After the release of 0.5.1 in 2019, we’ve been continuously improving drEEM for another major update.

The new version can be downloaded here.

For help on the installation and a really quick tour: https://youtu.be/9OyxSKEWmbE

New documentation

drEEM now features a full custom documentation including a number of tutorials, some of them brand new. You can call doc dreem and explore it. The function help for each of drEEM’s functions has also been moved to the help browser. To quickly access the function syntax, type help functionname in the console. To read more in depth about a function, type doc functionname.

A full list of the changes since v0.5.1:

NEW

  • Documentation was completely overhauled. Each function now has a html help file. These can be called by the command doc functionname or help functionname (& click on link). The old help in each m-file still exists, but is no longer updated.
  • openfluormatches: Plot exported results from database matches (openfluor.org)
  • randinitanal. Completely rewritten. Automatic detection parallel computing capabilities. Changes:
    • Allow user to cancel unfinished models (parallel mode).
    • Updated help section (minor fixes).
    • Fixed error in calculation of component size (field “compsize”).
    • User can specify whether PLS_toolbox or N-way toolbox should be used for PARAFAC.
    • Switched to input parsing of input arguments, but old input is also recognized.
    • Plots existing models if dataset with models is provided and no other inputs are given
  • splitanalysis. Completely rewritten. Automatic detection parallel computing capabilities. Changes:
    • User can specify whether PLS_toolbox or N-way toolbox should be used for PARAFAC.
    • Switched to input parsing of input arguments, but old input is also recognized.
    • User can track all models with detailed progress bar and cancel components if desired.
  • checkdataset. Troubleshooting function to validate a dataset structure and identify issues.
    • Function runs quietly in other functions and reports problems if they are found.
  • handlescatter: smootheem with new iterative interpolation method (inpainting).
  • dreemfig: A interal function that makes all of drEEM’s plots look much nicer.
  • Support for datacursor in various plotting functions. When using the cursor, more information is now shown, such as filename of the sample, wavelength, index of a sample or wavelength etc.

Modifications

  • normeem: Automated detection of blanks / low intensity samples. User is asked if sample-exclusion should occur.
  • normeem: New option allows automated choice between leaving and removing low-intensity samples.
  • nwayparafac: Minor changes to improve forward compatibility & speed.
  • fastnnls: Minor changes to improve speed.
  • nmodel: Minor changes to improve speed.
  • outliertest: Parallelization support & improved graphical output.
  • eemreview: Changed graphical layout. Now includes drop-down menu for sample selection and checkboxes for options.
  • fingerprint: New option to show scatter as lines (superimposed)

Deletions

  • prandinitanal: Function replaced with new randinitanal. Multitreading capabilities retained.
  • psplitanalysis: Function replaced with new version of splitanalysis. Multitreading capabilities retained.
  • multiwaitbar: Replaced with improved function (blockbar)