tidyproject

Build Institutional Memory and Learning:

Memory:

Consistent and tidy directory structure for all your projects
Long term reproducibility:
- Project library for each project: stores packages alongside project code (like packrat but lighter):
- Version control (git) compatibility: roll back your projects when needed.

Learning:

Code library: Store and share scripts, functions, templates in an ever improving repository of code
Search code library for keywords or raw text

Installation

install.packages("devtools")
devtools::install_github("tsahota/tidyproject")
library(tidyproject)

Quick Tutorial

Make a project

Make a tidyproject with

make_project("path/to/directory")

Open the newly created Rstudio project with File -> Open Project. Warning: do not use setwd() to open tidyprojects.

You should see a new directory structure. Opening the Rstudio project reconfigures default libraries to use the project library, e.g. try installing a package now:

devtools::install_github("tsahota/tidyproject")
library(tidyproject)

This package is now in your "ProjectLibrary" subdirectory. Loading packages from this tidyproject (e.g. with library), will cause packages in this specific project library load. If you want to switch projects, use Rstudio's "open project". Using setwd() is strongly discouraged.

Create a new script:

new_script("scriptname.R")

This will pre-fill some comment fields and store the script in your "Scripts" subdirectory.

Monitor your compliance

Check your tidyproject is set up correctly by typing the following:

check_session()

It complains about Renvironment_info.txt not being present. Take an snapshot of your R environment:

Renvironment_info()

This will search your scripts in your "Scripts" directory for package dependencies and output version and environment information into Renvironment_info.txt of the main directory. If you run check_session() again it should pass now. If tidyproject ever gives you errors, check_session() is a good first port of call.

Add a code library

If you have a directory of scripts somewhere (scripts can be in subdirectories) add it with the following:

options(code_library_path="path/to/code/repository")

Tip 1: Add this to your user ~/.Rprofile (create it if it doesn't exist) to avoid doing this every R session (or R_HOME/etc/Rprofile.site if you want this to apply for all users).

Tip 2: Add multiple directories to the code_library_path by specifying a vector of directory paths.

Use code library

View code library with:

code_library()

Preview code with:

preview("nameofscript.R")

copy code into your project "Scripts" subdirectory with:

copy_script("nameofscript.R")

copy other types of files into other subdirectories (e.g. "Models") with:

copy_file("stantemplate.stan","Models")

Search for code

To list all R scripts in the ./Scripts subdirectory:

ls_scripts("./Scripts")

More refined searching is most easily accomplished with the pipe symbol, %>%, e.g. to find all scripts in ./Scripts that contain the text text_to_match:

ls_scripts("./Scripts") %>% search_raw("text_to_match")

To find all scripts in the Code Library that contain the text text_to_match:

ls_code_library() %>% search_raw("text_to_match")

To find all scripts in Code Library that match the keyword keyword_to_match:

ls_code_library() %>% search_keyword("keyword_to_match")

Chain multiple commands for more targetted searching:

ls_code_library() %>%
  search_keyword("keyword_to_match") %>%
  search_raw("text_to_match")

rgray1/tidyproject