https://github.com/baumer-lab/fertile

creating optimal conditions for reproducibility
https://github.com/baumer-lab/fertile

r reproducibility reproducible-research tidyverse workflow

Last synced: 3 months ago
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creating optimal conditions for reproducibility

• Host: GitHub
• URL: https://github.com/baumer-lab/fertile
• Owner: baumer-lab
• License: gpl-3.0
• Created: 2018-08-03T18:29:12.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2021-04-15T12:49:30.000Z (over 3 years ago)
• Last Synced: 2024-06-11T08:50:05.027Z (5 months ago)
• Topics: r, reproducibility, reproducible-research, tidyverse, workflow
• Language: R
• Homepage:
• Size: 4.48 MB
• Stars: 52
• Watchers: 3
• Forks: 4
• Open Issues: 16
• Metadata Files:
  • Readme: README.Rmd
  • License: LICENSE

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• jimsghstars - baumer-lab/fertile - creating optimal conditions for reproducibility (R)

README

        
---

output: github_document

---

```{r, echo = FALSE, message = FALSE, warning = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "README-"

)

```

```{r, include = FALSE}

library(fertile)

library(tidyverse)

miceps <- system.file("extdata/project_miceps.zip", package = "fertile") %>%

  sandbox()

```

[![Travis-CI Build Status](https://travis-ci.org/baumer-lab/fertile.svg?branch=master)](https://travis-ci.org/baumer-lab/fertile)

[![Codecov test coverage](https://codecov.io/gh/baumer-lab/fertile/branch/master/graph/badge.svg)](https://codecov.io/gh/baumer-lab/fertile?branch=master)

[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)

# fertile: creating optimal conditions for reproducibility 

**Tools to make achieving R project reproducibility easy!**

## Why `fertile`?

- Addresses all different reproducibility aspects in one place

- Simple functions w/ minimal arguments

- Minimal prior knowledge required

- `R`-specific features

- Customizable to your needs

- Has educational features

## Sample Project 

`miceps`: variable containing path to directory containing following project:



## Easily Create Reproducibility Reports

```{r badges, eval = FALSE}

proj_badges(miceps)

```



$~$



## Run Reproducibility Checks

`fertile` contains 16 checks on different aspects of reproducibility:



$~$

Run them individually or in customizable groupings, w/ `proj_check()`, `proj_check_some()`, or `proj_check_badge()`

```{r}

# Individual check

has_well_commented_code(miceps)

```

```{r}

# Combined checks

proj_check_badge(miceps, "documentation")

```

## Warnings For Potentially Non-Reproducible Commands

```{r, error = TRUE}

read_csv("/Users/audreybertin/Documents/fertile/project_miceps/mice.csv")

```

```{r, error = TRUE}

setwd(miceps)

```

Several data-reading functions built in to `fertile`'s warning system:



$~$

Customize warning system by:

- Adding functions (`add_shim()`, `add_all_possible_shims()`)

```{r addshim, eval = FALSE}

# Add stats::write.ftable to the warning system

add_shim(func = "write.ftable", package = "stats")

```

- Editing functions (`edit_shims()`)

- Disabling warnings for user-added functions (`unload_shims()`)

- Enabling warnings for user-added functions (`load_shims()`) --- this is the *default* setting.

## Installation

You can install `fertile` from GitHub with:

```{r gh-installation, eval = FALSE}

# install.packages("remotes")

remotes::install_github("baumer-lab/fertile")

```

## Citation

```{r citation}

citation("fertile")

```

The `fertile` release at the time of publication for the above citation can be found here: