Changes in version 2024.1.24

- reformat NEWS.
- fix man pages for CRAN.

Changes in version 2017.08.15

- remove binSum.
- add cDPA_interface.

Changes in version 2017.06.20

- depend on penaltyLearning, delete related code in this pkg.

Changes in version 2016.08.06

- Suggest ggplot2 >= 2.0, new geom_tallrect implementation.
- cDPA C code now computes total Poisson loss which is consistent with the PoissonLoss R function, and with other packages (Segmentor3IsBack, coseg). It has been significantly cleaned up (duplication removed).

Changes in version 2015.04.07

- move joint segmentation code to PeakSegJoint package.

Changes in version 2015.04.02

- multiSampleSegZoom C function.
- R implementation of multiSampleSegSome.

Changes in version 2015.03.27

- Scripts up to Step4 under exec/

Changes in version 2015.03.23

- Error checking in binSum.
- chrom and sample ratio features in exec/Step1.R

Changes in version 2015.03.16

- multiSampleSeg Optimal and Heuristic C code.

Changes in version 2015.03.11

- clusterPeaks C code.
- LinDynProg.c renamed to cDPA to be consistent with paper.

Changes in version 2015.03.05

- Do not use GSL headers for positive infinity cost; instead use INFINITY defined in "math.h"

Changes in version 2015.03.03

- fista.R interval regression code.
- binSum C code sets count to -1 for profiles that are too short for the number of bins requested.

Changes in version 2015.02.27

- binSum C code for quickly computing sums over bins of constant size.

Changes in version 2014.11.10

- warning when user requests X peaks but that model is infeasible.