Package index • protocolhelper

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_person_info(): Helper function to check if person 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.