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

Source: R/create_protocol.R
create_protocol.Rd

This function will create a new folder based on values that are passed on via the parameters and creates a R-markdown (bookdown) skeleton based on a template file to start working on a new protocol. The function is (partly) interactive and will ask for the title, optional subtitle, the authors, reviewers, file manager and keywords. These metadata (YAML section of index.Rmd file) will then be filled in automatically. The other metadata still need to be passed to the arguments of the function

  • see examples section. Optionally, the rmarkdown chapters are rendered to an html file which will be saved in a matching subfolder of the docs folder.

Usage

create_protocol(
  protocol_type = c("sfp", "spp", "sap", "sop", "sip"),
  short_title,
  version_number = get_version_number(),
  theme = NULL,
  project_name = NULL,
  language = c("nl", "en"),
  from_docx = NULL,
  protocol_number = NULL,
  template = protocol_type,
  render = FALSE
)

create_sfp(
  short_title,
  version_number = get_version_number(),
  theme = c("generic", "water", "air", "soil", "vegetation", "species"),
  language = c("nl", "en"),
  from_docx = NULL,
  protocol_number = NULL,
  template = c("sfp", "generic"),
  render = FALSE
)

create_spp(
  short_title,
  version_number = get_version_number(),
  project_name,
  language = c("nl", "en"),
  from_docx = NULL,
  protocol_number = NULL,
  template = c("spp"),
  render = FALSE
)

create_sap(
  short_title,
  version_number = get_version_number(),
  language = c("nl", "en"),
  from_docx = NULL,
  protocol_number = NULL,
  template = c("sap", "generic"),
  render = FALSE
)

create_sip(
  short_title,
  version_number = get_version_number(),
  language = c("nl", "en"),
  from_docx = NULL,
  protocol_number = NULL,
  template = c("sip", "generic"),
  render = FALSE
)

create_sop(
  short_title,
  version_number = get_version_number(),
  language = c("nl", "en"),
  from_docx = NULL,
  protocol_number = NULL,
  template = c("sop", "generic"),
  render = FALSE
)

Arguments

protocol_type

Either sfp (standard field protocol), spp ( standard project protocol), sap (standard analytical protocol), sip ( standard instrument protocol), sop (standard operating protocol)

short_title

A character string of less than 20 characters to use in folder and file names

version_number

A version number of the form YYYY.##. The default is a function which will determine this number automatically. It should normally not be changed.

theme

A character string equal to one of "generic" (default), "water", "air", "soil", "vegetation" or "species". It is used as the folder location (source/sfp/theme) where standard field protocols that belong to the same theme will be stored. Ignored if protocol_type is other than "sfp".

project_name

A character string that is used as the folder location (source/spp/project_name) where project-specific protocols that belong to the same project will be stored. Preferably a short name or acronym. If the folder does not exist, it will be created. Ignored if protocol_type is other than "spp".

language

Language of the protocol, either "nl" (Dutch), the default, or "en" (English).

from_docx

A character string with the path (absolute or relative) to a .docx file containing a pre-existing protocol. Please make sure to copy-paste all relevant meta-data from the .docx file to the corresponding parameters of this function. If nothing is provided (i.e. default = NULL), an empty template will be used.

protocol_number

A character string giving the protocol number. This parameter should normally not be specified (i.e. NULL), unless from_docx is specified. A protocol number is a three digit string where the first digit corresponds with a theme and the last two digits identify a protocol within a theme for standard field protocols. A protocol number for other protocol types is just a three digit string. If NULL (the default), a protocol number will be determined automatically based on pre-existing protocol numbers. Note that for backwards compatibility with protocol numbers that were already in use at INBO, we made a list of reserved numbers. These reserved numbers will not be used when protocol_number is NULL. The only time you will need to explicitly pass a protocol number to the protocol_number argument is when you want to migrate a pre-existing INBO protocol to protocolsource and hence use one of the reserved numbers. Protocol numbers that are already in use in protocolsource can be retrieved with get_protocolnumbers().

template

Which template to use? Default is set equal to protocol_type. However, you can also set this to "generic" in which case a simplified template will be used that can be used as an alternative to the default templates.

render

Whether or not to render the protocol to html. Defaults to FALSE.

Details

It is assumed that the source folder is a subfolder of an RStudio project with git version control. A target folder to which files will be written will be created as subdirectories beneath source. The subfolder structure is of the form /sfp/<theme>/<sfp>_<protocolnumber>_<language>_<short_title>/ for standard field protocols. Or /spp/<project_name>/<spp>_<protocolnumber>_<language>_<short_title>/ for standard project protocols. Or /sip/<sip>_<protocolnumber>_<language>_<short_title>/ for sips (and analogous for sop and sap). The folder names are determined by the corresponding arguments of the function. A matching subfolder structure will be created beneath the docs folder (and output files needed for rendering to html output will be placed in it if render = TRUE. The template Rmarkdown files and the Rmarkdown files that result from converting a docx protocol (see from_docx argument), will be written to the target folder beneath source. Template Rmarkdown files with the same name as Rmarkdown files that result from converting a docx protocol will be overwritten by the latter. Besides Rmarkdown files, this target folder will also contain files needed to render to a Bookdown gitbook such as a _bookdown.yml and _output.yml. The NEWS.md file must be used to document the changes between revisions of the protocol. Furthermore, a data and a media folder will be created as subdirectories of the target folder. The media folder can be used to store image files and will contain image files extracted from the docx protocol when the from_docx argument is used. The data folder can be used to store tabular data that are needed for the protocol.

See also

Other creation: add_dependencies(), add_one_subprotocol(), add_subprotocols(), insert_protocolsection(), update_protocol(), update_version_number()

Examples

if (FALSE) { # \dontrun{
protocolhelper::create_protocol(
  protocol_type = "sfp",
  short_title = "water 1",
  theme = "water", language = "en")
} # }