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new_compendium.Rd
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new_compendium.Rd
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/new_compendium.R
\name{new_compendium}
\alias{new_compendium}
\title{Create an R compendium structure}
\usage{
new_compendium(
compendium = NULL,
license = "GPL (>= 2)",
status = NULL,
lifecycle = NULL,
contributing = TRUE,
code_of_conduct = TRUE,
vignette = FALSE,
test = FALSE,
create_repo = TRUE,
private = FALSE,
gh_check = FALSE,
codecov = FALSE,
website = FALSE,
gh_render = FALSE,
gh_citation = FALSE,
given = NULL,
family = NULL,
email = NULL,
orcid = NULL,
organisation = NULL,
renv = FALSE,
dockerfile = FALSE,
overwrite = FALSE,
quiet = FALSE
)
}
\arguments{
\item{compendium}{A character vector specifying the folders to be created.
See \code{\link[=add_compendium]{add_compendium()}} for further information.}
\item{license}{A character vector of length 1. The license to be used for
this project. Run \code{\link[=get_licenses]{get_licenses()}} to choose an appropriate one. Default
is \code{license = 'GPL (>= 2)'}
The license can be changed later by calling \code{\link[=add_license]{add_license()}} (and
\code{\link[=add_license_badge]{add_license_badge()}} or \code{\link[=refresh]{refresh()}} to update the corresponding badge in
the README).}
\item{status}{A character vector of length 1. The status of the project
according to the standard defined by the \url{https://www.repostatus.org}
project. One among \code{'concept'}, \code{'wip'}, \code{'suspended'}, \code{'abandoned'},
\code{'active'}, \code{'inactive'}, or \code{'unsupported'}. See \code{\link[=add_repostatus_badge]{add_repostatus_badge()}}
for further information.
This argument is used to add a badge to the \code{README.Rmd} to help visitors
to better understand your project. Default is \code{status = NULL}.
This status can be added/changed later by using \code{\link[=add_repostatus_badge]{add_repostatus_badge()}}.}
\item{lifecycle}{A character vector of length 1. The life cycle stage of
the project according to the standard defined at
\url{https://lifecycle.r-lib.org/articles/stages.html}. One among
\code{'experimental'}, \code{'stable'}, \code{'deprecated'}, or \code{'superseded'}.
See \code{\link[=add_lifecycle_badge]{add_lifecycle_badge()}} for further information.
This argument is used to add a badge to the \code{README.Rmd} to help visitors
to better understand your project. Default is \code{lifecycle = NULL}.
This stage can be added/changed later by using \code{\link[=add_lifecycle_badge]{add_lifecycle_badge()}}.}
\item{contributing}{A logical value. If \code{TRUE} (default) adds a
\code{CONTRIBUTING.md} file and \code{ISSUE_TEMPLATES}. See \code{\link[=add_contributing]{add_contributing()}} for
further information.}
\item{code_of_conduct}{A logical value. If \code{TRUE} (default) adds a
\code{CODE_OF_CONDUCT.md} file. See \code{\link[=add_code_of_conduct]{add_code_of_conduct()}} for further
information.}
\item{vignette}{A logical value. If \code{TRUE} creates a vignette in
\verb{vignettes/}. Packages \href{https://yihui.org/knitr/}{\code{knitr}} and
\href{https://rmarkdown.rstudio.com/}{\code{rmarkdown}} are also added to the
\code{Suggests} field in the \code{DESCRIPTION} file. Default is \code{FALSE}.}
\item{test}{A logical value. If \code{TRUE} initializes units tests by running
\code{\link[usethis:use_testthat]{usethis::use_testthat()}}.
Package \href{https://testthat.r-lib.org}{\code{testthat}} is also added to the
\code{Suggests} field in the \code{DESCRIPTION} file. Default is \code{FALSE}.}
\item{create_repo}{A logical value. If \code{TRUE} (default) creates a repository
(public if \code{private = FALSE} or private if \code{private = TRUE}) on GitHub.
See the section \strong{Creating a GitHub repo} of the help page of
\code{\link[=new_package]{new_package()}}.}
\item{private}{A logical value. If \code{TRUE} creates a private repository on
user GitHub account (or organisation). Default is \code{private = FALSE}.}
\item{gh_check}{A logical value. If \code{TRUE} configures GitHub
Actions to automatically check and test the package after each push. This
will run \verb{R CMD check} on the three major operating systems (Ubuntu, macOS,
and Windows) on the latest release of R. See \code{\link[=add_github_actions_check]{add_github_actions_check()}}
for further information.
If \code{create_repo = FALSE} this argument is ignored. Default is \code{FALSE}.}
\item{codecov}{A logical value. If \code{TRUE} configures GitHub Actions to
automatically report the code coverage of units tests after each push.
See \code{\link[=add_github_actions_codecov]{add_github_actions_codecov()}} for further information.
If \code{create_repo = FALSE} this argument is ignored. Default is \code{FALSE}.}
\item{website}{A logical value. If \code{TRUE} configures GitHub
Actions to automatically build and deploy the package website
(using \href{https://pkgdown.r-lib.org/index.html}{\code{pkgdown}})
after each push. A \strong{gh-pages} branch will be created using
\code{\link[usethis:use_github_pages]{usethis::use_github_pages()}} and the GitHub repository will be
automatically configured to deploy website.
If \code{create_repo = FALSE} this argument is ignored. Default is \code{FALSE}.}
\item{gh_render}{A logical value. If \code{TRUE} configures GitHub
Actions to automatically knit the \code{README.Rmd} after each push.
See \code{\link[=add_github_actions_render]{add_github_actions_render()}} for further information.
If \code{create_repo = FALSE} this argument is ignored. Default is \code{FALSE}.}
\item{gh_citation}{A logical value. If \code{TRUE} configures GitHub
Actions to automatically update the \code{CITATION.cff} file.
See \code{\link[=add_github_actions_citation]{add_github_actions_citation()}} for further information.
If \code{create_repo = FALSE} this argument is ignored. Default is \code{FALSE}.}
\item{given}{A character vector of length 1. The given name of the
maintainer of the package. If \code{NULL} (default) the function will try to
get this value by reading the \code{.Rprofile} file.
For further information see \code{\link[=set_credentials]{set_credentials()}}.}
\item{family}{A character vector of length 1. The family name of the
maintainer of the package. If \code{NULL} (default) the function will try to
get this value by reading the \code{.Rprofile} file.
For further information see \code{\link[=set_credentials]{set_credentials()}}.}
\item{email}{A character vector of length 1. The email address of the
maintainer of the package. If \code{NULL} (default) the function will try to
get this value by reading the \code{.Rprofile} file.
For further information see \code{\link[=set_credentials]{set_credentials()}}.}
\item{orcid}{A character vector of length 1. The ORCID of the maintainer of
the package. If \code{NULL} (default) the function will try to get this value
by reading the \code{.Rprofile} file.
For further information see \code{\link[=set_credentials]{set_credentials()}}.}
\item{organisation}{A character vector of length 1. The GitHub organisation
to host the repository. If defined it will overwrite the GitHub pseudo.
Default is \code{organisation = NULL} (the GitHub pseudo will be used).}
\item{renv}{A logical value. If \code{TRUE} initializes an \code{renv} environment for
the project by running \code{\link[renv:init]{renv::init()}}.
Package \href{https://rstudio.github.io/renv/}{\code{renv}} is also added to the
\code{Imports} field in the \code{DESCRIPTION} file. Default is \code{FALSE}.}
\item{dockerfile}{A logical value. If \code{TRUE} creates an \code{Dockerfile} for
the project. See \code{\link[=add_dockerfile]{add_dockerfile()}} for further detail. Default is \code{FALSE}.}
\item{overwrite}{A logical value. If \code{TRUE} files written from templates and
modified by user are erased. Default is \code{overwrite = FALSE}.
\strong{Be careful while using this argument}.}
\item{quiet}{A logical value. If \code{TRUE} messages are deleted. Default is
\code{FALSE}.}
}
\value{
No return value.
}
\description{
This function creates a research compendium (i.e. a predefined files/folders
structure) to help user organizing files/folders to run analysis.
In addition to common R packages files/folders (see \code{\link[=new_package]{new_package()}} for
further information) this function will created these following folders:
\itemize{
\item \verb{data/}: a folder to store raw data. Note that these data must never be
modified. If user want to modify them it is recommended to export new data
in \verb{outputs/}.
\item \verb{analyses/}: a folder to write analyses instructions, i.e. R scripts. If
user need to create R functions it is recommended to write them in the \verb{R/}
folder.
\item \verb{outputs/}: a folder to store intermediate and final outputs generated by
the R scripts.
\item \verb{figures/}: a folder to store figures generated by the R scripts.
}
This function also creates a Make-like R file (\code{make.R}). This file contains
two main lines:
\itemize{
\item \code{devtools::install_deps()}: downloads the external dependencies required
by the project (an alternative to \code{install.packages()}). Ideal for sharing;
\item \code{devtools::load_all()}: loads external dependencies and R functions (an
alternative to \code{library()} and \code{source()} respectively).
}
As the user writes R scripts he/she can add the following line in this file:
\code{source(here::here("rscripts", "script_X.R"))}. Then he/she can source the
entire \code{make.R} to run analysis. The function \code{\link[=add_dependencies]{add_dependencies()}} can be
used to automatically add external dependencies in the \code{DESCRIPTION} file.
It is recommended, for a better reproducibility, to call external
dependencies as \code{pkg::fun()} or with \verb{@import} or \verb{@importFrom} in R
functions instead of using \code{library()}.
All these files/folders are added to the \code{.Rbuildignore} so the rest of the
project (e.g. R functions) can be used (or installed) as a R package.
}
\examples{
\dontrun{
library(rcompendium)
## Define **ONCE FOR ALL** your credentials ----
set_credentials(given = "John", family = "Doe",
email = "john.doe@domain.com",
orcid = "9999-9999-9999-9999", protocol = "ssh")
## Create an R package ----
new_compendium()
## Start adding data and developing functions and scripts ----
## ...
## Update package (documentation, dependencies, README, check) ----
refresh()
}
}
\seealso{
Other setup functions:
\code{\link{new_package}()},
\code{\link{refresh}()},
\code{\link{set_credentials}()}
}
\concept{setup functions}