# John Muschelli

#### ariExtra

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Leverages the 'ari' package and other tools to create automated courses from slides and a script. Also, uploads these to 'YouTube' and other services using 'tuber' package.

#### brainR

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This includes functions for creating 3D and 4D images using 'WebGL', 'rgl', and 'JavaScript' commands. This package relies on the X toolkit ('XTK', <https://github.com/xtk/X#readme>).

#### cifti

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Functions for the input/output and visualization of medical imaging data in the form of 'CIFTI' files <https://www.nitrc.org/projects/cifti/>.

#### diffr

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An R interface to the 'codediff' JavaScript library (a copy of which is included in the package). Allows for visualization of the difference between 2 files, usually text files or R scripts, in a browser.

#### fedreporter

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Downloads data from Federal 'RePORTER' <https://api.federalreporter.nih.gov/> using the Federal 'RePORTER' API. Allows the user to search job projects from different government agencies.

#### freesurfer

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Wrapper functions that interface with 'Freesurfer' <https://surfer.nmr.mgh.harvard.edu/>, a powerful and commonly-used 'neuroimaging' software, using system commands. The goal is to be able to interface with 'Freesurfer' completely in R, where you pass R objects of class 'nifti', implemented by package 'oro.nifti', and the function executes an 'Freesurfer' command and returns an R object of class 'nifti' or necessary output.

#### fslr

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Wrapper functions that interface with 'FSL' <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>, a powerful and commonly-used 'neuroimaging' software, using system commands. The goal is to be able to interface with 'FSL' completely in R, where you pass R objects of class 'nifti', implemented by package 'oro.nifti', and the function executes an 'FSL' command and returns an R object of class 'nifti' if desired.

#### gcite

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Scrapes Google Citation pages and creates data frames of citations over time.

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Functions to read in the geometry format under the 'Neuroimaging' 'Informatics' Technology Initiative ('NIfTI'), called 'GIFTI' <https://www.nitrc.org/projects/gifti/>. These files contain surfaces of brain imaging data.

#### glassdoor

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Interacts with the 'Glassdoor' API <https://www.glassdoor.com/developer/index.htm>. Allows the user to search job statistics, employer statistics, and job progression, where 'Glassdoor' provides a breakdown of other jobs a person did after their current one.

#### kirby21.base

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Multi-modal magnetic resonance imaging ('MRI') data from the 'Kirby21' 'reproducibility' study <https://www.nitrc.org/projects/multimodal/>, including functional and structural imaging.

#### kirby21.fmri

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Functional magnetic resonance imaging ('fMRI') data from the 'Kirby21' 'reproducibility' study <doi:10.1016/j.neuroimage.2010.11.047>.

#### kirby21.t1

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Structural T1 magnetic resonance imaging ('MRI') data from the 'Kirby21' 'reproducibility' study <doi:10.1016/j.neuroimage.2010.11.047>.

#### leanpubr

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Provides access to the 'Leanpub' API <https://leanpub.com/help/api> for gathering information about publications and submissions to the 'Leanpub' platform.

#### matlabr

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Provides users to call MATLAB from using the "system" command. Allows users to submit lines of code or MATLAB m files. This is in comparison to 'R.matlab', which creates a MATLAB server.

#### mscstts

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R Client for the Microsoft Cognitive Services 'Text-to-Speech' REST API, including voice synthesis. A valid account must be registered at the Microsoft Cognitive Services website <https://azure.microsoft.com/services/cognitive-services/> in order to obtain a (free) API key. Without an API key, this package will not work properly.

#### neurobase

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Base package for 'Neuroconductor', which includes many helper functions that interact with objects of class 'nifti', implemented by package 'oro.nifti', for reading/writing and also other manipulation functions.

#### neurocInstall

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Installs 'Neuroconductor' packages from the release repository <https://neuroconductor.org/releases/> or from 'GitHub'.

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#### neurovault

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Uses 'Neurovault' API <https://neurovault.org/api-docs> to download statistical maps of the human brain stored on that platform.

#### nsrr

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Allows users to access data from the National Sleep Research Resource ('NSRR') <https://sleepdata.org/>.

#### papayar

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Users pass images and objects of class 'nifti' from the 'oro.nifti' package to a Papaya, an interactive lightweight JavaScript viewer. Although many packages can view individual slices or projections of image and matrix data, this package allows for quick and easy interactive browsing of images. The viewer is based off of the Mango software, which is a lightweight medical image viewer.

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Implements a converter for 'Axivity' Continuous Wave 'Accelerometer' ('CWA') data files <https://axivity.com/> to CSV. A CSV reader wrapper function for the output of the converted file is also provided.

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#### spm12r

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Installs 'SPM12' to the R library directory and has associated functions for 'fMRI' and general imaging utilities, called through 'MATLAB'.

#### stapler

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An implementation of Simultaneous Truth and Performance Level Estimation (STAPLE) <doi:10.1109/TMI.2004.828354>. This method is used when there are multiple raters for an object, typically an image, and this method fuses these ratings into one rating. It uses an expectation-maximization method to estimate this rating and the individual specificity/sensitivity for each rater.

#### text2speech

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Unifies different text to speech engines, such as Google, Microsoft, and Amazon. Text synthesis can be done in any engine with a simple switch of an argument denoting the service requested. The 'aws.polly' package has been orphaned and can be found from the CRAN archives.

#### WhiteStripe

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Shinohara (2014) <DOI:10.1016/j.nicl.2014.08.008> introduced 'WhiteStripe', an intensity-based normalization of T1 and T2 images, where normal appearing white matter performs well, but requires segmentation. This method performs white matter mean and standard deviation estimates on data that has been rigidly-registered to the 'MNI' template and uses histogram-based methods.

#### ActFrag

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Recent studies haven shown that, on top of total daily active/sedentary volumes, the time accumulation strategies provide more sensitive information. This package provides functions to extract commonly used fragmentation metrics to quantify such time accumulation strategies based on minute level actigraphy-measured activity counts data.

#### ActivityIndex

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Reads raw 'accelerometry' from 'GT3X+' data and plain table data to calculate Activity Index from 'Bai et al.' (2016) <doi:10.1371/journal.pone.0160644>. The Activity Index refers to the square root of the second-level average variance of the three 'accelerometry' axes.

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Designed for optimal use in performing fast, accurate walking strides segmentation from high-density data collected from a wearable accelerometer worn during continuous walking activity.

#### ari

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Create videos from 'R Markdown' documents, or images and audio files. These images can come from image files or HTML slides, and the audio files can be provided by the user or computer voice narration can be created using 'Amazon Polly'. The purpose of this package is to allow users to create accessible, translatable, and reproducible lecture videos. See <https://aws.amazon.com/polly/> for more information.

#### crsra

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Tidies and performs preliminary analysis of 'Coursera' research export data. These export data can be downloaded by anyone who has classes on Coursera and wants to analyze the data. Coursera is one of the leading providers of MOOCs and was launched in January 2012. With over 25 million learners, Coursera is the most popular provider in the world being followed by EdX, the MOOC provider that was a result of a collaboration between Harvard University and MIT, with over 10 million users. Coursera has over 150 university partners from 29 countries and offers a total of 2000+ courses from computer science to philosophy. Besides, Coursera offers 180+ specialization, Coursera's credential system, and four fully online Masters degrees. For more information about Coursera check Coursera's About page on <https://blog.coursera.org/about/>.

#### docxtractr

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'Microsoft Word' 'docx' files provide an 'XML' structure that is fairly straightforward to navigate, especially when it applies to 'Word' tables and comments. Tools are provided to determine table count/structure, comment count and also to extract/clean tables and comments from 'Microsoft Word' 'docx' documents. There is also nascent support for '.doc' and '.pptx' files.

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Call 'Google Cloud' machine learning APIs for text and speech tasks. Call the 'Cloud Translation' API <https://cloud.google.com/translate/> for detection and translation of text, the 'Natural Language' API <https://cloud.google.com/natural-language/> to analyse text for sentiment, entities or syntax, the 'Cloud Speech' API <https://cloud.google.com/speech/> to transcribe sound files to text and the 'Cloud Text-to-Speech' API <https://cloud.google.com/text-to-speech/> to turn text into sound files.

#### gganatogram

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Create anatograms, tool that enables the user to visualize data sets directly on representations of a body of various species. These are commonly used to graphically explore large-scale human gene expression data.

#### iglu

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Implements a wide range of metrics for measuring glucose control and glucose variability based on continuous glucose monitoring data. The list of implemented metrics is summarized in Rodbard (2009) <doi:10.1089/dia.2009.0015>. Additional visualization tools include time-series and lasagna plots.

#### imbibe

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Provides a set of fast, chainable image-processing operations which are applicable to images of two, three or four dimensions, particularly medical images.

#### knitr

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Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.

#### nitrcbot

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Parses and downloads images from various 'NeuroImaging Tools and Resources Collaboratory' <https://www.nitrc.org> sets.

#### oasis

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Trains and makes predictions from the OASIS method, described in detail in the paper "OASIS is Automated Statistical Inference for Segmentation, with applications to multiple sclerosis lesion segmentation in MRI" <doi:10.1016/j.nicl.2013.03.002>. OASIS is a method for multiple sclerosis (MS) lesion segmentation on structural magnetic resonance image (MRI) studies. OASIS creates probability maps of lesion presence using the FLAIR, T2, T1, and PD structural MRI volumes. This packages allows for training of the OASIS model and prediction of OASIS probability maps from a trained model with user supplied studies that have a gold standard lesion segmentation masks. The package will also create OASIS probability maps for MRI studies using the OASIS model from the OASIS paper if no gold standard lesion segmentation masks are available.

#### officer

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Access and manipulate 'Microsoft Word' and 'Microsoft PowerPoint' documents from R. The package focuses on tabular and graphical reporting from R; it also provides two functions that let users get document content into data objects. A set of functions lets add and remove images, tables and paragraphs of text in new or existing documents. The package does not require any installation of Microsoft products to be able to write Microsoft files.

#### oro.nifti

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Functions for the input/output and visualization of medical imaging data that follow either the 'ANALYZE', 'NIfTI' or 'AFNI' formats. This package is part of the Rigorous Analytics bundle.

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Implements a high performance C++ parser for 'ActiGraph' 'GT3X'/'GT3X+' data format (with extension '.gt3x') for 'accelerometer' samples. Activity samples can be easily read into a matrix or data.frame. This allows for storing the raw 'accelerometer' samples in the original binary format to reserve space.

#### riskRegression

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Implementation of the following methods for event history analysis. Risk regression models for survival endpoints also in the presence of competing risks are fitted using binomial regression based on a time sequence of binary event status variables. A formula interface for the Fine-Gray regression model and an interface for the combination of cause-specific Cox regression models. A toolbox for assessing and comparing performance of risk predictions (risk markers and risk prediction models). Prediction performance is measured by the Brier score and the area under the ROC curve for binary possibly time-dependent outcome. Inverse probability of censoring weighting and pseudo values are used to deal with right censored data. Lists of risk markers and lists of risk models are assessed simultaneously. Cross-validation repeatedly splits the data, trains the risk prediction models on one part of each split and then summarizes and compares the performance across splits.

#### ROpenCVLite

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Installs 'OpenCV' for use by other packages. 'OpenCV' <https://opencv.org/> is library of programming functions mainly aimed at real-time computer vision. This 'Lite' version contains the stable base version of 'OpenCV' and does not contain any of its externally contributed modules.

#### rticles

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A suite of custom R Markdown formats and templates for authoring journal articles and conference submissions.

#### runstats

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Provides methods for fast computation of running sample statistics for time series. These include: (1) mean, (2) standard deviation, and (3) variance over a fixed-length window of time-series, (4) correlation, (5) covariance, and (6) Euclidean distance (L2 norm) between short-time pattern and time-series. Implemented methods utilize Convolution Theorem to compute convolutions via Fast Fourier Transform (FFT).

#### scifigure

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Users may specify what fundamental qualities of a new study have or have not changed in an attempt to reproduce or replicate an original study. A comparison of the differences is visualized. Visualization approach follows 'Patil', 'Peng', and 'Leek' (2016) <doi:10.1101/066803>.

#### spant

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Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.

#### sublime

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Creates probability maps of incident and enlarging lesion voxels from a baseline and followup magnetic resonance imaging study in patients with multiple sclerosis.

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#### Rvision

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This package uses the OpenCV library to provide R users with methods to read and manipulate video and image files, as well as camera streams.

#### slidex

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This package is designed to extract information from Microsoft PowerPoint slides, and then put that information into an R Markdown document with a {xaringan} <https://github.com/yihui/xaringan> YAML. If the xaringan package is also installed, beautiful html slides can then be produced by knitting the RMD. At present, the package exports one function, convert_pptx, which converts a .pptx file to R Markdown. The package is not intended to be all encompassing or provide perfect conversion. Rather, it should get you about 90% of the way there for about 80% of use cases. Given the idiosyncrasies of different slide show presentations, it is expected that some manual editing of the resulting RMD will need to be completed to get the HTML slides to look exactly as you want them, but most of the hard work should be done for you. Importantly, the package maintains and provides the proper code for any images that were embedded in the .pptx slides, as well as links. Tables are also generally maintained, although they may require some manual editing if complex spanner heads and merged cells were used in the original table. Nested bulleted lists should also be maintained.