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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
<!-- badges: start -->
[](https://www.repostatus.org/#active)
[](https://lifecycle.r-lib.org/articles/stages.html#maturing-1)
[](https://www.gnu.org/licenses/gpl-3.0.html)
[](https://github.com/inbo/checklist/releases)
[](https://github.com/inbo/checklist/actions)
[](https://app.codecov.io/gh/inbo/checklist?branch=main)
[](https://doi.org/10.5281/zenodo.4028303)
<!-- badges: end -->
# The Checklist Package <img src="man/figures/logo.svg" align="right" alt="A hexagon with the word checklist" width="120" />
```{r setup, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE, comment = "#>", fig.path = "man/figures/README-",
out.width = "100%", eval = FALSE
)
```
The goal of `checklist` is to provide an elaborate and strict set of checks for R packages and R code.
## Installation
You can install the package from the [INBO universe](https://inbo.r-universe.dev/builds) via
```{r universe}
# Enable the INBO universe
options(
repos = c(
inbo = "https://inbo.r-universe.dev", CRAN = "https://cloud.r-project.org"
)
)
# Install the packages
install.packages("checklist")
```
If that doesn't work, you can install the version from [GitHub](https://github.com/inbo/checklist/) with:
```{r installation}
# install.packages("remotes")
remotes::install_github("inbo/checklist")
```
## Setting a default organisation
We created `checklist` with the Research Institute for Nature and Forest (INBO) in mind.
When you don't specify the organisation, `checklist` assumes the code was written by INBO personnel.
INBO has specific requirements which are not relevant for external users of `checklist`.
When you are not writing code for INBO, we recommend that you set a default `organisation`.
Below we specify the defaults for INBO.
More details in `vignette("organisation", package = "checklist")`.
```{r organisation}
library(checklist)
org <- organisation$new(
github = "inbo", community = "inbo", email = "[email protected]",
rightsholder = "Research Institute for Nature and Forest (INBO)",
funder = "Research Institute for Nature and Forest (INBO)",
organisation = list(
"inbo.be" = list(
affiliation = c(
en = "Research Institute for Nature and Forest (INBO)",
nl = "Instituut voor Natuur en Bosonderzoek (INBO)"
),
orcid = TRUE
)
)
)
default_organisation(org = org)
```
## Using `checklist` on a package.
Before you can run the checks, you must initialise `checklist` on the package.
Either use `create_package()` to create a new package from scratch.
Or use `setup_package()` on an existing package.
More details in `vignette("getting_started", package = "checklist")`.
```{r package-initialise}
create_package()
```
Once initialised, you can run all the checks with `check_package()`.
Or run the individual checks.
```{r package-checks}
check_cran()
check_description()
check_documentation()
check_lintr()
check_filename()
check_folder()
update_citation()
```
To allow some of the warnings or notes, first run the checks and store them in an object.
Update `checklist.yml` by writing that object.
```{r package-allow-warnings}
x <- check_package()
write_checklist(x)
```
## Using `checklist` on a project.
Before you can run the checks, you must initialise `checklist` on the project.
Either use `create_project()` to create a new package from scratch.
Or use `setup_project()` on an existing package.
More details in `vignette("getting_started_project", package = "checklist")`.
```{r project-initialise}
library(checklist)
create_project()
```
Once initialised, you can run all the checks with `check_project()`.
Or run the individual checks.
```{r project-checks}
check_lintr()
check_filename()
check_folder()
update_citation()
```
To allow some of the warnings or notes, first run the checks and store them in an object.
Update `checklist.yml` by writing that object.
```{r project-allow-warnings}
x <- check_project()
write_checklist(x)
```