├── .Rbuildignore ├── data ├── README.md ├── 2-6-data │ ├── boxplot │ │ ├── lda.png │ │ ├── nb.png │ │ ├── kknn.png │ │ ├── rpart.png │ │ └── ranger.png │ ├── Heatmapa_piekna_missing.png │ ├── Heatmapa_piekna_wszystkie.png │ ├── datasets_frame.csv │ ├── rpart.csv │ ├── lda.csv │ ├── ranger.csv │ ├── nb.csv │ └── kknn.csv ├── interpretability_3_5_results.csv └── 1-8-reproducibility-journal-and-language │ └── results.csv ├── latex ├── after_body.tex ├── before_body.tex └── preamble.tex ├── 2-0-imputation.Rmd ├── book.pdf ├── 3-0-interpretability.Rmd ├── 1-4-img ├── fig1.png ├── fig2.png ├── fig3.png ├── fig4.png ├── fig5.png ├── fig6.png ├── fig7.png └── fig8.png ├── images ├── 2-4-0.png ├── 2-4-1.png ├── 2-4-2.png ├── 3-5-1.png ├── 3-5-2.png ├── 3-5-3.png ├── 3-5-4.png ├── 3-6-1.png ├── 3-6-2.png ├── 3-6-3.png ├── 3-6-4.png ├── 3-6-5.png ├── 3-6-6.png ├── 3-6-7.png ├── 3-6-8.png ├── 3-6-9.png ├── cover.png ├── 2-1-PCA.png ├── 2-1-time.png ├── 3-5-bfg.png ├── 3-5-bfl.png ├── 3-5-byg.png ├── 3-5-byl.png ├── 3-6-10.png ├── 3-6-11.png ├── 3-6-12.png ├── 3-6-13.png ├── 3-7-eda.png ├── 3-8-BUT.png ├── by-nc-sa.png ├── 2-1-ranks.png ├── 3-8-HIDDEN.png ├── 3-8-KLAPEK.png ├── 3-8-KURTKA.png ├── 3-8-LOGREG.png ├── 2-1-workflow.png ├── 3-4-results.png ├── 3-7-algorithm.png ├── 3-7-boxplot.png ├── 3-7-density.png ├── 3-8-KMEANS_1.png ├── 3-8-KMEANS_2.png ├── 2-3-methodology.png ├── 2-3-times_plot.png ├── 3-2-pdp_basic_Z.png ├── 3-8-BUT_HIDDEN.png ├── 3-8-HIDDEN_All.png ├── 3-8-KMEANS_ALL.png ├── 3-8-KNNMODEL_1.png ├── 2-1-influence-NA.png ├── 2-3-measures_plot.png ├── 2-3-rankings_plot.png ├── 3-2-rpart_result.png ├── 3-8-BlackBoxCONV_1.png ├── 3-8-CONVAUTOENC_1.png ├── 3-8-KURTKA_HIDDEN.png └── 3-8-SVDAUTOENC_1.png ├── 1-5-files ├── plot1.png └── plot2.png ├── 2-5-images ├── all1.PNG ├── all2.PNG ├── big1.PNG ├── big2.PNG ├── small1.PNG ├── small2.PNG ├── 27_colic.png ├── 29_credit.png ├── 4_labor.png ├── 56_vote.png ├── Legenda.PNG ├── overall.png ├── 188_eucalyptus.png ├── 55_hepatitis.png └── 944_echoMonths.png ├── 3-8-plots ├── BUT.png ├── HIDDEN.png ├── KLAPEK.png ├── KURTKA.png ├── LOGREG.png ├── BUT_HIDDEN.png ├── KMEANS_1.png ├── KMEANS_2.png ├── KNNMODEL_1.png ├── SVDAUTOENC_1.png ├── BlackBoxCONV_1.png ├── CONVAUTOENC_1.png └── KURTKA_HIDDEN.png ├── docs ├── 1-4-img │ ├── fig1.png │ ├── fig2.png │ ├── fig3.png │ ├── fig4.png │ ├── fig5.png │ ├── fig6.png │ ├── fig7.png │ └── fig8.png ├── images │ ├── 2-4-0.png │ ├── 2-4-1.png │ ├── 2-4-2.png │ ├── 3-5-1.png │ ├── 3-5-2.png │ ├── 3-5-3.png │ ├── 3-5-4.png │ ├── 3-6-1.png │ ├── 3-6-2.png │ ├── 3-6-3.png │ ├── 3-6-4.png │ ├── 3-6-5.png │ ├── 3-6-6.png │ ├── 3-6-7.png │ ├── 3-6-8.png │ ├── 3-6-9.png │ ├── cover.png │ ├── 2-1-PCA.png │ ├── 2-1-time.png │ ├── 3-5-bfg.png │ ├── 3-5-bfl.png │ ├── 3-5-byg.png │ ├── 3-5-byl.png │ ├── 3-6-10.png │ ├── 3-6-11.png │ ├── 3-6-12.png │ ├── 3-6-13.png │ ├── 3-7-eda.png │ ├── by-nc-sa.png │ ├── 2-1-ranks.png │ ├── 3-8-HIDDEN.png │ ├── 3-8-KLAPEK.png │ ├── 3-8-KURTKA.png │ ├── 3-8-LOGREG.png │ ├── 2-1-workflow.png │ ├── 3-4-results.png │ ├── 3-7-algorithm.png │ ├── 3-7-boxplot.png │ ├── 3-7-density.png │ ├── 3-8-KMEANS_1.png │ ├── 3-8-KMEANS_2.png │ ├── 2-3-times_plot.png │ ├── 3-2-pdp_basic_Z.png │ ├── 3-8-HIDDEN_All.png │ ├── 3-8-KMEANS_ALL.png │ ├── 3-8-KNNMODEL_1.png │ ├── 2-1-influence-NA.png │ ├── 2-3-measures_plot.png │ ├── 2-3-rankings_plot.png │ ├── 3-2-rpart_result.png │ ├── 3-8-BlackBoxCONV_1.png │ ├── 3-8-CONVAUTOENC_1.png │ ├── 3-8-KURTKA_HIDDEN.png │ ├── 3-8-SVDAUTOENC_1.png │ └── pdp_basic_Z_ranger.png ├── 1-5-files │ ├── plot1.png │ └── plot2.png ├── 2-5-images │ ├── all1.PNG │ ├── all2.PNG │ ├── big1.PNG │ ├── big2.PNG │ ├── small1.PNG │ ├── small2.PNG │ ├── 27_colic.png │ ├── 29_credit.png │ ├── 4_labor.png │ ├── 56_vote.png │ ├── Legenda.PNG │ ├── overall.png │ ├── 188_eucalyptus.png │ ├── 55_hepatitis.png │ └── 944_echoMonths.png ├── 1-6-files │ ├── art_freq.png │ ├── chunk_freq.png │ ├── group_freq.png │ ├── korelacje_celu_grupy.png │ ├── korelacje_celu_chunki2.png │ ├── korelacje_celu_artykoly.png │ ├── srednia_dlugosc_celu_chunki.png │ ├── srednia_dlugosc_celu_grupy.png │ ├── reprodukowalnosc_celu_chunki.png │ └── srednia_dlugosc_celu_artykoly.png ├── 2-2-files │ ├── rankingAll.png │ ├── rankingGood.png │ ├── imputationTimesBoxplot.png │ └── imputationTimesScatter.png ├── 3-1-graphs │ ├── DecisionTree.jpg │ └── CompareModels_2.png ├── 3-2-graphs │ ├── rpart_result.png │ └── pdp_basic_Z_ranger.png ├── data │ └── 2-6-data │ │ ├── boxplot │ │ ├── lda.png │ │ ├── nb.png │ │ ├── kknn.png │ │ ├── rpart.png │ │ └── ranger.png │ │ ├── Heatmapa_piekna_missing.png │ │ └── Heatmapa_piekna_wszystkie.png ├── 1-2-files │ └── Summary_of_marking_articles.png ├── libs │ ├── gitbook │ │ ├── css │ │ │ ├── fontawesome │ │ │ │ └── fontawesome-webfont.ttf │ │ │ ├── plugin-clipboard.css │ │ │ ├── plugin-table.css │ │ │ ├── plugin-search.css │ │ │ ├── plugin-bookdown.css │ │ │ └── plugin-fontsettings.css │ │ └── js │ │ │ ├── plugin-clipboard.js │ │ │ ├── jquery.highlight.js │ │ │ ├── plugin-sharing.js │ │ │ ├── plugin-fontsettings.js │ │ │ ├── plugin-search.js │ │ │ └── plugin-bookdown.js │ ├── kePrint │ │ └── kePrint.js │ └── header-attrs │ │ └── header-attrs.js ├── css │ └── style.css └── book_files │ └── figure-html │ ├── plot-mark-language-1.svg │ ├── plot-value-language-1.svg │ ├── plot-mark-journal-1.svg │ ├── plot-value-journal-1.svg │ ├── unnamed-chunk-10-1.svg │ ├── plot-mark-both-1.svg │ ├── plot-value-both-1.svg │ └── unnamed-chunk-15-1.svg ├── 1-6-files ├── art_freq.png ├── chunk_freq.png ├── group_freq.png ├── korelacje_celu_grupy.png ├── korelacje_celu_chunki.png ├── korelacje_celu_chunki2.png ├── korelacje_celu_artykoly.png ├── srednia_dlugosc_celu_chunki.png ├── srednia_dlugosc_celu_grupy.png ├── reprodukowalnosc_celu_chunki.png ├── srednia_dlugosc_celu_artykoly.png ├── articles.csv ├── generowanie_obrazkow.R └── groups.csv ├── 2-2-files ├── rankingAll.png ├── rankingGood.png ├── imputationTimesBoxplot.png └── imputationTimesScatter.png ├── 3-1-graphs ├── CompareModels.png ├── DecisionTree.jpg └── CompareModels_2.png ├── DESCRIPTION ├── 1-2-files ├── Summary_of_marking_articles.png └── code.R ├── .gitignore ├── .travis.yml ├── 1-7-data ├── issuescompare.csv ├── repro.csv └── corr.csv ├── 9-0-references.Rmd ├── Makefile ├── _bookdown.yml ├── 8-0-acknowledgements.Rmd ├── 1-0-reproducibility.Rmd ├── css └── style.css ├── _output.yml ├── README.md ├── .github └── workflows │ ├── check_pr.yml │ └── bookdown.yml ├── index.Rmd └── 3-3-interpretable-higgs.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- 1 | ^.*\.Rproj$ 2 | ^\.Rproj\.user$ 3 | -------------------------------------------------------------------------------- /data/README.md: -------------------------------------------------------------------------------- 1 | Here add datasets needed for chapters 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https://raw.githubusercontent.com/DominikRafacz/2020L-WB-Book/master/docs/libs/gitbook/css/fontawesome/fontawesome-webfont.ttf -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | .Ruserdata 5 | *.swp 6 | _book 7 | _bookdown_files 8 | _main.Rmd 9 | *.log 10 | *.Rproj 11 | book.tex 12 | packages.bib 13 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | language: r 2 | pandoc_version: 1.19.2.1 3 | sudo: required 4 | cache: 5 | packages: true 6 | before_install: 7 | - sudo apt-get install libv8-dev 8 | before_script: 9 | - chmod +x ./_build.sh 10 | script: ./_build.sh 11 | 12 | -------------------------------------------------------------------------------- /1-7-data/issuescompare.csv: -------------------------------------------------------------------------------- 1 | "","name","value","n" 2 | "1","api",-1,1 3 | "2","api",0,15 4 | "3","api",1,2 5 | "4","names",-1,1 6 | "5","names",0,14 7 | "6","names",1,3 8 | "7","results",-1,1 9 | "8","results",0,15 10 | "9","results",1,2 11 | -------------------------------------------------------------------------------- /9-0-references.Rmd: -------------------------------------------------------------------------------- 1 | `r if (knitr:::is_html_output()) '# References {-}'` 2 | 3 | ```{r include=FALSE} 4 | # generate a BibTeX database automatically for some R packages 5 | knitr::write_bib(c( 6 | .packages(), 'bookdown', 'knitr', 'rmarkdown' 7 | ), 'packages.bib') 8 | ``` 9 | 10 | -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- 1 | all: html pdf epub 2 | 3 | html: *.Rmd 4 | Rscript -e "bookdown::render_book('./', 'bookdown::gitbook')" 5 | 6 | pdf: *.Rmd 7 | Rscript -e "bookdown::render_book('./', 'bookdown::pdf_book')" 8 | 9 | epub : *.Rmd 10 | Rscript -e "bookdown::render_book('./', 'bookdown::epub_book')" 11 | 12 | -------------------------------------------------------------------------------- /_bookdown.yml: -------------------------------------------------------------------------------- 1 | book_filename: book 2 | repo: https://github.com/mini-pw/2020L-WB-Book 3 | output_dir: docs 4 | clean: [packages.bib, bookdown.bbl] 5 | delete_merged_file: true 6 | language: 7 | label: 8 | fig: "FIGURE " 9 | tab: "TABLE " 10 | ui: 11 | edit: "Edit" 12 | chapter_name: "Chapter " 13 | -------------------------------------------------------------------------------- /8-0-acknowledgements.Rmd: -------------------------------------------------------------------------------- 1 | # Acknowledgements 2 | 3 | This project is inspired by a fantastic book [Limitations of Interpretable Machine Learning Methods](https://compstat-lmu.github.io/iml_methods_limitations/) created at the Department of Statistics, LMU Munich. 4 | We used the LIML project as cornerstone for this reopsitory. 5 | -------------------------------------------------------------------------------- /docs/libs/kePrint/kePrint.js: -------------------------------------------------------------------------------- 1 | $(document).ready(function(){ 2 | if (typeof $('[data-toggle="tooltip"]').tooltip === 'function') { 3 | $('[data-toggle="tooltip"]').tooltip(); 4 | } 5 | if ($('[data-toggle="popover"]').popover === 'function') { 6 | $('[data-toggle="popover"]').popover(); 7 | } 8 | }); 9 | -------------------------------------------------------------------------------- /docs/libs/gitbook/css/plugin-clipboard.css: -------------------------------------------------------------------------------- 1 | div.sourceCode { 2 | position: relative; 3 | } 4 | 5 | .copy-to-clipboard-button { 6 | position: absolute; 7 | right: 0; 8 | top: 0; 9 | visibility: hidden; 10 | } 11 | 12 | .copy-to-clipboard-button:focus { 13 | outline: 0; 14 | } 15 | 16 | div.sourceCode:hover > .copy-to-clipboard-button { 17 | visibility: visible; 18 | } 19 | -------------------------------------------------------------------------------- /latex/before_body.tex: -------------------------------------------------------------------------------- 1 | % you may need to leave a few empty pages before the dedication page 2 | 3 | %\cleardoublepage\newpage\thispagestyle{empty}\null 4 | %\cleardoublepage\newpage\thispagestyle{empty}\null 5 | %\cleardoublepage\newpage 6 | \thispagestyle{empty} 7 | 8 | \begin{center} 9 | \end{center} 10 | 11 | \setlength{\abovedisplayskip}{-5pt} 12 | \setlength{\abovedisplayshortskip}{-5pt} 13 | -------------------------------------------------------------------------------- /1-0-reproducibility.Rmd: -------------------------------------------------------------------------------- 1 | # Reproducibility of scientific papers {#reproducibility} 2 | 3 | This chapter contains a wide range of studies on the reproducibility of scientific articles. 4 | Each subsection is a self-contained paper answering a different research problem. 5 | 6 | Please, note that each subsection contains a work of different authors and therefore subsections may differ at some points, for example, definitions of reproducibility used in particular studies. -------------------------------------------------------------------------------- /css/style.css: -------------------------------------------------------------------------------- 1 | p.caption { 2 | color: #777; 3 | margin-top: 10px; 4 | } 5 | p code { 6 | white-space: inherit; 7 | } 8 | pre { 9 | word-break: normal; 10 | word-wrap: normal; 11 | } 12 | pre code { 13 | white-space: inherit; 14 | } 15 | p.flushright { 16 | text-align: right; 17 | } 18 | blockquote > p:last-child { 19 | text-align: right; 20 | } 21 | blockquote > p:first-child { 22 | text-align: inherit; 23 | } 24 | 25 | 26 | #which-neighbours-affected-house-prices-in-the-90s p 27 | { 28 | text-align: justify; 29 | text-justify: inter-word; 30 | } -------------------------------------------------------------------------------- /docs/css/style.css: -------------------------------------------------------------------------------- 1 | p.caption { 2 | color: #777; 3 | margin-top: 10px; 4 | } 5 | p code { 6 | white-space: inherit; 7 | } 8 | pre { 9 | word-break: normal; 10 | word-wrap: normal; 11 | } 12 | pre code { 13 | white-space: inherit; 14 | } 15 | p.flushright { 16 | text-align: right; 17 | } 18 | blockquote > p:last-child { 19 | text-align: right; 20 | } 21 | blockquote > p:first-child { 22 | text-align: inherit; 23 | } 24 | 25 | 26 | #which-neighbours-affected-house-prices-in-the-90s p 27 | { 28 | text-align: justify; 29 | text-justify: inter-word; 30 | } -------------------------------------------------------------------------------- /docs/libs/header-attrs/header-attrs.js: -------------------------------------------------------------------------------- 1 | // Pandoc 2.9 adds attributes on both header and div. We remove the former (to 2 | // be compatible with the behavior of Pandoc < 2.8). 3 | document.addEventListener('DOMContentLoaded', function(e) { 4 | var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); 5 | var i, h, a; 6 | for (i = 0; i < hs.length; i++) { 7 | h = hs[i]; 8 | if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 9 | a = h.attributes; 10 | while (a.length > 0) h.removeAttribute(a[0].name); 11 | } 12 | }); 13 | -------------------------------------------------------------------------------- /docs/libs/gitbook/css/plugin-table.css: -------------------------------------------------------------------------------- 1 | .book .book-body .page-wrapper .page-inner section.normal table{display:table;width:100%;border-collapse:collapse;border-spacing:0;overflow:auto}.book .book-body .page-wrapper .page-inner section.normal table td,.book .book-body .page-wrapper .page-inner section.normal table th{padding:6px 13px;border:1px solid #ddd}.book .book-body .page-wrapper .page-inner section.normal table tr{background-color:#fff;border-top:1px solid #ccc}.book .book-body .page-wrapper .page-inner section.normal table tr:nth-child(2n){background-color:#f8f8f8}.book .book-body .page-wrapper .page-inner section.normal table th{font-weight:700} 2 | -------------------------------------------------------------------------------- /data/2-6-data/datasets_frame.csv: -------------------------------------------------------------------------------- 1 | "data_nr";"data_name";"nr_instances";"nr_features";"nr_missing";"procent_missing" 2 | "1018";"ipums_la_99-small";8844;56;34843;0,07 3 | "1590";"adult";48842;13;6465;0,01 4 | "188";"eucalyptus";736;16;455;0,04 5 | "23381";"dresses-sales";500;13;955;0,15 6 | "27";"colic";368;20;1199;0,16 7 | "29";"credit-approval";690;16;67;0,01 8 | "38";"sick";3772;28;2293;0,02 9 | "4";"labor";57;17;326;0,34 10 | "40536";"SpeedDating";8378;123;18570;0,02 11 | "41278";"stem-okcupid";45907;20;139693;0,15 12 | "55";"hepatitis";155;20;167;0,05 13 | "56";"vote";435;17;392;0,05 14 | "6332";"cylinder-bands";540;34;999;0,05 15 | "944";"echoMonths";130;10;97;0,07 16 | -------------------------------------------------------------------------------- /1-7-data/repro.csv: -------------------------------------------------------------------------------- 1 | package,old.version,old.reproducibility,new.reproducibility,old.names.issues,new.names.issues,old.api.issues,new.api.issues,old.result.issues,new.result.issues 2 | VSURF,1.0.2,2,2,4,0,2,1,3,4 3 | MVN,3.8,1,3,0,0,0,7,0,0 4 | mldr,0.2.51,2,2,1,1,0,0,0,0 5 | fanplot,3.4.1,1,1,0,0,0,0,0,0 6 | Peptides,1.0.4,2,2,0,5,0,0,0,0 7 | cmvnorm,1.0-3,1,1,0,0,0,0,0,0 8 | factorplot,1.1,1,1,0,0,0,0,3,3 9 | FactoMineR,1.3,1,1,0,0,0,0,0,0 10 | gridGraphics,0.1-5,1,3,0,0,0,0,1,3 11 | phaseR,1.3,1,2,0,3,0,0,0,0 12 | betategarch,3,1,1,0,0,0,0,6,6 13 | tempdisagg,0.22,1,1,0,0,0,0,0,0 14 | mvtnorm,0.9-7,2,2,0,0,1,1,0,0 15 | brainR,1.2,1,1,0,0,0,0,0,0 16 | qmethod,1.3.0,2,2,0,0,0,0,1,1 17 | stringdist,0.7.2,1,1,0,0,1,1,1,1 18 | rotations,1.3,3,3,0,0,0,0,3,3 19 | ggmap,2.3,3,3,0,1,0,9,13,2 20 | -------------------------------------------------------------------------------- /docs/libs/gitbook/css/plugin-search.css: -------------------------------------------------------------------------------- 1 | .book .book-summary .book-search { 2 | padding: 6px; 3 | background: transparent; 4 | position: absolute; 5 | top: -50px; 6 | left: 0px; 7 | right: 0px; 8 | transition: top 0.5s ease; 9 | } 10 | .book .book-summary .book-search input, 11 | .book .book-summary .book-search input:focus, 12 | .book .book-summary .book-search input:hover { 13 | width: 100%; 14 | background: transparent; 15 | border: 1px solid #ccc; 16 | box-shadow: none; 17 | outline: none; 18 | line-height: 22px; 19 | padding: 7px 4px; 20 | color: inherit; 21 | box-sizing: border-box; 22 | } 23 | .book.with-search .book-summary .book-search { 24 | top: 0px; 25 | } 26 | .book.with-search .book-summary ul.summary { 27 | top: 50px; 28 | } 29 | .with-search .summary li[data-level] a[href*=".html#"] { 30 | display: none; 31 | } 32 | -------------------------------------------------------------------------------- /data/2-6-data/rpart.csv: -------------------------------------------------------------------------------- 1 | Dataset;Insert mean;Mice_pmm;VIM_knn;VIM_hotdeck;softImpute 2 | ipums_la_99-small;NA;NA;NA;NA;NA 3 | adult;0,902948166;0,902948166;0,902948166;0,902948166;0,902948166 4 | eucalyptus;0,881355932;0,906077348;0,792682927;0,875;0,895027624 5 | dresses-sales;NA;NA;NA;NA;NA 6 | colic;0,756756757;0,666666667;0,666666667;0,731707317;0,756756757 7 | credit-approval;0,885714286;0,885714286;0,885714286;0,885714286;0,885714286 8 | sick;0,985221675;0,983791402;0,98659139;0,988732394;0,990126939 9 | labor;0,75;0,333333333;0,666666667;0,75;0,428571429 10 | SpeedDating;1;1;1;1;1 11 | stem-okcupid;NA;NA;NA;NA;NA 12 | hepatitis;0,4;0,5;0,666666667;0,4;0,444444444 13 | vote;0,964912281;0,965517241;0,964912281;0,965517241;0,964912281 14 | cylinder-bands;0,732394366;0,722222222;0,732394366;0,732394366;0,732394366 15 | echoMonths;0,774193548;0,8125;0,774193548;0,774193548;0,774193548 16 | -------------------------------------------------------------------------------- /data/2-6-data/lda.csv: -------------------------------------------------------------------------------- 1 | Dataset;Insert mean;Mice_pmm;VIM_knn;VIM_hotdeck;softImpute 2 | ipums_la_99-small;0,285714286;0,317073171;0,290697674;0,24;0,285714286 3 | adult;0,89739403;0,898241042;0,898669797;0,898456328;0,89739403 4 | eucalyptus;0,9;0,905027933;0,893854749;0,893854749;0,906077348 5 | dresses-sales;NA;NA;NA;NA;NA 6 | colic;0,571428571;0,457142857;0,634146341;0,634146341;0,611111111 7 | credit-approval;0,874074074;NA;0,874074074;0,872180451;0,859259259 8 | sick;0,976939203;0,977003484;0,978336827;0,97632312;0,976906928 9 | labor;1;NA;0,8;1;0,857142857 10 | SpeedDating;0,994992847;0,995352163;0,994992847;0,99391771;0,994992847 11 | stem-okcupid;NA;NA;NA;NA;NA 12 | hepatitis;0,6;0,6;0,545454545;0,545454545;0,6 13 | vote;0,964912281;0,964912281;0,964912281;0,964912281;0,964912281 14 | cylinder-bands;0,647887324;NA;0,676470588;0,637681159;0,637681159 15 | echoMonths;0,864864865;NA;0,864864865;0,864864865;0,864864865 16 | -------------------------------------------------------------------------------- /1-7-data/corr.csv: -------------------------------------------------------------------------------- 1 | "reproducibility","names","api","results","api.and.results","github.stars","github.subscribers","github.contributors","github.adds","github.dels","github.commits","github.issues","github.open_issues","CI","versions" 2 | 0,-4,-1,1,0,16,4,1,4584,2814,37,5,1,1,2 3 | 2,0,7,0,7,0,2,0,0,0,0,4,1,0,12 4 | 0,0,0,0,0,17,7,2,2895,1400,113,30,3,1,6 5 | 0,0,0,0,0,0,1,1,64,21,4,0,0,0,0 6 | 0,5,0,0,0,23,3,6,61104,57711,178,30,1,0,10 7 | 0,0,0,0,0,2,1,1,1593,104,21,3,1,0,1 8 | 0,0,0,0,0,1,2,1,1540,1972,21,0,0,0,0 9 | 0,0,0,0,0,6,1,1,21213,5020,17,4,3,0,18 10 | 2,0,0,2,2,28,2,3,11161,8800,101,16,7,0,5 11 | 1,3,0,0,0,6,2,2,4459,2347,29,9,2,0,1 12 | 0,0,0,0,0,1,1,0,0,0,0,0,0,0,2 13 | 0,0,0,0,0,22,7,2,4637,4073,66,30,3,1,3 14 | 0,0,0,0,0,1,1,1,7290,4273,34,0,0,0,32 15 | 0,0,0,0,0,9,2,1,13572,6389,22,0,0,1,1 16 | 0,0,0,0,0,27,11,3,12355,10624,186,80,284,1,7 17 | 0,0,0,0,0,212,13,6,12192,7369,306,84,15,1,19 18 | 0,0,0,0,0,0,3,3,32217,30126,119,7,1,0,3 19 | 0,1,9,-11,-2,590,49,13,19336,14750,310,97,206,1,5 20 | -------------------------------------------------------------------------------- /data/2-6-data/ranger.csv: -------------------------------------------------------------------------------- 1 | Dataset;Insert mean;Mice_pmm;VIM_knn;VIM_hotdeck;softImpute 2 | ipums_la_99-small;0,184615385;0,15625;0,141732283;0,15503876;0,15625 3 | adult;0,914816997;0,915805988;0,915746127;0,915681536;0,915209847 4 | eucalyptus;0,908108108;0,908108108;0,918032787;0,908108108;0,902173913 5 | dresses-sales;0,757575758;0,715447154;0,723076923;0,723076923;0,763358779 6 | colic;0,666666667;0,6875;0,764705882;0,666666667;0,611111111 7 | credit-approval;0,881118881;NA;0,881118881;0,887323944;0,881118881 8 | sick;0,985974755;0,985283812;0,986666667;0,985283812;0,985974755 9 | labor;0,857142857;NA;0,857142857;0,857142857;0,857142857 10 | SpeedDating;0,995732575;0,995378599;0,996441281;0,995378599;0,995732575 11 | stem-okcupid;0,884918881;0,885217391;0,889460816;0,884813185;0,883368102 12 | hepatitis;0,666666667;0,666666667;0,75;0,5;0,444444444 13 | vote;0,974358974;0,982758621;0,973913043;0,965517241;0,974358974 14 | cylinder-bands;0,776119403;NA;0,794117647;0,8;0,764705882 15 | echoMonths;0,8125;NA;0,75;0,8125;0,787878788 16 | -------------------------------------------------------------------------------- /data/2-6-data/nb.csv: -------------------------------------------------------------------------------- 1 | Dataset;Insert mean;Mice_pmm;VIM_knn;VIM_hotdeck;softImpute 2 | ipums_la_99-small;0,124716553;0,125930166;0,126364159;0,123873874;0,124716553 3 | adult;0,886622751;0,887071207;0,887224726;0,887184688;0,886622751 4 | eucalyptus;0,863387978;0,87431694;0,886486486;0,87431694;0,868131868 5 | dresses-sales;0,672;0,666666667;0,698412698;0,64516129;0,704 6 | colic;0,518518519;0,465116279;0,528301887;0,565217391;0,528301887 7 | credit-approval;0,787096774;0,787096774;0,787096774;0,787096774;0,787096774 8 | sick;0,947521866;0,945215486;0,947521866;0,945215486;0,943065693 9 | labor;0,666666667;0,8;0,428571429;1;1 10 | SpeedDating;0,886345699;0,885025682;0,886874261;0,887573964;0,886345699 11 | stem-okcupid;0,844271413;0,857510671;0,843214943;0,857085048;0,844330112 12 | hepatitis;0,6;0,6;0,6;0,545454545;0,6 13 | vote;0,915254237;0,915254237;0,923076923;0,915254237;0,915254237 14 | cylinder-bands;0,564705882;0,384615385;0,571428571;0,542857143;0,551724138 15 | echoMonths;0,864864865;0,823529412;0,8;0,787878788;0,833333333 16 | -------------------------------------------------------------------------------- /data/2-6-data/kknn.csv: -------------------------------------------------------------------------------- 1 | Dataset;Insert mean;Mice_pmm;VIM_knn;VIM_hotdeck;softImpute 2 | ipums_la_99-small;0,220858896;0,201257862;0,242424242;0,209876543;0,220858896 3 | adult;0,88715382;0,888652671;0,888593105;0,889863159;0,88715382 4 | eucalyptus;0,857142857;0,852272727;0,852272727;0,857142857;0,857142857 5 | dresses-sales;0,742138365;0,742138365;0,742138365;0,742138365;0,713286713 6 | colic;0,565217391;0,571428571;0,604651163;0,577777778;0,510638298 7 | credit-approval;0,85106383;NA;0,85106383;0,85106383;0,842857143 8 | sick;0,979762736;0,978397213;0,979790941;0,978427279;0,978427279 9 | labor;0,666666667;NA;0,857142857;0,8;1 10 | SpeedDating;0,914166085;0,915620642;0,915998606;0,914642609;0,91454482 11 | stem-okcupid;0,883104245;0,883104245;0,883104245;0,883104245;0,883104245 12 | hepatitis;0,666666667;0,857142857;0,666666667;0,666666667;0,666666667 13 | vote;0,949152542;0,956521739;0,948275862;0,957264957;0,949152542 14 | cylinder-bands;0,763157895;NA;0,684931507;0,676056338;0,783783784 15 | echoMonths;0,777777778;NA;0,764705882;0,787878788;0,777777778 16 | -------------------------------------------------------------------------------- /docs/libs/gitbook/js/plugin-clipboard.js: -------------------------------------------------------------------------------- 1 | gitbook.require(["gitbook", "jQuery"], function(gitbook, $) { 2 | 3 | var copyButton = ''; 4 | var clipboard; 5 | 6 | gitbook.events.bind("page.change", function() { 7 | 8 | if (!ClipboardJS.isSupported()) return; 9 | 10 | // the page.change event is thrown twice: before and after the page changes 11 | if (clipboard) { 12 | // clipboard is already defined 13 | // we can deduct that we are before page changes 14 | clipboard.destroy(); // destroy the previous events listeners 15 | clipboard = undefined; // reset the clipboard object 16 | return; 17 | } 18 | 19 | $(copyButton).prependTo("div.sourceCode"); 20 | 21 | clipboard = new ClipboardJS(".copy-to-clipboard-button", { 22 | text: function(trigger) { 23 | return trigger.parentNode.textContent; 24 | } 25 | }); 26 | 27 | }); 28 | 29 | }); 30 | -------------------------------------------------------------------------------- /_output.yml: -------------------------------------------------------------------------------- 1 | bookdown::gitbook: 2 | dev: svglite 3 | css: css/style.css 4 | split_by: section 5 | config: 6 | toc: 7 | collapse: section 8 | before: | 9 |

  • ML Case Studies

    • 10 | after: | 11 |
  • Published with bookdown
    • 12 | download: [pdf, epub] 13 | edit: https://github.com/mini-pw/2020L-WB-Book/edit/master/%s 14 | sharing: 15 | github: yes 16 | facebook: no 17 | bookdown::html_chapters: 18 | css: [css/style.css, css/toc.css] 19 | bookdown::pdf_book: 20 | includes: 21 | in_header: latex/preamble.tex 22 | before_body: latex/before_body.tex 23 | after_body: latex/after_body.tex 24 | keep_tex: yes 25 | dev: "cairo_pdf" 26 | latex_engine: xelatex 27 | citation_package: natbib 28 | template: null 29 | pandoc_args: --top-level-division=chapter 30 | toc_depth: 1 31 | toc_unnumbered: no 32 | toc_appendix: yes 33 | quote_footer: ["\\VA{", "}{}"] 34 | bookdown::epub_book: 35 | dev: svglite 36 | stylesheet: css/style.css 37 | -------------------------------------------------------------------------------- /1-6-files/articles.csv: -------------------------------------------------------------------------------- 1 | "length","package.overview","object.construction","introduction.to.subject","method.implementation","addressing.an.issue","error.identification" 2 | 15,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 3 | 2,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE 4 | 9,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 5 | 45,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 6 | 125,TRUE,FALSE,TRUE,TRUE,FALSE,FALSE 7 | 57,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 8 | 9,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 9 | 18,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE 10 | 43,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 11 | 34,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 12 | 14,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE 13 | 36,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 14 | 10,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 15 | 5,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE 16 | 91,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 17 | 105,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 18 | 120,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE 19 | 34,TRUE,FALSE,TRUE,TRUE,FALSE,FALSE 20 | 34,TRUE,TRUE,FALSE,FALSE,TRUE,FALSE 21 | 94,TRUE,FALSE,FALSE,TRUE,TRUE,TRUE 22 | 9,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE 23 | 21,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE 24 | 46,TRUE,FALSE,FALSE,TRUE,TRUE,FALSE 25 | 42,TRUE,TRUE,TRUE,TRUE,TRUE,FALSE 26 | 115,TRUE,TRUE,FALSE,TRUE,TRUE,FALSE 27 | 170,TRUE,FALSE,TRUE,TRUE,TRUE,FALSE 28 | 19,TRUE,FALSE,TRUE,TRUE,TRUE,FALSE 29 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # ML Case Studies 2 | 3 | by **Evidence Based Machine Learning Lab** 4 | 5 | ebook: https://mini-pw.github.io/2020L-WB-Book 6 | 7 | 8 | ## How this book came about 9 | 10 | This book is the result of a student projects for [Case Studies](https://github.com/mini-pw/2020L-WarsztatyBadawcze) course at the Warsaw University of Technology. Each team prepared an article on one of the topics selected from reproducibility, imputation, and interpretability. 11 | 12 | This project is inspired by a fantastic books [Limitations of Interpretable Machine Learning Methods](https://compstat-lmu.github.io/iml_methods_limitations/) done at the Department of Statistics, LMU Munich and [XAI Stories. Case studies for eXplainable Artificial Intelligence](https://pbiecek.github.io/xai_stories/) done at the Warsaw University of Technology and at the University of Warsaw. 13 | 14 | We used the LIML project as the cornerstone for this repository. 15 | 16 | ## How to build the book 17 | 18 | Step 1: Clone or download the repository https://github.com/mini-pw/2020L-WB-Book. 19 | 20 | Step 2: Install dependencies 21 | 22 | ``` 23 | devtools::install_dev_deps() 24 | ``` 25 | 26 | Step 3: Render the book (R commands) 27 | 28 | ```{r} 29 | # HTML 30 | bookdown::render_book('./', 'bookdown::gitbook') 31 | # PDF 32 | bookdown::render_book('./', 'bookdown::pdf_book') 33 | ``` 34 | 35 | -------------------------------------------------------------------------------- /.github/workflows/check_pr.yml: -------------------------------------------------------------------------------- 1 | on: 2 | pull_request: 3 | branches: 4 | - master 5 | 6 | name: check PR 7 | 8 | jobs: 9 | build: 10 | runs-on: macOS-latest 11 | steps: 12 | - name: Checkout repo 13 | uses: actions/checkout@v2 14 | 15 | - name: Setup R 16 | uses: r-lib/actions/setup-r@master 17 | 18 | - name: Install pandoc and pandoc citeproc 19 | run: | 20 | brew install pandoc 21 | brew install pandoc-citeproc 22 | - name: Cache Renv packages 23 | uses: actions/cache@v1 24 | with: 25 | path: $HOME/.local/share/renv 26 | key: r-${{ hashFiles('renv.lock') }} 27 | restore-keys: r- 28 | 29 | - name: Cache bookdown results 30 | uses: actions/cache@v1 31 | with: 32 | path: _bookdown_files 33 | key: bookdown-${{ hashFiles('**/*Rmd') }} 34 | restore-keys: bookdown- 35 | 36 | - name: Install packages 37 | run: | 38 | R -e 'install.packages("renv")' 39 | R -e 'install.packages("bookdown")' 40 | R -e 'install.packages("ggplot2")' 41 | R -e 'install.packages("svglite")' 42 | R -e 'install.packages("dplyr")' 43 | R -e 'install.packages("kableExtra")' 44 | R -e 'install.packages("corrplot")' 45 | R -e 'install.packages("tidyr")' 46 | R -e 'install.packages("reshape2")' 47 | R -e 'renv::restore()' 48 | 49 | - name: Build site 50 | run: Rscript -e 'bookdown::render_book("index.Rmd", quiet = TRUE)' 51 | 52 | -------------------------------------------------------------------------------- /latex/preamble.tex: -------------------------------------------------------------------------------- 1 | \usepackage{booktabs} 2 | \usepackage{longtable} 3 | \usepackage[bf,singlelinecheck=off]{caption} 4 | 5 | \usepackage{url} 6 | 7 | % By default the URLs are put in typewriter type in the body and the 8 | % bibliography of the document when using the \url command. If you are 9 | % using many long URLs you may want to uncommennt the next line so they 10 | % are typeset a little smaller. 11 | \renewcommand{\UrlFont}{\small\tt} 12 | 13 | \usepackage{framed,color} 14 | \definecolor{shadecolor}{RGB}{248,248,248} 15 | 16 | \renewcommand{\textfraction}{0.05} 17 | \renewcommand{\topfraction}{0.8} 18 | \renewcommand{\bottomfraction}{0.8} 19 | \renewcommand{\floatpagefraction}{0.75} 20 | 21 | \renewenvironment{quote}{\begin{VF}}{\end{VF}} 22 | \let\oldhref\href 23 | \renewcommand{\href}[2]{#2\footnote{\url{#1}}} 24 | 25 | \makeatletter 26 | \newenvironment{kframe}{% 27 | \medskip{} 28 | \setlength{\fboxsep}{.8em} 29 | \def\at@end@of@kframe{}% 30 | \ifinner\ifhmode% 31 | \def\at@end@of@kframe{\end{minipage}}% 32 | \begin{minipage}{\columnwidth}% 33 | \fi\fi% 34 | \def\FrameCommand##1{\hskip\@totalleftmargin \hskip-\fboxsep 35 | \colorbox{shadecolor}{##1}\hskip-\fboxsep 36 | % There is no \\@totalrightmargin, so: 37 | \hskip-\linewidth \hskip-\@totalleftmargin \hskip\columnwidth}% 38 | \MakeFramed {\advance\hsize-\width 39 | \@totalleftmargin\z@ \linewidth\hsize 40 | \@setminipage}}% 41 | {\par\unskip\endMakeFramed% 42 | \at@end@of@kframe} 43 | \makeatother 44 | 45 | 46 | \usepackage{makeidx} 47 | \makeindex 48 | 49 | \urlstyle{tt} 50 | 51 | \usepackage{amsthm} 52 | \makeatletter 53 | \def\thm@space@setup{% 54 | \thm@preskip=8pt plus 2pt minus 4pt 55 | \thm@postskip=\thm@preskip 56 | } 57 | \makeatother 58 | 59 | \frontmatter 60 | -------------------------------------------------------------------------------- /.github/workflows/bookdown.yml: -------------------------------------------------------------------------------- 1 | on: 2 | push: 3 | branches: master 4 | paths-ignore: 5 | - 'docs/**' 6 | 7 | name: bookdown 8 | 9 | jobs: 10 | build: 11 | runs-on: macOS-latest 12 | steps: 13 | - name: Checkout repo 14 | uses: actions/checkout@v2 15 | 16 | - name: Setup R 17 | uses: r-lib/actions/setup-r@master 18 | 19 | - name: Install pandoc and pandoc citeproc 20 | run: | 21 | brew install pandoc 22 | brew install pandoc-citeproc 23 | - name: Cache Renv packages 24 | uses: actions/cache@v1 25 | with: 26 | path: $HOME/.local/share/renv 27 | key: r-${{ hashFiles('renv.lock') }} 28 | restore-keys: r- 29 | 30 | - name: Cache bookdown results 31 | uses: actions/cache@v1 32 | with: 33 | path: _bookdown_files 34 | key: bookdown-${{ hashFiles('**/*Rmd') }} 35 | restore-keys: bookdown- 36 | 37 | - name: Install packages 38 | run: | 39 | R -e 'install.packages("renv")' 40 | R -e 'install.packages("bookdown")' 41 | R -e 'install.packages("ggplot2")' 42 | R -e 'install.packages("svglite")' 43 | R -e 'install.packages("dplyr")' 44 | R -e 'install.packages("kableExtra")' 45 | R -e 'install.packages("corrplot")' 46 | R -e 'install.packages("tidyr")' 47 | R -e 'install.packages("reshape2")' 48 | R -e 'renv::restore()' 49 | 50 | - name: Build site 51 | run: Rscript -e 'bookdown::render_book("index.Rmd", quiet = TRUE)' 52 | 53 | - name: Commit results 54 | run: | 55 | git add . 56 | git commit -m 'Render book' || echo "No changes to commit" 57 | git push origin || echo "No changes to commit" 58 | -------------------------------------------------------------------------------- /1-2-files/code.R: -------------------------------------------------------------------------------- 1 | library(ggplot2) 2 | library(dplyr) 3 | library(reshape2) 4 | 5 | bincor <- c(NA, 5, 4, NA, NA, 5) 6 | grpstring <- c(NA, 5, 4.5, 5, 4, 5) 7 | mmpf <- c(NA, 5, NA, 5, 0, 1) 8 | realvams <- c(NA, 2.5, 5, 5, 5, 5) 9 | shadow <- c(5, 2.5, 2.5, 5, 4.5, 5) 10 | coutryshapes <- c(0, NA, NA, NA, NA, 4.5) 11 | tmvtnorm <- c(NA, 5, NA, NA, 2.5, 3) 12 | mcmc <- c(NA, 1, NA, 0.5, NA, 4) 13 | drawingdiagrams <- c(NA, 5, 3, 3, NA, 5) 14 | geospatial <- c(1, 5, 4.5, 4.5, NA, 5) 15 | rainbow <- c(NA, 3, 5, 5, NA, 5) 16 | stplanr <- c(NA, NA, NA, 1, NA, 5) 17 | rssampling <- c(NA, 5, NA, NA, 0.5, 5) 18 | fixedpoint <- c(NA, 5, 5, 5, 5, 3.5) 19 | nowcasting <- c(NA, 3.5, 4.5, 5, 5, 4) 20 | rasterimages <- c(2.5, 1.5, 5, 3.5, 5, 4.5) 21 | marks <- data.frame(t(data.frame(bincor, grpstring, mmpf, realvams, shadow, coutryshapes, tmvtnorm, 22 | mcmc, drawingdiagrams, geospatial, rainbow, stplanr, rssampling, 23 | fixedpoint, nowcasting, rasterimages))) 24 | colnames(marks) <- c("ext_resources", "compatibility", "graphics", "add_config", "randomness", "availability") 25 | 26 | 27 | 28 | marks %>% 29 | melt(id.vars = NULL) %>% 30 | group_by(variable) %>% 31 | mutate(n_checked = sum(!is.na(value))) %>% 32 | ggplot()+ 33 | geom_boxplot(aes(x = variable, y = value, fill = cut(n_checked, c(3, 8, 9.5, 11, 13, 15, 17), labels = c(4, 9, 10, 12, 14, 16))), 34 | outlier.shape=NA)+ 35 | geom_point(aes(x = variable, y = value), alpha = 0.4, size = 0.8)+ 36 | theme_bw() + 37 | scale_fill_manual( values = c('#f0f9e8','#ccebc5','#a8ddb5','#7bccc4','#43a2ca','#0868ac'))+ 38 | labs(fill = "Number of articles\nwith a mark", 39 | y = 'Marks distribution', 40 | title = 'Summary of marking the articles') + 41 | scale_x_discrete(name = 'Category', 42 | limits = c('ext_resources', 'randomness', 'graphics', 'add_config', 'compatibility', 'availability'), 43 | labels = c("External\nresources", "Resistance to\nrandomness", "Graphics", "Additional\nconfiguration", 44 | "Compatibility with\nolder versions", "Code availability")) 45 | 46 | 47 | 48 | -------------------------------------------------------------------------------- /data/interpretability_3_5_results.csv: -------------------------------------------------------------------------------- 1 | "";"task.id";"learner.id";"mse.test.mean";"mae.test.mean";"rsq.test.mean" 2 | "1";"Brute force";"regr.lm";29,1823649121806;4,30062066144669;0,88908642630914 3 | "2";"Brute force";"regr.glmnet";31,2899812517843;4,48711486459731;0,881550065031613 4 | "3";"Brute force";"regr.glmnet.optimized";29,8529487104456;4,3625274339313;0,886700934771772 5 | "4";"Brute force";"regr.rpart";73,7611405604666;6,73059359471656;0,721959456465732 6 | "5";"Brute force";"regr.ranger";21,5603429939546;3,45364954856109;0,918540756546873 7 | "6";"Brute force";"regr.svm";19,8700231403269;3,30123389562929;0,924787232983105 8 | "7";"By hand";"regr.lm";31,5560094478273;4,45428704336918;0,882099736001743 9 | "8";"By hand";"regr.glmnet";32,1327883695607;4,44175209276462;0,879988058038762 10 | "9";"By hand";"regr.glmnet.optimized";31,576019816282;4,44680237091941;0,882037058657926 11 | "10";"By hand";"regr.rpart";70,0570281540328;6,56489243396003;0,738742636976469 12 | "11";"By hand";"regr.ranger";25,0022178142404;3,83240399462384;0,90686415842268 13 | "12";"By hand";"regr.svm";18,7326622429411;3,19409070485136;0,930038749484442 14 | "13";"Plain concrete data";"regr.lm";110,311063794207;8,31823205678952;0,599772252225149 15 | "14";"Plain concrete data";"regr.glmnet";110,295634486819;8,32705977913484;0,599788997786959 16 | "15";"Plain concrete data";"regr.glmnet.optimized";110,303629001595;8,32017797907583;0,599787720855053 17 | "16";"Plain concrete data";"regr.rpart";86,0613643066016;7,25201571037859;0,687099976219574 18 | "17";"Plain concrete data";"regr.ranger";30,390004563917;4,03384292786329;0,890396910335718 19 | "18";"Plain concrete data";"regr.svm";45,9079829646728;4,91270625507088;0,834285530024648 20 | "19";"W/O outliers/influential";"regr.lm";60,8040921784569;6,23986341109415;0,772154166985926 21 | "20";"W/O outliers/influential";"regr.glmnet";60,8251956705515;6,24694780170259;0,772062913668611 22 | "21";"W/O outliers/influential";"regr.glmnet.optimized";60,805757554579;6,2411071066787;0,772145291938215 23 | "22";"W/O outliers/influential";"regr.rpart";71,0344803533818;6,63196762722823;0,732956393966613 24 | "23";"W/O outliers/influential";"regr.ranger";25,1538542089238;3,86933402166129;0,90513151339428 25 | "24";"W/O outliers/influential";"regr.svm";26,9005278691465;3,90686958272295;0,898529683542402 26 | -------------------------------------------------------------------------------- /index.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "ML Case Studies" 3 | author: "" 4 | date: "`r Sys.Date()`" 5 | documentclass: krantz 6 | bibliography: [book.bib, packages.bib] 7 | biblio-style: apalike 8 | link-citations: yes 9 | colorlinks: yes 10 | lot: False 11 | lof: False 12 | site: bookdown::bookdown_site 13 | description: "Case studies for reproducibility, imputation, and interpretability" 14 | graphics: yes 15 | cover-image: images/cover.png 16 | --- 17 | 18 | ```{r setup, include=FALSE} 19 | options( 20 | htmltools.dir.version = FALSE, formatR.indent = 2, width = 55, digits = 4 21 | ) 22 | output <- knitr::opts_knit$get("rmarkdown.pandoc.to") 23 | is.html = !is.null(output) && output == "html" 24 | ``` 25 | 26 | # Preface {-} 27 | 28 | ```{r cover, cache=FALSE, out.width="500", fig.align="center", echo=FALSE, eval = is.html} 29 | knitr::include_graphics('images/cover.png') 30 | ``` 31 | 32 | 33 | 34 | This book is the result of a student projects for [Case Studies](https://github.com/mini-pw/2020L-WarsztatyBadawcze) course at the Warsaw University of Technology. Each team prepared an article on one of the topics selected from reproducibility, imputation, and interpretability. 35 | 36 | This project is inspired by a book [Limitations of Interpretable Machine Learning Methods](https://compstat-lmu.github.io/iml_methods_limitations/) created at the Department of Statistics, LMU Munich [XAI Stories. Case studies for eXplainable Artificial Intelligence](https://pbiecek.github.io/xai_stories/) done at the Warsaw University of Technology and at the University of Warsaw. 37 | We used the LIML project as the cornerstone for this repository. 38 | 39 | The cover created by Anna Kozak. 40 | 41 | ![Creative Commons License](images/by-nc-sa.png) 42 | 43 | This book is licensed under the [Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License](http://creativecommons.org/licenses/by-nc-sa/4.0/). 44 | 45 | 46 | \mainmatter 47 | 48 | 49 | ## Technical Setup {-} 50 | The book chapters are written in the Markdown language. 51 | The simulations, data examples and visualizations were created with R [@rlang] and Python. 52 | The book was compiled with the bookdown package. 53 | We collaborated using git and github. 54 | For details, head over to the [book's repository](https://github.com/mini-pw/2020L-WB-Book). 55 | 56 | 57 | -------------------------------------------------------------------------------- /data/1-8-reproducibility-journal-and-language/results.csv: -------------------------------------------------------------------------------- 1 | Journal,Language,Title,StudentsMark,ReproducibilityValue 2 | JOSS,Python,Autorank: A Python package for automated ranking of classifiers,4,0.95 3 | JSTAT,R,Beyond Tandem Analysis: Joint Dimension Reduction and Clustering in R,5,1 4 | JSTAT,Python,CoClust: A Python Package for Co-Clustering,2,0.3 5 | JSTAT,R,corr2D: Implementation of Two-Dimensional Correlation Analysis in R,4,1 6 | JSTAT,R,frailtyEM: An R Package for Estimating Semiparametric Shared Frailty Models,4,0.79 7 | JOSS,Python,Graph Transliterator: A graph-based transliteration tool,4,0.93 8 | JMLR,Python,HyperTools: a Python Toolbox for Gaining Geometric Insights into High-Dimensional Data,5,0.96 9 | JOSS,R,iml: An R package for Interpretable Machine Learning,5,1 10 | JOSS,R,learningCurve: An implementation of Crawford's and Wright's learning curve production functions,5,1 11 | JOSS,R,mimosa: A Modern Graphical User Interface for 2-level Mixed Models,3,0.67 12 | JMLR,R,mlr: Machine Learning in R,4,0.98 13 | JMLR,R,Model-based Boosting 2.0,4,0.95 14 | JSTAT,Python,"Natter: A Python Natural Image Statistics Toolbox 15 | ",2,0 16 | JSTAT,R,Network Coincidence Analysis: The netCoin R Package,4,0.91 17 | JMLR,Python,OpenEnsembles: A Python Resource for Ensemble Clustering,2,0.78 18 | JOSS,R,origami: A Generalized Framework for Cross-Validation in R,5,1 19 | JOSS,Python,py-pde: A Python package for solving partial differential equations,2,0.86 20 | JOSS,Python,PyEscape: A narrow escape problem simulator packagefor Python,2,0.8 21 | JOSS,Python,Pyglmnet: Python implementation of elastic-net regularized generalized linear models,5,0.98 22 | JSTAT,Python,pyParticleEst: A Python Framework for Particle-Based Estimation Methods,3,0.67 23 | JSTAT,Python,"PypeR, A Python Package for Using R in Python",3,1 24 | JOSS,R,"Rclean: A Tool for Writing Cleaner, More Transparent Code",5,1 25 | JMLR,Python,RLPy: A Value-Function-Based Reinforcement Learning Framework for Education and Research,2,0.59 26 | JSTAT,R,rmcfs: An R Package for Monte Carlo Feature Selection and Interdependency Discovery,2,0.57 27 | JMLR,Python,Seglearn: A Python Package for Learning Sequences and Time Series,4,0.88 28 | JSTAT,Python,Simulated Data for Linear Regression with Structured and Sparse Penalties: Introducing pylearn-simulate,2,0.3 29 | JOSS,R,tacmagic: Positron emission tomography analysis in R,5,1 30 | JMLR,Python,TensorLy: Tensor Learning in Python,3,1 31 | JMLR,R,The flare Package for High Dimensional Linear Regression and Precision Matrix Estimation in R ,3,1 32 | JMLR,R,The huge Package for High-dimensional Undirected Graph Estimation in R ,3,1 33 | -------------------------------------------------------------------------------- /1-6-files/generowanie_obrazkow.R: -------------------------------------------------------------------------------- 1 | chnk <- read.csv("chunks.csv") 2 | grp <- read.csv("groups.csv") 3 | art <- read.csv("articles.csv") 4 | 5 | 6 | 7 | non_zero_mean <- function(vektor){ 8 | tmp <- vektor[vektor!=0] 9 | return(mean(tmp)) 10 | } 11 | 12 | 13 | 14 | 15 | # table of chuncks 16 | purpose <- chnk[,c(-1, -2)]*1 # we get rig of unnesesery columns and multyply by 1 to 17 | DataExplorer::plot_correlation(purpose) # convert logical into numeric 18 | 19 | 20 | reproducibility <- chnk[chnk$reproducibility.scale != -1,c(-1, -17)] * 1 # we get rid of "uncallable.code", 21 | # becouse it has reproducibility of -1 22 | 23 | tmp <- (reproducibility[,-1]*1 %*% reproducibility[,1]) %>% 24 | sapply(non_zero_mean) %>% as.data.frame() 25 | colnames(tmp) <- "correlation_with_reproducibility" 26 | tmp$ID <- rownames(tmp) 27 | 28 | tmp %>% 29 | ggplot(aes(x=reorder(ID, correlation_with_reproducibility), y=correlation_with_reproducibility, fill="red")) + 30 | geom_col(stat="identity") + 31 | theme(axis.text.x = element_text(size = 12, angle = 90, vjust=0.5), legend.position='none') + 32 | xlab("purpose of chunk") + ylab("mean reproducibility") 33 | 34 | 35 | 36 | 37 | 38 | tmp <- (chnk[,c(-1,-2)]*1 %*% chnk[,1]) %>% 39 | sapply(non_zero_mean) %>% as.data.frame() 40 | colnames(tmp) <- "length" 41 | tmp$ID <- rownames(tmp) 42 | tmp %>% 43 | ggplot(aes(x=reorder(ID, length, desc), y=length, fill = "Red")) + 44 | geom_col(stat="identity") + 45 | theme(axis.text.x = element_text(size = 12, angle = 90, vjust=0.5), legend.position='none') + 46 | xlab("purpose of chunk") + ylab("mean length") 47 | 48 | 49 | 50 | 51 | 52 | # table of groups 53 | purpose <- grp[,c(-1)]*1 54 | DataExplorer::plot_correlation(purpose) 55 | 56 | 57 | 58 | tmp <- (grp[,c(-1)]*1 %*% chnk[,1]) %>% sapply(non_zero_mean) %>% as.data.frame() 59 | colnames(tmp) <- "length" 60 | tmp$ID <- rownames(tmp) 61 | tmp %>% 62 | ggplot(aes(x=reorder(ID, length, desc), y=length, fill = "Red")) + 63 | geom_col(stat="identity") + 64 | theme(axis.text.x = element_text(size = 12, angle = 90, vjust=0.5), legend.position='none') + 65 | xlab("purpose of chunk") + ylab("mean length") 66 | 67 | 68 | 69 | 70 | # table of articles 71 | purpose <- art[,c(-1)]*1 72 | DataExplorer::plot_correlation(purpose) 73 | 74 | 75 | 76 | tmp <- (art[,c(-1)]*1 %*% art[,1]) %>% sapply(non_zero_mean) %>% as.data.frame() 77 | colnames(tmp) <- "length" 78 | tmp$ID <- rownames(tmp) 79 | tmp %>% 80 | ggplot(aes(x=reorder(ID, length, desc), y=length, fill = "Red")) + 81 | geom_col(stat="identity") + 82 | theme(axis.text.x = element_text(size = 12, angle = 90, vjust=0.5), legend.position='none') + 83 | xlab("purpose of chunk") + ylab("mean length") 84 | 85 | 86 | -------------------------------------------------------------------------------- /docs/libs/gitbook/css/plugin-bookdown.css: -------------------------------------------------------------------------------- 1 | .book .book-header h1 { 2 | padding-left: 20px; 3 | padding-right: 20px; 4 | } 5 | .book .book-header.fixed { 6 | position: fixed; 7 | right: 0; 8 | top: 0; 9 | left: 0; 10 | border-bottom: 1px solid rgba(0,0,0,.07); 11 | } 12 | span.search-highlight { 13 | background-color: #ffff88; 14 | } 15 | @media (min-width: 600px) { 16 | .book.with-summary .book-header.fixed { 17 | left: 300px; 18 | } 19 | } 20 | @media (max-width: 1240px) { 21 | .book .book-body.fixed { 22 | top: 50px; 23 | } 24 | .book .book-body.fixed .body-inner { 25 | top: auto; 26 | } 27 | } 28 | @media (max-width: 600px) { 29 | .book.with-summary .book-header.fixed { 30 | left: calc(100% - 60px); 31 | min-width: 300px; 32 | } 33 | .book.with-summary .book-body { 34 | transform: none; 35 | left: calc(100% - 60px); 36 | min-width: 300px; 37 | } 38 | .book .book-body.fixed { 39 | top: 0; 40 | } 41 | } 42 | 43 | .book .book-body.fixed .body-inner { 44 | top: 50px; 45 | } 46 | .book .book-body .page-wrapper .page-inner section.normal sub, .book .book-body .page-wrapper .page-inner section.normal sup { 47 | font-size: 85%; 48 | } 49 | 50 | @media print { 51 | .book .book-summary, .book .book-body .book-header, .fa { 52 | display: none !important; 53 | } 54 | .book .book-body.fixed { 55 | left: 0px; 56 | } 57 | .book .book-body,.book .book-body .body-inner, .book.with-summary { 58 | overflow: visible !important; 59 | } 60 | } 61 | .kable_wrapper { 62 | border-spacing: 20px 0; 63 | border-collapse: separate; 64 | border: none; 65 | margin: auto; 66 | } 67 | .kable_wrapper > tbody > tr > td { 68 | vertical-align: top; 69 | } 70 | .book .book-body .page-wrapper .page-inner section.normal table tr.header { 71 | border-top-width: 2px; 72 | } 73 | .book .book-body .page-wrapper .page-inner section.normal table tr:last-child td { 74 | border-bottom-width: 2px; 75 | } 76 | .book .book-body .page-wrapper .page-inner section.normal table td, .book .book-body .page-wrapper .page-inner section.normal table th { 77 | border-left: none; 78 | border-right: none; 79 | } 80 | .book .book-body .page-wrapper .page-inner section.normal table.kable_wrapper > tbody > tr, .book .book-body .page-wrapper .page-inner section.normal table.kable_wrapper > tbody > tr > td { 81 | border-top: none; 82 | } 83 | .book .book-body .page-wrapper .page-inner section.normal table.kable_wrapper > tbody > tr:last-child > td { 84 | border-bottom: none; 85 | } 86 | 87 | div.theorem, div.lemma, div.corollary, div.proposition, div.conjecture { 88 | font-style: italic; 89 | } 90 | span.theorem, span.lemma, span.corollary, span.proposition, span.conjecture { 91 | font-style: normal; 92 | } 93 | div.proof:after { 94 | content: "\25a2"; 95 | float: right; 96 | } 97 | .header-section-number { 98 | padding-right: .5em; 99 | } 100 | -------------------------------------------------------------------------------- /docs/libs/gitbook/js/jquery.highlight.js: -------------------------------------------------------------------------------- 1 | gitbook.require(["jQuery"], function(jQuery) { 2 | 3 | /* 4 | * jQuery Highlight plugin 5 | * 6 | * Based on highlight v3 by Johann Burkard 7 | * http://johannburkard.de/blog/programming/javascript/highlight-javascript-text-higlighting-jquery-plugin.html 8 | * 9 | * Code a little bit refactored and cleaned (in my humble opinion). 10 | * Most important changes: 11 | * - has an option to highlight only entire words (wordsOnly - false by default), 12 | * - has an option to be case sensitive (caseSensitive - false by default) 13 | * - highlight element tag and class names can be specified in options 14 | * 15 | * Copyright (c) 2009 Bartek Szopka 16 | * 17 | * Licensed under MIT license. 18 | * 19 | */ 20 | 21 | jQuery.extend({ 22 | highlight: function (node, re, nodeName, className) { 23 | if (node.nodeType === 3) { 24 | var match = node.data.match(re); 25 | if (match) { 26 | var highlight = document.createElement(nodeName || 'span'); 27 | highlight.className = className || 'highlight'; 28 | var wordNode = node.splitText(match.index); 29 | wordNode.splitText(match[0].length); 30 | var wordClone = wordNode.cloneNode(true); 31 | highlight.appendChild(wordClone); 32 | wordNode.parentNode.replaceChild(highlight, wordNode); 33 | return 1; //skip added node in parent 34 | } 35 | } else if ((node.nodeType === 1 && node.childNodes) && // only element nodes that have children 36 | !/(script|style)/i.test(node.tagName) && // ignore script and style nodes 37 | !(node.tagName === nodeName.toUpperCase() && node.className === className)) { // skip if already highlighted 38 | for (var i = 0; i < node.childNodes.length; i++) { 39 | i += jQuery.highlight(node.childNodes[i], re, nodeName, className); 40 | } 41 | } 42 | return 0; 43 | } 44 | }); 45 | 46 | jQuery.fn.unhighlight = function (options) { 47 | var settings = { className: 'highlight', element: 'span' }; 48 | jQuery.extend(settings, options); 49 | 50 | return this.find(settings.element + "." + settings.className).each(function () { 51 | var parent = this.parentNode; 52 | parent.replaceChild(this.firstChild, this); 53 | parent.normalize(); 54 | }).end(); 55 | }; 56 | 57 | jQuery.fn.highlight = function (words, options) { 58 | var settings = { className: 'highlight', element: 'span', caseSensitive: false, wordsOnly: false }; 59 | jQuery.extend(settings, options); 60 | 61 | if (words.constructor === String) { 62 | words = [words]; 63 | // also match 'foo-bar' if search for 'foo bar' 64 | if (/\s/.test(words[0])) words.push(words[0].replace(/\s+/, '-')); 65 | } 66 | words = jQuery.grep(words, function(word, i){ 67 | return word !== ''; 68 | }); 69 | words = jQuery.map(words, function(word, i) { 70 | return word.replace(/[-[\]{}()*+?.,\\^$|#\s]/g, "\\$&"); 71 | }); 72 | if (words.length === 0) { return this; } 73 | 74 | var flag = settings.caseSensitive ? "" : "i"; 75 | var pattern = "(" + words.join("|") + ")"; 76 | if (settings.wordsOnly) { 77 | pattern = "\\b" + pattern + "\\b"; 78 | } 79 | var re = new RegExp(pattern, flag); 80 | 81 | return this.each(function () { 82 | jQuery.highlight(this, re, settings.element, settings.className); 83 | }); 84 | }; 85 | 86 | }); 87 | -------------------------------------------------------------------------------- /docs/libs/gitbook/js/plugin-sharing.js: -------------------------------------------------------------------------------- 1 | gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) { 2 | var SITES = { 3 | 'github': { 4 | 'label': 'Github', 5 | 'icon': 'fa fa-github', 6 | 'onClick': function(e) { 7 | e.preventDefault(); 8 | var repo = $('meta[name="github-repo"]').attr('content'); 9 | if (typeof repo === 'undefined') throw("Github repo not defined"); 10 | window.open("https://github.com/"+repo); 11 | } 12 | }, 13 | 'facebook': { 14 | 'label': 'Facebook', 15 | 'icon': 'fa fa-facebook', 16 | 'onClick': function(e) { 17 | e.preventDefault(); 18 | window.open("http://www.facebook.com/sharer/sharer.php?u="+encodeURIComponent(location.href)); 19 | } 20 | }, 21 | 'twitter': { 22 | 'label': 'Twitter', 23 | 'icon': 'fa fa-twitter', 24 | 'onClick': function(e) { 25 | e.preventDefault(); 26 | window.open("http://twitter.com/intent/tweet?text="+document.title+"&url="+encodeURIComponent(location.href)+"&hashtags=rmarkdown,bookdown"); 27 | } 28 | }, 29 | 'linkedin': { 30 | 'label': 'LinkedIn', 31 | 'icon': 'fa fa-linkedin', 32 | 'onClick': function(e) { 33 | e.preventDefault(); 34 | window.open("https://www.linkedin.com/shareArticle?mini=true&url="+encodeURIComponent(location.href)+"&title="+encodeURIComponent(document.title)); 35 | } 36 | }, 37 | 'weibo': { 38 | 'label': 'Weibo', 39 | 'icon': 'fa fa-weibo', 40 | 'onClick': function(e) { 41 | e.preventDefault(); 42 | window.open("http://service.weibo.com/share/share.php?content=utf-8&url="+encodeURIComponent(location.href)+"&title="+encodeURIComponent(document.title)); 43 | } 44 | }, 45 | 'instapaper': { 46 | 'label': 'Instapaper', 47 | 'icon': 'fa fa-italic', 48 | 'onClick': function(e) { 49 | e.preventDefault(); 50 | window.open("http://www.instapaper.com/text?u="+encodeURIComponent(location.href)); 51 | } 52 | }, 53 | 'vk': { 54 | 'label': 'VK', 55 | 'icon': 'fa fa-vk', 56 | 'onClick': function(e) { 57 | e.preventDefault(); 58 | window.open("http://vkontakte.ru/share.php?url="+encodeURIComponent(location.href)); 59 | } 60 | } 61 | }; 62 | 63 | 64 | 65 | gitbook.events.bind("start", function(e, config) { 66 | var opts = config.sharing; 67 | if (!opts) return; 68 | 69 | // Create dropdown menu 70 | var menu = _.chain(opts.all) 71 | .map(function(id) { 72 | var site = SITES[id]; 73 | if (!site) return; 74 | return { 75 | text: site.label, 76 | onClick: site.onClick 77 | }; 78 | }) 79 | .compact() 80 | .value(); 81 | 82 | // Create main button with dropdown 83 | if (menu.length > 0) { 84 | gitbook.toolbar.createButton({ 85 | icon: 'fa fa-share-alt', 86 | label: 'Share', 87 | position: 'right', 88 | dropdown: [menu] 89 | }); 90 | } 91 | 92 | // Direct actions to share 93 | _.each(SITES, function(site, sideId) { 94 | if (!opts[sideId]) return; 95 | 96 | gitbook.toolbar.createButton({ 97 | icon: site.icon, 98 | label: site.label, 99 | title: site.label, 100 | position: 'right', 101 | onClick: site.onClick 102 | }); 103 | }); 104 | }); 105 | }); 106 | -------------------------------------------------------------------------------- /docs/libs/gitbook/js/plugin-fontsettings.js: -------------------------------------------------------------------------------- 1 | gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) { 2 | var fontState; 3 | 4 | var THEMES = { 5 | "white": 0, 6 | "sepia": 1, 7 | "night": 2 8 | }; 9 | 10 | var FAMILY = { 11 | "serif": 0, 12 | "sans": 1 13 | }; 14 | 15 | // Save current font settings 16 | function saveFontSettings() { 17 | gitbook.storage.set("fontState", fontState); 18 | update(); 19 | } 20 | 21 | // Increase font size 22 | function enlargeFontSize(e) { 23 | e.preventDefault(); 24 | if (fontState.size >= 4) return; 25 | 26 | fontState.size++; 27 | saveFontSettings(); 28 | }; 29 | 30 | // Decrease font size 31 | function reduceFontSize(e) { 32 | e.preventDefault(); 33 | if (fontState.size <= 0) return; 34 | 35 | fontState.size--; 36 | saveFontSettings(); 37 | }; 38 | 39 | // Change font family 40 | function changeFontFamily(index, e) { 41 | e.preventDefault(); 42 | 43 | fontState.family = index; 44 | saveFontSettings(); 45 | }; 46 | 47 | // Change type of color 48 | function changeColorTheme(index, e) { 49 | e.preventDefault(); 50 | 51 | var $book = $(".book"); 52 | 53 | if (fontState.theme !== 0) 54 | $book.removeClass("color-theme-"+fontState.theme); 55 | 56 | fontState.theme = index; 57 | if (fontState.theme !== 0) 58 | $book.addClass("color-theme-"+fontState.theme); 59 | 60 | saveFontSettings(); 61 | }; 62 | 63 | function update() { 64 | var $book = gitbook.state.$book; 65 | 66 | $(".font-settings .font-family-list li").removeClass("active"); 67 | $(".font-settings .font-family-list li:nth-child("+(fontState.family+1)+")").addClass("active"); 68 | 69 | $book[0].className = $book[0].className.replace(/\bfont-\S+/g, ''); 70 | $book.addClass("font-size-"+fontState.size); 71 | $book.addClass("font-family-"+fontState.family); 72 | 73 | if(fontState.theme !== 0) { 74 | $book[0].className = $book[0].className.replace(/\bcolor-theme-\S+/g, ''); 75 | $book.addClass("color-theme-"+fontState.theme); 76 | } 77 | }; 78 | 79 | function init(config) { 80 | var $bookBody, $book; 81 | 82 | //Find DOM elements. 83 | $book = gitbook.state.$book; 84 | $bookBody = $book.find(".book-body"); 85 | 86 | // Instantiate font state object 87 | fontState = gitbook.storage.get("fontState", { 88 | size: config.size || 2, 89 | family: FAMILY[config.family || "sans"], 90 | theme: THEMES[config.theme || "white"] 91 | }); 92 | 93 | update(); 94 | }; 95 | 96 | 97 | gitbook.events.bind("start", function(e, config) { 98 | var opts = config.fontsettings; 99 | if (!opts) return; 100 | 101 | // Create buttons in toolbar 102 | gitbook.toolbar.createButton({ 103 | icon: 'fa fa-font', 104 | label: 'Font Settings', 105 | className: 'font-settings', 106 | dropdown: [ 107 | [ 108 | { 109 | text: 'A', 110 | className: 'font-reduce', 111 | onClick: reduceFontSize 112 | }, 113 | { 114 | text: 'A', 115 | className: 'font-enlarge', 116 | onClick: enlargeFontSize 117 | } 118 | ], 119 | [ 120 | { 121 | text: 'Serif', 122 | onClick: _.partial(changeFontFamily, 0) 123 | }, 124 | { 125 | text: 'Sans', 126 | onClick: _.partial(changeFontFamily, 1) 127 | } 128 | ], 129 | [ 130 | { 131 | text: 'White', 132 | onClick: _.partial(changeColorTheme, 0) 133 | }, 134 | { 135 | text: 'Sepia', 136 | onClick: _.partial(changeColorTheme, 1) 137 | }, 138 | { 139 | text: 'Night', 140 | onClick: _.partial(changeColorTheme, 2) 141 | } 142 | ] 143 | ] 144 | }); 145 | 146 | 147 | // Init current settings 148 | init(opts); 149 | }); 150 | }); 151 | 152 | 153 | -------------------------------------------------------------------------------- /docs/book_files/figure-html/plot-mark-language-1.svg: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 2 39 | 3 40 | 4 41 | 5 42 | 43 | 44 | 45 | 46 | 47 | 48 | Python 49 | R 50 | Language 51 | StudentsMark 52 | 53 | -------------------------------------------------------------------------------- /docs/book_files/figure-html/plot-value-language-1.svg: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 0.00 41 | 0.25 42 | 0.50 43 | 0.75 44 | 1.00 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | Python 53 | R 54 | Language 55 | ReproducibilityValue 56 | 57 | -------------------------------------------------------------------------------- /docs/book_files/figure-html/plot-mark-journal-1.svg: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 2 41 | 3 42 | 4 43 | 5 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | JMLR 52 | JOSS 53 | JSTAT 54 | Journal 55 | StudentsMark 56 | 57 | -------------------------------------------------------------------------------- /1-6-files/groups.csv: -------------------------------------------------------------------------------- 1 | "length","package.usage","practical.use","method.comparison","generating.output","presenting.specification","data.preparation","occurrence.demonstration","introduction.to.analysis","possible.error" 2 | 15,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 3 | 2,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 4 | 9,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 5 | 45,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 6 | 25,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE 7 | 51,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE 8 | 17,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE 9 | 4,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE 10 | 28,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE 11 | 9,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 12 | 3,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 13 | 5,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 14 | 6,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 15 | 2,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 16 | 1,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 17 | 8,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 18 | 23,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 19 | 9,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE 20 | 12,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE 21 | 3,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 22 | 3,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 23 | 6,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 24 | 1,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 25 | 4,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 26 | 9,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 27 | 5,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 28 | 18,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 29 | 4,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 30 | 1,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 31 | 4,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 32 | 6,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 33 | 7,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 34 | 5,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 35 | 7,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 36 | 2,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 37 | 5,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 38 | 1,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE 39 | 6,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE 40 | 7,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE 41 | 5,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 42 | 10,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 43 | 14,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 44 | 3,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE 45 | 6,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 46 | 1,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 47 | 5,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 48 | 18,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE 49 | 4,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 50 | 8,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE 51 | 21,FALSE,FALSE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE 52 | 7,TRUE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE 53 | 8,TRUE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE 54 | 25,TRUE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE 55 | 16,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 56 | 39,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 57 | 25,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 58 | 25,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 59 | 16,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE 60 | 29,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE 61 | 59,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE 62 | 30,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE 63 | 2,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 64 | 9,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 65 | 4,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 66 | 19,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 67 | 34,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 68 | 30,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 69 | 36,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE 70 | 28,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE 71 | 4,FALSE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,TRUE,FALSE 72 | 5,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 73 | 1,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 74 | 2,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 75 | 15,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 76 | 1,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 77 | 2,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE 78 | 2,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 79 | 3,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 80 | 1,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 81 | 1,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 82 | 1,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE 83 | 2,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 84 | 6,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 85 | 7,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 86 | 23,TRUE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 87 | 10,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE 88 | 1,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 89 | 5,TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE 90 | 6,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE 91 | 9,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 92 | 6,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE 93 | 5,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 94 | 27,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,TRUE,FALSE 95 | 7,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE 96 | 10,TRUE,FALSE,TRUE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE 97 | 11,TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE 98 | 4,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 99 | 2,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 100 | 6,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 101 | 19,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE 102 | 9,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 103 | 10,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 104 | 10,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE 105 | 7,TRUE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,TRUE,TRUE 106 | 7,TRUE,FALSE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 107 | 23,TRUE,FALSE,FALSE,TRUE,FALSE,FALSE,FALSE,FALSE,FALSE 108 | 16,TRUE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE 109 | 30,TRUE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE 110 | 21,TRUE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE 111 | 20,TRUE,FALSE,FALSE,TRUE,FALSE,TRUE,FALSE,FALSE,FALSE 112 | 46,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE 113 | 19,TRUE,FALSE,TRUE,TRUE,FALSE,TRUE,FALSE,TRUE,FALSE 114 | -------------------------------------------------------------------------------- /docs/book_files/figure-html/plot-value-journal-1.svg: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 0.00 43 | 0.25 44 | 0.50 45 | 0.75 46 | 1.00 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | JMLR 56 | JOSS 57 | JSTAT 58 | Journal 59 | ReproducibilityValue 60 | 61 | -------------------------------------------------------------------------------- /docs/book_files/figure-html/unnamed-chunk-10-1.svg: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 8 30 | 1 31 | 2 32 | 0 33 | 5 34 | 0 35 | 0 36 | 0 37 | 2 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 1 53 | 2 54 | 3 55 | 1 56 | 2 57 | 3 58 | Reproducibility of the old version 59 | Reproducibility of the current version 60 | 61 | -------------------------------------------------------------------------------- /docs/libs/gitbook/js/plugin-search.js: -------------------------------------------------------------------------------- 1 | gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) { 2 | var index = null; 3 | var $searchInput, $searchLabel, $searchForm; 4 | var $highlighted = [], hi, hiOpts = { className: 'search-highlight' }; 5 | var collapse = false, toc_visible = []; 6 | 7 | // Use a specific index 8 | function loadIndex(data) { 9 | // [Yihui] In bookdown, I use a character matrix to store the chapter 10 | // content, and the index is dynamically built on the client side. 11 | // Gitbook prebuilds the index data instead: https://github.com/GitbookIO/plugin-search 12 | // We can certainly do that via R packages V8 and jsonlite, but let's 13 | // see how slow it really is before improving it. On the other hand, 14 | // lunr cannot handle non-English text very well, e.g. the default 15 | // tokenizer cannot deal with Chinese text, so we may want to replace 16 | // lunr with a dumb simple text matching approach. 17 | index = lunr(function () { 18 | this.ref('url'); 19 | this.field('title', { boost: 10 }); 20 | this.field('body'); 21 | }); 22 | data.map(function(item) { 23 | index.add({ 24 | url: item[0], 25 | title: item[1], 26 | body: item[2] 27 | }); 28 | }); 29 | } 30 | 31 | // Fetch the search index 32 | function fetchIndex() { 33 | return $.getJSON(gitbook.state.basePath+"/search_index.json") 34 | .then(loadIndex); // [Yihui] we need to use this object later 35 | } 36 | 37 | // Search for a term and return results 38 | function search(q) { 39 | if (!index) return; 40 | 41 | var results = _.chain(index.search(q)) 42 | .map(function(result) { 43 | var parts = result.ref.split("#"); 44 | return { 45 | path: parts[0], 46 | hash: parts[1] 47 | }; 48 | }) 49 | .value(); 50 | 51 | // [Yihui] Highlight the search keyword on current page 52 | $highlighted = results.length === 0 ? [] : $('.page-inner') 53 | .unhighlight(hiOpts).highlight(q, hiOpts).find('span.search-highlight'); 54 | scrollToHighlighted(0); 55 | 56 | return results; 57 | } 58 | 59 | // [Yihui] Scroll the chapter body to the i-th highlighted string 60 | function scrollToHighlighted(d) { 61 | var n = $highlighted.length; 62 | hi = hi === undefined ? 0 : hi + d; 63 | // navignate to the previous/next page in the search results if reached the top/bottom 64 | var b = hi < 0; 65 | if (d !== 0 && (b || hi >= n)) { 66 | var path = currentPath(), n2 = toc_visible.length; 67 | if (n2 === 0) return; 68 | for (var i = b ? 0 : n2; (b && i < n2) || (!b && i >= 0); i += b ? 1 : -1) { 69 | if (toc_visible.eq(i).data('path') === path) break; 70 | } 71 | i += b ? -1 : 1; 72 | if (i < 0) i = n2 - 1; 73 | if (i >= n2) i = 0; 74 | var lnk = toc_visible.eq(i).find('a[href$=".html"]'); 75 | if (lnk.length) lnk[0].click(); 76 | return; 77 | } 78 | if (n === 0) return; 79 | var $p = $highlighted.eq(hi); 80 | $p[0].scrollIntoView(); 81 | $highlighted.css('background-color', ''); 82 | // an orange background color on the current item and removed later 83 | $p.css('background-color', 'orange'); 84 | setTimeout(function() { 85 | $p.css('background-color', ''); 86 | }, 2000); 87 | } 88 | 89 | function currentPath() { 90 | var href = window.location.pathname; 91 | href = href.substr(href.lastIndexOf('/') + 1); 92 | return href === '' ? 'index.html' : href; 93 | } 94 | 95 | // Create search form 96 | function createForm(value) { 97 | if ($searchForm) $searchForm.remove(); 98 | if ($searchLabel) $searchLabel.remove(); 99 | if ($searchInput) $searchInput.remove(); 100 | 101 | $searchForm = $('
    ', { 102 | 'class': 'book-search', 103 | 'role': 'search' 104 | }); 105 | 106 | $searchLabel = $('