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NEWS for package 'gmkin'

gmkin 0.6-12 (2021-02-13)

  • Depend on mkin (>= 1.0.2) which preserves model names stored in 'mkinmod' objects, which were overwritten starting from mkin 1.0.0

  • Remove option to plot during fit, as mkin does not have this functionality any more

  • Another update of the 'FOCUS_2006' workspace to satisfy gmkin on windows

gmkin 0.6-11 (2021-02-12)

  • Adapt built-in 'FOCUS_2006' workspace to mkin 1.0.x as we have now have the 'deg_func' element in 'mkinmod' objects

  • The three HOWTO tests in the manual pass

gmkin 0.6-10 (2019-07-09)

  • Adapt to mkin, making the new way to fit variance by variable and the two-component error model available to gmkin

  • Use devEMF for better vector graphics export for Windows

  • Manual weighting is not possible as this functionality is currently not present in mkin versions >

gmkin 0.6-9 (2018-09-13)

  • Enable fits with the two-component error model during iterative reweighting (IRLS)

gmkin 0.6-8 (2016-01-25)

  • Formal improvements mainly in the docs

gmkin 0.6-7 (2017-03-06)

Bug fixes

  • The compiled versions of the models were removed from the model gallery in order to avoid invalid pointers.

Major changes

  • A howto section was added to the manual. The howtos are also useful as functionality tests.

gmkin 0.6-6 (2016-01-08)

Bug fixes

  • Activate the button "Keep changes" as soon as a dataset title is entered in the dataset editor so entered data can be kept.

  • Entering "x" into an input field triggered saving the file due to a peculiarity of the GAction implementation in gWidgetsWWW2. The keybinding was changed to "Shift-F12" (see below).

  • When data was entered manually, sometimes it could not be fitted as the override column was of type "character" instead of "numeric".

Major changes

  • Changed the keybinding for saving the current workspace to "Shift-F12"

Minor changes

  • The project file is now immediately shown with its full path in the project editor window after saving a file.

  • Do not show widgets for fit options in 'Configuration' tab when not fit is configured. Also inactivate the run button and show a message telling the user what to do to configure a fit.

gmkin 0.6-5 (2015-12-11)

Bug fixes

  • When configuring a fit using a model with use_of_ff = 'max', this was ignored when the model was loaded from a project file

  • The configure button was not disabled when switching a project (which clears model and dataset selections)

gmkin 0.6-4 (2015-12-09)

  • Various small corrections of unexpected or incorrect GUI behaviour. See git commit logs for details.

Bug fixes

  • Unchecking the pathway to sink in the model editor was ignored.

gmkin 0.6-3 (2015-11-28)

  • Various small layout and GUI logic improvements based on the suggestions by Stefan Meinecke (Umweltbundesamt Germany). Thanks, also for the financial support from the Umweltbundesamt!

Minor changes

  • Removed the 'Add' and 'Remove' buttons from the data editor, as adding rows leads to a corrupt state of the GUI

  • The button 'Keep changes' now asks if the currently selected model should be overwritten if the name was not changed

Bug fixes

  • In the model editor, the combobox for the 'to' field did not accept to be empty after holding a selection

  • Some graphical errors in the model gallery were fixed

  • Importing data in wide format corrupted the array of observed variables as mkin_wide_to_long returns 'name' as a factor

gmkin 0.6-2 (2015-11-10)

  • Make it possible to export model predictions as CSV

  • Bugfix on windows: Start a windows graphics device for plotting during the fit if none is active to avoid an error

  • Only tell the user that the fit can be aborted in the R console when gmkin is running in an interactive R session

gmkin 0.6-1 (2015-11-10)

  • Completely rewritten user interface with a three column layout

  • Introduce project management with the possibility to move datasets and models

  • Tabbed viewing area on the right, with workflow graph, data editor, the manual and changes in gmkin (this file)

  • Introduction of a workspace object as an R6 class 'gmkinws'

  • Simplify model specification by using a combobox with multiple selection for specifiying target variables (metabolites, target compartments)

  • Introduce a model gallery (loaded when the tab is selected the first time, as it loads slowly)

gmkin 0.5-10 (2015-05-08)

Minor changes

  • Updates to DESCRIPTION and

  • man/gmkin.Rd: Do not mark gmkin as being experimental any more

gmkin 0.5-8 (2014-11-25)

Minor changes

  • Adapt fit configuration to the fact that the default optimisation algorithm in mkin has been changed to Port

gmkin 0.5-7

New features

  • Installation is further simplified, as both gmkin and gWidgetsWWW2 are now available from R-Forge.

gmkin 0.5-6

New features

  • The plot of the current fit and the residuals can be saved as pdf or png file, on windows also as a windows metafile (wmf)

gmkin 0.5-5

Bug fixes

  • Prevent loading old gmkin workspace files created with mkin < 0.9-32 as they do not load properly

  • Fix saving summary files. They were all saved under the same name without a warning

gmkin 0.5-4

Bug fixes

  • A heading in the manual was fixed

gmkin 0.5-3

New features

  • First version installable from the package repository on r-forge

  • New vignette gmkin_manual

  • Small improvements in the model editor

gmkin 0.5-2

New features

  • Make Port and SANN optimisation algorithms from FME available to gmkin, in addition to the default algorithm Marq

  • Make it possible to specify the maximum number of iterations for these algorithms

  • Provide the possibility to save summaries as text file

  • Option to show the fitting process in a separate plot device, default is not to

  • Add an inital message explaining the use of the target input box of the model editor

Bug fixes

  • Sorting in the fit table now works correctly also for more than 9 fits

  • The fit table was not always updated (e.g. after deleting a fit) due to a bug introduced while fixing the bug above

Minor changes

  • The statusbar message was improved

  • This NEWS file was added, in markdown format for viewing on github

gmkin 0.5-1

  • This is the gmkin version presented at SETAC in Basel in May 2014