README.md

In rettopnivek/camrprojects: Portable Functions for R Projects at CAM-MGH

camrprojects

An R package with portable functions used in R projects for the Center for Addiction Medicine (CAM) at Massachusetts General Hospital (MGH).

Getting started

Prerequisites

First install the statistical software R. It is also recommended to install RStudio. Finally, the following R packages are required:

• devtools
• dplyr
• furrr
• httr
• jsonlite
• magrittr
• progress
• progressr
• purrr
• rlang
• stringr
• tidyr

Installation

To easily install the 'camrprojects' package, you'll need the 'devtools' package:

install.packages("devtools")
library(devtools)

The 'camrprojects' package can then be installed via the following command:

install_github("rettopnivek/camrprojects")

Using the package

To load the package:

library(camrprojects)

To list the available functions:

ls(pos = "package:camrprojects")

Details and examples for a specific function can be obtained via help( "function" ) substituting the appropriate function name for "function".

Standardized naming schemes

File names

To aid in file organization and interpretability, file names in CAM R projects will ideally follow the formats below:

• TXX-Description-MM_DD_YYYY.ext or...
• TXX-Description-Created_MM_DD_YYYY_at_H_M.ext.

The components of this naming scheme are: T - A letter for grouping and categorization. For example... * Files starting with 'R' or 'S' can refer to R scripts. * Files starting with 'D' can refer to data files (.RData, .csv, etc.). * Files starting with 'F' can refer to image files (.png, .pdf, etc.). * Files starting with 'W' can refer to Word documents. * Files starting with 'P' can refer to Powerpoint slides. * files starting with 'T' can refer to plain text files. XX - A numbering scheme from '01' onward. Description - A brief human-readable description of the file with words separated by underscores (e.g., 'Data_preparation' or 'Descriptive_summaries'). MM_DD_YYYY or Created_MM_DD_YYYY_at_H_M - the date or date and time when a file is created. This is most useful for data and output files.

Column names in data frames

Data frames containing data from CAM studies should preferably follow a consistent variable naming scheme. Ideally, variables will be in the style: GGG.TTT.Var_name or... GGG.TTT.Optional.Var_name.

Each component has a specific interpretation/use: GGG is a 3-letter abbreviation giving the overarching group for a variable (e.g., 'Identifiers', 'Session details', etc.); TTT is a 3-letter abbreviation for the type of data (e.g., 'Integer', 'Character string', etc.); Optional refers to an optional sub-category (e.g., indicators for time points like 'BL' for baseline and 'Y1' or 'Y2' or subsequent years); Var_name is a human-readable label (e.g., 'Treatment_groups', 'Session_dates', etc.).

The goal of this naming scheme is to 1) aid in filtering and selecting columns and 2) improve readability and interpretation of columns.

Data Dictionary Tools

Forthcoming.

Reading data from REDCap

Forthcoming.

Authors

Contributors

• Eylul Ackman
• Michael Pascale
• Kevin Potter
• William Schmitt
• Bryn Evohr

Current maintainers

• Kevin Potter
• Bryn Evohr

License

MIT

rettopnivek/camrprojects documentation built on March 26, 2024, 9:17 a.m.