├── .gitignore ├── 00-before-we-start.Rmd ├── 00-before-we-start.html ├── 01-intro-to-R.Rmd ├── 01-intro-to-R.html ├── 02-starting-with-data.Rmd ├── 02-starting-with-data.html ├── 03-data-frames.Rmd ├── 03-data-frames.html ├── 04-dplyr.Rmd ├── 04-dplyr.html ├── 05-data-visualization.Rmd ├── 05-data-visualization.html ├── 05-r-and-sql.Rmd ├── 05-visualisation-ggplot2.Rmd ├── CONDUCT.Rmd ├── CONDUCT.html ├── CONTRIBUTING.Rmd ├── CONTRIBUTING.html ├── Ecoli_genomes_with_SNPs_per_locus_tag.txt ├── Ecoli_metadata.csv ├── Ecoli_metadata.txt ├── LICENSE.Rmd ├── LICENSE.html ├── Makefile ├── README.md ├── R_visualization.md ├── _config.yml ├── _includes ├── anySetup.html ├── banner.html ├── footer.html ├── header.html ├── javascript.html ├── lesson-index.html ├── pythonSetup.html ├── rSetup.html ├── setup.html └── spreadsheetSetup.html ├── _layouts ├── lesson.html ├── slides.html └── workshop.html ├── _site.yml ├── css ├── bootstrap │ ├── bootstrap-responsive.css │ ├── bootstrap.css │ └── img │ │ ├── glyphicons-halflings-white.png │ │ └── glyphicons-halflings.png ├── lesson.css ├── pygments │ └── friendly.css ├── swc-bootstrap.css └── swc.css ├── data ├── Ecoli_genomes_with_SNPs_per_locus_tag.txt ├── Ecoli_metadata.csv └── Ecoli_metadata.txt ├── footer.html ├── img ├── DC-logo-vision.png ├── DC1_logo_small.png ├── DataONE_LOGO.jpg ├── R-ecology-correct-order-1.png ├── R-ecology-wrong-order-1.png ├── creative-commons-attribution-license.png ├── r-lesson-boxplot-1.png ├── r-lesson-correct-order-1.png ├── r-lesson-scatter-plot1-1.png ├── r-lesson-unnamed-chunk-10-1.png ├── r-lesson-unnamed-chunk-11-1.png ├── r-lesson-unnamed-chunk-13-1.png ├── r-lesson-unnamed-chunk-14-1.png ├── r-lesson-unnamed-chunk-3-1.png ├── r-lesson-unnamed-chunk-4-1.png ├── r-lesson-unnamed-chunk-5-1.png ├── r-lesson-unnamed-chunk-6-1.png ├── r-lesson-wrong-order-1.png ├── r_starting_example_script.png └── r_starting_how_it_should_like.png ├── index.Rmd ├── index.html ├── journal.pone.0081760.s004.csv ├── site_libs ├── bootstrap-3.3.5 │ ├── css │ │ ├── bootstrap-theme.css │ │ ├── bootstrap-theme.css.map │ │ ├── bootstrap-theme.min.css │ │ ├── bootstrap.css │ │ ├── bootstrap.css.map │ │ ├── bootstrap.min.css │ │ ├── cerulean.min.css │ │ ├── cosmo.min.css │ │ ├── flatly.min.css │ │ ├── fonts │ │ │ ├── Lato.ttf │ │ │ ├── LatoBold.ttf │ │ │ ├── LatoItalic.ttf │ │ │ ├── NewsCycle.ttf │ │ │ ├── NewsCycleBold.ttf │ │ │ ├── OpenSans.ttf │ │ │ ├── OpenSansBold.ttf │ │ │ ├── OpenSansBoldItalic.ttf │ │ │ ├── OpenSansItalic.ttf │ │ │ ├── OpenSansLight.ttf │ │ │ ├── OpenSansLightItalic.ttf │ │ │ ├── Raleway.ttf │ │ │ ├── RalewayBold.ttf │ │ │ ├── Roboto.ttf │ │ │ ├── RobotoBold.ttf │ │ │ ├── RobotoLight.ttf │ │ │ ├── RobotoMedium.ttf │ │ │ ├── SourceSansPro.ttf │ │ │ ├── SourceSansProBold.ttf │ │ │ ├── SourceSansProItalic.ttf │ │ │ ├── SourceSansProLight.ttf │ │ │ └── Ubuntu.ttf │ │ ├── journal.min.css │ │ ├── lumen.min.css │ │ ├── paper.min.css │ │ ├── readable.min.css │ │ ├── sandstone.min.css │ │ ├── simplex.min.css │ │ ├── spacelab.min.css │ │ ├── united.min.css │ │ └── yeti.min.css │ ├── fonts │ │ ├── glyphicons-halflings-regular.eot │ │ ├── glyphicons-halflings-regular.svg │ │ ├── glyphicons-halflings-regular.ttf │ │ ├── glyphicons-halflings-regular.woff │ │ └── glyphicons-halflings-regular.woff2 │ ├── js │ │ ├── bootstrap.js │ │ ├── bootstrap.min.js │ │ └── npm.js │ └── shim │ │ ├── html5shiv.min.js │ │ └── respond.min.js ├── font-awesome-5.0.13 │ ├── css │ │ └── fa-svg-with-js.css │ ├── fonts │ │ ├── fa-brands-400.ttf │ │ ├── fa-regular-400.ttf │ │ └── fa-solid-900.ttf │ └── js │ │ ├── fa-v4-shims.min.js │ │ └── fontawesome-all.min.js ├── jquery-1.11.3 │ └── jquery.min.js ├── jqueryui-1.11.4 │ ├── README │ ├── images │ │ ├── ui-icons_444444_256x240.png │ │ ├── ui-icons_555555_256x240.png │ │ ├── ui-icons_777620_256x240.png │ │ ├── ui-icons_777777_256x240.png │ │ ├── ui-icons_cc0000_256x240.png │ │ └── ui-icons_ffffff_256x240.png │ ├── index.html │ ├── jquery-ui.css │ 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