In beanumber/fertile: Creating Optimal Conditions for Reproducibility

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)

library(fertile)
library(tidyverse)


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

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

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()

# Individual check
has_well_commented_code(miceps)

# Combined checks
proj_check_badge(miceps, "documentation")

Warnings For Potentially Non-Reproducible Commands

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

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())

# 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:

# install.packages("remotes")
remotes::install_github("baumer-lab/fertile")

Citation

citation("fertile")

The fertile release at the time of publication for the above citation can be found here: https://github.com/baumer-lab/fertile/releases/tag/v1.0

beanumber/fertile documentation built on April 17, 2021, 4:33 a.m.