverging_bar.png +0 -0
  41. data/blogs/gknit/lst.rds +0 -0
  42. data/blogs/gknit/model.rb +1 -1
  43. data/blogs/gknit/stats.bib +0 -0
  44. data/blogs/manual/include_model_local_repro.Rmd +14 -0
  45. data/blogs/manual/include_model_local_repro.md +75 -0
  46. data/blogs/manual/lst.rds +0 -0
  47. data/blogs/manual/manual.Rmd +1582 -196
  48. data/blogs/manual/manual.log +1786 -0
  49. data/blogs/manual/manual.md +3107 -890
  50. data/blogs/manual/manual.tex +3018 -1086
  51. data/blogs/manual/manual_files/figure-html/bubble-1.png +0 -0
  52. data/blogs/manual/manual_files/figure-html/diverging_bar.png +0 -0
  53. data/blogs/manual/manual_files/figure-latex/bubble-1.png +0 -0
  54. data/blogs/manual/model.rb +41 -0
  55. data/blogs/nse_dplyr/nse_dplyr.Rmd +277 -151
  56. data/blogs/nse_dplyr/nse_dplyr.log +928 -0
  57. data/blogs/nse_dplyr/nse_dplyr.md +457 -293
  58. data/blogs/oh_my/not_so.rb +0 -0
  59. data/blogs/oh_my/oh_my.Rmd +1234 -25
  60. data/blogs/oh_my/oh_my.log +804 -0
  61. data/blogs/oh_my/oh_my.md +1808 -228
  62. data/blogs/oh_my/oh_my.tex +821 -0
  63. data/blogs/oh_my/old.Rmd +15 -14
  64. data/blogs/ruby_plot/ruby_plot.Rmd +58 -82
  65. data/blogs/ruby_plot/ruby_plot.log +885 -0
  66. data/blogs/ruby_plot/ruby_plot.md +71 -103
  67. data/blogs/ruby_plot/ruby_plot.tex +940 -0
  68. data/blogs/ruby_plot/ruby_plot_files/figure-html/dose_len.png +0 -0
  69. data/blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_delivery.png +0 -0
  70. data/blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_dose.png +0 -0
  71. data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_by_delivery_color.png +0 -0
  72. data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_by_delivery_color2.png +0 -0
  73. data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_decorations.png +0 -0
  74. data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_jitter.png +0 -0
  75. data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_points.png +0 -0
  76. data/blogs/ruby_plot/ruby_plot_files/figure-html/final_box_plot.png +0 -0
  77. data/blogs/ruby_plot/ruby_plot_files/figure-html/final_violin_plot.png +0 -0
  78. data/blogs/ruby_plot/ruby_plot_files/figure-html/violin_with_jitter.png +0 -0
  79. data/blogs/ruby_plot/ruby_plot_files/figure-latex/dose_len.png +0 -0
  80. data/blogs/ruby_plot/ruby_plot_files/figure-latex/facet_by_delivery.png +0 -0
  81. data/blogs/ruby_plot/ruby_plot_files/figure-latex/facet_by_dose.png +0 -0
  82. data/blogs/ruby_plot/ruby_plot_files/figure-latex/facets_by_delivery_color.png +0 -0
  83. data/blogs/ruby_plot/ruby_plot_files/figure-latex/facets_by_delivery_color2.png +0 -0
  84. data/blogs/ruby_plot/ruby_plot_files/figure-latex/facets_with_decorations.png +0 -0
  85. data/blogs/ruby_plot/ruby_plot_files/figure-latex/facets_with_jitter.png +0 -0
  86. data/blogs/ruby_plot/ruby_plot_files/figure-latex/facets_with_points.png +0 -0
  87. data/blogs/ruby_plot/ruby_plot_files/figure-latex/final_box_plot.png +0 -0
  88. data/blogs/ruby_plot/ruby_plot_files/figure-latex/final_violin_plot.png +0 -0
  89. data/blogs/ruby_plot/ruby_plot_files/figure-latex/violin_with_jitter.png +0 -0
  90. data/blogs/test/test.Rmd +14 -0
  91. data/examples/50Plots_MasterList/Images/midwest-scatterplot.PNG +0 -0
  92. data/examples/50Plots_MasterList/ScatterPlot.rb +0 -0
  93. data/examples/50Plots_MasterList/scatter_plot.rb +0 -0
  94. data/examples/Bibliography/master.bib +50 -0
  95. data/examples/Bibliography/stats.bib +72 -0
  96. data/examples/R/calc.R +0 -0
  97. data/examples/R/java_interop.R +0 -0
  98. data/examples/bioconductor_deseq2_airway/Documentation/DESeq2-airway-walkthrough.md +56 -0
  99. data/examples/bioconductor_deseq2_airway/bench_galaaz_three_same_process.rb +53 -0
  100. data/examples/bioconductor_deseq2_airway/bench_r_three_same_process.R +34 -0
  101. data/examples/bioconductor_deseq2_airway/deseq2_airway_galaaz.rb +33 -0
  102. data/examples/bioconductor_deseq2_airway/deseq2_airway_galaaz_optimized.rb +34 -0
  103. data/examples/bioconductor_deseq2_airway/deseq2_airway_minimal.R +30 -0
  104. data/examples/bioconductor_deseq2_airway/deseq2_airway_pipeline_for_bench.R +36 -0
  105. data/examples/islr/all.rb +13 -0
  106. data/examples/islr/ch2.spec.rb +37 -7
  107. data/examples/islr/ch3.spec.rb +11 -2
  108. data/examples/islr/ch3_boston.rb +27 -0
  109. data/examples/islr/ch3_multiple_regression.rb +0 -0
  110. data/examples/islr/ch6.spec.rb +24 -1
  111. data/examples/islr/x_y_rnorm.jpg +0 -0
  112. data/examples/latex_templates/Test-acm_article/Makefile +16 -0
  113. data/examples/latex_templates/Test-acm_article/Test-acm_article.Rmd +65 -0
  114. data/examples/latex_templates/Test-acm_article/acm_proc_article-sp.cls +1670 -0
  115. data/examples/latex_templates/Test-acm_article/sensys-abstract.cls +703 -0
  116. data/examples/latex_templates/Test-acm_article/sigproc.bib +59 -0
  117. data/examples/latex_templates/Test-acs_article/Test-acs_article.Rmd +260 -0
  118. data/examples/latex_templates/Test-acs_article/acs-Test-acs_article.bib +11 -0
  119. data/examples/latex_templates/Test-acs_article/acs-my_output.bib +11 -0
  120. data/examples/latex_templates/Test-acs_article/acstest.bib +17 -0
  121. data/examples/latex_templates/Test-aea_article/AEA.cls +1414 -0
  122. data/{blogs/gknit/marshal.dump → examples/latex_templates/Test-aea_article/BibFile.bib} +0 -0
  123. data/examples/latex_templates/Test-aea_article/Test-aea_article.Rmd +108 -0
  124. data/examples/latex_templates/Test-aea_article/aea.bst +1269 -0
  125. data/examples/latex_templates/Test-aea_article/multicol.sty +853 -0
  126. data/examples/latex_templates/Test-aea_article/references.bib +0 -0
  127. data/examples/latex_templates/Test-aea_article/setspace.sty +546 -0
  128. data/examples/latex_templates/Test-amq_article/Test-amq_article.Rmd +256 -0
  129. data/examples/latex_templates/Test-amq_article/Test-amq_article.pdfsync +3397 -0
  130. data/examples/latex_templates/Test-ams_article/Test-ams_article.Rmd +215 -0
  131. data/examples/latex_templates/Test-ams_article/amstest.bib +436 -0
  132. data/examples/latex_templates/Test-asa_article/Test-asa_article.Rmd +153 -0
  133. data/examples/latex_templates/Test-asa_article/agsm.bst +1353 -0
  134. data/examples/latex_templates/Test-asa_article/bibliography.bib +233 -0
  135. data/examples/latex_templates/Test-ieee_article/IEEEtran.bst +2409 -0
  136. data/examples/latex_templates/Test-ieee_article/IEEEtran.cls +6346 -0
  137. data/examples/latex_templates/Test-ieee_article/Test-ieee_article.Rmd +175 -0
  138. data/examples/latex_templates/Test-ieee_article/mybibfile.bib +20 -0
  139. data/examples/latex_templates/Test-rjournal_article/RJournal.sty +335 -0
  140. data/examples/latex_templates/Test-rjournal_article/RJreferences.bib +18 -0
  141. data/examples/latex_templates/Test-rjournal_article/Test-rjournal_article.Rmd +52 -0
  142. data/examples/latex_templates/Test-springer_article/Test-springer_article.Rmd +65 -0
  143. data/examples/latex_templates/Test-springer_article/bibliography.bib +26 -0
  144. data/examples/latex_templates/Test-springer_article/spbasic.bst +1658 -0
  145. data/examples/latex_templates/Test-springer_article/spmpsci.bst +1512 -0
  146. data/examples/latex_templates/Test-springer_article/spphys.bst +1443 -0
  147. data/examples/latex_templates/Test-springer_article/svglov3.clo +113 -0
  148. data/examples/latex_templates/Test-springer_article/svjour3.cls +1431 -0
  149. data/examples/misc/baseball.csv +0 -0
  150. data/examples/misc/ggplot.rb +3 -2
  151. data/examples/misc/moneyball.rb +0 -0
  152. data/examples/misc/subsetting.rb +0 -0
  153. data/examples/multithread_shards_to_r/shards_to_r.rb +67 -0
  154. data/examples/rmarkdown/svm-rmarkdown-anon-ms-example/svm-rmarkdown-anon-ms-example.Rmd +73 -0
  155. data/examples/rmarkdown/svm-rmarkdown-article-example/svm-rmarkdown-article-example.Rmd +382 -0
  156. data/examples/rmarkdown/svm-rmarkdown-beamer-example/svm-rmarkdown-beamer-example.Rmd +164 -0
  157. data/examples/rmarkdown/svm-rmarkdown-cv/svm-rmarkdown-cv.Rmd +92 -0
  158. data/examples/rmarkdown/svm-rmarkdown-syllabus-example/attend-grade-relationships.csv +482 -0
  159. data/examples/rmarkdown/svm-rmarkdown-syllabus-example/svm-rmarkdown-syllabus-example.Rmd +280 -0
  160. data/examples/rmarkdown/svm-xaringan-example/svm-xaringan-example.Rmd +386 -0
  161. data/examples/sthda_ggplot/README.md +0 -0
  162. data/examples/sthda_ggplot/RUN.md +41 -0
  163. data/examples/sthda_ggplot/all.rb +0 -0
  164. data/examples/sthda_ggplot/one_variable_continuous/density_gg.rb +0 -0
  165. data/examples/sthda_ggplot/one_variable_continuous/geom_area.rb +0 -0
  166. data/examples/sthda_ggplot/one_variable_continuous/geom_density.rb +2 -0
  167. data/examples/sthda_ggplot/one_variable_continuous/geom_dotplot.rb +0 -0
  168. data/examples/sthda_ggplot/one_variable_continuous/geom_freqpoly.rb +0 -0
  169. data/examples/sthda_ggplot/one_variable_continuous/geom_histogram.rb +0 -0
  170. data/examples/sthda_ggplot/one_variable_continuous/histogram_density.rb +0 -0
  171. data/examples/sthda_ggplot/one_variable_continuous/stat.rb +0 -0
  172. data/examples/sthda_ggplot/one_variable_discrete/bar.rb +0 -0
  173. data/examples/sthda_ggplot/qplots/box_violin_dot.rb +0 -0
  174. data/examples/sthda_ggplot/qplots/scatter_plots.rb +0 -0
  175. data/examples/sthda_ggplot/scatter_gg.rb +0 -0
  176. data/examples/sthda_ggplot/two_variables_cont_bivariate/geom_bin2d.rb +0 -0
  177. data/examples/sthda_ggplot/two_variables_cont_bivariate/geom_density2d.rb +0 -0
  178. data/examples/sthda_ggplot/two_variables_cont_bivariate/geom_hex.rb +0 -0
  179. data/examples/sthda_ggplot/two_variables_cont_cont/geom_point.rb +0 -0
  180. data/examples/sthda_ggplot/two_variables_cont_cont/geom_smooth.rb +0 -0
  181. data/examples/sthda_ggplot/two_variables_cont_cont/misc.rb +0 -0
  182. data/examples/sthda_ggplot/two_variables_cont_function/geom_area.rb +4 -3
  183. data/examples/sthda_ggplot/two_variables_disc_cont/geom_bar.rb +0 -0
  184. data/examples/sthda_ggplot/two_variables_disc_cont/geom_boxplot.rb +0 -0
  185. data/examples/sthda_ggplot/two_variables_disc_cont/geom_dotplot.rb +0 -0
  186. data/examples/sthda_ggplot/two_variables_disc_cont/geom_jitter.rb +0 -0
  187. data/examples/sthda_ggplot/two_variables_disc_cont/geom_line.rb +0 -0
  188. data/examples/sthda_ggplot/two_variables_disc_cont/geom_violin.rb +0 -0
  189. data/examples/sthda_ggplot/two_variables_disc_disc/geom_jitter.rb +0 -0
  190. data/examples/sthda_ggplot/two_variables_error/geom_crossbar.rb +0 -0
  191. data/ext/new_bridge/Makefile +46 -0
  192. data/ext/new_bridge/galaaz_gatekeeper_phase0.cpp +12 -0
  193. data/ext/new_bridge/galaaz_gatekeeper_phase1.cpp +1639 -0
  194. data/lib/R_interface/galaaz_device.R +20 -0
  195. data/lib/R_interface/include_engine.R +109 -0
  196. data/lib/R_interface/new_bridge_adapter.rb +824 -0
  197. data/lib/R_interface/r.rb +177 -25
  198. data/lib/R_interface/r_arrow.rb +113 -0
  199. data/lib/R_interface/r_libs.R +4 -4
  200. data/lib/R_interface/r_methods.rb +13 -116
  201. data/lib/R_interface/r_module_s.rb +0 -0
  202. data/lib/R_interface/rbinary_operators.rb +20 -2
  203. data/lib/R_interface/rclosure.rb +5 -1
  204. data/lib/R_interface/rdata_frame.rb +34 -70
  205. data/lib/R_interface/rdevice.rb +125 -0
  206. data/lib/R_interface/rdevices.R +0 -0
  207. data/lib/R_interface/renvironment.rb +10 -4
  208. data/lib/R_interface/rexpression.rb +5 -1
  209. data/lib/R_interface/rindexed_object.rb +41 -13
  210. data/lib/R_interface/rlanguage.rb +20 -62
  211. data/lib/R_interface/rlist.rb +115 -25
  212. data/lib/R_interface/rlogical_operators.rb +0 -0
  213. data/lib/R_interface/rmatrix.rb +2 -11
  214. data/lib/R_interface/rmd_indexed_object.rb +5 -1
  215. data/lib/R_interface/robject.rb +348 -290
  216. data/lib/R_interface/rpkg.rb +1 -0
  217. data/lib/R_interface/rsupport.rb +610 -331
  218. data/lib/R_interface/rsupport_scope.rb +2 -1
  219. data/lib/R_interface/rsymbol.rb +50 -0
  220. data/lib/R_interface/ruby_callback.rb +2 -3
  221. data/lib/R_interface/ruby_extensions.rb +225 -175
  222. data/lib/R_interface/runary_operators.rb +0 -0
  223. data/lib/R_interface/rvector.rb +147 -31
  224. data/lib/galaaz.rb +0 -0
  225. data/lib/galaaz_jruby.rb +22 -0
  226. data/lib/gknit/diagnostics.rb +50 -0
  227. data/lib/gknit/draft.rb +111 -0
  228. data/lib/gknit/include_engine.rb +15 -7
  229. data/lib/gknit/knitr_engine.rb +223 -107
  230. data/lib/gknit/rb_engine.rb +3 -3
  231. data/lib/gknit/ruby_engine.rb +0 -0
  232. data/lib/gknit.rb +3 -0
  233. data/lib/new_bridge/bootstrap/windows_bootstrap.rb +285 -0
  234. data/lib/new_bridge/envelope.rb +51 -0
  235. data/lib/new_bridge/eval_result.rb +26 -0
  236. data/lib/new_bridge/framing.rb +39 -0
  237. data/lib/new_bridge/instance_pool_client.rb +38 -0
  238. data/lib/new_bridge/r_instance_manager.rb +404 -0
  239. data/lib/new_bridge/session_client.rb +530 -0
  240. data/lib/new_bridge/tcp_framed.rb +44 -0
  241. data/lib/new_bridge.rb +9 -0
  242. data/lib/util/exec_ruby.rb +95 -46
  243. data/lib/util/inline_file.rb +35 -30
  244. data/new_bridge_specs/benchmark_phase5_5_unboxing_spec.rb +96 -0
  245. data/new_bridge_specs/eval_r_async_spec.rb +113 -0
  246. data/new_bridge_specs/integration_phase5_1_concurrent_spec.rb +50 -0
  247. data/new_bridge_specs/integration_phase5_1_eval_spec.rb +16 -0
  248. data/new_bridge_specs/integration_phase5_1_r_api_spec.rb +25 -0
  249. data/new_bridge_specs/integration_phase5_1_smoke_spec.rb +31 -0
  250. data/new_bridge_specs/integration_phase5_2_dataframe_unboxing_spec.rb +19 -0
  251. data/new_bridge_specs/integration_phase5_2_handle_eval_unboxing_spec.rb +25 -0
  252. data/new_bridge_specs/integration_phase5_3_callback_args_spec.rb +28 -0
  253. data/new_bridge_specs/integration_phase5_3_callback_error_spec.rb +22 -0
  254. data/new_bridge_specs/integration_phase5_3_callback_timeout_spec.rb +28 -0
  255. data/new_bridge_specs/integration_phase5_3_callbacks_smoke_spec.rb +22 -0
  256. data/new_bridge_specs/integration_phase5_3_edge_cases_spec.rb +52 -0
  257. data/new_bridge_specs/integration_phase5_3_nested_spec.rb +30 -0
  258. data/new_bridge_specs/integration_phase5_4_concurrent_sessions_spec.rb +53 -0
  259. data/new_bridge_specs/integration_phase5_4_nested_session_callbacks_spec.rb +49 -0
  260. data/new_bridge_specs/integration_phase5_4_session_routing_spec.rb +38 -0
  261. data/new_bridge_specs/integration_phase5_5_stress_concurrency_spec.rb +52 -0
  262. data/new_bridge_specs/integration_phase5_5_unbox_walk_spec.rb +46 -0
  263. data/new_bridge_specs/phase0_protocol_spec.rb +96 -0
  264. data/new_bridge_specs/phase1_req_ret_spec.rb +66 -0
  265. data/new_bridge_specs/phase2_multi_instance_spec.rb +67 -0
  266. data/new_bridge_specs/phase3_callbacks_spec.rb +71 -0
  267. data/new_bridge_specs/phase4_2_hardening_spec.rb +252 -0
  268. data/new_bridge_specs/phase4_3_r_instance_manager_spec.rb +85 -0
  269. data/new_bridge_specs/phase4_nested_callbacks_spec.rb +123 -0
  270. data/r_requires/ggplot.rb +0 -0
  271. data/r_requires/knitr.rb +0 -0
  272. data/specs/all.rb +15 -11
  273. data/specs/arrow_from_ruby_batches_spec.rb +50 -0
  274. data/specs/arrow_semantics_spec.rb +64 -0
  275. data/specs/bridge_concurrent_spec.rb +46 -0
  276. data/specs/bridge_nested_spec.rb +25 -0
  277. data/specs/dataframe_semantics_spec.rb +122 -0
  278. data/specs/dataframe_single_index_logical_filter_spec.rb +21 -0
  279. data/specs/dispatch_probe_cache_spec.rb +38 -0
  280. data/specs/dispatch_probe_error_class_fallback_spec.rb +20 -0
  281. data/specs/dispatch_probe_fallback_spec.rb +18 -0
  282. data/specs/environment_semantics_spec.rb +89 -0
  283. data/specs/field_access_spec.rb +31 -0
  284. data/specs/figures/bg.jpeg +0 -0
  285. data/specs/figures/bg.png +0 -0
  286. data/specs/figures/bg.svg +168 -57
  287. data/specs/figures/dose_len.png +0 -0
  288. data/specs/figures/no_args.jpeg +0 -0
  289. data/specs/figures/no_args.png +0 -0
  290. data/specs/figures/no_args.svg +168 -57
  291. data/specs/figures/width_height.jpeg +0 -0
  292. data/specs/figures/width_height.png +0 -0
  293. data/specs/figures/width_height_units1.jpeg +0 -0
  294. data/specs/figures/width_height_units1.png +0 -0
  295. data/specs/figures/width_height_units2.jpeg +0 -0
  296. data/specs/figures/width_height_units2.png +0 -0
  297. data/specs/formula_semantics_spec.rb +81 -0
  298. data/specs/galaaz_util_exec_ruby_spec.rb +85 -0
  299. data/specs/galaaz_util_inline_file_spec.rb +54 -0
  300. data/specs/gknit_cli_option_permutation_spec.rb +24 -0
  301. data/specs/gknit_include_engine_spec.rb +72 -0
  302. data/specs/gknit_install_timeout_report_spec.rb +69 -0
  303. data/specs/gknit_internal_error_report_spec.rb +57 -0
  304. data/specs/gknit_vector_map_output_spec.rb +59 -0
  305. data/specs/globalenv_guardrail_spec.rb +52 -0
  306. data/specs/language_expression_semantics_spec.rb +145 -0
  307. data/specs/list_semantics_spec.rb +111 -0
  308. data/specs/new_bridge_bulk_dataframe_transfer_spec.rb +44 -0
  309. data/specs/new_bridge_bulk_vector_transfer_spec.rb +73 -0
  310. data/specs/new_bridge_callback_timeout_spec.rb +69 -0
  311. data/specs/new_bridge_eval_r_fallback_spec.rb +55 -0
  312. data/specs/nil_null_spec.rb +42 -0
  313. data/specs/object_build_phase2_spec.rb +53 -0
  314. data/specs/phase1_callback_bridge_spec.rb +84 -0
  315. data/specs/phase2_gknit_generic_rendering_guardrail_spec.rb +46 -0
  316. data/specs/phase2_gknit_no_raw_code_leakage_spec.rb +43 -0
  317. data/specs/phase3_gknit_generic_graphics_capture_spec.rb +71 -0
  318. data/specs/plot_device_semantics_spec.rb +28 -0
  319. data/specs/plot_snapshot_semantics_spec.rb +58 -0
  320. data/specs/protocol_result_spec.rb +236 -0
  321. data/specs/r_batch_fail_fast_spec.rb +47 -0
  322. data/specs/r_bridge_bootstrap_spec.rb +11 -0
  323. data/specs/r_devices.spec.rb +1 -1
  324. data/specs/r_eval.spec.rb +16 -18
  325. data/specs/r_function.spec.rb +1 -1
  326. data/specs/r_instance_manager_spec.rb +285 -0
  327. data/specs/r_list_apply.spec.rb +15 -15
  328. data/specs/r_matrix.spec.rb +0 -0
  329. data/specs/r_nse.spec.rb +5 -5
  330. data/specs/r_object_send_dispatch_spec.rb +13 -0
  331. data/specs/r_vector_comparator_spec.rb +8 -0
  332. data/specs/r_vector_creation.spec.rb +0 -0
  333. data/specs/r_vector_functions.spec.rb +0 -0
  334. data/specs/r_vector_object.spec.rb +0 -0
  335. data/specs/r_vector_operators.spec.rb +0 -0
  336. data/specs/r_vector_structured_scalar_reads_spec.rb +35 -0
  337. data/specs/r_vector_subsetting.spec.rb +0 -0
  338. data/specs/range_helper_spec.rb +21 -0
  339. data/specs/rsupport_scope_spec.rb +28 -0
  340. data/specs/rsupport_var_name_thread_safety_spec.rb +24 -0
  341. data/specs/scalar_character_spec.rb +44 -0
  342. data/specs/scoped_symbol_dsl_refinement_spec.rb +40 -0
  343. data/specs/session_env_bridge_spec.rb +25 -0
  344. data/specs/simplecov_bootstrap_spec.rb +10 -0
  345. data/specs/spec_helper.rb +10 -0
  346. data/specs/tmp.rb +41 -20
  347. data/specs/unboxing_recursion_regression_spec.rb +30 -0
  348. data/specs/unboxing_spec.rb +49 -0
  349. data/specs/verify_callbacks.rb +42 -0
  350. data/sty/galaaz.sty +0 -0
  351. data/version.rb +1 -1
  352. metadata +239 -71
  353. data/blogs/galaaz_ggplot/galaaz_ggplot.aux +0 -41
  354. data/blogs/galaaz_ggplot/galaaz_ggplot.html +0 -705
  355. data/blogs/galaaz_ggplot/galaaz_ggplot.out +0 -10
  356. data/blogs/galaaz_ggplot/galaaz_ggplot.pdf +0 -0
  357. data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-latex/midwest_rb.pdf +0 -0
  358. data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-latex/scatter_plot_rb.pdf +0 -0
  359. data/blogs/galaaz_ggplot/midwest.html +0 -188
  360. data/blogs/gknit/gknit.html +0 -2266
  361. data/blogs/gknit/gknit.pdf +0 -0
  362. data/blogs/gknit/gknit.tex +0 -1358
  363. data/blogs/manual/graph.rb +0 -29
  364. data/blogs/manual/manual.html +0 -2995
  365. data/blogs/manual/manual.pdf +0 -0
  366. data/blogs/manual/manual_files/figure-latex/diverging_bar.pdf +0 -0
  367. data/blogs/nse_dplyr/nse_dplyr.html +0 -960
  368. data/blogs/nse_dplyr/nse_dplyr.pdf +0 -0
  369. data/blogs/nse_dplyr/nse_dplyr.tex +0 -1373
  370. data/blogs/oh_my/oh_my.html +0 -680
  371. data/blogs/ruby_plot/ruby_plot.Rmd_external_figs +0 -662
  372. data/blogs/ruby_plot/ruby_plot.html +0 -729
  373. data/blogs/ruby_plot/ruby_plot.pdf +0 -0
  374. data/blogs/ruby_plot/ruby_plot_files/figure-html/dose_len.svg +0 -57
  375. data/blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_delivery.svg +0 -106
  376. data/blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_dose.svg +0 -110
  377. data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_by_delivery_color.svg +0 -174
  378. data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_by_delivery_color2.svg +0 -236
  379. data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_jitter.svg +0 -296
  380. data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_points.svg +0 -236
  381. data/blogs/ruby_plot/ruby_plot_files/figure-html/final_box_plot.svg +0 -218
  382. data/blogs/ruby_plot/ruby_plot_files/figure-html/final_violin_plot.svg +0 -128
  383. data/blogs/ruby_plot/ruby_plot_files/figure-html/violin_with_jitter.svg +0 -150
  384. data/examples/paper/paper.rb +0 -36
  385. data/specs/r_dataframe.spec.rb +0 -379
  386. data/specs/r_environment.spec.rb +0 -140
  387. data/specs/r_formula.spec.rb +0 -232
  388. data/specs/r_language.spec.rb +0 -112
  389. data/specs/r_list.spec.rb +0 -293
  390. data/specs/r_plots.spec.rb +0 -72
  391. data/specs/ruby_expression.spec.rb +0 -315
@@ -0,0 +1,164 @@
1
+ ---
2
+ title: An Example R Markdown Document
3
+ subtitle: (A Subtitle Would Go Here if This Were a Class)
4
+ author: Steven V. Miller
5
+ institute: Department of Political Science
6
+ titlegraphic: ./orange-purple.png
7
+ fontsize: 10pt
8
+ output:
9
+ beamer_presentation:
10
+ template: ~/desenv/galaaz/sty/svm-r-markdown-templates/svm-latex-beamer.tex
11
+ keep_tex: true
12
+ # toc: true
13
+ slide_level: 2
14
+ ioslides_presentation:
15
+ smaller: true
16
+ logo: png-tiger-paw-open-2000.png
17
+ make149: true
18
+ ---
19
+
20
+ <style>
21
+ slides > slide.backdrop {
22
+ background: white;
23
+ border-bottom: 0px;
24
+ box-shadow: 0 0 0;
25
+ }
26
+
27
+
28
+ slides > slide {
29
+ font-family: 'Open Sans', Helvetica, Arial, sans-serif;
30
+ border-bottom: 3px solid #F66733;
31
+ box-shadow: 0 3px 0 #522D80;
32
+
33
+ }
34
+
35
+ .title-slide hgroup h1 {
36
+ color: #522D80;
37
+ }
38
+
39
+
40
+
41
+ h2 {
42
+
43
+ color: #522D80;
44
+ }
45
+
46
+ slides > slide.dark {
47
+ background: #522D80 !important;
48
+ border-bottom: 0;
49
+ box-shadow: 0 0 0;
50
+ }
51
+
52
+ .segue h2 {
53
+ color: white;
54
+ }
55
+
56
+ slides > slide.title-slide {
57
+ border-bottom: 0;
58
+ box-shadow: 0 0 0;
59
+ }
60
+
61
+ ol, ul {
62
+
63
+ padding-bottom: 10px;
64
+
65
+ }
66
+
67
+ </style>
68
+
69
+
70
+
71
+ # Pop Songs and Political Science
72
+
73
+ ## Sheena Easton and Game Theory
74
+
75
+ Sheena Easton describes the following scenario for her baby:
76
+
77
+ 1. Takes the morning train
78
+ 2. Works from nine 'til five
79
+ 3. Takes another train home again
80
+ 4. Finds Sheena Easton waiting for him
81
+
82
+ Sheena Easton and her baby are playing a **zero-sum (total conflict) game**.
83
+
84
+ - Akin to Holmes-Moriarty game (see: von Neumann and Morgenstern)
85
+ - Solution: **mixed strategy**
86
+
87
+ ## Rick Astley's Re-election Platform
88
+
89
+ Rick Astley's campaign promises:
90
+
91
+ - Never gonna give you up.
92
+ - Never gonna let you down.
93
+ - Never gonna run around and desert you.
94
+ - Never gonna make you cry.
95
+ - Never gonna say goodbye.
96
+ - Never gonna tell a lie and hurt you.
97
+
98
+ Whereas these pledges conform to the preferences of the **median voter**, we expect
99
+ Congressman Astley to secure re-election.
100
+
101
+ ## Caribbean Queen and Operation Urgent Fury
102
+
103
+ Billy Ocean released "Caribbean Queen" in 1984.
104
+
105
+ - Emphasized sharing the same dream
106
+ - Hearts beating as one
107
+
108
+ "Caribbean Queen" is about the poor execution of Operation Urgent Fury.
109
+
110
+ - Echoed JCS chairman David Jones' frustrations with military establishment.
111
+
112
+ Billy Ocean is advocating for what became the Goldwater-Nichols Act.
113
+
114
+ - Wanted to take advantage of **economies of scale**, resolve **coordination problems** in U.S. military.
115
+
116
+ ## The Good Day Hypothesis
117
+
118
+ We know the following about Ice Cube's day.
119
+
120
+ 1. The Lakers beat the Supersonics.
121
+ 2. No helicopter looked for a murder.
122
+ 3. Consumed Fatburger at 2 a.m.
123
+ 4. Goodyear blimp: "Ice Cube's a pimp."
124
+
125
+ This leads to two different hypotheses:
126
+
127
+ - $H_0$: Ice Cube's day is statistically indistinguishable from a typical day.
128
+ - $H_1$: Ice Cube is having a good (i.e. greater than average) day.
129
+
130
+ These hypotheses are tested using archival data of Ice Cube's life.
131
+
132
+ # Example R code
133
+ ## Example R stuff
134
+
135
+ ```{r cars, echo = TRUE}
136
+ summary(cars)
137
+ ```
138
+
139
+ ## Slide with Plot
140
+
141
+ ```{r pressure}
142
+ # plot(pressure)
143
+ # function plot is not available in fastR -- should use ggplot
144
+ ```
145
+
146
+ ## ggplot code
147
+
148
+ ```{r createdata, dev = "png", echo=TRUE, eval=FALSE}
149
+ df <- data.frame(x = rnorm(1000))
150
+ x <- df$x
151
+ base <- ggplot(df, aes(x)) + geom_density() + scale_x_continuous(limits = c(-5, 5))
152
+ base + stat_function(fun = dnorm, colour = "red")
153
+ ```
154
+
155
+
156
+ ## Another Plot
157
+
158
+ ```{r plotit, dev = "png", echo=FALSE}
159
+ library(ggplot2)
160
+ df <- data.frame(x = rnorm(1000))
161
+ x <- df$x
162
+ base <- ggplot(df, aes(x)) + geom_density() + scale_x_continuous(limits = c(-5, 5))
163
+ base + stat_function(fun = dnorm, colour = "red")
164
+ ```
@@ -0,0 +1,92 @@
1
+ ---
2
+ output:
3
+ pdf_document:
4
+ latex_engine: pdflatex
5
+ template: /home/rbotafogo/desenv/galaaz/sty/svm-r-markdown-templates/svm-latex-cv.tex
6
+ geometry: margin=1in
7
+
8
+ title: "CV"
9
+ author: William Sealy Gosset
10
+
11
+ jobtitle: "Chief Brewer, Arthur Guinness & Son"
12
+ address: "Guinness Brewery · Park Royal · London NW10 7RR, UK"
13
+ fontawesome: yes
14
+ email: guinness@consumer-care.net
15
+ # github: svmiller
16
+ # twitter: stevenvmiller
17
+ #osf: "Enter 5 digit osf string here"
18
+ phone: "+353 1 408 4800"
19
+ web: guinness.com
20
+ updated: no
21
+
22
+ keywords: R Markdown, academic CV, template
23
+
24
+ fontfamily: mathpazo
25
+ fontfamilyoptions: sc, osf
26
+ fontsize: 11pt
27
+ linkcolor: blue
28
+ urlcolor: blue
29
+ ---
30
+
31
+ # Employment
32
+
33
+ *Arthur Guinness & Son*
34
+
35
+ Chief Brewer (Park Royal) \hfill 1935-1937
36
+
37
+ Researcher (Dublin) \hfill 1899-1935
38
+
39
+ # Education
40
+
41
+ *New College, Oxford University*, B.A. Chemistry \hfill 1899
42
+
43
+
44
+ # Publications
45
+
46
+ ## Books
47
+
48
+ Pearson, E.S. and John Wishart (eds.). 1943. *"Student's" Collected Papers* London: Biometrika Office.
49
+
50
+ ## Journal Articles
51
+
52
+ Student. 1938. "Comparison between Balanced and Random Arrangements on Field Plots." *Biometrika* 29(3-4): 363--378.
53
+
54
+ Student. 1936. "Co-operation in Large Scale Experiments." *Supplement to Journal of the Royal Statistical Society* 3(2): 115--136.
55
+
56
+ Student. 1931. "On the *z* Test." *Biometrika* 23(3-4): 407-408.
57
+
58
+ Student. 1931. "The Lanarkshire Milk Experiment." *Biometrika* 23(3-4): 398--406.
59
+
60
+ Student. 1929. "Statistics in Biological Research." *Nature* 124: 93
61
+
62
+ Student. 1927. "Errors of Routine Analysis." *Biometrika* 19(1-2): 151--164.
63
+
64
+ Student. 1926. "Mathematics and Agronomy." *Journal of the American Society of Agronomy* 18.
65
+
66
+ Student. 1925. "New Tables for Testing the Significance of Observations." *Metron* 5(3): 105--108.
67
+
68
+ Student. 1923. "On Testing Varieties of Cereals." *Biometrika* 15(3-4): 271--293.
69
+
70
+ Student. 1921. "An Experimental Determination of the Probable Error of Dr. Spearman's Correlation Co-efficient" *Biometrika* 13(2-3): 263--282.
71
+
72
+ Student. 1917. "Tables for Estimating the Probability That the Given Mean of a Unique Sample of Observations Lies between $-\infty$ and Any Given Distance of the Mean of the Population from Which the Sample Is Drawn." *Biometrika* 11(4): 414--417.
73
+
74
+ Student. 1909. "The Distribution of the Means of Samples Which Are Not Drawn at Random." *Biometrika* 7(1-2): 210--214.
75
+
76
+ Student. 1908. "Probable Error of a Correlation Coefficient." *Biometrika* 6(2-3): 302--310.
77
+
78
+ Student. 1908. "The Probable Error of a Mean." *Biometrika* 6(1): 1--25.
79
+
80
+ Student. 1907. "On the Error of Counting with a Haemacytometer." *Biometrika* 5(3): 351--360.
81
+
82
+ ## Other Publications
83
+
84
+ Student. 1905. "The Pearson Co-efficient of Correlation." Supplement to Report of 1904, Arthur Guinness Son & Company.
85
+
86
+ Student. 1904. "The Application of the 'Law of Error' to the Work of the Brewery." Report, Arthur Guinness Son & Company.
87
+
88
+ # References
89
+
90
+ Available upon request, though likely would include Karl Pearson and Ronald A. Fisher. Please
91
+ send corrections, feedback, or details of missed publications (of which there are probably
92
+ a few) to svmille@clemson.edu.