Document Structure

Main file and sub documents:

The document is structured in a main document (open_science_paper.Rnw) located in the Open-Science-Paper root folder and several sub documents. The main document includes all of the sub documents as child elements via noweb code chunks. They look like shown in the example box below. Usually you do not have to edit the main file, except you like to change a class option or add another subdocument to your paper.

<<subdoc_content_header, child='usr/subdocuments/osp_header.Rnw', eval=T>>=
@

The root folder contains two folders that separates a document space from a user modification space.

usr folder:

└── usr
    ├── cache
    ├── graphics
    │   ├── dynamic
    │   └── static
    ├── statistics
    │   ├── datasave
    │   └── rproject
    └── subdocuments
        ├── bibliography
        │   └── open_science_paper.bib
        ├── chapters
        │   ├── chunks
        │   ├── osp_abstract_section.Rnw
        │   ├── osp_acknowledgements_section.Rnw
        │   ├── osp_bibliography_section.Rnw
        │   ├── osp_discussion_section.Rnw
        │   ├── osp_header.Rnw
        │   ├── osp_introduction_section.Rnw
        │   ├── osp_material_methods_section.Rnw
        │   └── osp_results_section.Rnw
        └── options
            ├── osp_document_options.sty
            └── osp_global_knitr_options.Rnw

• cache: Contains the Knitr cache
• graphics:
  • static: Put static graphics in here
  • dynamic: Default output folder for the generated Knitr graphics
• statistics:
  • datasave: Put your primary research data into it
  • rproject: Use if for R scripts or fill it with the maketask initrproject
• subdocuments:
  • bibliography: The bibliography file
  • chapters: All the document chapter files
  • options: The global Knitr configuration and the style file for user changes

osp folder:

Open-Science-Paper related stuff like examples and logo graphics.

• data: The template for the github hook and the example for a csv file for the header information
• graphics: Open-Science-Paper logos
• server: Continous interation server for the document
• subdocuments: Exampel data and empty files for the makefile switch and the class file

├── osp
│   ├── data
│   │   ├── ospGitHook
│   │   └── ospHeaderTable.csv
│   ├── graphics
│   │   ├── MapPelargoniumSidoides.pdf
│   │   ├── open-science-papers-footer-logo-black.pdf
│   │   ├── open-science-papers-footer-logo-black.svg
│   │   ├── open-science-papers-footer-logo-gray.pdf
│   │   ├── open-science-papers-footer-logo-gray.svg
│   │   ├── open-science-papers-logos-all.svg
│   │   ├── open-science-papers-title-header-logo.pdf
│   │   ├── open-science-paper-title-header-logo.svg
│   │   └── Pelargoniumsidoides.png
│   ├── server
│   │   └── buildserver.rb
│   └── subdocuments
│       ├── exmpl
│       │   ├── bibliography
│       │   │   └── open_science_paper.bib
│       │   ├── chapters
│       │   │   ├── chunks
│       │   │   ├── osp_abstract_section.Rnw
│       │   │   ├── osp_acknowledgements_section.Rnw
│       │   │   ├── osp_bibliography_section.Rnw
│       │   │   ├── osp_discussion_section.Rnw
│       │   │   ├── osp_header.Rnw
│       │   │   ├── osp_introduction_section.Rnw
│       │   │   ├── osp_material_methods_section.Rnw
│       │   │   ├── osp_results_section.Rnw
│       │   │   └── osp_results_section.tex
│       │   ├── options
│       │   │   ├── osp_document_options.sty
│       │   │   └── osp_global_knitr_options.Rnw
│       │   └── README.md
│       ├── open_science_paper.cls
│       └── temp
│           ├── bibliography
│           │   └── open_science_paper.bib
│           ├── chapters
│           │   ├── chunks
│           │   ├── osp_abstract_section.Rnw
│           │   ├── osp_acknowledgements_section.Rnw
│           │   ├── osp_bibliography_section.Rnw
│           │   ├── osp_discussion_section.Rnw
│           │   ├── osp_header.Rnw
│           │   ├── osp_introduction_section.Rnw
│           │   ├── osp_material_methods_section.Rnw
│           │   ├── osp_results_section.Rnw
│           │   └── osp_results_section.tex
│           ├── options
│           │   ├── osp_document_options.sty
│           │   └── osp_global_knitr_options.Rnw
│           └── README.md

Full structure overview

.
├── makefile
├── open_science_paper.pdf
├── open_science_paper.Rnw
├── osp
│   ├── data
│   │   ├── ospGitHook
│   │   └── ospHeaderTable.csv
│   ├── graphics
│   │   ├── MapPelargoniumSidoides.pdf
│   │   ├── open-science-papers-footer-logo-black.pdf
│   │   ├── open-science-papers-footer-logo-black.svg
│   │   ├── open-science-papers-footer-logo-gray.pdf
│   │   ├── open-science-papers-footer-logo-gray.svg
│   │   ├── open-science-papers-logos-all.svg
│   │   ├── open-science-papers-title-header-logo.pdf
│   │   ├── open-science-paper-title-header-logo.svg
│   │   └── Pelargoniumsidoides.png
│   ├── server
│   │   └── buildserver.rb
│   └── subdocuments
│       ├── exmpl
│       │   ├── bibliography
│       │   │   └── open_science_paper.bib
│       │   ├── chapters
│       │   │   ├── chunks
│       │   │   ├── osp_abstract_section.Rnw
│       │   │   ├── osp_acknowledgements_section.Rnw
│       │   │   ├── osp_bibliography_section.Rnw
│       │   │   ├── osp_discussion_section.Rnw
│       │   │   ├── osp_header.Rnw
│       │   │   ├── osp_introduction_section.Rnw
│       │   │   ├── osp_material_methods_section.Rnw
│       │   │   ├── osp_results_section.Rnw
│       │   │   └── osp_results_section.tex
│       │   ├── options
│       │   │   ├── osp_document_options.sty
│       │   │   └── osp_global_knitr_options.Rnw
│       │   └── README.md
│       ├── open_science_paper.cls
│       └── temp
│           ├── bibliography
│           │   └── open_science_paper.bib
│           ├── chapters
│           │   ├── chunks
│           │   ├── osp_abstract_section.Rnw
│           │   ├── osp_acknowledgements_section.Rnw
│           │   ├── osp_bibliography_section.Rnw
│           │   ├── osp_discussion_section.Rnw
│           │   ├── osp_header.Rnw
│           │   ├── osp_introduction_section.Rnw
│           │   ├── osp_material_methods_section.Rnw
│           │   ├── osp_results_section.Rnw
│           │   └── osp_results_section.tex
│           ├── options
│           │   ├── osp_document_options.sty
│           │   └── osp_global_knitr_options.Rnw
│           └── README.md
├── README.md
└── usr
    ├── cache
    ├── graphics
    │   ├── dynamic
    │   └── static
    ├── statistics
    │   ├── datasave
    │   └── rproject
    └── subdocuments
        ├── bibliography
        │   └── open_science_paper.bib
        ├── chapters
        │   ├── chunks
        │   ├── osp_abstract_section.Rnw
        │   ├── osp_acknowledgements_section.Rnw
        │   ├── osp_bibliography_section.Rnw
        │   ├── osp_discussion_section.Rnw
        │   ├── osp_header.Rnw
        │   ├── osp_introduction_section.Rnw
        │   ├── osp_material_methods_section.Rnw
        │   └── osp_results_section.Rnw
        └── options
            ├── osp_document_options.sty
            └── osp_global_knitr_options.Rnw

28 directories, 55 files