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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 Fri Jun 24, 2022 made by Micah Jeppesen

  • inst/apodize2d: Updated to work with Octave v6 and higher with change in logic of data types.

  • inst/autophase2d: Updated to work with Octave v6 and higher with change in logic of data types.

  • inst/backscaleplot: Added functionality for 2D NMR - Needs testing to confirm proper functionality.

  • inst/binadapt: Updated to work with Octave v6 and higher with change in logic of data types.

  • inst/binadapt2d: Updated to work with Octave v6 and higher with change in logic of data types.

  • inst/coshift: Added functionality for 2D NMR - Real implementation of superimposed 2d matrices.

  • inst/decompose2d: Updated to work with Octave v6 and higher with change in logic of data types.

  • inst/estnoise: Added functionality for 2D NMR - binary work was completed by Brad, but the logic front end needed work.

  • inst/lorentz2d: New function to allow for creation of theoretical lorentzian peaks from user input criteria.

  • inst/max2d: New function for the convenience of examining 2d nmr spectra before binning.

  • inst/mean2d: New function for the convenience of examining 2d nmr spectra before binning.

  • inst/min2d: New function for the convenience of examining 2d nmr spectra before binning.

  • inst/nmrft2d: Updated to work with Octave v6 and higher with change in logic of data types.

  • inst/nmrist: Updated to work with Octave v6 and higher with change in logic of data types.

  • inst/norm2d: New function for the convenience of examining 2d nmr spectra before binning.

  • inst/peakpick: Added functionality for 2D NMR - binary work was completed by Brad, but the logic front end needed work.

  • inst/phase2d: Updated to work with Octave v6 and higher with change in logic of data types.

  • inst/plotspectra2d: A visualization function for convenience of viewing multiple 2D NMR spectra in combination.

  • inst/rotatespectra2d: A convenience function for the manipulation of 2D NMR spectra that may have been incorrectly processed.

  • inst/ransy2d: New function for the use of the ransy dissemination protocol for 2D NMR spectra.

  • inst/realnmr: Updated to work with Octave v6 and higher with change in logic of data types.

  • inst/rmnoise: Added functionality for 2D NMR - binary work was completed by Brad, but the logic front end needed work.

  • inst/rmobs: Added functionality for 2D NMR - due to the cell data type of 2D NMR this function needed work.

  • inst/rmvar: Added functionality for 2D NMR - due to the nature of the structure of 2D data this function is a convenience function.

  • inst/std2d: New function for the convenience of examining 2d nmr spectra before binning.

  • inst/zerofill2d: Updated to work with Octave v6 and higher with change in logic of data types.

  • inst/lorentz: Bug fix - previous version was likely broken during Octave updates.

  • inst/cvscoresplot3: Bug fix - had a plotting bug with 3d figures.

  • inst/loadingsplot: Bug fix - had a plotting bug with 3d figures.

  • inst/scoresplot3: Bug fix - had a plotting bug with 3d figures.

  • inst/loadfid: Added convenience check for installation of NMRPipe, this allows the user to launch octave from any shell and have full use of MVAPACK.

  • inst/loadnmr: Added convenience check for installation of NMRPipe, this allows the user to launch octave from any shell and have full use of MVAPACK.

  • inst/loadser: Added convenience check for installation of NMRPipe, this allows the user to launch octave from any shell and have full use of MVAPACK.

  • inst/ransy1d: Expansion of usability incorporating an abscissa input option, this removes the required findnearest function call.

  • inst/scoresplot: Updated to return the figure handle optionally.

  • inst/scoresplot2: Updated to return the figure handle optionally.

  • inst/biplot: New function for the visualization of PCA data.

  • inst/biplot2: New function for the visualization of PCA data.

  • inst/biplot3: New function for the visualization of PCA data.

  • inst/combinespectra1d: New function for the convenience of dealing with multiple data sets that must be processed separately and be combined later.

  • inst/fcpv: New function for creating a fold change and p value structure pipeline, with outputs like volcanoplot and autoBVBplot.

  • inst/loadingsplot2: New function to accommodate loadingsplot3.

  • inst/loadingsplot3: New function for the visualization of 3 dimensional loadings data.

  • inst/scatter_legend_capable: A new helper function for volcanoplot.

  • inst/sref: A new function to allow linear scaling of a dataset to a reference peak.

  • inst/volcanoplot: A new function for the visualization of fold change and pvalue data.

  • inst/autoBVBPlot: A new function for the automatic creation of sets of box plots, violin plots, and beeswarm plots based on statistically significant data.

  • CITATION: Allows user to simply get the correct citation for MVAPACK by typing "citation mvapack" in an octave environment.

  • pre_install.m: A courtesy function to allow mvapack to check conditions on install and show visuals to user to confirm action.

  • post_install.m: A courtesy function to allow mvapack to confirm installation and visualize to the user.

  • uninst/: A file of previously incorporated, but soon to be removed files. This doesn't affect the end user.

  • inprogress/: A file of functions that are not completed, but will be reworked in future editions.

Changes from Fri May 07, 2021 made by Christopher Jurich

  • mvapack/src/external/boost: Removed external project dependencies so that MVAPACK compiles exclusively from source code in the project.

  • ChangeLog: Removed deprecated function calls and behavior from existing C++ bindings. Generalized Makefile to work across different versions of octave.

  • Fuction Files: Aggregated a number of missing function files into mvapack/inst.

  • Documentation Update: Reconciled differences between documentation and available function files.

  • inst/baseline_noise_estimation: Initial implementation - utility function that helps estimate the noise-to-signal ratio for a given extracted ion chromatogram (EIC).

  • inst/baseline_subtraction: Initial implementation - method that performs asymmetric least squares (ALS) baseline subtraction on an EIC.

  • inst/create_eics: Initial implementation - creates folder of EICs from various open-source file formats of replicate data.

  • inst/efficient_filter: Initial implementation - rapid application of a filter to a waveform. Uses C++ bindings.

  • inst/gauss_baseline_noise: Initial implementation - determines baseline noise using second derivative gaussian wavelet.

  • inst/gauss_deriv_peak_picking: Initial implementation - picks peak using second derivate gaussian wavelet.

  • inst/gaussian_coefficients: Initial implementation - generates the coefficients for a second derivative gaussian wavelet.

  • inst/impute: Initial implementation - all purpose matrix imputation method for a matrix of feature peaks.

  • inst/impute_mean: Initial implementation - imputation of feature matrix using mean of existing methods.

  • inst/load_peaks: Initial implementation - utility method to load peaks from .csv file.

  • inst/pick_peaks: Initial implementation - picks peaks from a folder of EIC .csv files.

  • inst/prepare_eic: Initial implementation - preparation function for raw eic data needed for peak picking.

  • inst/quantile_normalize: Initial implementation - quantile normalization method for feature matrices. Based on BioConductorR version.

  • inst/save_peaks: Initial implementation - utility method for saving a matrix of peaks to a .csv file.

Changes from Thu Jul 11, 2019 made by Eli Riekeberg

  • doc/RANDOMFORESTREADME.txt: added explanation of how random forest algorithm implemented and examples of it's use.

  • examples/: Added an examples folder, containing small text file of example coffees data and example Random Forest and SVM script.

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) 2021 University of Nebraska Board of Regents.