| 3c1313d | Andreas Raue | 10 November 2015, 13:56:26 UTC | bug fix for cases where output was requested | 10 November 2015, 13:56:26 UTC |
| cad3c62 | Clemens Kreutz | 10 November 2015, 13:49:08 UTC | Bug fix occuring in arLhsSampleSizeCalculation if called via arFitLHS(smallNumber) | 10 November 2015, 13:49:08 UTC |
| f2c1476 | Joep Vanlier | 09 November 2015, 16:36:25 UTC | merge | 09 November 2015, 16:36:25 UTC |
| 161c8d5 | Joep Vanlier | 09 November 2015, 16:34:00 UTC | Added support for RANDOMs in arExport. Improved figure legend location arPlotY. Suppressed annoying output arPlotter. | 09 November 2015, 16:34:00 UTC |
| 8b9edf5 | Max Schelker | 09 November 2015, 15:23:10 UTC | minor | 09 November 2015, 15:23:10 UTC |
| 1f86a5f | Lorenz Adlung | 04 November 2015, 14:01:10 UTC | arMergeFits of chosen workspaces edited online with Bitbucket | 04 November 2015, 14:01:10 UTC |
| ea59386 | Helge Hass | 03 November 2015, 14:09:15 UTC | minor fix | 03 November 2015, 14:09:15 UTC |
| 73856a5 | Max Schelker | 02 November 2015, 13:26:04 UTC | Merge | 02 November 2015, 13:26:04 UTC |
| f32fc0c | Max Schelker | 02 November 2015, 13:25:46 UTC | Merge | 02 November 2015, 13:25:46 UTC |
| 5f3ff12 | Clemens Kreutz | 01 November 2015, 09:29:06 UTC | 1) arFitLHS now calls arLhsSampleSizeCalculation.m 2) Call arFitLHS(8,[],[],true) is now feasible. | 01 November 2015, 09:29:06 UTC |
| 2b88184 | Clemens Kreutz | 31 October 2015, 21:59:02 UTC | New function: Sample size calculation for LHS | 31 October 2015, 21:59:02 UTC |
| adae663 | Clemens Kreutz | 31 October 2015, 20:59:43 UTC | Bug fix (error if field does not exist) | 31 October 2015, 20:59:43 UTC |
| 19369d2 | Clemens Kreutz | 31 October 2015, 20:53:15 UTC | Bug fix (error if field does not exist) | 31 October 2015, 20:53:15 UTC |
| fcff228 | Max Schelker | 30 October 2015, 15:50:16 UTC | minor | 30 October 2015, 15:50:16 UTC |
| 2c64a18 | Clemens Kreutz | 30 October 2015, 14:13:49 UTC | Small change in the Setup of the DREAM Example. | 30 October 2015, 14:13:49 UTC |
| 18513ee | Clemens Kreutz | 30 October 2015, 14:11:15 UTC | New ple functionalities: 1) pleGlobals.mode=5 enforces that the threshold or the bounds are reached by the number of specified steps (samplesize). Usually the samplesize can be decreased compared to pleGlobals.mode=1. Can only be used via arPLEInit([],[],5). 2) ple with option "force" 3) Loading and saving: pleGlobals is also saved in workspace.mat if arSave is executed. It is used if the profile calculation saved in result.mat is not finished. This prevents unintended overwriting of old results if ple is aborted. | 30 October 2015, 14:11:15 UTC |
| 018854a | Joep Vanlier | 30 October 2015, 10:28:39 UTC | Merge | 30 October 2015, 10:28:39 UTC |
| b5a8da4 | Joep Vanlier | 30 October 2015, 10:28:21 UTC | Added more descriptive error messages for incorrectly specified input functions. | 30 October 2015, 10:28:21 UTC |
| 6fbf3c1 | Bernhard Steiert | 29 October 2015, 13:59:29 UTC | Fix issue #49 | 29 October 2015, 13:59:29 UTC |
| a812cb6 | Joep Vanlier | 27 October 2015, 14:39:47 UTC | minor | 27 October 2015, 14:39:47 UTC |
| bbd69fa | Joep Vanlier | 27 October 2015, 14:37:25 UTC | bugfix | 27 October 2015, 14:37:25 UTC |
| 56d3edd | Joep Vanlier | 27 October 2015, 14:32:28 UTC | Added option to add description to data file input change. | 27 October 2015, 14:32:28 UTC |
| 21ded04 | Joep Vanlier | 27 October 2015, 09:45:29 UTC | merge | 27 October 2015, 09:45:29 UTC |
| 981aaac | Joep Vanlier | 27 October 2015, 09:45:11 UTC | Added sensitivity RHS contributions. Fitting compartment volumes should now be possible without problems. | 27 October 2015, 09:45:11 UTC |
| 512b6fd | Andreas Raue | 23 October 2015, 20:12:29 UTC | Remove all paper related files from Repository | 23 October 2015, 20:12:29 UTC |
| 8a915bd | Joep Vanlier | 23 October 2015, 17:20:28 UTC | Fixed minor bug in arPrint | 23 October 2015, 17:20:28 UTC |
| 64107d3 | Joep Vanlier | 23 October 2015, 16:39:31 UTC | Clemens's earlier push | 23 October 2015, 16:39:31 UTC |
| dce4c21 | Joep Vanlier | 23 October 2015, 16:35:54 UTC | Reverted bad merge | 23 October 2015, 16:35:54 UTC |
| 5748b5b | Joep Vanlier | 23 October 2015, 15:34:56 UTC | Merge | 23 October 2015, 15:34:56 UTC |
| 19ee0b1 | Joep Vanlier | 23 October 2015, 15:34:44 UTC | Added warning & sensitivities for volume parameters | 23 October 2015, 15:34:44 UTC |
| 0fbbd2c | Clemens Kreutz | 23 October 2015, 13:41:13 UTC | Zusammenführen | 23 October 2015, 13:41:13 UTC |
| 2cdc8da | Clemens Kreutz | 23 October 2015, 13:15:09 UTC | New option for logging within optimization, new config: ar.config.logFitting, new sub-function in arFit.m: arLogFitDetailed. | 23 October 2015, 13:15:09 UTC |
| 48b343b | Joep Vanlier | 23 October 2015, 11:49:50 UTC | Fixed bug associated with new negative state detection (field may not exist when there is no data) | 23 October 2015, 11:49:50 UTC |
| b88c1ca | Joep Vanlier | 23 October 2015, 11:44:25 UTC | Added free volume parameters to parameters list. To do: appropriate sensitivities | 23 October 2015, 11:44:25 UTC |
| 2ae94cd | Joep Vanlier | 22 October 2015, 15:29:38 UTC | merge | 22 October 2015, 15:29:38 UTC |
| 4cae05a | Joep Vanlier | 22 October 2015, 15:29:25 UTC | Added 'exact' option to arFindPar. Monotonic spline extrapolates with last tangent now. | 22 October 2015, 15:29:25 UTC |
| 6f5a2eb | Helge Hass | 22 October 2015, 15:10:36 UTC | minor change in PB | 22 October 2015, 15:10:36 UTC |
| 28ca4ca | Helge Hass | 22 October 2015, 15:05:08 UTC | Merge (grrr) | 22 October 2015, 15:05:08 UTC |
| ed42ef6 | Helge Hass | 22 October 2015, 15:01:17 UTC | delete tmp variables of versioning | 22 October 2015, 15:01:17 UTC |
| 89efe5a | Clemens Kreutz | 22 October 2015, 09:51:05 UTC | Allows to call arSetPars with another ar-struct, e.g. from a workspace. The new potential call arSetPars(ar2) alters the global ar by using info in ar2. | 22 October 2015, 09:51:05 UTC |
| 2424777 | Joep Vanlier | 19 October 2015, 11:16:10 UTC | pleSmooth: added comment symbol to make sure the entire help appears | 19 October 2015, 11:16:10 UTC |
| ee0bed1 | Joep Vanlier | 14 October 2015, 15:27:14 UTC | bugfix (thanks Tim!) | 14 October 2015, 15:27:14 UTC |
| 64bfb01 | Joep Vanlier | 14 October 2015, 08:59:41 UTC | accidental change plePlotMulti again | 14 October 2015, 08:59:41 UTC |
| 441dd34 | Joep Vanlier | 14 October 2015, 08:56:52 UTC | merge | 14 October 2015, 08:56:52 UTC |
| b47a281 | Joep Vanlier | 14 October 2015, 08:56:43 UTC | Changed str2double to str2num in arFindData. str2double would return NaN for (value), while str2num succesfully parses it to the correct numeric value. | 14 October 2015, 08:56:43 UTC |
| a51d11b | Helge Hass | 13 October 2015, 15:31:36 UTC | save revision information in ar struct for crosscheck later on | 13 October 2015, 15:31:36 UTC |
| edddb46 | Joep Vanlier | 13 October 2015, 14:08:15 UTC | undo a change I only use locally | 13 October 2015, 14:08:15 UTC |
| 272759b | Joep Vanlier | 13 October 2015, 14:07:15 UTC | Added negative timepoint integers to the regular expression mask | 13 October 2015, 14:07:15 UTC |
| 1848faa | Joep Vanlier | 13 October 2015, 12:39:23 UTC | Refactored spline derivative derivation to be more succinct and safer. Can also have expressions containing splines now, e.g. spline5(args) * exp(-k*t) | 13 October 2015, 12:39:23 UTC |
| e4268d2 | Joep Vanlier | 13 October 2015, 10:28:36 UTC | bugfix monotonic splines | 13 October 2015, 10:28:36 UTC |
| f208d63 | Joep Vanlier | 12 October 2015, 17:35:19 UTC | merge | 12 October 2015, 17:35:19 UTC |
| e3a1444 | Joep Vanlier | 12 October 2015, 17:35:04 UTC | Added monotonic splines (do not wobble due to monotonicity between knots). See Examples/MonotoneSpline | 12 October 2015, 17:35:04 UTC |
| 2cb03a7 | Lorenz Adlung | 12 October 2015, 08:15:35 UTC | Should resolve issue #20 arLoadData.m edited online with Bitbucket | 12 October 2015, 08:15:35 UTC |
| c807628 | Andreas Raue | 07 October 2015, 16:04:32 UTC | simplified and improved section. Now only shows red if parameter are fitted. | 07 October 2015, 16:04:32 UTC |
| 52dda1b | Andreas Raue | 07 October 2015, 15:59:08 UTC | improved query for parameters close to bound = red colored lines in arPrint Not it is relative to the set ub and lb distance | 07 October 2015, 15:59:08 UTC |
| 45e3992 | Joep Vanlier | 06 October 2015, 16:58:09 UTC | Added the option in pleSmooth to specify a point and direction manually. | 06 October 2015, 16:58:09 UTC |
| 1dc4b42 | Joep Vanlier | 06 October 2015, 11:50:09 UTC | merge | 06 October 2015, 11:50:09 UTC |
| f4ad5d6 | Joep Vanlier | 06 October 2015, 11:49:51 UTC | Minor bugfix: Make sure that silent plot is actually silent. | 06 October 2015, 11:49:51 UTC |
| bb267e5 | Clemens Kreutz | 05 October 2015, 18:31:42 UTC | ar.config.useLHS=0: uniform between ar.lb and ar.ub; ar.config.useLHS=2: randn if prior available. | 05 October 2015, 18:31:42 UTC |
| 86e42fa | Bernhard Steiert | 05 October 2015, 09:16:24 UTC | Small change in detection of negative states | 05 October 2015, 09:16:24 UTC |
| 1e7eed2 | Andreas Raue | 02 October 2015, 13:52:01 UTC | helper functions for random effects implementation | 02 October 2015, 13:52:01 UTC |
| 14f1f0c | Andreas Raue | 01 October 2015, 18:01:11 UTC | New type of RANDOM effect: normal distribution | 01 October 2015, 18:01:11 UTC |
| 058ca73 | Andreas Raue | 01 October 2015, 18:00:45 UTC | implemented exclusion of +/- Inf data from residuals | 01 October 2015, 18:00:45 UTC |
| 59246c5 | Andreas Raue | 01 October 2015, 18:00:09 UTC | added help text | 01 October 2015, 18:00:09 UTC |
| 24850f5 | Bernhard Steiert | 30 September 2015, 16:05:41 UTC | Fix issue #47 | 30 September 2015, 16:05:41 UTC |
| b96c323 | Max Schelker | 28 September 2015, 18:22:58 UTC | updates ignore file | 28 September 2015, 18:22:58 UTC |
| 98dcfda | Max Schelker | 28 September 2015, 18:17:55 UTC | fixes issue #45 | 28 September 2015, 18:17:55 UTC |
| 92ba1ba | Max Schelker | 28 September 2015, 17:50:24 UTC | workaround for R2015b compatibility | 28 September 2015, 17:50:24 UTC |
| 8ceb8dd | Max Schelker | 22 September 2015, 12:45:46 UTC | improvements in correlation plot | 22 September 2015, 12:45:46 UTC |
| ef99bf3 | Joep Vanlier | 21 September 2015, 09:41:53 UTC | Some updates w.r.t. the new stoichiometry feature | 21 September 2015, 09:41:53 UTC |
| 1b9493a | JoepVanlier | 17 September 2015, 17:07:22 UTC | Also updated MASSACTION mode for non-unity stoichiometry | 17 September 2015, 17:07:22 UTC |
| d03b72a | JoepVanlier | 17 September 2015, 16:31:37 UTC | removed some unnecessary output during compiling which I accidentally committed with the last commit | 17 September 2015, 16:31:37 UTC |
| df1693b | JoepVanlier | 17 September 2015, 16:28:06 UTC | Added option to use more complex stoichiometry in rates e.g. 5 A + 4 B -> C | 17 September 2015, 16:28:06 UTC |
| a6e79c3 | Bernhard Steiert | 16 September 2015, 12:39:22 UTC | Suppressing output of each initial likelihood value when performing LHS | 16 September 2015, 12:39:22 UTC |
| 2afdf58 | Bernhard Steiert | 16 September 2015, 12:12:25 UTC | Improvement in arChi2.m: After ODE solver crashes, it is restarted with modified settings. | 16 September 2015, 12:12:25 UTC |
| 5fe5809 | Clemens Kreutz | 16 September 2015, 09:02:28 UTC | Change of arFits.m from 21.5.15 had a bug. Some old fits were kept were it was not intended. This is now fixed. | 16 September 2015, 09:02:28 UTC |
| ec98601 | Max Schelker | 11 September 2015, 15:32:33 UTC | added useful tools from Matlab fileexchange | 11 September 2015, 15:32:33 UTC |
| 0667b9e | Bernhard Steiert | 11 September 2015, 10:11:14 UTC | Merge | 11 September 2015, 10:11:14 UTC |
| 04030dd | Bernhard Steiert | 11 September 2015, 09:55:34 UTC | PPL bug fix | 11 September 2015, 09:55:34 UTC |
| 28ea062 | Andreas Raue | 09 September 2015, 19:16:31 UTC | bug fix | 09 September 2015, 19:16:31 UTC |
| 8726d8b | Helge Hass | 08 September 2015, 14:53:19 UTC | Merge | 08 September 2015, 14:53:19 UTC |
| d109729 | Helge Hass | 08 September 2015, 14:45:29 UTC | better thresholds for observation-specific integrator tolerances. New steady state solver function which sets input to 0 and allows to solve for kinetic parameters if needed | 08 September 2015, 14:45:29 UTC |
| 8befc59 | Lorenz Adlung | 01 September 2015, 12:34:02 UTC | Minor fix of arLoadModel.m from commit 1ac65bb edited online with Bitbucket | 01 September 2015, 12:34:02 UTC |
| f8a70a4 | Helge Hass | 20 August 2015, 08:59:28 UTC | bugfix plotting of DR with prediction profiles | 20 August 2015, 08:59:28 UTC |
| 6648e99 | Joep Vanlier | 18 August 2015, 16:20:55 UTC | merge | 18 August 2015, 16:20:55 UTC |
| a69cc54 | Joep Vanlier | 18 August 2015, 16:20:37 UTC | Refined arFindData.m | 18 August 2015, 16:20:37 UTC |
| 7fe3aac | Bernhard Steiert | 18 August 2015, 13:16:13 UTC | Merge | 18 August 2015, 13:16:13 UTC |
| 819f0ab | Joep Vanlier | 18 August 2015, 12:55:45 UTC | Simplified arFindData.m (pull recommended if you use this function) | 18 August 2015, 12:55:45 UTC |
| 120d1b9 | Bernhard Steiert | 18 August 2015, 12:53:55 UTC | Small change in pleSmooth to prevent oversensitivity | 18 August 2015, 12:53:55 UTC |
| dd022c0 | Bernhard Steiert | 18 August 2015, 12:19:34 UTC | pleSmooth now also works for connecting local optima | 18 August 2015, 12:19:34 UTC |
| 41e0674 | Joep Vanlier | 18 August 2015, 12:12:27 UTC | merge | 18 August 2015, 12:12:27 UTC |
| f5f45f1 | Joep Vanlier | 18 August 2015, 12:11:10 UTC | Fixed bug in condition filter of arFindData. | 18 August 2015, 12:11:10 UTC |
| ca4eae8 | Joep Vanlier | 14 August 2015, 14:32:19 UTC | Change in arLoadModel.m: Do not add DERIVE variable in DERIVE expression as a new internal parameter | 14 August 2015, 14:32:19 UTC |
| d63e86b | Joep Vanlier | 13 August 2015, 16:43:14 UTC | Added extra flag to look for fixed pars to arPrint | 13 August 2015, 16:43:14 UTC |
| b3f15ee | Joep Vanlier | 11 August 2015, 17:03:01 UTC | Added warning message for when arLoadData can't find the corresponding csv or xls file. Also note that this can potentially lead to a crash (should add some error handling there too!) | 11 August 2015, 17:03:01 UTC |
| ca7bcca | Joep Vanlier | 11 August 2015, 14:42:08 UTC | Fixed typo in arSubPlotter | 11 August 2015, 14:42:08 UTC |
| 75cc406 | Joep Vanlier | 07 August 2015, 14:21:33 UTC | minor change | 07 August 2015, 14:21:33 UTC |
| 6afafd4 | Joep Vanlier | 07 August 2015, 14:18:05 UTC | merge | 07 August 2015, 14:18:05 UTC |
| f4b46f5 | Joep Vanlier | 07 August 2015, 14:17:54 UTC | Updated bibliography (for later) | 07 August 2015, 14:17:54 UTC |
| 1eae56b | Joep Vanlier | 07 August 2015, 14:12:02 UTC | retry mechanism for pleExtend | 07 August 2015, 14:12:02 UTC |
