prodigenr

https://rostools.github.io/prodigenr/
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An R package for creating standardized project directory structures with template files for data...
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### Example: Setting up a new project in a temporary directory

Source: https://rostools.github.io/prodigenr/reference/setup_project.html

Demonstrates how to use setup_project to create a new project in a temporary location. It also shows how to subsequently add Git to the project using setup_with_git.

```R
if (FALSE) { # \dontrun{
# Use a temporary location
new_proj_name <- fs::path_temp("DiabetesCancer")
setup_project(new_proj_name)
# After the new project opens up, add Git with:
setup_with_git()
} # }
```

--------------------------------

### Example Usage of create_report and create_slides

Source: https://rostools.github.io/prodigenr/reference/create_doc.html

Demonstrates the usage of `create_report()` and `create_slides()` functions. This example is typically run interactively and is marked as non-runnable.

```r
if (FALSE) { # \dontrun{
create_report()
create_slides()
} # }
```

--------------------------------

### Install prodigenr from GitHub

Source: https://rostools.github.io/prodigenr/index.html

Install the development version of the prodigenr package from GitHub using the pak package.

```r
# install.packages("pak")
pak::pak("rostools/prodigenr")
```

--------------------------------

### Install prodigenr from CRAN

Source: https://rostools.github.io/prodigenr/index.html

Install the released version of the prodigenr package from CRAN.

```r
install.packages("prodigenr")
```

--------------------------------

### List Available Templates

Source: https://rostools.github.io/prodigenr/reference/template_list.html

Use this function to get a list of available templates within an R package. The function returns a character vector.

```R
template_list
```

```R
template_list
#> [1] "report" "slides"
```

--------------------------------

### setup_with_git()

Source: https://rostools.github.io/prodigenr/reference/index.html

Sets up Git for the project.

```APIDOC
## setup_with_git()

### Description
Setup Git to the project.

### Parameters

#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
None

### Response
#### Success Response
None

#### Response Example
None
```

--------------------------------

### Set up a new project directory

Source: https://rostools.github.io/prodigenr/index.html

Use the setup_project() command in the R console to create a new project directory with template files. Specify the desired path for the project.

```r
library(prodigenr)
setup_project("~/Desktop/DiseaseDiet")
```

--------------------------------

### setup_project()

Source: https://rostools.github.io/prodigenr/reference/index.html

Sets up a standardized folder and file structure for a research analysis project.

```APIDOC
## setup_project()

### Description
Setup a standardized folder and file structure for a research analysis project.

### Parameters

#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
None

### Response
#### Success Response
None

#### Response Example
None
```

--------------------------------

### Initialize Git in a Project

Source: https://rostools.github.io/prodigenr/reference/setup_with_git.html

Run this function inside the project directory to add Git and a .gitignore file. It is a simplified version of usethis::use_git().

```r
setup_with_git()
```

--------------------------------

### Initialize Project Structure

Source: https://rostools.github.io/prodigenr/reference/setup_project.html

Sets up a common folder and file infrastructure for a new research project. This function also adds essential files to kickstart the project and can integrate Git.

```R
setup_project(path)
```

--------------------------------

### Create a basic Quarto slide presentation

Source: https://rostools.github.io/prodigenr/reference/create_doc.html

Use `create_slides()` to generate a Quarto file for slide presentations in the `docs/` folder. This is a wrapper for `create_doc(type = "slides")`.

```r
create_slides()
```

--------------------------------

### create_slides()

Source: https://rostools.github.io/prodigenr/reference/index.html

Creates a basic Quarto slides presentation from a template.

```APIDOC
## create_slides()

### Description
Create a basic Quarto slides presentation from a template.

### Parameters

#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
None

### Response
#### Success Response
None

#### Response Example
None
```

--------------------------------

### Create a Quarto document (report or slides)

Source: https://rostools.github.io/prodigenr/reference/create_doc.html

The main function `create_doc` allows specifying the document type as either 'report' or 'slides'. It creates the respective Quarto file in the `docs/` folder.

```r
create_doc(type = c("report", "slides"))
```

--------------------------------

### create_doc()

Source: https://rostools.github.io/prodigenr/reference/index.html

Creates a basic Quarto document from a specified template.

```APIDOC
## create_doc()

### Description
Create a basic Quarto document from a template.

### Parameters

#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
None

### Response
#### Success Response
None

#### Response Example
None
```

--------------------------------

### List available document templates

Source: https://rostools.github.io/prodigenr/articles/prodigenr.html

View the available document templates that can be created using the `create_*()` functions. Currently, 'report' and 'slides' are supported.

```R
template_list
```

--------------------------------

### create_doc

Source: https://rostools.github.io/prodigenr/reference/create_doc.html

Creates a manuscript/report or slide Quarto file and saves it into the `docs/` folder.

```APIDOC
## create_doc

### Description
Creates manuscript/report or slide Quarto file and saves it into the `docs/` folder.

### Arguments

* **type** (string) - Required - The file type (e.g. report, slides).

### Value
A created `.qmd` file in the `docs/` folder.

### Functions
* `create_report()`: Creates a report Quarto document in the `docs/` folder.
* `create_slides()`: Creates a Quarto document for making slides in the `docs/` folder.

### Examples
```r
if (FALSE) { # \dontrun{
create_report()
create_slides()
} # }
```
```

--------------------------------

### Create a new report file

Source: https://rostools.github.io/prodigenr/index.html

Once inside a prodigenr project, use create_report() to add a manuscript or report Quarto file.

```r
create_report()
```

--------------------------------

### create_report()

Source: https://rostools.github.io/prodigenr/reference/index.html

Creates a basic Quarto report from a template.

```APIDOC
## create_report()

### Description
Create a basic Quarto report from a template.

### Parameters

#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
None

### Response
#### Success Response
None

#### Response Example
None
```

--------------------------------

### create_report

Source: https://rostools.github.io/prodigenr/reference/create_doc.html

Creates a report Quarto document in the `docs/` folder.

```APIDOC
## create_report

### Description
Creates a report Quarto document in the `docs/` folder.

### Examples
```r
if (FALSE) { # \dontrun{
create_report()
} # }
```
```

--------------------------------

### List available project templates

Source: https://rostools.github.io/prodigenr/index.html

The template_list command displays the names of all available project template files that can be used with prodigenr.

```r
template_list
#> [1] "report" "slides"
```

--------------------------------

### Add a new document to the project

Source: https://rostools.github.io/prodigenr/articles/prodigenr.html

After creating a project, use `create_*()` commands within the project's RStudio console to add new document templates like slides or reports to the 'docs/' folder.

```R
# you need to run these in the project's console
create_slides()
```

--------------------------------

### Open prodigenr introduction vignette

Source: https://rostools.github.io/prodigenr/index.html

Access the detailed introduction vignette for prodigenr to learn more about its features and usage.

```r
vignette('prodigenr', 'prodigenr')
```

--------------------------------

### template_list

Source: https://rostools.github.io/prodigenr/reference/index.html

Lists project templates available within prodigenr.

```APIDOC
## template_list

### Description
List project templates within prodigenr.

### Parameters

#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
None

### Response
#### Success Response
None

#### Response Example
None
```

--------------------------------

### BibTeX Citation for prodigenr

Source: https://rostools.github.io/prodigenr/authors.html

This is the BibTeX entry for citing the prodigenr R package. It includes the title, author, year, package version, and URLs for the project website and GitHub repository.

```bibtex
@Manual{
  title = {prodigenr: Research Project Directory Generator},
  author = {Luke Johnston},
  year = {2024},
  note = {R package version 0.7.0.9000,
    https://rostools.github.io/prodigenr/},
  url = {https://github.com/rostools/prodigenr},
}
```
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