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.
- checksums.yaml +4 -4
- data/CHANGELOG.md +26 -0
- data/LICENSE +0 -0
- data/README.md +3123 -882
- data/Rakefile +62 -41
- data/bin/galaaz-bootstrap +137 -0
- data/bin/galaaz-jruby +14 -0
- data/bin/galaaz_jruby_env.inc.sh +6 -0
- data/bin/gbookdown +64 -0
- data/bin/gknit +223 -6
- data/bin/gknit-draft +105 -0
- data/bin/gknit-draft.rb +28 -0
- data/bin/gknit_Rscript +127 -0
- data/bin/grun +27 -1
- data/bin/gstudio +49 -4
- data/bin/{gstudio.rb → gstudio_irb.rb} +0 -0
- data/bin/gstudio_pry.rb +7 -0
- data/bin/install-tinytex +6 -0
- data/bin/run_all_rspec +43 -0
- data/bin/run_example +14 -0
- data/bin/run_old_rspec +19 -0
- data/bin/run_rspec +23 -0
- data/bin/run_rspec_subset +38 -0
- data/bin/run_slow_rspec +19 -0
- data/blogs/R-on-Rails-Planning-Document.md +940 -0
- data/blogs/README.md +100 -0
- data/blogs/galaaz_ggplot/galaaz_ggplot.Rmd +38 -66
- data/blogs/galaaz_ggplot/galaaz_ggplot.log +754 -0
- data/blogs/galaaz_ggplot/galaaz_ggplot.md +364 -0
- data/blogs/galaaz_ggplot/galaaz_ggplot.tex +607 -0
- data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-html/midwest_rb.png +0 -0
- data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-html/scatter_plot_rb.png +0 -0
- data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-markdown_github/midwest_rb.png +0 -0
- data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-markdown_github/scatter_plot_rb.png +0 -0
- data/blogs/galaaz_ggplot/midwest.Rmd +3 -3
- data/blogs/galaaz_ggplot/midwest_external_png +0 -0
- data/blogs/gknit/gknit.Rmd +52 -55
- data/blogs/gknit/gknit.md +94 -94
- data/blogs/gknit/gknit_files/figure-html/bubble-1.png +0 -0
- data/blogs/gknit/gknit_files/figure-html/diverging_bar.png +0 -0
- data/blogs/gknit/lst.rds +0 -0
- data/blogs/gknit/model.rb +1 -1
- data/blogs/gknit/stats.bib +0 -0
- data/blogs/manual/include_model_local_repro.Rmd +14 -0
- data/blogs/manual/include_model_local_repro.md +75 -0
- data/blogs/manual/lst.rds +0 -0
- data/blogs/manual/manual.Rmd +1582 -196
- data/blogs/manual/manual.log +1786 -0
- data/blogs/manual/manual.md +3107 -890
- data/blogs/manual/manual.tex +3018 -1086
- data/blogs/manual/manual_files/figure-html/bubble-1.png +0 -0
- data/blogs/manual/manual_files/figure-html/diverging_bar.png +0 -0
- data/blogs/manual/manual_files/figure-latex/bubble-1.png +0 -0
- data/blogs/manual/model.rb +41 -0
- data/blogs/nse_dplyr/nse_dplyr.Rmd +277 -151
- data/blogs/nse_dplyr/nse_dplyr.log +928 -0
- data/blogs/nse_dplyr/nse_dplyr.md +457 -293
- data/blogs/oh_my/not_so.rb +0 -0
- data/blogs/oh_my/oh_my.Rmd +1234 -25
- data/blogs/oh_my/oh_my.log +804 -0
- data/blogs/oh_my/oh_my.md +1808 -228
- data/blogs/oh_my/oh_my.tex +821 -0
- data/blogs/oh_my/old.Rmd +15 -14
- data/blogs/ruby_plot/ruby_plot.Rmd +58 -82
- data/blogs/ruby_plot/ruby_plot.log +885 -0
- data/blogs/ruby_plot/ruby_plot.md +71 -103
- data/blogs/ruby_plot/ruby_plot.tex +940 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/dose_len.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_delivery.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_dose.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_by_delivery_color.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_by_delivery_color2.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_decorations.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_jitter.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_points.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/final_box_plot.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/final_violin_plot.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/violin_with_jitter.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/dose_len.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/facet_by_delivery.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/facet_by_dose.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/facets_by_delivery_color.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/facets_by_delivery_color2.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/facets_with_decorations.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/facets_with_jitter.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/facets_with_points.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/final_box_plot.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/final_violin_plot.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/violin_with_jitter.png +0 -0
- data/blogs/test/test.Rmd +14 -0
- data/examples/50Plots_MasterList/Images/midwest-scatterplot.PNG +0 -0
- data/examples/50Plots_MasterList/ScatterPlot.rb +0 -0
- data/examples/50Plots_MasterList/scatter_plot.rb +0 -0
- data/examples/Bibliography/master.bib +50 -0
- data/examples/Bibliography/stats.bib +72 -0
- data/examples/R/calc.R +0 -0
- data/examples/R/java_interop.R +0 -0
- data/examples/bioconductor_deseq2_airway/Documentation/DESeq2-airway-walkthrough.md +56 -0
- data/examples/bioconductor_deseq2_airway/bench_galaaz_three_same_process.rb +53 -0
- data/examples/bioconductor_deseq2_airway/bench_r_three_same_process.R +34 -0
- data/examples/bioconductor_deseq2_airway/deseq2_airway_galaaz.rb +33 -0
- data/examples/bioconductor_deseq2_airway/deseq2_airway_galaaz_optimized.rb +34 -0
- data/examples/bioconductor_deseq2_airway/deseq2_airway_minimal.R +30 -0
- data/examples/bioconductor_deseq2_airway/deseq2_airway_pipeline_for_bench.R +36 -0
- data/examples/islr/all.rb +13 -0
- data/examples/islr/ch2.spec.rb +37 -7
- data/examples/islr/ch3.spec.rb +11 -2
- data/examples/islr/ch3_boston.rb +27 -0
- data/examples/islr/ch3_multiple_regression.rb +0 -0
- data/examples/islr/ch6.spec.rb +24 -1
- data/examples/islr/x_y_rnorm.jpg +0 -0
- data/examples/latex_templates/Test-acm_article/Makefile +16 -0
- data/examples/latex_templates/Test-acm_article/Test-acm_article.Rmd +65 -0
- data/examples/latex_templates/Test-acm_article/acm_proc_article-sp.cls +1670 -0
- data/examples/latex_templates/Test-acm_article/sensys-abstract.cls +703 -0
- data/examples/latex_templates/Test-acm_article/sigproc.bib +59 -0
- data/examples/latex_templates/Test-acs_article/Test-acs_article.Rmd +260 -0
- data/examples/latex_templates/Test-acs_article/acs-Test-acs_article.bib +11 -0
- data/examples/latex_templates/Test-acs_article/acs-my_output.bib +11 -0
- data/examples/latex_templates/Test-acs_article/acstest.bib +17 -0
- data/examples/latex_templates/Test-aea_article/AEA.cls +1414 -0
- data/{blogs/gknit/marshal.dump → examples/latex_templates/Test-aea_article/BibFile.bib} +0 -0
- data/examples/latex_templates/Test-aea_article/Test-aea_article.Rmd +108 -0
- data/examples/latex_templates/Test-aea_article/aea.bst +1269 -0
- data/examples/latex_templates/Test-aea_article/multicol.sty +853 -0
- data/examples/latex_templates/Test-aea_article/references.bib +0 -0
- data/examples/latex_templates/Test-aea_article/setspace.sty +546 -0
- data/examples/latex_templates/Test-amq_article/Test-amq_article.Rmd +256 -0
- data/examples/latex_templates/Test-amq_article/Test-amq_article.pdfsync +3397 -0
- data/examples/latex_templates/Test-ams_article/Test-ams_article.Rmd +215 -0
- data/examples/latex_templates/Test-ams_article/amstest.bib +436 -0
- data/examples/latex_templates/Test-asa_article/Test-asa_article.Rmd +153 -0
- data/examples/latex_templates/Test-asa_article/agsm.bst +1353 -0
- data/examples/latex_templates/Test-asa_article/bibliography.bib +233 -0
- data/examples/latex_templates/Test-ieee_article/IEEEtran.bst +2409 -0
- data/examples/latex_templates/Test-ieee_article/IEEEtran.cls +6346 -0
- data/examples/latex_templates/Test-ieee_article/Test-ieee_article.Rmd +175 -0
- data/examples/latex_templates/Test-ieee_article/mybibfile.bib +20 -0
- data/examples/latex_templates/Test-rjournal_article/RJournal.sty +335 -0
- data/examples/latex_templates/Test-rjournal_article/RJreferences.bib +18 -0
- data/examples/latex_templates/Test-rjournal_article/Test-rjournal_article.Rmd +52 -0
- data/examples/latex_templates/Test-springer_article/Test-springer_article.Rmd +65 -0
- data/examples/latex_templates/Test-springer_article/bibliography.bib +26 -0
- data/examples/latex_templates/Test-springer_article/spbasic.bst +1658 -0
- data/examples/latex_templates/Test-springer_article/spmpsci.bst +1512 -0
- data/examples/latex_templates/Test-springer_article/spphys.bst +1443 -0
- data/examples/latex_templates/Test-springer_article/svglov3.clo +113 -0
- data/examples/latex_templates/Test-springer_article/svjour3.cls +1431 -0
- data/examples/misc/baseball.csv +0 -0
- data/examples/misc/ggplot.rb +3 -2
- data/examples/misc/moneyball.rb +0 -0
- data/examples/misc/subsetting.rb +0 -0
- data/examples/multithread_shards_to_r/shards_to_r.rb +67 -0
- data/examples/rmarkdown/svm-rmarkdown-anon-ms-example/svm-rmarkdown-anon-ms-example.Rmd +73 -0
- data/examples/rmarkdown/svm-rmarkdown-article-example/svm-rmarkdown-article-example.Rmd +382 -0
- data/examples/rmarkdown/svm-rmarkdown-beamer-example/svm-rmarkdown-beamer-example.Rmd +164 -0
- data/examples/rmarkdown/svm-rmarkdown-cv/svm-rmarkdown-cv.Rmd +92 -0
- data/examples/rmarkdown/svm-rmarkdown-syllabus-example/attend-grade-relationships.csv +482 -0
- data/examples/rmarkdown/svm-rmarkdown-syllabus-example/svm-rmarkdown-syllabus-example.Rmd +280 -0
- data/examples/rmarkdown/svm-xaringan-example/svm-xaringan-example.Rmd +386 -0
- data/examples/sthda_ggplot/README.md +0 -0
- data/examples/sthda_ggplot/RUN.md +41 -0
- data/examples/sthda_ggplot/all.rb +0 -0
- data/examples/sthda_ggplot/one_variable_continuous/density_gg.rb +0 -0
- data/examples/sthda_ggplot/one_variable_continuous/geom_area.rb +0 -0
- data/examples/sthda_ggplot/one_variable_continuous/geom_density.rb +2 -0
- data/examples/sthda_ggplot/one_variable_continuous/geom_dotplot.rb +0 -0
- data/examples/sthda_ggplot/one_variable_continuous/geom_freqpoly.rb +0 -0
- data/examples/sthda_ggplot/one_variable_continuous/geom_histogram.rb +0 -0
- data/examples/sthda_ggplot/one_variable_continuous/histogram_density.rb +0 -0
- data/examples/sthda_ggplot/one_variable_continuous/stat.rb +0 -0
- data/examples/sthda_ggplot/one_variable_discrete/bar.rb +0 -0
- data/examples/sthda_ggplot/qplots/box_violin_dot.rb +0 -0
- data/examples/sthda_ggplot/qplots/scatter_plots.rb +0 -0
- data/examples/sthda_ggplot/scatter_gg.rb +0 -0
- data/examples/sthda_ggplot/two_variables_cont_bivariate/geom_bin2d.rb +0 -0
- data/examples/sthda_ggplot/two_variables_cont_bivariate/geom_density2d.rb +0 -0
- data/examples/sthda_ggplot/two_variables_cont_bivariate/geom_hex.rb +0 -0
- data/examples/sthda_ggplot/two_variables_cont_cont/geom_point.rb +0 -0
- data/examples/sthda_ggplot/two_variables_cont_cont/geom_smooth.rb +0 -0
- data/examples/sthda_ggplot/two_variables_cont_cont/misc.rb +0 -0
- data/examples/sthda_ggplot/two_variables_cont_function/geom_area.rb +4 -3
- data/examples/sthda_ggplot/two_variables_disc_cont/geom_bar.rb +0 -0
- data/examples/sthda_ggplot/two_variables_disc_cont/geom_boxplot.rb +0 -0
- data/examples/sthda_ggplot/two_variables_disc_cont/geom_dotplot.rb +0 -0
- data/examples/sthda_ggplot/two_variables_disc_cont/geom_jitter.rb +0 -0
- data/examples/sthda_ggplot/two_variables_disc_cont/geom_line.rb +0 -0
- data/examples/sthda_ggplot/two_variables_disc_cont/geom_violin.rb +0 -0
- data/examples/sthda_ggplot/two_variables_disc_disc/geom_jitter.rb +0 -0
- data/examples/sthda_ggplot/two_variables_error/geom_crossbar.rb +0 -0
- data/ext/new_bridge/Makefile +46 -0
- data/ext/new_bridge/galaaz_gatekeeper_phase0.cpp +12 -0
- data/ext/new_bridge/galaaz_gatekeeper_phase1.cpp +1639 -0
- data/lib/R_interface/galaaz_device.R +20 -0
- data/lib/R_interface/include_engine.R +109 -0
- data/lib/R_interface/new_bridge_adapter.rb +824 -0
- data/lib/R_interface/r.rb +177 -25
- data/lib/R_interface/r_arrow.rb +113 -0
- data/lib/R_interface/r_libs.R +4 -4
- data/lib/R_interface/r_methods.rb +13 -116
- data/lib/R_interface/r_module_s.rb +0 -0
- data/lib/R_interface/rbinary_operators.rb +20 -2
- data/lib/R_interface/rclosure.rb +5 -1
- data/lib/R_interface/rdata_frame.rb +34 -70
- data/lib/R_interface/rdevice.rb +125 -0
- data/lib/R_interface/rdevices.R +0 -0
- data/lib/R_interface/renvironment.rb +10 -4
- data/lib/R_interface/rexpression.rb +5 -1
- data/lib/R_interface/rindexed_object.rb +41 -13
- data/lib/R_interface/rlanguage.rb +20 -62
- data/lib/R_interface/rlist.rb +115 -25
- data/lib/R_interface/rlogical_operators.rb +0 -0
- data/lib/R_interface/rmatrix.rb +2 -11
- data/lib/R_interface/rmd_indexed_object.rb +5 -1
- data/lib/R_interface/robject.rb +348 -290
- data/lib/R_interface/rpkg.rb +1 -0
- data/lib/R_interface/rsupport.rb +610 -331
- data/lib/R_interface/rsupport_scope.rb +2 -1
- data/lib/R_interface/rsymbol.rb +50 -0
- data/lib/R_interface/ruby_callback.rb +2 -3
- data/lib/R_interface/ruby_extensions.rb +225 -175
- data/lib/R_interface/runary_operators.rb +0 -0
- data/lib/R_interface/rvector.rb +147 -31
- data/lib/galaaz.rb +0 -0
- data/lib/galaaz_jruby.rb +22 -0
- data/lib/gknit/diagnostics.rb +50 -0
- data/lib/gknit/draft.rb +111 -0
- data/lib/gknit/include_engine.rb +15 -7
- data/lib/gknit/knitr_engine.rb +223 -107
- data/lib/gknit/rb_engine.rb +3 -3
- data/lib/gknit/ruby_engine.rb +0 -0
- data/lib/gknit.rb +3 -0
- data/lib/new_bridge/bootstrap/windows_bootstrap.rb +285 -0
- data/lib/new_bridge/envelope.rb +51 -0
- data/lib/new_bridge/eval_result.rb +26 -0
- data/lib/new_bridge/framing.rb +39 -0
- data/lib/new_bridge/instance_pool_client.rb +38 -0
- data/lib/new_bridge/r_instance_manager.rb +404 -0
- data/lib/new_bridge/session_client.rb +530 -0
- data/lib/new_bridge/tcp_framed.rb +44 -0
- data/lib/new_bridge.rb +9 -0
- data/lib/util/exec_ruby.rb +95 -46
- data/lib/util/inline_file.rb +35 -30
- data/new_bridge_specs/benchmark_phase5_5_unboxing_spec.rb +96 -0
- data/new_bridge_specs/eval_r_async_spec.rb +113 -0
- data/new_bridge_specs/integration_phase5_1_concurrent_spec.rb +50 -0
- data/new_bridge_specs/integration_phase5_1_eval_spec.rb +16 -0
- data/new_bridge_specs/integration_phase5_1_r_api_spec.rb +25 -0
- data/new_bridge_specs/integration_phase5_1_smoke_spec.rb +31 -0
- data/new_bridge_specs/integration_phase5_2_dataframe_unboxing_spec.rb +19 -0
- data/new_bridge_specs/integration_phase5_2_handle_eval_unboxing_spec.rb +25 -0
- data/new_bridge_specs/integration_phase5_3_callback_args_spec.rb +28 -0
- data/new_bridge_specs/integration_phase5_3_callback_error_spec.rb +22 -0
- data/new_bridge_specs/integration_phase5_3_callback_timeout_spec.rb +28 -0
- data/new_bridge_specs/integration_phase5_3_callbacks_smoke_spec.rb +22 -0
- data/new_bridge_specs/integration_phase5_3_edge_cases_spec.rb +52 -0
- data/new_bridge_specs/integration_phase5_3_nested_spec.rb +30 -0
- data/new_bridge_specs/integration_phase5_4_concurrent_sessions_spec.rb +53 -0
- data/new_bridge_specs/integration_phase5_4_nested_session_callbacks_spec.rb +49 -0
- data/new_bridge_specs/integration_phase5_4_session_routing_spec.rb +38 -0
- data/new_bridge_specs/integration_phase5_5_stress_concurrency_spec.rb +52 -0
- data/new_bridge_specs/integration_phase5_5_unbox_walk_spec.rb +46 -0
- data/new_bridge_specs/phase0_protocol_spec.rb +96 -0
- data/new_bridge_specs/phase1_req_ret_spec.rb +66 -0
- data/new_bridge_specs/phase2_multi_instance_spec.rb +67 -0
- data/new_bridge_specs/phase3_callbacks_spec.rb +71 -0
- data/new_bridge_specs/phase4_2_hardening_spec.rb +252 -0
- data/new_bridge_specs/phase4_3_r_instance_manager_spec.rb +85 -0
- data/new_bridge_specs/phase4_nested_callbacks_spec.rb +123 -0
- data/r_requires/ggplot.rb +0 -0
- data/r_requires/knitr.rb +0 -0
- data/specs/all.rb +15 -11
- data/specs/arrow_from_ruby_batches_spec.rb +50 -0
- data/specs/arrow_semantics_spec.rb +64 -0
- data/specs/bridge_concurrent_spec.rb +46 -0
- data/specs/bridge_nested_spec.rb +25 -0
- data/specs/dataframe_semantics_spec.rb +122 -0
- data/specs/dataframe_single_index_logical_filter_spec.rb +21 -0
- data/specs/dispatch_probe_cache_spec.rb +38 -0
- data/specs/dispatch_probe_error_class_fallback_spec.rb +20 -0
- data/specs/dispatch_probe_fallback_spec.rb +18 -0
- data/specs/environment_semantics_spec.rb +89 -0
- data/specs/field_access_spec.rb +31 -0
- data/specs/figures/bg.jpeg +0 -0
- data/specs/figures/bg.png +0 -0
- data/specs/figures/bg.svg +168 -57
- data/specs/figures/dose_len.png +0 -0
- data/specs/figures/no_args.jpeg +0 -0
- data/specs/figures/no_args.png +0 -0
- data/specs/figures/no_args.svg +168 -57
- data/specs/figures/width_height.jpeg +0 -0
- data/specs/figures/width_height.png +0 -0
- data/specs/figures/width_height_units1.jpeg +0 -0
- data/specs/figures/width_height_units1.png +0 -0
- data/specs/figures/width_height_units2.jpeg +0 -0
- data/specs/figures/width_height_units2.png +0 -0
- data/specs/formula_semantics_spec.rb +81 -0
- data/specs/galaaz_util_exec_ruby_spec.rb +85 -0
- data/specs/galaaz_util_inline_file_spec.rb +54 -0
- data/specs/gknit_cli_option_permutation_spec.rb +24 -0
- data/specs/gknit_include_engine_spec.rb +72 -0
- data/specs/gknit_install_timeout_report_spec.rb +69 -0
- data/specs/gknit_internal_error_report_spec.rb +57 -0
- data/specs/gknit_vector_map_output_spec.rb +59 -0
- data/specs/globalenv_guardrail_spec.rb +52 -0
- data/specs/language_expression_semantics_spec.rb +145 -0
- data/specs/list_semantics_spec.rb +111 -0
- data/specs/new_bridge_bulk_dataframe_transfer_spec.rb +44 -0
- data/specs/new_bridge_bulk_vector_transfer_spec.rb +73 -0
- data/specs/new_bridge_callback_timeout_spec.rb +69 -0
- data/specs/new_bridge_eval_r_fallback_spec.rb +55 -0
- data/specs/nil_null_spec.rb +42 -0
- data/specs/object_build_phase2_spec.rb +53 -0
- data/specs/phase1_callback_bridge_spec.rb +84 -0
- data/specs/phase2_gknit_generic_rendering_guardrail_spec.rb +46 -0
- data/specs/phase2_gknit_no_raw_code_leakage_spec.rb +43 -0
- data/specs/phase3_gknit_generic_graphics_capture_spec.rb +71 -0
- data/specs/plot_device_semantics_spec.rb +28 -0
- data/specs/plot_snapshot_semantics_spec.rb +58 -0
- data/specs/protocol_result_spec.rb +236 -0
- data/specs/r_batch_fail_fast_spec.rb +47 -0
- data/specs/r_bridge_bootstrap_spec.rb +11 -0
- data/specs/r_devices.spec.rb +1 -1
- data/specs/r_eval.spec.rb +16 -18
- data/specs/r_function.spec.rb +1 -1
- data/specs/r_instance_manager_spec.rb +285 -0
- data/specs/r_list_apply.spec.rb +15 -15
- data/specs/r_matrix.spec.rb +0 -0
- data/specs/r_nse.spec.rb +5 -5
- data/specs/r_object_send_dispatch_spec.rb +13 -0
- data/specs/r_vector_comparator_spec.rb +8 -0
- data/specs/r_vector_creation.spec.rb +0 -0
- data/specs/r_vector_functions.spec.rb +0 -0
- data/specs/r_vector_object.spec.rb +0 -0
- data/specs/r_vector_operators.spec.rb +0 -0
- data/specs/r_vector_structured_scalar_reads_spec.rb +35 -0
- data/specs/r_vector_subsetting.spec.rb +0 -0
- data/specs/range_helper_spec.rb +21 -0
- data/specs/rsupport_scope_spec.rb +28 -0
- data/specs/rsupport_var_name_thread_safety_spec.rb +24 -0
- data/specs/scalar_character_spec.rb +44 -0
- data/specs/scoped_symbol_dsl_refinement_spec.rb +40 -0
- data/specs/session_env_bridge_spec.rb +25 -0
- data/specs/simplecov_bootstrap_spec.rb +10 -0
- data/specs/spec_helper.rb +10 -0
- data/specs/tmp.rb +41 -20
- data/specs/unboxing_recursion_regression_spec.rb +30 -0
- data/specs/unboxing_spec.rb +49 -0
- data/specs/verify_callbacks.rb +42 -0
- data/sty/galaaz.sty +0 -0
- data/version.rb +1 -1
- metadata +239 -71
- data/blogs/galaaz_ggplot/galaaz_ggplot.aux +0 -41
- data/blogs/galaaz_ggplot/galaaz_ggplot.html +0 -705
- data/blogs/galaaz_ggplot/galaaz_ggplot.out +0 -10
- data/blogs/galaaz_ggplot/galaaz_ggplot.pdf +0 -0
- data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-latex/midwest_rb.pdf +0 -0
- data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-latex/scatter_plot_rb.pdf +0 -0
- data/blogs/galaaz_ggplot/midwest.html +0 -188
- data/blogs/gknit/gknit.html +0 -2266
- data/blogs/gknit/gknit.pdf +0 -0
- data/blogs/gknit/gknit.tex +0 -1358
- data/blogs/manual/graph.rb +0 -29
- data/blogs/manual/manual.html +0 -2995
- data/blogs/manual/manual.pdf +0 -0
- data/blogs/manual/manual_files/figure-latex/diverging_bar.pdf +0 -0
- data/blogs/nse_dplyr/nse_dplyr.html +0 -960
- data/blogs/nse_dplyr/nse_dplyr.pdf +0 -0
- data/blogs/nse_dplyr/nse_dplyr.tex +0 -1373
- data/blogs/oh_my/oh_my.html +0 -680
- data/blogs/ruby_plot/ruby_plot.Rmd_external_figs +0 -662
- data/blogs/ruby_plot/ruby_plot.html +0 -729
- data/blogs/ruby_plot/ruby_plot.pdf +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/dose_len.svg +0 -57
- data/blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_delivery.svg +0 -106
- data/blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_dose.svg +0 -110
- data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_by_delivery_color.svg +0 -174
- data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_by_delivery_color2.svg +0 -236
- data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_jitter.svg +0 -296
- data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_points.svg +0 -236
- data/blogs/ruby_plot/ruby_plot_files/figure-html/final_box_plot.svg +0 -218
- data/blogs/ruby_plot/ruby_plot_files/figure-html/final_violin_plot.svg +0 -128
- data/blogs/ruby_plot/ruby_plot_files/figure-html/violin_with_jitter.svg +0 -150
- data/examples/paper/paper.rb +0 -36
- data/specs/r_dataframe.spec.rb +0 -379
- data/specs/r_environment.spec.rb +0 -140
- data/specs/r_formula.spec.rb +0 -232
- data/specs/r_language.spec.rb +0 -112
- data/specs/r_list.spec.rb +0 -293
- data/specs/r_plots.spec.rb +0 -72
- data/specs/ruby_expression.spec.rb +0 -315
|
@@ -0,0 +1,175 @@
|
|
|
1
|
+
---
|
|
2
|
+
title: Bare Demo of IEEEtran.cls for IEEE Conferences
|
|
3
|
+
affiliation:
|
|
4
|
+
## use one only of the following
|
|
5
|
+
# author-columnar: true ## one column per author
|
|
6
|
+
institution-columnar: true ## one column per institution (multiple autors eventually)
|
|
7
|
+
# wide: true ## one column wide author/affiliation fields
|
|
8
|
+
|
|
9
|
+
institution:
|
|
10
|
+
- name: Georgia Institute of Technology
|
|
11
|
+
department: School of Electrical and Computer Engineering
|
|
12
|
+
location: Atlanta, Georgia 30332--0250
|
|
13
|
+
email: ece@datech.edu
|
|
14
|
+
mark: 1
|
|
15
|
+
author:
|
|
16
|
+
- name: Michael Shell
|
|
17
|
+
- name: Twentieth Century Fox
|
|
18
|
+
location: Springfield, USA
|
|
19
|
+
mark: 2
|
|
20
|
+
author:
|
|
21
|
+
- name: Homer Simpson
|
|
22
|
+
email: homer@thesimpsons.com
|
|
23
|
+
- name: Starfleet Academy
|
|
24
|
+
location: San Francisco, California 96678-2391
|
|
25
|
+
other: "Telephone: (800) 555--1212, Fax: (888) 555--1212"
|
|
26
|
+
mark: 3
|
|
27
|
+
author:
|
|
28
|
+
- name: Montgomery Scott
|
|
29
|
+
- name: Tyrell Inc.
|
|
30
|
+
location: 123 Replicant Street, Los Angeles, USA 90210--4321
|
|
31
|
+
mark: 4
|
|
32
|
+
author:
|
|
33
|
+
- name: Eldon Tyrell
|
|
34
|
+
email: eldon@starfleet-academy.star
|
|
35
|
+
- name: Roy Batty
|
|
36
|
+
email: roy@replicant.offworld
|
|
37
|
+
abstract: |
|
|
38
|
+
The abstract goes here.
|
|
39
|
+
On multiple lines eventually.
|
|
40
|
+
|
|
41
|
+
bibliography: mybibfile.bib
|
|
42
|
+
output: rticles::ieee_article
|
|
43
|
+
---
|
|
44
|
+
|
|
45
|
+
Introduction
|
|
46
|
+
=============
|
|
47
|
+
<!-- no \IEEEPARstart -->
|
|
48
|
+
This demo file is intended to serve as a ``starter file''
|
|
49
|
+
for IEEE conference papers produced under \LaTeX\ using
|
|
50
|
+
IEEEtran.cls version 1.8b and later.
|
|
51
|
+
<!-- You must have at least 2 lines in the paragraph with the drop letter -->
|
|
52
|
+
<!-- (should never be an issue) -->
|
|
53
|
+
I wish you the best of success.
|
|
54
|
+
|
|
55
|
+
|
|
56
|
+
## Subsection Heading Here
|
|
57
|
+
Subsection text here.
|
|
58
|
+
|
|
59
|
+
### Subsubsection Heading Here
|
|
60
|
+
Subsubsection text here.
|
|
61
|
+
|
|
62
|
+
<!-- An example of a floating figure using the graphicx package. -->
|
|
63
|
+
<!-- Note that \label must occur AFTER (or within) \caption. -->
|
|
64
|
+
<!-- For figures, \caption should occur after the \includegraphics. -->
|
|
65
|
+
<!-- Note that IEEEtran v1.7 and later has special internal code that -->
|
|
66
|
+
<!-- is designed to preserve the operation of \label within \caption -->
|
|
67
|
+
<!-- even when the captionsoff option is in effect. However, because -->
|
|
68
|
+
<!-- of issues like this, it may be the safest practice to put all your -->
|
|
69
|
+
<!-- \label just after \caption rather than within \caption{}. -->
|
|
70
|
+
|
|
71
|
+
<!-- Reminder: the "draftcls" or "draftclsnofoot", not "draft", class -->
|
|
72
|
+
<!-- option should be used if it is desired that the figures are to be -->
|
|
73
|
+
<!-- displayed while in draft mode. -->
|
|
74
|
+
|
|
75
|
+
<!-- \begin{figure}[!t] -->
|
|
76
|
+
<!-- \centering -->
|
|
77
|
+
<!-- \includegraphics[width=2.5in]{myfigure} -->
|
|
78
|
+
<!-- where an .eps filename suffix will be assumed under latex, -->
|
|
79
|
+
<!-- and a .pdf suffix will be assumed for pdflatex; or what has been declared -->
|
|
80
|
+
<!-- via \DeclareGraphicsExtensions. -->
|
|
81
|
+
<!-- \caption{Simulation results for the network.} -->
|
|
82
|
+
<!-- \label{fig_sim} -->
|
|
83
|
+
<!-- \end{figure} -->
|
|
84
|
+
|
|
85
|
+
<!-- Note that the IEEE typically puts floats only at the top, even when this -->
|
|
86
|
+
<!-- results in a large percentage of a column being occupied by floats. -->
|
|
87
|
+
|
|
88
|
+
|
|
89
|
+
<!-- An example of a double column floating figure using two subfigures. -->
|
|
90
|
+
<!-- (The subfig.sty package must be loaded for this to work.) -->
|
|
91
|
+
<!-- The subfigure \label commands are set within each subfloat command, -->
|
|
92
|
+
<!-- and the \label for the overall figure must come after \caption. -->
|
|
93
|
+
<!-- \hfil is used as a separator to get equal spacing. -->
|
|
94
|
+
<!-- Watch out that the combined width of all the subfigures on a -->
|
|
95
|
+
<!-- line do not exceed the text width or a line break will occur. -->
|
|
96
|
+
|
|
97
|
+
<!-- \begin{figure*}[!t] -->
|
|
98
|
+
<!-- \centering -->
|
|
99
|
+
<!-- \subfloat[Case I]{\includegraphics[width=2.5in]{box}% -->
|
|
100
|
+
<!-- \label{fig_first_case}} -->
|
|
101
|
+
<!-- \hfil -->
|
|
102
|
+
<!-- \subfloat[Case II]{\includegraphics[width=2.5in]{box}% -->
|
|
103
|
+
<!-- \label{fig_second_case}} -->
|
|
104
|
+
<!-- \caption{Simulation results for the network.} -->
|
|
105
|
+
<!-- \label{fig_sim} -->
|
|
106
|
+
<!-- \end{figure*} -->
|
|
107
|
+
|
|
108
|
+
<!-- Note that often IEEE papers with subfigures do not employ subfigure -->
|
|
109
|
+
<!-- captions (using the optional argument to \subfloat[]), but instead will -->
|
|
110
|
+
<!-- reference/describe all of them (a), (b), etc., within the main caption. -->
|
|
111
|
+
<!-- Be aware that for subfig.sty to generate the (a), (b), etc., subfigure -->
|
|
112
|
+
<!-- labels, the optional argument to \subfloat must be present. If a -->
|
|
113
|
+
<!-- subcaption is not desired, just leave its contents blank, -->
|
|
114
|
+
<!-- e.g., \subfloat[]. -->
|
|
115
|
+
|
|
116
|
+
|
|
117
|
+
<!-- An example of a floating table. Note that, for IEEE style tables, the -->
|
|
118
|
+
<!-- \caption command should come BEFORE the table and, given that table -->
|
|
119
|
+
<!-- captions serve much like titles, are usually capitalized except for words -->
|
|
120
|
+
<!-- such as a, an, and, as, at, but, by, for, in, nor, of, on, or, the, to -->
|
|
121
|
+
<!-- and up, which are usually not capitalized unless they are the first or -->
|
|
122
|
+
<!-- last word of the caption. Table text will default to \footnotesize as -->
|
|
123
|
+
<!-- the IEEE normally uses this smaller font for tables. -->
|
|
124
|
+
<!-- The \label must come after \caption as always. -->
|
|
125
|
+
|
|
126
|
+
<!-- \begin{table}[!t] -->
|
|
127
|
+
<!-- % increase table row spacing, adjust to taste -->
|
|
128
|
+
<!-- \renewcommand{\arraystretch}{1.3} -->
|
|
129
|
+
<!-- if using array.sty, it might be a good idea to tweak the value of -->
|
|
130
|
+
<!-- \extrarowheight as needed to properly center the text within the cells -->
|
|
131
|
+
<!-- \caption{An Example of a Table} -->
|
|
132
|
+
<!-- \label{table_example} -->
|
|
133
|
+
<!-- \centering -->
|
|
134
|
+
<!-- % Some packages, such as MDW tools, offer better commands for making tables -->
|
|
135
|
+
<!-- % than the plain LaTeX2e tabular which is used here. -->
|
|
136
|
+
<!-- \begin{tabular}{|c||c|} -->
|
|
137
|
+
<!-- \hline -->
|
|
138
|
+
<!-- One & Two\\ -->
|
|
139
|
+
<!-- \hline -->
|
|
140
|
+
<!-- Three & Four\\ -->
|
|
141
|
+
<!-- \hline -->
|
|
142
|
+
<!-- \end{tabular} -->
|
|
143
|
+
<!-- \end{table} -->
|
|
144
|
+
|
|
145
|
+
|
|
146
|
+
<!-- Note that the IEEE does not put floats in the very first column -->
|
|
147
|
+
<!-- - or typically anywhere on the first page for that matter. Also, -->
|
|
148
|
+
<!-- in-text middle ("here") positioning is typically not used, but it -->
|
|
149
|
+
<!-- is allowed and encouraged for Computer Society conferences (but -->
|
|
150
|
+
<!-- not Computer Society journals). Most IEEE journals/conferences use -->
|
|
151
|
+
<!-- top floats exclusively. -->
|
|
152
|
+
<!-- Note that, LaTeX2e, unlike IEEE journals/conferences, places -->
|
|
153
|
+
<!-- footnotes above bottom floats. This can be corrected via the -->
|
|
154
|
+
<!-- \fnbelowfloat command of the stfloats package. -->
|
|
155
|
+
|
|
156
|
+
|
|
157
|
+
Conclusion
|
|
158
|
+
============
|
|
159
|
+
The conclusion goes here.
|
|
160
|
+
|
|
161
|
+
<!-- conference papers do not normally have an appendix -->
|
|
162
|
+
|
|
163
|
+
Acknowledgment {#acknowledgment}
|
|
164
|
+
==============
|
|
165
|
+
|
|
166
|
+
The authors would like to thank...
|
|
167
|
+
|
|
168
|
+
Bibliography styles
|
|
169
|
+
===================
|
|
170
|
+
|
|
171
|
+
Here are two sample references: @Feynman1963118 [@Dirac1953888].
|
|
172
|
+
|
|
173
|
+
\newpage
|
|
174
|
+
References {#references .numbered}
|
|
175
|
+
==========
|
|
@@ -0,0 +1,20 @@
|
|
|
1
|
+
@article{Dirac1953888,
|
|
2
|
+
title = "The lorentz transformation and absolute time",
|
|
3
|
+
journal = "Physica",
|
|
4
|
+
volume = "19",
|
|
5
|
+
number = "1--12",
|
|
6
|
+
pages = "888--896",
|
|
7
|
+
year = "1953",
|
|
8
|
+
doi = "10.1016/S0031-8914(53)80099-6",
|
|
9
|
+
author = "P.A.M. Dirac"
|
|
10
|
+
}
|
|
11
|
+
|
|
12
|
+
@article{Feynman1963118,
|
|
13
|
+
title = "The theory of a general quantum system interacting with a linear dissipative system",
|
|
14
|
+
journal = "Annals of Physics ",
|
|
15
|
+
volume = "24",
|
|
16
|
+
pages = "118--173",
|
|
17
|
+
year = "1963",
|
|
18
|
+
doi = "10.1016/0003-4916(63)90068-X",
|
|
19
|
+
author = "R.P Feynman and F.L {Vernon Jr.}"
|
|
20
|
+
}
|
|
@@ -0,0 +1,335 @@
|
|
|
1
|
+
% Package `RJournal' to use with LaTeX2e
|
|
2
|
+
% Copyright (C) 2010 by the R Foundation
|
|
3
|
+
% Copyright (C) 2013 by the R Journal
|
|
4
|
+
%
|
|
5
|
+
% Originally written by Kurt Hornik and Friedrich Leisch with subsequent
|
|
6
|
+
% edits by the editorial board
|
|
7
|
+
|
|
8
|
+
\NeedsTeXFormat{LaTeX2e}[1995/12/01]
|
|
9
|
+
\ProvidesPackage{RJournal}[2013/08/27 v0.13 RJournal package]
|
|
10
|
+
|
|
11
|
+
\RequirePackage{tikz}
|
|
12
|
+
|
|
13
|
+
% Overall page layout, fonts etc -----------------------------------------------
|
|
14
|
+
|
|
15
|
+
% Issues of of \emph{The R Journal} are created from the standard \LaTeX{}
|
|
16
|
+
% document class \pkg{report}.
|
|
17
|
+
|
|
18
|
+
\RequirePackage{geometry}
|
|
19
|
+
\geometry{a4paper,
|
|
20
|
+
textwidth=14cm, top=1cm, bottom=1cm,
|
|
21
|
+
includehead,includefoot,centering,
|
|
22
|
+
footskip=1.5cm}
|
|
23
|
+
\raggedbottom
|
|
24
|
+
|
|
25
|
+
\RequirePackage{fancyhdr}
|
|
26
|
+
\fancyhead{}
|
|
27
|
+
\fancyheadoffset{2cm}
|
|
28
|
+
\fancyhead[L]{\textsc{\RJ@sectionhead}}
|
|
29
|
+
\fancyhead[R]{\thepage}
|
|
30
|
+
\fancyfoot{}
|
|
31
|
+
\fancyfoot[L]{The R Journal Vol. \RJ@volume/\RJ@number, \RJ@month}
|
|
32
|
+
\fancyfoot[R]{ISSN 2073-4859}
|
|
33
|
+
\pagestyle{fancy}
|
|
34
|
+
|
|
35
|
+
% We use the following fonts (all with T1 encoding):
|
|
36
|
+
%
|
|
37
|
+
% rm & palatino
|
|
38
|
+
% tt & inconsolata
|
|
39
|
+
% sf & helvetica
|
|
40
|
+
% math & palatino
|
|
41
|
+
|
|
42
|
+
\RequirePackage{microtype}
|
|
43
|
+
|
|
44
|
+
\RequirePackage[scaled=0.92]{helvet}
|
|
45
|
+
\RequirePackage{palatino,mathpazo}
|
|
46
|
+
\RequirePackage[scaled=1.02]{inconsolata}
|
|
47
|
+
\RequirePackage[T1]{fontenc}
|
|
48
|
+
|
|
49
|
+
\RequirePackage[hyphens]{url}
|
|
50
|
+
\RequirePackage[pagebackref]{hyperref}
|
|
51
|
+
\renewcommand{\backref}[1]{[p#1]}
|
|
52
|
+
|
|
53
|
+
% Dark blue colour for all links
|
|
54
|
+
\RequirePackage{color}
|
|
55
|
+
\definecolor{link}{rgb}{0.45,0.51,0.67}
|
|
56
|
+
\hypersetup{
|
|
57
|
+
colorlinks,%
|
|
58
|
+
citecolor=link,%
|
|
59
|
+
filecolor=link,%
|
|
60
|
+
linkcolor=link,%
|
|
61
|
+
urlcolor=link
|
|
62
|
+
}
|
|
63
|
+
|
|
64
|
+
% Give the text a little room to breath
|
|
65
|
+
\setlength{\parskip}{3pt}
|
|
66
|
+
\RequirePackage{setspace}
|
|
67
|
+
\setstretch{1.05}
|
|
68
|
+
|
|
69
|
+
% Issue and article metadata ---------------------------------------------------
|
|
70
|
+
|
|
71
|
+
% Basic front matter information about the issue: volume, number, and
|
|
72
|
+
% date.
|
|
73
|
+
|
|
74
|
+
\newcommand{\volume}[1]{\def\RJ@volume{#1}}
|
|
75
|
+
\newcommand{\volnumber}[1]{\def\RJ@number{#1}}
|
|
76
|
+
\renewcommand{\month}[1]{\def\RJ@month{#1}}
|
|
77
|
+
\renewcommand{\year}[1]{\def\RJ@year{#1}}
|
|
78
|
+
|
|
79
|
+
|
|
80
|
+
% Individual articles correspond to
|
|
81
|
+
% chapters, and are contained in |article| environments. This makes it
|
|
82
|
+
% easy to have figures counted within articles and hence hyperlinked
|
|
83
|
+
% correctly.
|
|
84
|
+
|
|
85
|
+
% An article has an author, a title, and optionally a subtitle. We use
|
|
86
|
+
% the obvious commands for specifying these. Articles will be put in certain
|
|
87
|
+
% journal sections, named by \sectionhead.
|
|
88
|
+
|
|
89
|
+
\newcommand {\sectionhead} [1]{\def\RJ@sectionhead{#1}}
|
|
90
|
+
\renewcommand{\author} [1]{\def\RJ@author{#1}}
|
|
91
|
+
\renewcommand{\title} [1]{\def\RJ@title{#1}}
|
|
92
|
+
\newcommand {\subtitle} [1]{\def\RJ@subtitle{#1}}
|
|
93
|
+
|
|
94
|
+
% Control appearance of titles: make slightly smaller than usual, and
|
|
95
|
+
% suppress section numbering. See http://tex.stackexchange.com/questions/69749
|
|
96
|
+
% for why we don't use \setcounter{secnumdepth}{-1}
|
|
97
|
+
|
|
98
|
+
\usepackage[medium]{titlesec}
|
|
99
|
+
\usepackage{titletoc}
|
|
100
|
+
\titleformat{\section} {\normalfont\large\bfseries}{}{0em}{}
|
|
101
|
+
\titleformat{\subsection}{\normalfont\normalsize\bfseries}{}{0em}{}
|
|
102
|
+
\titlecontents{chapter} [0em]{}{}{}{\titlerule*[1em]{.}\contentspage}
|
|
103
|
+
|
|
104
|
+
% Article layout ---------------------------------------------------------------
|
|
105
|
+
|
|
106
|
+
% Environment |article| clears the article header information at its beginning.
|
|
107
|
+
% We use |\FloatBarrier| from the placeins package to keep floats within
|
|
108
|
+
% the article.
|
|
109
|
+
\RequirePackage{placeins}
|
|
110
|
+
\newenvironment{article}{\author{}\title{}\subtitle{}\FloatBarrier}{\FloatBarrier}
|
|
111
|
+
|
|
112
|
+
% Refereed articles should have an abstract, so we redefine |\abstract| to
|
|
113
|
+
% give the desired style
|
|
114
|
+
|
|
115
|
+
\renewcommand{\abstract}[1]{%
|
|
116
|
+
\setstretch{1}%
|
|
117
|
+
\noindent%
|
|
118
|
+
\small%
|
|
119
|
+
\textbf{Abstract} #1
|
|
120
|
+
}
|
|
121
|
+
|
|
122
|
+
% The real work is done by a redefined version of |\maketitle|. Note
|
|
123
|
+
% that even though we do not want chapters (articles) numbered, we
|
|
124
|
+
% need to increment the chapter counter, so that figures get correct
|
|
125
|
+
% labelling.
|
|
126
|
+
|
|
127
|
+
\renewcommand{\maketitle}{%
|
|
128
|
+
\noindent
|
|
129
|
+
\chapter{\RJ@title}\refstepcounter{chapter}
|
|
130
|
+
\ifx\empty\RJ@subtitle
|
|
131
|
+
\else
|
|
132
|
+
\noindent\textbf{\RJ@subtitle}
|
|
133
|
+
\par\nobreak\addvspace{\baselineskip}
|
|
134
|
+
\fi
|
|
135
|
+
\ifx\empty\RJ@author
|
|
136
|
+
\else
|
|
137
|
+
\noindent\textit{\RJ@author}
|
|
138
|
+
\par\nobreak\addvspace{\baselineskip}
|
|
139
|
+
\fi
|
|
140
|
+
\@afterindentfalse\@nobreaktrue\@afterheading
|
|
141
|
+
}
|
|
142
|
+
|
|
143
|
+
% Now for some ugly redefinitions. We do not want articles to start a
|
|
144
|
+
% new page. (Actually, we do, but this is handled via explicit
|
|
145
|
+
% \newpage
|
|
146
|
+
%
|
|
147
|
+
% The name@of@eq is a hack to get hyperlinks to equations to work
|
|
148
|
+
% within each article, even though there may be multiple eq.(1)
|
|
149
|
+
% \begin{macrocode}
|
|
150
|
+
\renewcommand\chapter{\secdef\RJ@chapter\@schapter}
|
|
151
|
+
\providecommand{\nohyphens}{%
|
|
152
|
+
\hyphenpenalty=10000\exhyphenpenalty=10000\relax}
|
|
153
|
+
\newcommand{\RJ@chapter}{%
|
|
154
|
+
\edef\name@of@eq{equation.\@arabic{\c@chapter}}%
|
|
155
|
+
\renewcommand{\@seccntformat}[1]{}%
|
|
156
|
+
\@startsection{chapter}{0}{0mm}{%
|
|
157
|
+
-2\baselineskip \@plus -\baselineskip \@minus -.2ex}{\p@}{%
|
|
158
|
+
\phantomsection\normalfont\huge\bfseries\raggedright}}
|
|
159
|
+
|
|
160
|
+
% Book reviews should appear as sections in the text and in the pdf bookmarks,
|
|
161
|
+
% however we wish them to appear as chapters in the TOC. Thus we define an
|
|
162
|
+
% alternative to |\maketitle| for reviews.
|
|
163
|
+
\newcommand{\review}[1]{
|
|
164
|
+
\pdfbookmark[1]{#1}{#1}
|
|
165
|
+
\section*{#1}
|
|
166
|
+
\addtocontents{toc}{\protect\contentsline{chapter}{#1}{\thepage}{#1.1}}
|
|
167
|
+
}
|
|
168
|
+
|
|
169
|
+
% We want bibliographies as starred sections within articles.
|
|
170
|
+
%
|
|
171
|
+
\RequirePackage[sectionbib,round]{natbib}
|
|
172
|
+
\bibliographystyle{abbrvnat}
|
|
173
|
+
|
|
174
|
+
% Equations, figures and tables are counted within articles, but we do
|
|
175
|
+
% not show the article number. For equations it becomes a bit messy to avoid
|
|
176
|
+
% having hyperref getting it wrong.
|
|
177
|
+
|
|
178
|
+
% \numberwithin{equation}{chapter}
|
|
179
|
+
\renewcommand{\theequation}{\@arabic\c@equation}
|
|
180
|
+
\renewcommand{\thefigure}{\@arabic\c@figure}
|
|
181
|
+
\renewcommand{\thetable}{\@arabic\c@table}
|
|
182
|
+
|
|
183
|
+
% Issue layout -----------------------------------------------------------------
|
|
184
|
+
|
|
185
|
+
% Need to provide our own version of |\tableofcontents|. We use the
|
|
186
|
+
% tikz package to get the rounded rectangle. Notice that |\section*|
|
|
187
|
+
% is really the same as |\chapter*|.
|
|
188
|
+
\renewcommand{\contentsname}{Contents}
|
|
189
|
+
\renewcommand\tableofcontents{%
|
|
190
|
+
\vspace{1cm}
|
|
191
|
+
\section*{\contentsname}
|
|
192
|
+
{ \@starttoc{toc} }
|
|
193
|
+
}
|
|
194
|
+
|
|
195
|
+
\renewcommand{\titlepage}{%
|
|
196
|
+
\thispagestyle{empty}
|
|
197
|
+
\hypersetup{
|
|
198
|
+
pdftitle={The R Journal Volume \RJ@volume/\RJ@number, \RJ@month \RJ@year},%
|
|
199
|
+
pdfauthor={R Foundation for Statistical Computing},%
|
|
200
|
+
}
|
|
201
|
+
\noindent
|
|
202
|
+
\begin{center}
|
|
203
|
+
\fontsize{50pt}{50pt}\selectfont
|
|
204
|
+
The \raisebox{-8pt}{\includegraphics[height=77pt]{Rlogo-4}}\hspace{10pt}
|
|
205
|
+
Journal
|
|
206
|
+
|
|
207
|
+
\end{center}
|
|
208
|
+
{\large \hfill Volume \RJ@volume/\RJ@number, \RJ@month{} \RJ@year \quad}
|
|
209
|
+
|
|
210
|
+
\rule{\textwidth}{1pt}
|
|
211
|
+
\begin{center}
|
|
212
|
+
{\Large A peer-reviewed, open-access publication of the \\
|
|
213
|
+
R Foundation for Statistical Computing}
|
|
214
|
+
\end{center}
|
|
215
|
+
|
|
216
|
+
% And finally, put in the TOC box. Note the way |tocdepth| is adjusted
|
|
217
|
+
% before and after producing the TOC: thus, we can ensure that only
|
|
218
|
+
% articles show up in the printed TOC, but that in the PDF version,
|
|
219
|
+
% bookmarks are created for sections and subsections as well (provided
|
|
220
|
+
% that the non-starred forms are used).
|
|
221
|
+
\setcounter{tocdepth}{0}
|
|
222
|
+
\tableofcontents
|
|
223
|
+
\setcounter{tocdepth}{2}
|
|
224
|
+
\clearpage
|
|
225
|
+
}
|
|
226
|
+
|
|
227
|
+
% Text formatting --------------------------------------------------------------
|
|
228
|
+
|
|
229
|
+
\newcommand{\R}{R}
|
|
230
|
+
\newcommand{\address}[1]{\addvspace{\baselineskip}\noindent\emph{#1}}
|
|
231
|
+
\newcommand{\email}[1]{\href{mailto:#1}{\normalfont\texttt{#1}}}
|
|
232
|
+
|
|
233
|
+
% Simple font selection is not good enough. For example, |\texttt{--}|
|
|
234
|
+
% gives `\texttt{--}', i.e., an endash in typewriter font. Hence, we
|
|
235
|
+
% need to turn off ligatures, which currently only happens for commands
|
|
236
|
+
% |\code| and |\samp| and the ones derived from them. Hyphenation is
|
|
237
|
+
% another issue; it should really be turned off inside |\samp|. And
|
|
238
|
+
% most importantly, \LaTeX{} special characters are a nightmare. E.g.,
|
|
239
|
+
% one needs |\~{}| to produce a tilde in a file name marked by |\file|.
|
|
240
|
+
% Perhaps a few years ago, most users would have agreed that this may be
|
|
241
|
+
% unfortunate but should not be changed to ensure consistency. But with
|
|
242
|
+
% the advent of the WWW and the need for getting `|~|' and `|#|' into
|
|
243
|
+
% URLs, commands which only treat the escape and grouping characters
|
|
244
|
+
% specially have gained acceptance
|
|
245
|
+
|
|
246
|
+
\DeclareRobustCommand\code{\bgroup\@noligs\@codex}
|
|
247
|
+
\def\@codex#1{\texorpdfstring%
|
|
248
|
+
{{\normalfont\ttfamily\hyphenchar\font=-1 #1}}%
|
|
249
|
+
{#1}\egroup}
|
|
250
|
+
\newcommand{\kbd}[1]{{\normalfont\texttt{#1}}}
|
|
251
|
+
\newcommand{\key}[1]{{\normalfont\texttt{\uppercase{#1}}}}
|
|
252
|
+
\DeclareRobustCommand\samp{`\bgroup\@noligs\@sampx}
|
|
253
|
+
\def\@sampx#1{{\normalfont\texttt{#1}}\egroup'}
|
|
254
|
+
\newcommand{\var}[1]{{\normalfont\textsl{#1}}}
|
|
255
|
+
\let\env=\code
|
|
256
|
+
\newcommand{\file}[1]{{`\normalfont\textsf{#1}'}}
|
|
257
|
+
\let\command=\code
|
|
258
|
+
\let\option=\samp
|
|
259
|
+
\newcommand{\dfn}[1]{{\normalfont\textsl{#1}}}
|
|
260
|
+
% \acronym is effectively disabled since not used consistently
|
|
261
|
+
\newcommand{\acronym}[1]{#1}
|
|
262
|
+
\newcommand{\strong}[1]{\texorpdfstring%
|
|
263
|
+
{{\normalfont\fontseries{b}\selectfont #1}}%
|
|
264
|
+
{#1}}
|
|
265
|
+
\let\pkg=\strong
|
|
266
|
+
\newcommand{\CRANpkg}[1]{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}%
|
|
267
|
+
\let\cpkg=\CRANpkg
|
|
268
|
+
\newcommand{\ctv}[1]{\href{http://CRAN.R-project.org/view=#1}{\emph{#1}}}
|
|
269
|
+
\newcommand{\BIOpkg}[1]{\href{http://www.bioconductor.org/packages/release/bioc/html/#1.html}{\pkg{#1}}}
|
|
270
|
+
|
|
271
|
+
% Example environments ---------------------------------------------------------
|
|
272
|
+
\RequirePackage{fancyvrb}
|
|
273
|
+
\RequirePackage{alltt}
|
|
274
|
+
|
|
275
|
+
\DefineVerbatimEnvironment{example}{Verbatim}{}
|
|
276
|
+
\renewenvironment{example*}{\begin{alltt}}{\end{alltt}}
|
|
277
|
+
|
|
278
|
+
% Support for output from Sweave, and generic session style code
|
|
279
|
+
% These used to have fontshape=sl for Sinput/Scode/Sin, but pslatex
|
|
280
|
+
% won't use a condensed font in that case.
|
|
281
|
+
|
|
282
|
+
\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontsize=\small}
|
|
283
|
+
\DefineVerbatimEnvironment{Soutput}{Verbatim}{fontsize=\small}
|
|
284
|
+
\DefineVerbatimEnvironment{Scode}{Verbatim}{fontsize=\small}
|
|
285
|
+
\DefineVerbatimEnvironment{Sin}{Verbatim}{fontsize=\small}
|
|
286
|
+
\DefineVerbatimEnvironment{Sout}{Verbatim}{fontsize=\small}
|
|
287
|
+
\newenvironment{Schunk}{}{}
|
|
288
|
+
|
|
289
|
+
% Mathematics ------------------------------------------------------------------
|
|
290
|
+
|
|
291
|
+
% The implementation of |\operatorname| is similar to the mechanism
|
|
292
|
+
% \LaTeXe{} uses for functions like sin and cos, and simpler than the
|
|
293
|
+
% one of \AmSLaTeX{}. We use |\providecommand| for the definition in
|
|
294
|
+
% order to keep the one of the \pkg{amstex} if this package has
|
|
295
|
+
% already been loaded.
|
|
296
|
+
% \begin{macrocode}
|
|
297
|
+
\providecommand{\operatorname}[1]{%
|
|
298
|
+
\mathop{\operator@font#1}\nolimits}
|
|
299
|
+
\RequirePackage{amsfonts}
|
|
300
|
+
|
|
301
|
+
\renewcommand{\P}{%
|
|
302
|
+
\mathop{\operator@font I\hspace{-1.5pt}P\hspace{.13pt}}}
|
|
303
|
+
\newcommand{\E}{%
|
|
304
|
+
\mathop{\operator@font I\hspace{-1.5pt}E\hspace{.13pt}}}
|
|
305
|
+
\newcommand{\VAR}{\operatorname{var}}
|
|
306
|
+
\newcommand{\COV}{\operatorname{cov}}
|
|
307
|
+
\newcommand{\COR}{\operatorname{cor}}
|
|
308
|
+
|
|
309
|
+
% Figures ----------------------------------------------------------------------
|
|
310
|
+
|
|
311
|
+
\RequirePackage[font=small,labelfont=bf]{caption}
|
|
312
|
+
|
|
313
|
+
% Wide environments for figures and tables -------------------------------------
|
|
314
|
+
\RequirePackage{environ}
|
|
315
|
+
|
|
316
|
+
% An easy way to make a figure span the full width of the page
|
|
317
|
+
\NewEnviron{widefigure}[1][]{
|
|
318
|
+
\begin{figure}[#1]
|
|
319
|
+
\advance\leftskip-2cm
|
|
320
|
+
\begin{minipage}{\dimexpr\textwidth+4cm\relax}%
|
|
321
|
+
\captionsetup{margin=2cm}
|
|
322
|
+
\BODY
|
|
323
|
+
\end{minipage}%
|
|
324
|
+
\end{figure}
|
|
325
|
+
}
|
|
326
|
+
|
|
327
|
+
\NewEnviron{widetable}[1][]{
|
|
328
|
+
\begin{table}[#1]
|
|
329
|
+
\advance\leftskip-2cm
|
|
330
|
+
\begin{minipage}{\dimexpr\textwidth+4cm\relax}%
|
|
331
|
+
\captionsetup{margin=2cm}
|
|
332
|
+
\BODY
|
|
333
|
+
\end{minipage}%
|
|
334
|
+
\end{table}
|
|
335
|
+
}
|
|
@@ -0,0 +1,18 @@
|
|
|
1
|
+
@Manual{R,
|
|
2
|
+
title = {R: A Language and Environment for Statistical Computing},
|
|
3
|
+
author = {{R Core Team}},
|
|
4
|
+
organization = {R Foundation for Statistical Computing},
|
|
5
|
+
address = {Vienna, Austria},
|
|
6
|
+
year = {2012},
|
|
7
|
+
note = {{ISBN} 3-900051-07-0},
|
|
8
|
+
url = {http://www.R-project.org/},
|
|
9
|
+
}
|
|
10
|
+
|
|
11
|
+
@article{ihaka:1996,
|
|
12
|
+
Author = {Ihaka, Ross and Gentleman, Robert},
|
|
13
|
+
Journal = {Journal of Computational and Graphical Statistics},
|
|
14
|
+
Number = 3,
|
|
15
|
+
Pages = {299--314},
|
|
16
|
+
Title = {R: A Language for Data Analysis and Graphics},
|
|
17
|
+
Volume = 5,
|
|
18
|
+
Year = 1996}
|
|
@@ -0,0 +1,52 @@
|
|
|
1
|
+
---
|
|
2
|
+
title: Capitalized Title Here
|
|
3
|
+
author:
|
|
4
|
+
- name: Author One
|
|
5
|
+
affiliation: Affiliation
|
|
6
|
+
address:
|
|
7
|
+
- line 1
|
|
8
|
+
- line 2
|
|
9
|
+
email: author1@work
|
|
10
|
+
- name: Author Two
|
|
11
|
+
affiliation: Affiliation
|
|
12
|
+
address:
|
|
13
|
+
- line 1
|
|
14
|
+
- line 2
|
|
15
|
+
email: author2@work
|
|
16
|
+
abstract: >
|
|
17
|
+
An abstract of less than 150 words.
|
|
18
|
+
output:
|
|
19
|
+
rticles::rjournal_article:
|
|
20
|
+
includes:
|
|
21
|
+
in_header: preamble.tex
|
|
22
|
+
---
|
|
23
|
+
|
|
24
|
+
## Introduction
|
|
25
|
+
|
|
26
|
+
Introductory section which may include references in parentheses
|
|
27
|
+
\citep{R}, or cite a reference such as \citet{R} in the text.
|
|
28
|
+
|
|
29
|
+
## Section title in sentence case
|
|
30
|
+
|
|
31
|
+
This section may contain a figure such as Figure \ref{figure:rlogo}.
|
|
32
|
+
|
|
33
|
+
\begin{figure}[htbp]
|
|
34
|
+
\centering
|
|
35
|
+
\includegraphics{Rlogo}
|
|
36
|
+
\caption{The logo of R.}
|
|
37
|
+
\label{figure:rlogo}
|
|
38
|
+
\end{figure}
|
|
39
|
+
|
|
40
|
+
## Another section
|
|
41
|
+
|
|
42
|
+
There will likely be several sections, perhaps including code snippets, such as:
|
|
43
|
+
|
|
44
|
+
```{r}
|
|
45
|
+
x <- 1:10
|
|
46
|
+
x
|
|
47
|
+
```
|
|
48
|
+
|
|
49
|
+
## Summary
|
|
50
|
+
|
|
51
|
+
This file is only a basic article template. For full details of _The R Journal_ style and information on how to prepare your article for submission, see the [Instructions for Authors](https://journal.r-project.org/share/author-guide.pdf).
|
|
52
|
+
\bibliography{RJreferences}
|
|
@@ -0,0 +1,65 @@
|
|
|
1
|
+
---
|
|
2
|
+
title: Title here
|
|
3
|
+
subtitle: Do you have a subtitle? If so, write it here
|
|
4
|
+
titlerunning: Short form of title (if too long for head)
|
|
5
|
+
authorrunning: Short form of author list if too long for running head
|
|
6
|
+
thanks: |
|
|
7
|
+
Grants or other notes about the article that should go on the front
|
|
8
|
+
page should be placed here. General acknowledgments should be placed at the
|
|
9
|
+
end of the article.
|
|
10
|
+
|
|
11
|
+
authors:
|
|
12
|
+
- name: Äüthör 1
|
|
13
|
+
address: Department of YYY, University of XXX
|
|
14
|
+
email: abc@def
|
|
15
|
+
|
|
16
|
+
- name: Âuthóř 2
|
|
17
|
+
address: Department of ZZZ, University of WWW
|
|
18
|
+
email: djf@wef
|
|
19
|
+
|
|
20
|
+
keywords:
|
|
21
|
+
- key
|
|
22
|
+
- dictionary
|
|
23
|
+
- word
|
|
24
|
+
|
|
25
|
+
#PACS:
|
|
26
|
+
#- PAC1
|
|
27
|
+
#- superPAC
|
|
28
|
+
|
|
29
|
+
MSC:
|
|
30
|
+
- MSC code 1
|
|
31
|
+
- MSC code 2
|
|
32
|
+
|
|
33
|
+
abstract: |
|
|
34
|
+
The text of your abstract. 150 -- 250 words.
|
|
35
|
+
|
|
36
|
+
bibliography: bibliography.bib
|
|
37
|
+
output: rticles::springer_article
|
|
38
|
+
---
|
|
39
|
+
|
|
40
|
+
# Introduction {#intro}
|
|
41
|
+
|
|
42
|
+
Your text comes here. Separate text sections with
|
|
43
|
+
|
|
44
|
+
# Section title {#sec:1}
|
|
45
|
+
|
|
46
|
+
Text with citations by @Galyardt14mmm, [@Mislevy06Cog].
|
|
47
|
+
|
|
48
|
+
## Subsection title {#sec:2}
|
|
49
|
+
|
|
50
|
+
as required. Don't forget to give each section
|
|
51
|
+
and subsection a unique label (see Sect. \ref{sec:1}).
|
|
52
|
+
|
|
53
|
+
#### Paragraph headings
|
|
54
|
+
|
|
55
|
+
Use paragraph headings as needed.
|
|
56
|
+
|
|
57
|
+
\begin{align}
|
|
58
|
+
a^2+b^2=c^2
|
|
59
|
+
\end{align}
|
|
60
|
+
|
|
61
|
+
|
|
62
|
+
|
|
63
|
+
|
|
64
|
+
|
|
65
|
+
# References
|
|
@@ -0,0 +1,26 @@
|
|
|
1
|
+
%% Copied from asa_article template
|
|
2
|
+
|
|
3
|
+
|
|
4
|
+
@incollection{Galyardt14mmm,
|
|
5
|
+
Author = {April Galyardt},
|
|
6
|
+
Booktitle = {Handbook of Mixed Membership Models},
|
|
7
|
+
Date-Added = {2014-08-21 21:18:27 +0000},
|
|
8
|
+
Date-Modified = {2014-08-21 21:18:27 +0000},
|
|
9
|
+
Editor = {Edoardo M. Airoldi and David Blei and Erosheva, Elena and Fienberg, Stephen E.},
|
|
10
|
+
Publisher = {Chapman and Hall},
|
|
11
|
+
Title = {Interpreting Mixed Membership Models: Implications of Erosheva's Representation Theorem},
|
|
12
|
+
Year = {2014}
|
|
13
|
+
}
|
|
14
|
+
|
|
15
|
+
|
|
16
|
+
@incollection{Mislevy06Cog,
|
|
17
|
+
Author = {Robert Mislevy},
|
|
18
|
+
Booktitle = {Educational Assessment},
|
|
19
|
+
Chapter = {8},
|
|
20
|
+
Date-Added = {2014-08-21 20:58:59 +0000},
|
|
21
|
+
Date-Modified = {2014-08-21 20:58:59 +0000},
|
|
22
|
+
Editor = {Robert L. Brennan},
|
|
23
|
+
Publisher = {American Council on Education and Praeger Publishers},
|
|
24
|
+
Title = {Cognitive Psychology and Educational Assessment},
|
|
25
|
+
Year = {2006}
|
|
26
|
+
}
|