├── .gitignore ├── .gitmodules ├── CONTRIBUTING.md ├── Gemfile ├── LICENSE.md ├── Makefile ├── README.md ├── _config.yml ├── _honor_roll ├── BTopcuoglu.jpg ├── BTopcuoglu.yml ├── TonimaRahman.jpg ├── TonimaRahman.yml ├── _template.yml ├── index.md ├── jcgneto.jpg ├── jcgneto.yml ├── priscalim00.jpg ├── priscalim00.yml ├── pschloss.jpg ├── pschloss.yml ├── tomkoset.jpg └── tomkoset.yml ├── _reproducible_research ├── 01_introduction.html ├── 02_reproducibility.html ├── 03_first_steps.html ├── 04_hpc.html ├── 05_documentation.html ├── 06_organization.html ├── 07_version_control.html ├── 08_automation.html ├── 09_programmatic_analyses.html ├── 10_literate_programming.html ├── 11_makefiles.html ├── 12_collaboration_personal.html ├── 13_collaboration_others.html ├── 14_open_science.html └── 2018_07_12_IMMSA.html ├── assets ├── fonts │ ├── DroidSerif-Bold.ttf │ ├── DroidSerif-BoldItalic.ttf │ ├── DroidSerif-Italic.ttf │ ├── DroidSerif.ttf │ ├── UbuntuMono-Bold.ttf │ ├── UbuntuMono-BoldItalic.ttf │ ├── UbuntuMono-Italic.ttf │ ├── UbuntuMono-Regular.ttf │ ├── YanoneKaffeesatz-Bold.ttf │ ├── YanoneKaffeesatz-ExtraLight.ttf │ ├── YanoneKaffeesatz-Light.ttf │ └── YanoneKaffeesatz-Regular.ttf └── images │ ├── 538_analysis_dag.png │ ├── 538_article_screen_shot.png │ ├── 538_brittany_distribution.png │ ├── 538_males_distribution.png │ ├── 538_repository.png │ ├── 538_schloss_report.png │ ├── a_lot_of_talking.gif │ ├── all-hail-reproducibility.png │ ├── analysis_paths.png │ ├── analysis_paths.pptx │ ├── animated-nmds.gif │ ├── asm-reproducibility-blurb.png │ ├── asm-reproducibility.jpg │ ├── available_upon_request.png │ ├── awesomesauce.gif │ ├── aws_ami_selection.png │ ├── aws_ec2_dashboard.png │ ├── aws_instance_type.png │ ├── aws_instances_dashboard.png │ ├── aws_key_pair.png │ ├── aws_services.png │ ├── aws_splash.png │ ├── aws_storage.png │ ├── aws_tutorial.png │ ├── aws_view_instances.png │ ├── begley-replicability.png │ ├── beyonce.png │ ├── boss.gif │ ├── bourne_table.png │ ├── brogrammer.gif │ ├── catterplots.png │ ├── click_settings_to_transfer.png │ ├── close_issue.png │ ├── contributing_md.png │ ├── create_new_issue.png │ ├── draw-an-owl-meme.jpg │ ├── edit_issue.png │ ├── edit_license.png │ ├── figshare.png │ ├── filezilla_apply_ok_filter.png │ ├── filezilla_approve_host_key.png │ ├── filezilla_aws_connected.png │ ├── filezilla_aws_dns.png │ ├── filezilla_aws_host_info.png │ ├── filezilla_create_filter.png │ ├── filezilla_double_click_behavior.png │ ├── filezilla_empty_directory.png │ ├── filezilla_filter_effect.png │ ├── filezilla_filter_name.png │ ├── filezilla_filters.png │ ├── filezilla_find_keypair.png │ ├── filezilla_fresh.png │ ├── filezilla_keypair_loaded.png │ ├── filezilla_program_filter.png │ ├── filezilla_random_picture.png │ ├── filezilla_refrehsed_directory.png │ ├── filezilla_select_server.png │ ├── filezilla_sftp_settings.png │ ├── filezilla_view.png │ ├── flux_configuration.jpg │ ├── flux_configuration.pptx │ ├── forked_repository.png │ ├── forking.png │ ├── gganimate.gif │ ├── git_commit_2x.png │ ├── github-Kozich_ReAnalysis_AEM_2013-repository.png │ ├── github-create-new-repository.png │ ├── github-edit-readme.png │ ├── github-new-repository-instructions.png │ ├── github-new-repository.png │ ├── github-signup.png │ ├── github-user-home.png │ ├── good_job.gif │ ├── goto_issues_repo.png │ ├── hadley-style-guide.png │ ├── high-five.gif │ ├── hooke_microscope.png │ ├── issue_001.png │ ├── issue_004.png │ ├── issue_04_closed.png │ ├── issue_04_create_pr.png │ ├── issue_04_pr_accepted.png │ ├── issue_04_pr_branch_deleted.png │ ├── issue_04_pr_feedback_iteration_1.png │ ├── issue_04_pr_feedback_iteration_2.png │ ├── issue_04_pr_final.png │ ├── issue_04_pr_iteration_1.png │ ├── issue_04_pr_iteration_2.png │ ├── issue_04_pr_merge.png │ ├── issues_002_and_003_close.png │ ├── jir.jpg │ ├── kozich-figure-4.png │ ├── kozich_scaling_up.png │ ├── kozich_scaling_up_marked.png │ ├── kozich_table_2.png │ ├── leeuwenhoek-doodle.gif │ ├── leeuwenhoek_microscope.png │ ├── license.png │ ├── mater-git-r-done.jpg │ ├── melba_roy.jpg │ ├── new_github_branch.png │ ├── new_issue_contribution.png │ ├── new_issues.png │ ├── new_organization.png │ ├── new_organization_signup.png │ ├── nih-grant-guideline.jpg │ ├── noble-figure-1.png │ ├── obama.gif │ ├── open_access.png │ ├── orcid.png │ ├── otherpeoplesdata.png │ ├── password.png │ ├── pebkac.jpg │ ├── phd-final-doc.gif │ ├── phd-story-told-in-filenames.gif │ ├── practice_citation.png │ ├── practice_html_basic.png │ ├── practice_html_code_chunk.png │ ├── practice_html_echo_false.png │ ├── practice_html_inline_dry_formatting.png │ ├── practice_html_inline_formatting.png │ ├── practice_html_title_author.png │ ├── practice_html_with_figure.png │ ├── practice_html_with_table.png │ ├── practice_references.png │ ├── preprints.png │ ├── press_fork_button.png │ ├── preventitive-medicine.jpg │ ├── prinz-replicability.png │ ├── repro_contingency_table.png │ ├── repro_contingency_table_exercise.png │ ├── repro_contingency_table_mine.png │ ├── riffomonas_splash_page.png │ ├── rmarkdown-flow.png │ ├── schloss-notebook.jpg │ ├── schloss_rubric.png │ ├── select_license.png │ ├── select_were_to_fork.png │ ├── sheep-cheering.gif │ ├── steve_martin_fork.gif │ ├── swc-git-staging-area.svg │ ├── teamwork.gif │ ├── topics_add.png │ ├── topics_link.png │ ├── topics_list.png │ ├── topics_reproducible_paper.png │ ├── transfer_ownership_button.png │ ├── transfer_pending.png │ ├── transfer_pending_update.png │ ├── transfer_repository_checks.png │ ├── transfer_success.png │ ├── transfer_team_access.png │ ├── watson_crick.png │ ├── wesanderson.png │ ├── write_paper.png │ └── you.gif ├── codemeta.json ├── favicon.ico ├── index.md ├── issue_template.md ├── mbio.csl ├── paper.bib ├── paper.md └── rr_notes_prep.md /.gitignore: -------------------------------------------------------------------------------- 1 | _site 2 | .sass-cache 3 | .jekyll-metadata 4 | 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