├── .Rbuildignore ├── .gitattributes ├── .gitignore ├── .travis.yml ├── CNAME ├── DESCRIPTION ├── LICENSE ├── README.md ├── _bookdown.yml ├── _output.yml ├── acknowledgements.Rmd ├── alternative-outputs-and-exts.Rmd ├── appendix-a-template.Rmd ├── appendix-b-faq.Rmd ├── appendix-c-html-extensions.Rmd ├── book.bib ├── book.js ├── caption-reference-eqn.Rmd ├── changing-figures.Rmd ├── citations-and-styles.Rmd ├── cite-fig-tab-sec.Rmd ├── common-problems.Rmd ├── data ├── create-oz-data.R ├── gapminder.csv └── oz_gapminder.csv ├── examples ├── book-demo.Rmd ├── data │ ├── gapminder.csv │ └── oz_gapminder.csv ├── demo-gapminder.Rmd └── intro-doc.Rmd ├── exercises ├── 01-rmd-example │ └── 01-rmd-example.Rmd ├── 02-rmd-figures-chunks │ └── 02-rmd-figures-chunks.Rmd ├── 03-rmd-lm-tables-inline-eqn │ └── 03-rmd-lm-tables-inline-eqn.Rmd ├── 04-rmd-global-opts-device │ └── 04-rmd-global-opts-device.Rmd ├── 05-rmd-bib-polish │ ├── 05-rmd-bib-polish.Rmd │ └── packages.bib ├── 06-rmd-find-errors │ └── 06-rmd-find-errors.Rmd └── 10-polished-example │ ├── 10-polished-example.Rmd │ ├── bmj.csl │ └── packages.bib ├── figs ├── ansi-keyboard.png ├── rmd-report-example-all-data.png ├── rmd-report-example.png ├── rstudio-create-proj-1.png ├── rstudio-create-proj-2.png ├── rstudio-create-proj-3.png ├── rstudio-create-proj-4.png ├── rstudio-knit-button.png ├── rstudio-remove-data.png ├── rstudio-screenshot.png └── ssa-logo.png ├── figures-tables-captions.Rmd ├── header.html ├── index.Rmd ├── inst └── WORDLIST ├── installation.Rmd ├── keyboard-shortcuts.Rmd ├── krantz.cls ├── latex ├── after_body.tex ├── before_body.tex └── preamble.tex ├── license.Rmd ├── logo.png ├── math.Rmd ├── next-steps.Rmd ├── packages.bib ├── pdf-html-word.Rmd ├── references.Rmd ├── rmd4sci.Rproj ├── rstudio.Rmd ├── style.css ├── tests └── spelling.R ├── tic.R ├── using-rmd.Rmd ├── why-rmd.Rmd └── workflow.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | *.Rmd linguist-detectable 2 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/.travis.yml -------------------------------------------------------------------------------- /CNAME: -------------------------------------------------------------------------------- 1 | rmd4sci.njtierney.com 2 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/README.md -------------------------------------------------------------------------------- /_bookdown.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/_bookdown.yml -------------------------------------------------------------------------------- /_output.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/_output.yml -------------------------------------------------------------------------------- /acknowledgements.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/acknowledgements.Rmd -------------------------------------------------------------------------------- /alternative-outputs-and-exts.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/alternative-outputs-and-exts.Rmd -------------------------------------------------------------------------------- /appendix-a-template.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/appendix-a-template.Rmd -------------------------------------------------------------------------------- /appendix-b-faq.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/appendix-b-faq.Rmd -------------------------------------------------------------------------------- /appendix-c-html-extensions.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/appendix-c-html-extensions.Rmd -------------------------------------------------------------------------------- /book.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/book.bib -------------------------------------------------------------------------------- /book.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/book.js -------------------------------------------------------------------------------- /caption-reference-eqn.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/caption-reference-eqn.Rmd -------------------------------------------------------------------------------- /changing-figures.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/changing-figures.Rmd -------------------------------------------------------------------------------- /citations-and-styles.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/citations-and-styles.Rmd -------------------------------------------------------------------------------- /cite-fig-tab-sec.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/cite-fig-tab-sec.Rmd -------------------------------------------------------------------------------- /common-problems.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/common-problems.Rmd -------------------------------------------------------------------------------- /data/create-oz-data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/data/create-oz-data.R -------------------------------------------------------------------------------- /data/gapminder.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/data/gapminder.csv -------------------------------------------------------------------------------- /data/oz_gapminder.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/data/oz_gapminder.csv -------------------------------------------------------------------------------- /examples/book-demo.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/examples/book-demo.Rmd -------------------------------------------------------------------------------- /examples/data/gapminder.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/examples/data/gapminder.csv -------------------------------------------------------------------------------- /examples/data/oz_gapminder.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/examples/data/oz_gapminder.csv -------------------------------------------------------------------------------- /examples/demo-gapminder.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/examples/demo-gapminder.Rmd -------------------------------------------------------------------------------- /examples/intro-doc.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/examples/intro-doc.Rmd -------------------------------------------------------------------------------- /exercises/01-rmd-example/01-rmd-example.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/exercises/01-rmd-example/01-rmd-example.Rmd -------------------------------------------------------------------------------- /exercises/02-rmd-figures-chunks/02-rmd-figures-chunks.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/exercises/02-rmd-figures-chunks/02-rmd-figures-chunks.Rmd -------------------------------------------------------------------------------- /exercises/03-rmd-lm-tables-inline-eqn/03-rmd-lm-tables-inline-eqn.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/exercises/03-rmd-lm-tables-inline-eqn/03-rmd-lm-tables-inline-eqn.Rmd -------------------------------------------------------------------------------- /exercises/04-rmd-global-opts-device/04-rmd-global-opts-device.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/exercises/04-rmd-global-opts-device/04-rmd-global-opts-device.Rmd -------------------------------------------------------------------------------- /exercises/05-rmd-bib-polish/05-rmd-bib-polish.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/exercises/05-rmd-bib-polish/05-rmd-bib-polish.Rmd -------------------------------------------------------------------------------- /exercises/05-rmd-bib-polish/packages.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/exercises/05-rmd-bib-polish/packages.bib -------------------------------------------------------------------------------- /exercises/06-rmd-find-errors/06-rmd-find-errors.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/exercises/06-rmd-find-errors/06-rmd-find-errors.Rmd -------------------------------------------------------------------------------- /exercises/10-polished-example/10-polished-example.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/exercises/10-polished-example/10-polished-example.Rmd -------------------------------------------------------------------------------- /exercises/10-polished-example/bmj.csl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/exercises/10-polished-example/bmj.csl -------------------------------------------------------------------------------- /exercises/10-polished-example/packages.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/exercises/10-polished-example/packages.bib -------------------------------------------------------------------------------- /figs/ansi-keyboard.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/figs/ansi-keyboard.png -------------------------------------------------------------------------------- /figs/rmd-report-example-all-data.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/figs/rmd-report-example-all-data.png -------------------------------------------------------------------------------- /figs/rmd-report-example.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/figs/rmd-report-example.png -------------------------------------------------------------------------------- /figs/rstudio-create-proj-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/figs/rstudio-create-proj-1.png -------------------------------------------------------------------------------- /figs/rstudio-create-proj-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/figs/rstudio-create-proj-2.png -------------------------------------------------------------------------------- /figs/rstudio-create-proj-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/figs/rstudio-create-proj-3.png -------------------------------------------------------------------------------- /figs/rstudio-create-proj-4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/figs/rstudio-create-proj-4.png -------------------------------------------------------------------------------- /figs/rstudio-knit-button.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/figs/rstudio-knit-button.png -------------------------------------------------------------------------------- /figs/rstudio-remove-data.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/figs/rstudio-remove-data.png -------------------------------------------------------------------------------- /figs/rstudio-screenshot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/figs/rstudio-screenshot.png -------------------------------------------------------------------------------- /figs/ssa-logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/figs/ssa-logo.png -------------------------------------------------------------------------------- /figures-tables-captions.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/figures-tables-captions.Rmd -------------------------------------------------------------------------------- /header.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/header.html -------------------------------------------------------------------------------- /index.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/index.Rmd -------------------------------------------------------------------------------- /inst/WORDLIST: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/inst/WORDLIST -------------------------------------------------------------------------------- /installation.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/installation.Rmd -------------------------------------------------------------------------------- /keyboard-shortcuts.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/keyboard-shortcuts.Rmd -------------------------------------------------------------------------------- /krantz.cls: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/krantz.cls -------------------------------------------------------------------------------- /latex/after_body.tex: -------------------------------------------------------------------------------- 1 | \backmatter 2 | \printindex 3 | -------------------------------------------------------------------------------- /latex/before_body.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/latex/before_body.tex -------------------------------------------------------------------------------- /latex/preamble.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/latex/preamble.tex -------------------------------------------------------------------------------- /license.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/license.Rmd -------------------------------------------------------------------------------- /logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/logo.png -------------------------------------------------------------------------------- /math.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/math.Rmd -------------------------------------------------------------------------------- /next-steps.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/next-steps.Rmd -------------------------------------------------------------------------------- /packages.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/packages.bib -------------------------------------------------------------------------------- /pdf-html-word.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/pdf-html-word.Rmd -------------------------------------------------------------------------------- /references.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/references.Rmd -------------------------------------------------------------------------------- /rmd4sci.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/rmd4sci.Rproj -------------------------------------------------------------------------------- /rstudio.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/rstudio.Rmd -------------------------------------------------------------------------------- /style.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/style.css -------------------------------------------------------------------------------- /tests/spelling.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/tests/spelling.R -------------------------------------------------------------------------------- /tic.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/tic.R -------------------------------------------------------------------------------- /using-rmd.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/using-rmd.Rmd -------------------------------------------------------------------------------- /why-rmd.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/why-rmd.Rmd -------------------------------------------------------------------------------- /workflow.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/njtierney/rmd4sci/HEAD/workflow.Rmd --------------------------------------------------------------------------------