Last updated: 2019-11-12

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Knit directory: smash-paper/analysis/

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File Version Author Date Message
html e574eec Peter Carbonetto 2019-05-29 Removed code chunk from home page.
Rmd bffeca4 Peter Carbonetto 2019-05-29 wflow_publish(“analysis/index.Rmd”)
html 29686e2 Peter Carbonetto 2019-05-29 More testing of wflow_publish() on index.Rmd.
html 23277ee Peter Carbonetto 2019-05-29 Testing workflowr::wflow_publish on index.Rmd.
Rmd d787b97 Peter Carbonetto 2019-05-29 wflow_publish(“analysis/index.Rmd”)
html ee4e1ef Peter Carbonetto 2019-03-14 Re-built home page with updated citation info; addresses Issue #2.
Rmd 2d1870b Peter Carbonetto 2019-03-14 Updated LICENSE; updated main workflowr page.
html bf8b368 Peter Carbonetto 2018-12-21 Fixed plots for Bursts simulations.
Rmd b9f5cd3 Peter Carbonetto 2018-12-21 wflow_publish(c(“index.Rmd”, “poisson.Rmd”))
html c815163 Peter Carbonetto 2018-12-21 Added info about Poisson results in output directory.
Rmd 840ef19 Peter Carbonetto 2018-12-20 wflow_publish(“index.Rmd”)
html 7dc40a9 Peter Carbonetto 2018-12-20 Revised license info given in home page.
Rmd 52a763f Peter Carbonetto 2018-12-20 wflow_publish(“index.Rmd”)
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Rmd 2ddb601 Peter Carbonetto 2018-12-06 I have an initial setup of the Shiny server document.
html 8caff70 Peter Carbonetto 2018-12-06 Re-built the workflowr pages after several minor changes to the text
Rmd c589dbb Peter Carbonetto 2018-12-06 wflow_publish(c(“index.Rmd”, “gaussian_signals.Rmd”,
Rmd d82c55d Peter Carbonetto 2018-12-04 Added shiny page to home.
Rmd ef0b2de Peter Carbonetto 2018-12-04 Minor edits to home page.
html 35f03c0 Peter Carbonetto 2018-12-04 Changed title of gaussian_signals.Rmd.
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html 6d2dec3 Peter Carbonetto 2018-11-09 Added link to TOC in home page.
Rmd 049dcbb Peter Carbonetto 2018-11-08 Moved around some files and revised TOC in home page.
html 40956da Peter Carbonetto 2018-11-08 Another minor edit to the home page.
Rmd a181e84 Peter Carbonetto 2018-11-08 wflow_publish(“index.Rmd”)
html 04a6b8a Peter Carbonetto 2018-11-08 Adjusted formatting of TOC in home page.
Rmd 1b61bd1 Peter Carbonetto 2018-11-08 wflow_publish(“index.Rmd”)
html 5bfcb05 Peter Carbonetto 2018-11-08 Fixing up the TOC for the home page.
Rmd 58539f5 Peter Carbonetto 2018-11-08 wflow_publish(“index.Rmd”)
html e6a06ed Peter Carbonetto 2018-11-08 Re-built the home page; wflow_publish(“index.Rmd”)
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Rmd e94d1ce Peter Carbonetto 2018-11-06 wflow_publish(“index.Rmd”)
html 762f342 Peter Carbonetto 2018-11-06 Some more minor fixes to the home page.
html 4c88a8b Peter Carbonetto 2018-11-06 A few more fixes to the home page.
Rmd 7caace6 Peter Carbonetto 2018-11-06 wflow_publish(“index.Rmd”)
html 145b7e5 Peter Carbonetto 2018-11-06 A few improvements to the home page.
Rmd 4baa137 Peter Carbonetto 2018-11-06 wflow_publish(“index.Rmd”)
html 0328612 Peter Carbonetto 2018-11-06 Re-built the home page after revamping it.
Rmd aa4437d Peter Carbonetto 2018-11-06 wflow_publish(“index.Rmd”)
Rmd 27bb547 Peter Carbonetto 2018-11-06 Greatly simplified the README.
html 0a6b926 Peter Carbonetto 2018-10-18 Adjusted workflowr site rendering.
html c0faf17 Peter Carbonetto 2018-10-18 Added links to analyses in home page.
Rmd 40ad2f2 Peter Carbonetto 2018-10-18 wflow_publish(“index.Rmd”)
html 4005f5e Peter Carbonetto 2018-08-23 Created home page for the first time.
html 0797696 Peter Carbonetto 2018-08-23 Build site.
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This repository contains data and R source code accompanying our manuscript,

Zhengrong Xing, Peter Carbonetto and Matthew Stephens (2019). Flexible signal denoising via flexible empirical Bayes shrinkage. arXiv:1605.07787.

If you find any of the source code in this repository useful for your work, please cite our paper.

The new methods can be found in the smashr package.

Contents

The following analyses generate some of the empirical results presented in Xing, Carbonetto & Stephens (2019). If you encounter a problem running any of the R code in these examples, please post an issue.

Illustrative applications

  1. Motorcycle acceleration data.

  2. ChIP-seq data.

What’s included in the git repository

See here for the source repository. This is the overall structure of the repository:

├── analysis
├── code
├── data
├── docs
├── dsc
├── output
└── shiny

License

Copyright (c) 2016-2019, Zhengrong Xing, Peter Carbonetto & Matthew Stephens.

Our numerical comparisons make use of some of the functions from WaveLab, so we have included the WaveLab source code in this repository. See the COPYING.m Wavelab850 subdirectory for more information about distributing WaveLab.

Our numerical comparisons also use of some functions from GaussianWaveDen, so we have included the GaussianWaveDen source in this repository. For information about distributing GaussianWaveDen, see the copyright.m in the WavDen subdirectory. Note that we made one small improvement to the code in blockJS.m to prevent an error that occurs when running the code in newer versions of MATLAB.

All other source code and software in this repository are made available under the terms of the MIT license. See the LICENSE file in the git repository for the full text of the license.

Credits

This project was developed by Zhengrong Xing at the University of Chicago, with support and contributions from Peter Carbonetto and Matthew Stephens.