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MVAPACK Change Log

This page displays a formatted history of changes that have been made to publicly released versions of the MVAPACK toolbox.

Changes from Thu Jun 18, 2015 made by Bradley Worley

  • inst/cvpls.m: updated to more accurate Q-squared calculations.

  • inst/cvopls.m: updated to more accurate Q-squared calculations.

  • inst/cvlda.m: updated to more accurate Q-squared calculations.

  • inst/cvanova.m: corrected error in mean square error calculations. given the updated cross-validation estimates of responses in the PLS and OPLS CV functions (above), it made sense to re-evaluate the way CV-ANOVA computed its MSE values and F-statistics.

  • inst/permtest.m: corrected error in p-value calculations. p-values are now calculated non-parametrically, as should be the case in permutation testing.

Changes from Wed Jun 03, 2015 made by Bradley Worley

  • inst/pca.m: implemented monte carlo leave-n-out (modified K+E) internal cross-validation for PCA models.

  • inst/opls.m: added orthogonal components into internal cross-val.

  • inst/mbopls.m: added initial implementation of multiblock opls.

Changes from Thu Apr 16, 2015 made by Bradley Worley

  • inst/ist.m: finalized implementation of iterative soft thresholding for reconstruction of nonuniformly sampled HSQC spectra.

  • inst/binadapt.m: added resolution parameter to generalized adaptive intelligent binning functions.

  • inst/binunif.m: added two-dimensional uniform binning support.

Changes from Mon Jan 05, 2015 made by Bradley Worley

  • inst/roi2data.m: added support for conversion of regions of interest in 1D and 2D spectral data into proper data matrices.

  • inst/data2roi.m: added support for back-transforming data matrices into partial 1D or 2D spectral data based on defined regions of interest.

Changes from Mon Nov 03, 2014 made by Bradley Worley

  • ChangeLog: retroactively documented all changes from initial public release to the current date.

Changes from Fri Oct 31, 2014 made by Bradley Worley

  • inst/binmanual.m: added support for both 1D and 2D manual ROI-based spectral binning.

  • inst/nmrist.m: added support for Iterative Soft Thresholding reconstruction of nonuniformly sampled 2D NMR data.

  • inst/roiplot.m: added support for both 1D and 2D ROI plotting.

Changes from Fri May 23, 2014 made by Bradley Worley

  • inst/cvscores.m: added support for computation of cross-validated scores.

  • inst/cvscoresplot.m: added support for 2D and 3D cross-validated scores scatter plots.

  • inst/permdensity.m: added support for kernel density estimation of permutation test results.

  • inst/permscatter.m: moved scatterplot-based permutation test result plotting into permscatter().

  • inst/susplot.m: added support for SUS-plot generation.

Changes from Tue Apr 01, 2014 made by Bradley Worley

  • inst/loadascii.m: added support for loading ASCII text files as MVAPACK data matrix/abscissa pairs.

Changes from Wed Mar 26, 2014 made by Bradley Worley

  • inst/mbpls.m: added support for multiblock PLS (MB-PLS) using the MBPLS algorithm with block scaling.

  • inst/svdpca.m: removed obsolete code for SVD-based PCA calculation.

Changes from Wed Feb 26, 2014 made by Bradley Worley

  • inst/apodize.m: added support for both 1D and 2D NMR apodization.

  • inst/autophase.m: added support for both 1D and 2D NMR autophasing.

  • inst/bin2roi.m: added bin2roi() function that converts bin centers and widths into general regions of interest.

  • inst/binadapt.m: added support for both 1D and 2D adaptive intelligent binning. two-dimensional support uses the newly developed Generalized Adaptive Intelligent (GAI) binning algorithm.

  • inst/binmanual.m: added support for binning from general regions of interest.

  • inst/cvpca.m: shifted PCA leave-one-out cross-validation into its own function, cvpca(), in case re-validation or use elsewhere is required later.

  • inst/cwt.m: added cwt() for continuous wavelet transforms of vector data. currently, only the mexican hat wavelet is supported.

  • inst/decompose.m: added initial (unfinished) implementation of CRAFT, based on frequency subdivision in time (FIR filtering and decimation) followed by reversible-jump Markov-chain Monte Carlo for signal estimation.

  • inst/estnoise.m: wrote a simple noise floor estimation routine.

  • inst/integrals.m: implemented support for calculating integrals and areas under the curve for spectral regions of interest.

  • inst/mbpca.m: added support for multiblock PCA (MB-PCA) using the CPCA-W algorithm.

  • inst/nmrft.m: added support for both 1D and 2D NMR (fast) Fourier transformation.

  • inst/nusft.m: added a (slow) implementation of the nonuniform DFT for NMR datasets.

  • inst/peakpick.m: implemented 1D NMR peak picking based on a CWT ridge-tracing approach.

  • inst/phase.m: added support for both 1D and 2D NMR phasing.

  • inst/*roi*.m: added support for general regions of interest.

  • inst/simplex_whiten.m: added whitening-method phase correction objective function.

  • inst/ussr.m: added Uncomplicated Statistical Spectral Remodeling support.

  • inst/zerofill.m: added support for both 1D and 2D NMR zero-filling.

Changes from Mon Oct 28, 2013 made by Bradley Worley

  • inst/loadnmr.m: consolidated bruker/agilent NMR data loading code into loadnmr().

  • inst/acquparms_agilent.m: added support for varian/agilent procpar file parsing.

  • inst/acquparms_bruker.m: moved bruker acqu*s file parsing code from acquparms.m to make acquparms.m vendor-neutral.

  • inst/acquparms.m: consolidated bruker/agilent acquisition parameter file parsing code into acquparms.m.

Changes from Thu Sep 19, 2013 made by Bradley Worley

  • inst/stocsy.m: added initial (unfinished) implementation of STOCSY.

Changes from Sun Sep 08, 2013 made by Bradley Worley

  • inst/pca.m: moved official PCA implementation to NIPALS algorithm utilizing C++ code for component computations.

  • inst/pls.m: added C++ code for PLS component computations.

  • inst/svdpca.m: moved unofficial SVD-based PCA implementation to svdpca().

Changes from Thu Sep 05, 2013 made by Bradley Worley

  • ChangeLog: released first official Octave package of MVAPACK and uploaded source code to <bionmr.unl.edu>.

MVAPACK is open source and freely available for academic use. Industrial users may contact Robert Powers for licensing details.

Copyright (C) 2014 University of Nebraska Board of Regents.