Reference

Protocol creation and updating

Functions for starting work on a new protocol or update a protocol

add_dependencies()

Adds dependencies to the YAML of an index.Rmd file

add_one_subprotocol()

Helper function to add one sub-protocol to a project-specific protocol of which it is a dependency

add_subprotocols()

Render all sub-protocols belonging to a main protocol to single markdown files

create_protocol() create_sfp() create_spp() create_sap() create_sip() create_sop()

Create a folder with a bookdown (R markdown) template to start a new protocol and optionally render to html

insert_protocolsection()

Function to add a chapter or a section of a published protocol for re-use in another protocol

update_protocol()

Preparatory steps to start the update of a pre-existing version of a protocol

update_version_number()

Updates the version number in the YAML section of a protocol index.Rmd file and optionally in protocol NEWS.md

docx convertion

Functions to convert docx to markdown

add_captions()

Touch up figure and table captions after using convert_docx_to_rmd()

convert_docx_to_rmd()

Convert a docx-file (a protocol) to an (R)markdown file

Protocol checking

Functions to check if protocols comply with standards

check_all()

Check protocol frontmatter and structure

check_all_author_info()

Helper function to check if author information is correct

check_frontmatter()

Checks protocol metadata

check_structure()

Checks protocol document structure

protocolcheck

The protocolcheck R6 class

validate_orcid()

validate an ORCID string

Utility functions

Functions that can be useful when working with protocols

add_label()

Helper function to create labelled captions for pander tables

get_path_to_protocol()

Function to get (or set) the full path to a protocol

get_protocol_type()

Get protocol type from protocol code

get_protocolnumbers()

Function to list all occupied protocol numbers

get_short_titles()

Function to list all short titles that are already in use.

get_version_number()

Get version number for a protocol

increment_version_number()

Increment version number

Protocol preview

Function to render a protocol

render_protocol()

Function to render a protocol to html and pdf.