Software

R packages for wearables, neuroimaging, and talking to other tools.

Most of my work ends up as an R package: more than 30 on CRAN, plus many more on GitHub. My newer work on wearables lives with the JHU Wearables group and installs together via activerse. Filter by topic on the right.

activerse

Attach the whole family of actigraphy packages at once, tidyverse-style.
wearablesGitHub

actibase

Baseline functions for actigraphy and activity processing and analysis.
wearablesCRAN downloads for actibase

actiread

Read actigraphy and activity data from many devices.
wearablesCRAN downloads for actiread

actimetrics

Create metrics for actigraphy and activity analysis.
wearablesCRAN downloads for actimetrics

actisomni

Create sleep measures from actigraphy data.
wearablesCRAN downloads for actisomni

actiplot

Plotting minute-level activity data.
wearablesvisualizationCRAN downloads for actiplot

actiquantiles

Map activity data to normalized quantiles.
wearablesCRAN downloads for actiquantiles

mapnhanespa

Map quantiles for physical activity from NHANES.
wearablesCRAN downloads for mapnhanespa

actisensorlog

Summarize SensorLog / SensorLogger phone activity data.
wearablesCRAN downloads for actisensorlog

actiwalkability

Access the EPA Walkability Index.
wearablesinterfacesCRAN downloads for actiwalkability

actinet

Estimate human activity from accelerometry data.
wearablesCRAN downloads for actinet

stepcount

Estimate step counts from accelerometry data (wraps OxWearables stepcount).
wearablesCRAN downloads for stepcount

walking

Segment accelerometry data into walking bouts using open-source methods.
wearablesCRAN downloads for walking

asleep

Estimate sleep from accelerometry data.
wearablesCRAN downloads for asleep

sleeper

Estimate sleep status from wrist-worn accelerometry data.
wearablesCRAN downloads for sleeper

stepcadence

Compute cadence metrics from NHANES step-count data.
wearablesGitHub

write.gt3x

Write ActiGraph GT3X files.
wearablesGitHub

fslr

Wrapper functions for FSL (FMRIB Software Library).
neuroimagingCRAN downloads for fslr

neurobase

Neuroconductor base package with helper functions for nifti objects.
neuroimagingCRAN downloads for neurobase

freesurfer

Wrapper functions for FreeSurfer.
neuroimagingCRAN downloads for freesurfer

WhiteStripe

White-matter normalization for magnetic resonance images.
neuroimagingCRAN downloads for WhiteStripe

stapler

Simultaneous Truth and Performance Level Estimation (STAPLE).
neuroimagingstatisticsCRAN downloads for stapler

gifti

Read neuroimaging GIFTI files with geometry information.
neuroimagingCRAN downloads for gifti

cifti

Toolbox for Connectivity Informatics Technology Initiative (CIFTI) files.
neuroimagingCRAN downloads for cifti

neurohcp

Interface to the Human Connectome Project data.
neuroimaginginterfacesCRAN downloads for neurohcp

brainR

Helper functions to misc3d and rgl for interactive 3D brain imaging.
neuroimagingvisualizationCRAN downloads for brainR

kirby21.base

Example data from the multi-modal MRI reproducibility resource (also kirby21.t1, kirby21.fmri).
neuroimagingdataCRAN downloads for kirby21.base

ichseg

Intracerebral hemorrhage segmentation of CT scans.
neuroimagingGitHub

lungct

Segmentation and analysis of lung CT scans.
neuroimagingGitHub

extrantsr

Additional functionality and extensions to ANTsR.
neuroimagingGitHub

spm12r

R interface for SPM12 (Statistical Parametric Mapping) processing.
neuroimagingGitHub

papayar

View medical research images with the Papaya JavaScript viewer.
neuroimagingvisualizationGitHub

dcm2niir

R wrapper for the dcm2nii DICOM converter.
neuroimagingGitHub

neurovault

NeuroVault database API access.
neuroimaginginterfacesGitHub

cforward

Forward selection using concordance / C-index.
statisticsCRAN downloads for cforward

diffr

Display differences between two files using the Codediff library.
visualizationCRAN downloads for diffr

rscopus

Scopus database API interface.
interfacesCRAN downloads for rscopus

gcite

Google Scholar citation parser.
interfacesCRAN downloads for gcite

matlabr

An interface for MATLAB using system calls.
interfacesCRAN downloads for matlabr

text2speech

Text-to-speech conversion across several cloud services.
interfacesCRAN downloads for text2speech

mscstts

R client for the Microsoft Cognitive Services text-to-speech REST API.
interfacesCRAN downloads for mscstts

glassdoor

Interface to the Glassdoor API.
interfacesCRAN downloads for glassdoor

nsrr

Interface to the National Sleep Research Resource.
interfacesGitHub

didactr

Tools for creating automated courses.
teachingGitHub
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