| d0a33df | JoepVanlier | 19 May 2015, 13:37:10 UTC | Added proper error handling for equilibration steps | 19 May 2015, 13:37:10 UTC |
| 64cc2d7 | JoepVanlier | 19 May 2015, 09:16:42 UTC | Edited arFindInputs to work with condition inputs rather than data inputs. Also updated the event example. | 19 May 2015, 09:16:42 UTC |
| 09d7f32 | JoepVanlier | 18 May 2015, 16:27:05 UTC | arGet function (added by Clemens Blank), used to extract data structures from the ar struct | 18 May 2015, 16:27:05 UTC |
| 397d6b3 | JoepVanlier | 18 May 2015, 16:19:54 UTC | Removed OSX Desktop Services Store files | 18 May 2015, 16:19:54 UTC |
| 283af28 | JoepVanlier | 18 May 2015, 16:11:58 UTC | Added verbose mode to arPrintSteadyState and added a sanity check to arSteadyState. | 18 May 2015, 16:11:58 UTC |
| 46cf8a2 | JoepVanlier | 18 May 2015, 15:45:10 UTC | Helper function to print pre-equilibration information | 18 May 2015, 15:45:10 UTC |
| 13d6024 | Clemens Kreutz | 18 May 2015, 11:43:00 UTC | Bug fix. The bug occurred if several d2d projects are in matlab's search path and therefore the path to arClusterCompiledHook.m was wrong. | 18 May 2015, 11:43:00 UTC |
| 31f1e44 | Clemens Kreutz | 18 May 2015, 11:35:23 UTC | Bug fix arCompare | 18 May 2015, 11:35:23 UTC |
| 55cb0ac | Clemens Kreutz | 18 May 2015, 10:41:46 UTC | Bug fix. | 18 May 2015, 10:41:46 UTC |
| 9cf50c2 | Max Schelker | 14 May 2015, 18:15:34 UTC | minor | 14 May 2015, 18:15:34 UTC |
| f4ec212 | Lorenz Adlung | 14 May 2015, 14:32:09 UTC | New Example | 14 May 2015, 14:32:09 UTC |
| 911591c | Lorenz Adlung | 14 May 2015, 14:20:28 UTC | arLoadPars adapted to workspace_pars_only.mat | 14 May 2015, 14:20:28 UTC |
| 5f25484 | Bernhard Steiert | 12 May 2015, 16:16:09 UTC | Small fix in plePlotMulti (thanks Raphael) | 12 May 2015, 16:16:09 UTC |
| fa121c2 | Max Schelker | 08 May 2015, 13:42:35 UTC | Merge | 08 May 2015, 13:42:35 UTC |
| 137f281 | Max Schelker | 08 May 2015, 13:41:02 UTC | added extracting sundials tar in windows. Please check if it still works on unix! | 08 May 2015, 13:41:02 UTC |
| be70ab7 | Andreas Raue | 08 May 2015, 12:56:26 UTC | small changes | 08 May 2015, 12:56:26 UTC |
| 1120b8e | Max Schelker | 07 May 2015, 21:21:08 UTC | added comment | 07 May 2015, 21:21:08 UTC |
| 311b1df | Max Schelker | 07 May 2015, 21:19:27 UTC | copy dll files to working directory if they are not in Windows folder (useful for users on Windows machines without admin privileges) | 07 May 2015, 21:19:27 UTC |
| 358d9ff | Lorenz Adlung | 06 May 2015, 11:46:02 UTC | Should resolve issue #28 arCheck.m edited online with Bitbucket | 06 May 2015, 11:46:02 UTC |
| 89d1934 | Andreas Raue | 04 May 2015, 20:51:42 UTC | added sys/time.h support for Windows, check out arPlotClockTimes to see how different threads and conditions are timed. | 04 May 2015, 20:51:42 UTC |
| b12fcd2 | Andreas Raue | 04 May 2015, 20:12:04 UTC | I improved the way arCompileAll is removing unused parameters from the whole compiled model. It fixes cases where parameter are without effect, a left over from CONDITIONS... Please let me know if you run into any issues with that. | 04 May 2015, 20:12:04 UTC |
| 943a971 | Andreas Raue | 04 May 2015, 20:09:34 UTC | improved new plot functions | 04 May 2015, 20:09:34 UTC |
| d6767a4 | Clemens Kreutz | 30 April 2015, 17:03:31 UTC | Bug fix. | 30 April 2015, 17:03:31 UTC |
| b6aa939 | Max Schelker | 30 April 2015, 16:59:02 UTC | Merge | 30 April 2015, 16:59:02 UTC |
| 94c6bc0 | Max Schelker | 30 April 2015, 16:57:21 UTC | corrected typos | 30 April 2015, 16:57:21 UTC |
| 0ddad5e | Andreas Raue | 30 April 2015, 00:54:41 UTC | small bug fix | 30 April 2015, 00:54:41 UTC |
| 9654a0c | Max Schelker | 29 April 2015, 14:43:43 UTC | fixes bug in arLoadData when having more than one model | 29 April 2015, 14:43:43 UTC |
| e226212 | Andreas Raue | 28 April 2015, 14:09:35 UTC | surpress unneccessary output from archi2 | 28 April 2015, 14:09:35 UTC |
| aac9618 | Andreas Raue | 27 April 2015, 15:43:12 UTC | some random changes | 27 April 2015, 15:43:12 UTC |
| 2cf0faf | JoepVanlier | 27 April 2015, 10:04:52 UTC | Added experimental support for more accurate step functions (inactive by default). Only works with events enabled and inputs classified. | 27 April 2015, 10:04:52 UTC |
| 42af98b | Clemens Kreutz | 24 April 2015, 10:06:10 UTC | Making the different possibilities to call arChi2 easier to understand. | 24 April 2015, 10:06:10 UTC |
| 2848f24 | Clemens Kreutz | 24 April 2015, 10:00:28 UTC | Bug fix (occurring for several models, data sets, ...) | 24 April 2015, 10:00:28 UTC |
| 02af026 | Andreas Raue | 23 April 2015, 20:49:01 UTC | bug fix | 23 April 2015, 20:49:01 UTC |
| d08d0f4 | Andreas Raue | 23 April 2015, 19:19:57 UTC | small fixes | 23 April 2015, 19:19:57 UTC |
| 9e313c1 | Andreas Raue | 23 April 2015, 19:18:49 UTC | bug fix | 23 April 2015, 19:18:49 UTC |
| 02f8d27 | JoepVanlier | 23 April 2015, 17:01:43 UTC | merge | 23 April 2015, 17:01:43 UTC |
| 710ee2a | JoepVanlier | 23 April 2015, 17:00:42 UTC | Added a function to recursively deepcopy a structure. Useful for when you want to have multiple ar structs around (see function description). | 23 April 2015, 17:00:42 UTC |
| 0ff9514 | Clemens Kreutz | 23 April 2015, 13:31:43 UTC | New function for comparing two ar structures (or parts of it), | 23 April 2015, 13:31:43 UTC |
| 683c42f | Andreas Raue | 23 April 2015, 13:17:49 UTC | improvements in parameter plotting functions | 23 April 2015, 13:17:49 UTC |
| 31d93cb | JoepVanlier | 23 April 2015, 12:12:54 UTC | Added residual error checking | 23 April 2015, 12:12:54 UTC |
| 7cd0f31 | Andreas Raue | 23 April 2015, 11:55:01 UTC | order struct fields | 23 April 2015, 11:55:01 UTC |
| 3b4683c | Clemens Kreutz | 23 April 2015, 10:01:23 UTC | A new function for evaluating the dependency on the ODE tolerances. | 23 April 2015, 10:01:23 UTC |
| 302ff50 | JoepVanlier | 22 April 2015, 15:39:04 UTC | minor fix in arPrint | 22 April 2015, 15:39:04 UTC |
| 3c98d72 | JoepVanlier | 22 April 2015, 15:14:50 UTC | Added some filters to arPrint that make it easier to work with larger models | 22 April 2015, 15:14:50 UTC |
| 66521a6 | Andreas Raue | 21 April 2015, 15:24:08 UTC | small bug fix | 21 April 2015, 15:24:08 UTC |
| 30fcb06 | Andreas Raue | 21 April 2015, 14:58:40 UTC | improvements in plotting guis | 21 April 2015, 14:58:40 UTC |
| 80f8a03 | Clemens Kreutz | 21 April 2015, 12:50:38 UTC | New function for evaluating the impact of the integration tolerances on residuals, sres, and chi2. | 21 April 2015, 12:50:38 UTC |
| 3720e7a | Clemens Kreutz | 21 April 2015, 12:48:47 UTC | Bug fix concerning arPrint red color for unlog parameters | 21 April 2015, 12:48:47 UTC |
| 709aa63 | Andreas Raue | 20 April 2015, 17:31:39 UTC | corrected bug for fast plotting of steady state constraint lines | 20 April 2015, 17:31:39 UTC |
| d49c103 | JoepVanlier | 18 April 2015, 10:50:53 UTC | fixed confusing typo in description | 18 April 2015, 10:50:53 UTC |
| c67a1a6 | Andreas Raue | 18 April 2015, 00:39:28 UTC | partially reversed changes from last commit | 18 April 2015, 00:39:28 UTC |
| b526593 | Andreas Raue | 18 April 2015, 00:38:36 UTC | changes in model template | 18 April 2015, 00:38:36 UTC |
| b0e45f5 | Andreas Raue | 17 April 2015, 01:57:05 UTC | update und unit calculations, this still does not work... | 17 April 2015, 01:57:05 UTC |
| 28d73d5 | Andreas Raue | 16 April 2015, 21:04:04 UTC | First part of attempt to automatically calculate parameter units... stay tuned | 16 April 2015, 21:04:04 UTC |
| 3836b0d | JoepVanlier | 16 April 2015, 13:24:52 UTC | small fix | 16 April 2015, 13:24:52 UTC |
| 778217d | JoepVanlier | 16 April 2015, 09:57:34 UTC | Edited description a little bit | 16 April 2015, 09:57:34 UTC |
| 5d830c6 | JoepVanlier | 16 April 2015, 09:46:40 UTC | Cleaned up the function a bit and added function to restrict to dynamic parameters | 16 April 2015, 09:46:40 UTC |
| 2f13d90 | JoepVanlier | 16 April 2015, 09:17:04 UTC | Added function to facilitate scripts which automate parameter manipulation. | 16 April 2015, 09:17:04 UTC |
| d313925 | JoepVanlier | 15 April 2015, 16:58:49 UTC | Fixed description for helper functions | 15 April 2015, 16:58:49 UTC |
| 0d8d5d0 | JoepVanlier | 15 April 2015, 16:53:57 UTC | Generalized the new helper functions a bit and added a few more that I've been using. | 15 April 2015, 16:53:57 UTC |
| 4b0efdf | Andreas Raue | 15 April 2015, 16:10:45 UTC | changes in arSave, does also save the parameter matrixes from fits in smaller file changes in arLoadPars, now accepts and ar struct changes in stringListChooser, display correct likelihood vales in preview | 15 April 2015, 16:10:45 UTC |
| 1f7d08b | Andreas Raue | 15 April 2015, 14:53:40 UTC | updates in ple function | 15 April 2015, 14:53:40 UTC |
| bb3ff08 | JoepVanlier | 15 April 2015, 12:27:42 UTC | merge | 15 April 2015, 12:27:42 UTC |
| 6a0d0f5 | JoepVanlier | 15 April 2015, 12:23:07 UTC | Two helper functions to make working with steady states a bit easier | 15 April 2015, 12:23:07 UTC |
| 3929836 | Clemens Kreutz | 15 April 2015, 11:47:13 UTC | The ylims of the axes are adapted if the parameters are changed by the tuner (otherwise the trajectories can move out the currently shown y-range). | 15 April 2015, 11:47:13 UTC |
| ed19b91 | Clemens Kreutz | 15 April 2015, 11:43:55 UTC | Parameters from another project-folder can be loaded. | 15 April 2015, 11:43:55 UTC |
| 4837a6d | Clemens Kreutz | 15 April 2015, 11:39:27 UTC | Latex is started with an option which prevent stopping/waiting of matlab if packages are missing. | 15 April 2015, 11:39:27 UTC |
| af5a2b9 | Joep Vanlier | 15 April 2015, 10:00:28 UTC | Made sure state omission field doesn't accidentally get passed as tStart | 15 April 2015, 10:00:28 UTC |
| 4055fb7 | Joep Vanlier | 14 April 2015, 16:24:25 UTC | Added exclusion list to steady state equilibration | 14 April 2015, 16:24:25 UTC |
| 0bd64d3 | Joep Vanlier | 10 April 2015, 13:01:13 UTC | Small optimization in arReport: ver('MATLAB') was a hot line while profiling arReport; hence I cached its result | 10 April 2015, 13:01:13 UTC |
| 195d0c6 | Joep Vanlier | 09 April 2015, 16:20:56 UTC | merge | 09 April 2015, 16:20:56 UTC |
| d7c9748 | Joep Vanlier | 09 April 2015, 16:20:34 UTC | Slightly more informative error message | 09 April 2015, 16:20:34 UTC |
| dbc55ff | Clemens Kreutz | 09 April 2015, 15:47:03 UTC | Function for recompiling a previously saved model without setup, i.e. without arLoadModel/arLoadData | 09 April 2015, 15:47:03 UTC |
| 83d6eed | Joep Vanlier | 09 April 2015, 08:41:55 UTC | Forgot to update C version number | 09 April 2015, 08:41:55 UTC |
| c238bbc | Joep Vanlier | 08 April 2015, 20:58:23 UTC | Fixed a bug in the event system. Should only have affected simulations with events before t=0 and no events after t=0. | 08 April 2015, 20:58:23 UTC |
| 7eab57f | Andreas Raue | 07 April 2015, 20:58:23 UTC | minor fixes | 07 April 2015, 20:58:23 UTC |
| e245127 | Andreas Raue | 07 April 2015, 20:58:08 UTC | bug fixes in new plot function | 07 April 2015, 20:58:08 UTC |
| 1377c3c | Andreas Raue | 07 April 2015, 20:57:48 UTC | new GUI, arSubPlotter, check it out! Improvements in arParameters | 07 April 2015, 20:57:48 UTC |
| 41a00b8 | Andreas Raue | 07 April 2015, 20:57:18 UTC | improved thread handling | 07 April 2015, 20:57:18 UTC |
| a24be09 | Andreas Raue | 05 April 2015, 00:42:32 UTC | update arParameters | 05 April 2015, 00:42:32 UTC |
| c6e06c7 | Andreas Raue | 04 April 2015, 20:35:46 UTC | New GUI: arParameters, basically an arTuner but in form of a table. | 04 April 2015, 20:35:46 UTC |
| 01250fe | Andreas Raue | 04 April 2015, 19:37:27 UTC | small changes to gui files | 04 April 2015, 19:37:27 UTC |
| f208784 | Andreas Raue | 03 April 2015, 21:38:00 UTC | implemented CVODES SetMaxStep functionality, see ar.config.maxstepsize | 03 April 2015, 21:38:00 UTC |
| 6e491c8 | Andreas Raue | 03 April 2015, 13:32:27 UTC | improved plotting | 03 April 2015, 13:32:27 UTC |
| b9fcee1 | Andreas Raue | 29 March 2015, 20:08:08 UTC | improved function, can now limit to only common parameters. | 29 March 2015, 20:08:08 UTC |
| 64a60bf | Andreas Raue | 29 March 2015, 16:40:22 UTC | two small improvements | 29 March 2015, 16:40:22 UTC |
| a859acf | Andreas Raue | 28 March 2015, 17:22:12 UTC | improved function, now work also if project was not yet compiled and linked. Great for debugging parameter conditions... | 28 March 2015, 17:22:12 UTC |
| a6fefef | Andreas Raue | 28 March 2015, 15:56:57 UTC | minor semantic correction in c code | 28 March 2015, 15:56:57 UTC |
| a84f288 | Joep Vanlier | 27 March 2015, 18:22:05 UTC | When equilibration is coupled to a target condition that does not have a specific parameter; a warning is thrown and the sensitivities of that parameter are not adjusted. | 27 March 2015, 18:22:05 UTC |
| 8a37131 | Joep Vanlier | 27 March 2015, 17:04:14 UTC | With the new plotting, the error bars occasionally don't show up under linux. Revert to old plotting under Linux until cause is found. | 27 March 2015, 17:04:14 UTC |
| b6ff87f | Joep Vanlier | 27 March 2015, 16:44:11 UTC | Remove events before tstart upon linkage since arSteadyState depends on first event being at the start. | 27 March 2015, 16:44:11 UTC |
| 2a02600 | Joep Vanlier | 27 March 2015, 13:59:25 UTC | Merge | 27 March 2015, 13:59:25 UTC |
| e307f14 | Joep Vanlier | 27 March 2015, 13:59:14 UTC | Make sure that simulation-only runs (equilibration and such) do not fill data structures | 27 March 2015, 13:59:14 UTC |
| d271f66 | Clemens Kreutz | 27 March 2015, 10:59:11 UTC | Inconvenience fixed for new plots (Problem was that if figures are saved and latex packages are missing Matlab stopped and seemed to not respond any more.) | 27 March 2015, 10:59:11 UTC |
| cba917e | Joep Vanlier | 26 March 2015, 23:00:11 UTC | Forgot to update C version number | 26 March 2015, 23:00:11 UTC |
| f67bc2b | Joep Vanlier | 26 March 2015, 22:52:03 UTC | Improved description | 26 March 2015, 22:52:03 UTC |
| 4987c6a | Joep Vanlier | 26 March 2015, 21:02:34 UTC | Fixed bug in pre-equilibration | 26 March 2015, 21:02:34 UTC |
| d6147fd | Joep Vanlier | 26 March 2015, 16:51:43 UTC | Set master flag to zero upon clear too | 26 March 2015, 16:51:43 UTC |
| dd271fd | Joep Vanlier | 26 March 2015, 16:35:51 UTC | Only update steady state sensitivities if necessary | 26 March 2015, 16:35:51 UTC |
| c49b7af | Joep Vanlier | 26 March 2015, 16:28:48 UTC | Added waitbars and minor fixes | 26 March 2015, 16:28:48 UTC |
