tdhock/change-tutorial

Materials for the useR2017 tutorial on changepoint detection

This repository contains code for the useR2017 tutorial “Introduction to optimal changepoint detection algorithms” by Toby Dylan Hocking and Rebecca Killick.

Rebecca: Unsupervised changepoint detection 90 minutes video. Source Rmd.

Toby: Supervised changepoint detection NAU copy, 90 minutes video. Source Rmd.

• Do the exercises during class on this Rcloud notebook https://rcloud.social/edit.html?notebook=3e66297efb401bc0c6333ad517804f85 (make sure to click the fork so you can makes changes). source: Supervised-exercises.R

TODOs

For a more advanced tutorial, check out coarseDataTools::EMforCFR, adapEnetClass, icenReg, and non-linear models.

Try `cv.glmnet(family=”poisson”)` for predicting the number of changepoints.

Copy and adapt tutorial materials from Rebecca’s eRum2016 workshop.

depmixS4.models.R tries to fit an HMM to the neuroblastoma data set, but I ran into depmixS4.bugs.R – I emailed the author <[email protected]> on May 31 but I haven’t heard anything yet.

9 June 2017

Compare with BIC from PELT/fpop pelt.fpop.R

27 Apr 2017

Compiled Rmd HTML Supervised changepoint tutorial, first draft, source: Supervised.Rmd.

28 Feb 2017

montreal-biohackathon-2017.org describes a changepoint detection challenge for a 24 hour Biohackathon.

13 Feb 2017

figure-regression-interactive-some.R creates 5 plot interactive data viz.

9 Feb 2017

figure-regression-interactive-some.R for interactive figure with a few profiles that we can zoom in to. http://bl.ocks.org/tdhock/raw/9fc37a7aaf291cef364aab3fb41dd898/

figure-regression-interactive.R for comparing BIC and learned model on entire neuroblastoma data set.

penaltyLearning package for exactModelSelection and targetInterval.

25 Nov 2016

Begin breakpoint.learning.cv.R which will read breakpoint.learning.RData and estimate breakpoint predicted test error via 6-fold cross-validation (including BIC, mBIC, supervised penalty learning via iregnet).

change-tutorial's Issues

Error when assigning values to 'TPR' column in data.table

Hi @tdhock, I'm encountering an error while running the code in the figure-regression-interactive-some.R file. Specifically, the error occurs on the following line:

change-tutorial/figure-regression-interactive-some.R

Line 194 in 8df639e

auc[, TPR := c(0.85, 0.9)]

The error message I'm receiving is:

Error in `[.data.table`(auc, , `:=`(TPR, c(0.85, 0.9))) : 
  Supplied 2 items to be assigned to 1 items of column 'TPR'. If you wish to 'recycle' the RHS please use rep() to make this intent clear to readers of your code.

I'm a bit confused about why this error is occurring. It seems that the code is trying to assign two values (0.85 and 0.9) to the 'TPR' column, but the error suggests there's only one item in the column to assign to.
Could you please give me some guidance on what might be causing this error and how can I modify the code to correctly assign these values to the 'TPR' column?

Thank you very much for your time and guidace