The Ontario Neurodegenerative Disease Research Initiative (ONDRI) is a series of studies of neurodegenerative and cerebrovascular diseases. For an overview of the foundational prospective, observational, longitudinal study at baseline see this preprint. For more general information on the project, visit ondri.ca, and follow the study on Twitter: @ONDRISTUDY.
ondri-nibs page is a github organization page for the Ontario
Neurodegenerative Disease Research Initiative’s (ONDRI) Neuroinformatics
& Biostatistics (NIBS) team to house materials for public (and internal)
Generally, this organization page has multiple repositories, each repository contains a unique item (e.g., Shiny apps, packages) or conceptual content (e.g., documentation). This page will provide links to each of those as the project grows and changes.
To note, all materials here are licensed as follows unless otherwise stated:
GPL-3 for software
CC-BY for documentation
If you use or adapt any materials here, please ensure you correctly do so according to their licenses and with full attribution.
This repository is a single file to keep track of all contributors to the NIBS material provided here.
This repository is a home for all the external facing (and some internally useful) documentation.
This repository provides two “toy” data sets. These data sets help illustrate a few things:
Each one shows how a tabular and non-tabular data set would be constructed
The data are synthetic, and also provide an illustrative data set for use with all of the apps and methods here (e.g., standards, data preparation, outlier detection)
See also this video for an explanation of the standards we implemented for the data
This repository is a simple
package with one primary function
ONDRI_df(). Its goal is to read in a
DICT.csv that are part of the ONDRI data packages, and
automatically handle some of the specifics about our data packages. That
Recoding and preserving the different missing data, as defined in the ONDRI standards.
Include information from the dictionary—such as
DATA_TYPES—as part of a
Some printing utilities to help see ONDRI’s data types and ONDRI’s missing coded data in the data packages
Some simple subsetting functions based on data types.
This repository houses a
R package designed with one purpose: to provide a color
palette package with the official ONDRI colors.
This repository houses a
lightweight package to provide an
RMarkdown template so that we can
have harmonized looking documents.
This repository houses an R package that emphasizes structural data checks, primarily formatting, filenames, valid MISSING codes, checks for complete data packages (e.g., DATA, DICT, README). This R package does not perform project-specific checks (e.g., for valid participants or date ranges). Please see the Standards App for (some) of those specifics.
This repository houses a heavy-duty app to check data standards for ONDRI and related projects, as well as custom projects and basic data checks.
This repository houses an app meant primarily for some fundamental but rudimentary data inspection and preparation. This app is meant for use with ONDRI data and, in particular, as the step between the standards checks and the outlier analyses (though this app can be used for inspection and preparation for other analyses).
This repository houses an app meant primarily for implementation of the ONDRI outliers detection pipeline. In short, it provides visualization and report generation based on the techniques found in the Outliers and Robust Structures (OuRS) package.
Some of the packages and utilities here depend on materials found elsewhere. In most cases these are utilities generally found (e.g., tidyverse). Some specific materials that are necessary for much of the NIBS pipelines are found at Derek’s github page and include:
The Outliers and Robust Structures (OuRS) package
The Generalized singular value decomposition package
The Generalized partial least squares package
This organization page will also include apps and packages for other tools as they are developed.