├── .gitignore ├── Makefile ├── contents ├── chapter_01_datascience │ ├── Makefile │ ├── chapter_01_datascience.Rmd │ └── chapter_01_datascience_slides.Rmd ├── chapter_02_introduction │ ├── Makefile │ ├── chapter_02_introduction.Rmd │ ├── chapter_02_introduction_slides.Rmd │ ├── data │ │ └── weight.csv │ ├── icons │ │ ├── FilterIcon.png │ │ ├── executeCode.png │ │ ├── import_dataset.png │ │ ├── installPackage.png │ │ ├── outline.png │ │ ├── refreshPackages.png │ │ ├── saveSourceDoc.png │ │ ├── section.png │ │ ├── sourceActiveDocument.png │ │ ├── stock_new.png │ │ ├── updatePackages.png │ │ └── viewerStop.png │ └── rstudio_screenshots │ │ ├── install_packages.png │ │ ├── packages_pane.png │ │ ├── read_csv.png │ │ ├── rstudio_when_open_first.png │ │ └── rstudio_with_editor.png ├── chapter_03_wrangling │ ├── Makefile │ ├── chapter_03_wrangling.Rmd │ ├── chapter_03_wrangling_slides.Rmd │ └── data │ │ ├── blp-trials-short.txt │ │ ├── blp_stimuli.csv │ │ ├── repeated_measured_a.csv │ │ └── repeated_measured_b.csv ├── chapter_04_visualization │ ├── Makefile │ ├── chapter_04_visualization.Rmd │ ├── chapter_04_visualization_slides.Rmd │ └── data │ │ ├── FatRats.csv │ │ ├── TitanicSurvival.csv │ │ ├── carprice.csv │ │ ├── quartet.csv │ │ ├── sleepstudy.csv │ │ └── weight.csv ├── chapter_05_exploratory │ ├── Makefile │ ├── chapter_05_exploratory.Rmd │ ├── chapter_05_exploratory_slides.Rmd │ ├── crop_pdf │ └── data │ │ └── nominal_gdp_per_capita.csv ├── chapter_06_programming │ ├── Makefile │ ├── chapter_06_programming.Rmd │ └── chapter_06_programming_slides.Rmd ├── chapter_07_reproducible │ ├── Makefile │ ├── chapter_07_reproducible.Rmd │ ├── chapter_07_reproducible_slides.Rmd │ ├── crop_pdf │ ├── examples │ │ ├── example-1.Rmd │ │ ├── example-10.Rmd │ │ ├── example-11.Rmd │ │ ├── example-12.Rmd │ │ ├── example-13.Rmd │ │ ├── example-14.Rmd │ │ ├── example-15.Rmd │ │ ├── example-16.Rmd │ │ ├── example-17.Rmd │ │ ├── example-18.Rmd │ │ ├── example-19.Rmd │ │ ├── example-2.Rmd │ │ ├── example-20.Rmd │ │ ├── example-21.Rmd │ │ ├── example-22.Rmd │ │ ├── example-23.Rmd │ │ ├── example-24.Rmd │ │ ├── example-25.Rmd │ │ ├── example-26.Rmd │ │ ├── example-27.Rmd │ │ ├── example-28.Rmd │ │ ├── example-29.Rmd │ │ ├── example-3.Rmd │ │ ├── example-30.Rmd │ │ ├── example-31.Rmd │ │ ├── example-32.Rmd │ │ ├── example-33.Rmd │ │ ├── example-34.Rmd │ │ ├── example-35.Rmd │ │ ├── example-36.Rmd │ │ ├── example-37.Rmd │ │ ├── example-38.Rmd │ │ ├── example-39.Rmd │ │ ├── example-4.Rmd │ │ ├── example-40.Rmd │ │ ├── example-41.Rmd │ │ ├── example-42.Rmd │ │ ├── example-43.Rmd │ │ ├── example-44.Rmd │ │ ├── example-5.Rmd │ │ ├── example-6.Rmd │ │ ├── example-7.Rmd │ │ ├── example-8.Rmd │ │ ├── example-9.Rmd │ │ ├── example.csv │ │ ├── python_code_1.Rmd │ │ ├── python_code_2.Rmd │ │ ├── refs.bib │ │ ├── utils.R │ │ └── weight.csv │ ├── include_graphics │ │ ├── github_screenshot.png │ │ └── knitDocument.png │ ├── utils.py │ └── venv_setup.sh ├── chapter_08_inference │ ├── Makefile │ ├── chapter_08_inference.Rmd │ ├── chapter_08_inference_slides.Rmd │ └── data │ │ └── housing.csv ├── chapter_09_linear │ ├── Makefile │ ├── chapter_09_linear.Rmd │ ├── chapter_09_linear_slides.Rmd │ └── data │ │ └── weight.csv ├── chapter_10_logistic │ ├── Makefile │ ├── chapter_10_logistic.Rmd │ ├── chapter_10_logistic_slides.Rmd │ └── data │ │ ├── affairs.csv │ │ ├── lbw.csv │ │ ├── weather.csv │ │ └── weight.csv ├── chapter_11_generalized │ ├── Makefile │ ├── chapter_11_generalized.Rmd │ ├── chapter_11_generalized_slides.Rmd │ └── data │ │ ├── DoctorAUS.csv │ │ ├── Insurance.csv │ │ ├── affairs.csv │ │ ├── biochemist.csv │ │ ├── golf_putts.csv │ │ ├── lbw.csv │ │ ├── smoking.csv │ │ └── weight.csv ├── chapter_12_multilevel │ ├── Makefile │ ├── chapter_12_multilevel.Rmd │ ├── chapter_12_multilevel_slides.Rmd │ ├── data │ │ ├── alcohol.csv │ │ ├── blp-short2.csv │ │ ├── blp-trials-short.txt │ │ ├── classroom.csv │ │ ├── mathachieve.csv │ │ ├── mathachieveschool.csv │ │ └── rats.csv │ ├── include │ │ ├── J_binomial.tex │ │ ├── J_binomial_s.tex │ │ ├── classroom.tex │ │ ├── classroom_s.tex │ │ ├── crossed_structures.tex │ │ ├── crossed_structures_s.tex │ │ ├── multilevel_alcohol.tex │ │ ├── multilevel_alcohol_s.tex │ │ ├── multilevel_binomial.tex │ │ ├── multilevel_binomial_s.tex │ │ ├── multilevel_sleepstudy.tex │ │ ├── multilevel_sleepstudy_s.tex │ │ ├── nonmultilevel_alcohol.tex │ │ ├── nonmultilevel_alcohol_s.tex │ │ ├── nonmultilevel_sleepstudy.tex │ │ ├── nonmultilevel_sleepstudy_s.tex │ │ ├── sleepstudy_j.tex │ │ └── sleepstudy_j_s.tex │ └── preamble.tex ├── chapter_13_nlregression │ ├── Makefile │ ├── chapter_13_nlregression.Rmd │ ├── chapter_13_nlregression_slides.Rmd │ ├── data │ │ ├── GSSvocab.csv │ │ ├── funct_theme_pts.csv │ │ └── golf_putts.csv │ └── includes │ │ ├── golf_putting_v2.pdf │ │ └── golf_putting_v2.svg ├── chapter_14_sem │ ├── Makefile │ ├── chapter_14_sem.Rmd │ ├── chapter_14_sem_slides.Rmd │ ├── data │ │ ├── grad.csv │ │ └── sat_act.csv │ └── src │ │ └── fa_parallel_src.R ├── chapter_15_hpc │ ├── Makefile │ ├── chapter_15_hpc.Rmd │ ├── chapter_15_hpc_slides.Rmd │ ├── code.cpp │ ├── data │ │ ├── affairs.csv │ │ └── housing.csv │ └── smra-package.R ├── chapter_16_shiny │ ├── Makefile │ ├── chapter_16_shiny.Rmd │ ├── chapter_16_shiny_slides.Rmd │ ├── data │ │ └── housing.csv │ ├── include │ │ ├── app_window.png │ │ ├── app_window_.png │ │ ├── app_window_gghist_.png │ │ ├── create_app.pdf │ │ ├── create_app.svg │ │ ├── false_discovery.png │ │ ├── file_new_file_shiny.png │ │ ├── file_new_file_shiny_.png │ │ ├── interacting_widgets.pdf │ │ ├── interacting_widgets_a.png │ │ ├── interacting_widgets_b.png │ │ ├── learnr.png │ │ ├── likelihood_screenshot_.png │ │ ├── new_shiny_dialog.png │ │ ├── new_shiny_dialog_.png │ │ ├── rmarkdownshiny.png │ │ ├── selected_region.png │ │ └── zoomed.png │ └── shiny │ │ ├── falsediscovery │ │ └── app.R │ │ ├── gghistogram │ │ ├── app.R │ │ └── housing.csv │ │ ├── learnr │ │ └── example.Rmd │ │ ├── likelihood │ │ └── app.R │ │ ├── markdown │ │ └── report.Rmd │ │ ├── selecting │ │ └── app.R │ │ └── zooming │ │ └── app.R ├── chapter_17_stan │ ├── Makefile │ ├── chapter_17_stan.Rmd │ ├── chapter_17_stan_slides.Rmd │ ├── data │ │ ├── MathPlacement.csv │ │ ├── biochemist.csv │ │ ├── loaded_dice.csv │ │ └── weight.csv │ ├── header.tex │ ├── requirements.txt │ ├── scripts │ │ ├── _m_dice_3.R │ │ ├── common.R │ │ ├── lmm.R │ │ ├── logitreg.R │ │ ├── m_dice.R │ │ ├── m_dice_3.R │ │ ├── m_dice_3_2.R │ │ ├── m_dice_4.R │ │ ├── m_normal.R │ │ ├── mlreg.R │ │ ├── negbinreg.R │ │ ├── normlinear.R │ │ └── poisreg.R │ └── stan │ │ ├── coin_bernoulli.stan │ │ ├── lmm.stan │ │ ├── loaded_dice.stan │ │ ├── loaded_dice_binomial.stan │ │ ├── loaded_dice_for.stan │ │ ├── loaded_dice_logit.stan │ │ ├── loaded_dice_logit2.stan │ │ ├── logitreg.stan │ │ ├── mlreg.stan │ │ ├── negbinreg.stan │ │ ├── normal.stan │ │ ├── normlinear.stan │ │ └── poisreg.stan └── header.tex ├── docker ├── 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