README.Rmd

--- 
title: "README"
output: 
  md_document:
  variant: markdown_github
  
params:
  NVIpkg: "NVIpackager"
  pkg_path: !r  usethis::proj_path()
  first_copyright_year: "2021"
---

```{r, include = FALSE}
NVIpkg <- params$NVIpkg
pkg_path <- params$pkg_path
# NVIpkg <- stringi::stri_extract_last_words(usethis::proj_path())
NVIpkg_inline <- paste0("`", NVIpkg, "`")
logo_path <- ""
if (file.exists(paste0("./man/figures/", NVIpkg, "_logo.png"))) {
  logo_path <- paste0(' <img src="man/figures/', NVIpkg, '_logo.png" align="right" height="138" />')
}

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

`r paste0(NVIpkg, ": ", desc::desc_get_field(key = "Title"), logo_path)`  
================

<!-- README.md is generated from README.Rmd. Please edit that file -->

  - [Overview](#overview)
  - [Installation](#installation)
  - [Usage](#usage)
  - [Copyright and license](#copyright-and-license)
  - [Contributing](#contributing)

## Overview
```{r, include = FALSE}
description <- desc::desc_get_field(key = "Description")
```
`r paste0(NVIpkg_inline, 
   "", 
   sub(substr(description,1,1), tolower(substr(description,1,1)), description))`

```{r child=system.file('templates', "README_NVIverse.Rmd", package = "NVIpackager")}
```

## Installation
```{r child=system.file('templates', "README_installation.Rmd", package = "NVIpackager")}
```

## Usage
```{r child=system.file('templates', "README_usage_attach.Rmd", package = "NVIpackager")}
```

`r paste0(NVIpkg_inline, 
   "", 
   sub(substr(description,1,1), tolower(substr(description,1,1)), description))`
   
#### Create a NVIverse package skeleton
To set up a package skeleton you can use the following procedure:

1. Create a repository for the package at the NorwegianVeterinaryInstitute's GitHub account. Give the repository the name of the package.
    - Make a short descriptive text. This can later be used as the Title in the DESCRIPTION file. 
    - Choose between Public or Private. If unsure, start with Private. It is easy to change to Public later.
    - Mark for Add a README file.
    - Choose the .gitignore template for R.
    - Choose a licence, For example MIT or BSD 3-clause
2. Create the repository.
3. Fork the repository to your own GitHub account.
4. Create an R-studio project for the package. In R-studio
    - Choose New project -> Version control
    - Copy the directory at GitHub and paste it where asked in R-studio.
    - Select a directory in your PC for your package.
5. Create the package skeleton
    ``` {r, eval = FALSE} 
NVIpackager::create_NVIpkg_skeleton(license_keyword = "BSD_3_clause")
    ```
6. Modify the DESCRIPTION file
    - Copy the descriptive text into the Title field in the DESCRIPTION file.
    - Copy the descriptive text into the Description field in the DESCRIPTION file and eventually extend it.
7. Update README and Mypackage-package help with the last changes in the DESCRIPTION file. 
    ``` {r update_readme_text, message=FALSE, warnings=FALSE, echo=FALSE, prompt = FALSE, comment = ""} 
update_readme_text <- paste('document_NVIpkg(pkg = stringi::stri_extract_last_words(usethis::proj_path()),',
              '    pkg_path = usethis::proj_path(),',
              '    style = FALSE,',
              '    manual = "update",',
              '    contributing = FALSE,',
              '    readme = TRUE)',
              sep = '\n')
cat(update_readme_text, sep = "", fill = TRUE)
    ```

#### Maintenance of a NVIverse package
Functions for updating documentation, performing tests, build and install the package are collected in the file "./notes/develop.R". You can run the different sections stepwise during package maintenance and updating.
  

```{r child=system.file('templates', "README_usage_help.Rmd", package = "NVIpackager")}
```

## Copyright and license
```{r child=system.file('templates', "README_copyright_and_license.Rmd", package = "NVIpackager")}
```

## Contributing
```{r child=system.file('templates', "README_contributing.Rmd", package = "NVIpackager")}
```

<!-- Code of conduct -->
-----
```{r child=system.file('templates', "README_code_of_conduct.Rmd", package = "NVIpackager")}
```