| d72d4c2 | Andreas Raue | 06 March 2015, 00:17:07 UTC | Increase C version code, after Joep's submits today to prevent compatibility problems | 06 March 2015, 00:17:07 UTC |
| c957462 | Max Schelker | 05 March 2015, 14:59:14 UTC | minor | 05 March 2015, 14:59:14 UTC |
| ce501ee | Max Schelker | 05 March 2015, 14:09:51 UTC | minor | 05 March 2015, 14:09:51 UTC |
| 6ea74e4 | Joep Vanlier | 05 March 2015, 13:10:08 UTC | Merge | 05 March 2015, 13:10:08 UTC |
| df5750a | Joep Vanlier | 05 March 2015, 13:01:46 UTC | Added events for dealing with step inputs. See /Examples/Event_Test for more information. | 05 March 2015, 13:01:46 UTC |
| a5a1678 | Andreas Raue | 05 March 2015, 02:42:45 UTC | cover letter | 05 March 2015, 02:42:45 UTC |
| 71e2a83 | Andreas Raue | 05 March 2015, 01:11:25 UTC | final version to be submitted to all coauthors | 05 March 2015, 01:11:25 UTC |
| d46ec7a | Andreas Raue | 04 March 2015, 14:15:53 UTC | added additional supplementary files | 04 March 2015, 14:15:53 UTC |
| 6871078 | Andreas Raue | 02 March 2015, 14:46:58 UTC | improvements in arNetworkGraphCompartments function | 02 March 2015, 14:46:58 UTC |
| f244b75 | Andreas Raue | 02 March 2015, 00:48:13 UTC | compressed main text to fit on two pages again, by removing some acknowledgement that, because of the extended author list, are now redundant and some extensive affiliations. removed user guide section from supplement, we agreed on having this as a separate supplementary file | 02 March 2015, 00:48:13 UTC |
| 6e8159b | Max Schelker | 01 March 2015, 18:05:00 UTC | added new version of the figure to main text | 01 March 2015, 18:05:00 UTC |
| d0aeab8 | Lorenz Adlung | 01 March 2015, 09:15:24 UTC | d2dpaper_supplement.tex edited online with Bitbucket, minor typos | 01 March 2015, 09:15:24 UTC |
| dbcce9a | Clemens Kreutz | 27 February 2015, 14:57:33 UTC | Small change d2d paper | 27 February 2015, 14:57:33 UTC |
| 3980c8f | Lorenz Adlung | 27 February 2015, 11:16:08 UTC | d2dpaper.tex edited online with Bitbucket, minor typos | 27 February 2015, 11:16:08 UTC |
| b77510b | Clemens Kreutz | 27 February 2015, 11:05:14 UTC | ple.m now also accepts parameter names, cells of names and regular expressions. | 27 February 2015, 11:05:14 UTC |
| cfbd928 | Max Schelker | 27 February 2015, 09:48:42 UTC | corrected typos in supplement and main text. removed temp files (do not need to be in repo!) | 27 February 2015, 09:48:42 UTC |
| a1d87f2 | Andreas Raue | 27 February 2015, 03:25:53 UTC | major changes also on the supplementary text | 27 February 2015, 03:25:53 UTC |
| 4f6b490 | Andreas Raue | 27 February 2015, 02:37:34 UTC | I think we are almost there for the main text... | 27 February 2015, 02:37:34 UTC |
| 162a71a | Andreas Raue | 27 February 2015, 00:44:58 UTC | Backout changeset c660c354257f1f83632a8d04db31d48a311b7f87 | 27 February 2015, 00:44:58 UTC |
| 0349af7 | Andreas Raue | 27 February 2015, 00:21:35 UTC | added line breaks for better support of BitBucket | 27 February 2015, 00:21:35 UTC |
| 62d2fa9 | Max Schelker | 26 February 2015, 15:49:13 UTC | added funding to main text and another proposition for the figure | 26 February 2015, 15:49:13 UTC |
| f18481d | Clemens Kreutz | 26 February 2015, 15:44:12 UTC | Paper Supplement: Ein paar Änderungen in Andreas' Teil. | 26 February 2015, 15:44:12 UTC |
| b10252a | Clemens Kreutz | 26 February 2015, 14:46:51 UTC | Paper überarbeitet und gekürzt | 26 February 2015, 14:46:51 UTC |
| dc0a74b | Andreas Raue | 26 February 2015, 14:03:06 UTC | small fixes | 26 February 2015, 14:03:06 UTC |
| 32abf0f | Andreas Raue | 26 February 2015, 04:32:58 UTC | updated word count | 26 February 2015, 04:32:58 UTC |
| fc80d87 | Andreas Raue | 26 February 2015, 02:55:34 UTC | added reference in the main text to the user guide for the raia example as well as the respective section in the supplement. | 26 February 2015, 02:55:34 UTC |
| fd3b4eb | Andreas Raue | 26 February 2015, 02:42:50 UTC | included revisions from Berni and Max | 26 February 2015, 02:42:50 UTC |
| 445bc91 | Andreas Raue | 25 February 2015, 16:23:10 UTC | added generic figure for pathway generated by Graphviz | 25 February 2015, 16:23:10 UTC |
| 5a0d267 | Andreas Raue | 25 February 2015, 16:20:33 UTC | added Clemens and Birgit as authors | 25 February 2015, 16:20:33 UTC |
| d90f044 | Max Schelker | 25 February 2015, 16:09:22 UTC | added ylabels to figure | 25 February 2015, 16:09:22 UTC |
| d6a2d9d | Max Schelker | 25 February 2015, 15:58:42 UTC | updated figure for Application Note | 25 February 2015, 15:58:42 UTC |
| 3fa0dff | Max Schelker | 25 February 2015, 12:03:08 UTC | minor changes for cross platform compatibility | 25 February 2015, 12:03:08 UTC |
| 7d5702b | Max Schelker | 25 February 2015, 11:33:17 UTC | added first draft of figure for the application note. Cleaned up temporary latex files | 25 February 2015, 11:33:17 UTC |
| a58524b | Andreas Raue | 25 February 2015, 00:22:35 UTC | uploaded latex files for application note | 25 February 2015, 00:22:35 UTC |
| bb35523 | Andreas Raue | 24 February 2015, 19:44:38 UTC | minor | 24 February 2015, 19:44:38 UTC |
| 2bd322c | Andreas Raue | 24 February 2015, 19:39:17 UTC | bug fix in new plot function | 24 February 2015, 19:39:17 UTC |
| 77810b0 | Andreas Raue | 24 February 2015, 19:38:57 UTC | Few changes that make the example look nicer | 24 February 2015, 19:38:57 UTC |
| 91d643f | Andreas Raue | 24 February 2015, 17:09:42 UTC | bug fix in cluster function that lead to loss or results in some cases | 24 February 2015, 17:09:42 UTC |
| 927f9f6 | Andreas Raue | 24 February 2015, 17:08:51 UTC | improved model code for Raia example | 24 February 2015, 17:08:51 UTC |
| 9a71c9f | Andreas Raue | 24 February 2015, 17:08:21 UTC | bug fix in new plot functions | 24 February 2015, 17:08:21 UTC |
| 04aa6b4 | Andreas Raue | 24 February 2015, 17:07:56 UTC | added png output for windows systems for new plot functions | 24 February 2015, 17:07:56 UTC |
| 30382d3 | Andreas Raue | 24 February 2015, 17:07:29 UTC | improved code | 24 February 2015, 17:07:29 UTC |
| d59250e | Andreas Raue | 16 February 2015, 16:26:30 UTC | bug fix, is work now if no inputs available | 16 February 2015, 16:26:30 UTC |
| 27b402a | Andreas Raue | 16 February 2015, 16:25:45 UTC | bug fix, sets times correctly also if no dynamic variables | 16 February 2015, 16:25:45 UTC |
| 5ab5fef | Andreas Raue | 16 February 2015, 16:24:48 UTC | bug fix, now work also if there is no data loaded | 16 February 2015, 16:24:48 UTC |
| a695999 | Bernhard Steiert | 11 February 2015, 17:12:15 UTC | Small fix for matlab2tikz | 11 February 2015, 17:12:15 UTC |
| 00045bd | Bernhard Steiert | 11 February 2015, 11:08:02 UTC | Updated the ordering of arguments for arSimuData | 11 February 2015, 11:08:02 UTC |
| 69246fa | Andreas Raue | 11 February 2015, 00:09:36 UTC | Merge | 11 February 2015, 00:09:36 UTC |
| e5a6830 | Andreas Raue | 11 February 2015, 00:07:19 UTC | option to not remove the final mex file but clear the intermediate c files | 11 February 2015, 00:07:19 UTC |
| 4107b04 | Andreas Raue | 11 February 2015, 00:06:47 UTC | nice plot | 11 February 2015, 00:06:47 UTC |
| c48ebef | Andreas Raue | 11 February 2015, 00:06:33 UTC | small bug fixes | 11 February 2015, 00:06:33 UTC |
| 3e4f270 | Andreas Raue | 11 February 2015, 00:04:21 UTC | improved function to simulate and save artificial data. The second index argument is not the index of the plot as given by arPlotter, not the index of a singe data set. This has advantages when simulating dose response data. | 11 February 2015, 00:04:21 UTC |
| bd0ff20 | Bernhard Steiert | 09 February 2015, 13:16:05 UTC | Small fixes for fmincon | 09 February 2015, 13:16:05 UTC |
| 6d88f69 | Andreas Raue | 31 January 2015, 02:57:07 UTC | small bug in new function arRandomPars | 31 January 2015, 02:57:07 UTC |
| cc635c3 | Joep Vanlier | 30 January 2015, 10:59:49 UTC | Also checks for xlsx files when extension is specified as xls. | 30 January 2015, 10:59:49 UTC |
| 3f6c847 | Joep Vanlier | 30 January 2015, 10:47:26 UTC | merge after updating arLoadData with xlsx | 30 January 2015, 10:47:26 UTC |
| 3b2f48b | Joep Vanlier | 30 January 2015, 10:41:57 UTC | Added xlsx as supported format. | 30 January 2015, 10:41:57 UTC |
| 3b4ca50 | Clemens Kreutz | 29 January 2015, 09:29:17 UTC | Bug fix arHighlightY.m | 29 January 2015, 09:29:17 UTC |
| 54f5ca4 | Clemens Kreutz | 29 January 2015, 09:27:06 UTC | Extended functionality of arLoadPars.m | 29 January 2015, 09:27:06 UTC |
| 2964811 | Clemens Kreutz | 29 January 2015, 09:25:29 UTC | arPrint: Slightly extended functionality. | 29 January 2015, 09:25:29 UTC |
| bc60584 | Andreas Raue | 28 January 2015, 20:37:42 UTC | I changed the way how legends are created again. There was a bug for dose response data with multiple conditions in that earlier implementation. | 28 January 2015, 20:37:42 UTC |
| 6055389 | Andreas Raue | 28 January 2015, 13:51:05 UTC | Changed LHS sampling functions. I separated the code that generates random samples into a new function arRandomPars It now allows to both use Latin hyper cube sampling (LHS), but also standard random sampling from the specified prior. A more recent analysis by Viktoria Ehret showed that LHS only provides significant benefit for smaller parameter space. Therefore I decided to change the default to random sampling from the prior, which provides more benefits in my hands... | 28 January 2015, 13:51:05 UTC |
| 4cee49a | Wolfgang Mader | 28 January 2015, 10:38:06 UTC | Merge | 28 January 2015, 10:38:06 UTC |
| d486249 | Wolfgang Mader | 28 January 2015, 10:37:26 UTC | Checking for missing x-plot handle, using default system libs for pdflatex. | 28 January 2015, 10:37:26 UTC |
| 3d4e6d4 | Andreas Raue | 28 January 2015, 00:52:32 UTC | merge and added -dmeta as output format for windows systems (.emf files, vector graphic that can be imported to powerpoint directly) | 28 January 2015, 00:52:32 UTC |
| 1fc08b8 | Bernhard Steiert | 27 January 2015, 10:18:13 UTC | Reverted commit d825d444766d. | 27 January 2015, 10:18:13 UTC |
| b349bd7 | Bernhard Steiert | 27 January 2015, 10:10:19 UTC | Merge | 27 January 2015, 10:10:19 UTC |
| 61f5541 | Bernhard Steiert | 27 January 2015, 09:58:40 UTC | arPlot2 change: The figure is resized before PDF export. This generates consistent font sizes independent on the number of subplots. | 27 January 2015, 09:58:40 UTC |
| 137097b | Andreas Raue | 26 January 2015, 20:29:59 UTC | I don't understand this part and simplified it because I got errors there | 26 January 2015, 20:29:59 UTC |
| 49a8d6a | Andreas Raue | 26 January 2015, 20:29:28 UTC | small bug fixes | 26 January 2015, 20:29:28 UTC |
| 05d11f4 | Bernhard Steiert | 26 January 2015, 13:31:24 UTC | There is a small difference in the way arPlot and arPlot2 count X. This fix clears the line handle if arPlot2 is called after arPlot. There might be a more elegant solution for this issue. | 26 January 2015, 13:31:24 UTC |
| 9f990ee | Bernhard Steiert | 26 January 2015, 12:24:02 UTC | Small bug fixes | 26 January 2015, 12:24:02 UTC |
| 3701784 | Andreas Raue | 20 January 2015, 22:22:14 UTC | there was an issue if Observables or Derived variable would have the same name as a parameter defined previously. This would mess up and slow down some of the later calculation, although the calculations were not wrong. This fixes this issue and throws an error message now. | 20 January 2015, 22:22:14 UTC |
| aad7624 | Andreas Raue | 20 January 2015, 22:17:33 UTC | A few bug fixes for the new plotting function | 20 January 2015, 22:17:33 UTC |
| 0235df5 | Bernhard Steiert | 20 January 2015, 16:39:16 UTC | PDF Plots by running 'arPlot2(1)' are now generated by default with matlab2tikz on Unix and Mac. Please revert if you have other preferences or experience any problems! | 20 January 2015, 16:39:16 UTC |
| 15c0b75 | Andreas Raue | 20 January 2015, 16:03:16 UTC | small bug fix in new plot functions | 20 January 2015, 16:03:16 UTC |
| 10aa517 | Andreas Raue | 20 January 2015, 02:20:34 UTC | This submit closes the branch "New Plot Functions" | 20 January 2015, 02:20:34 UTC |
| a86eaa9 | Andreas Raue | 20 January 2015, 02:17:19 UTC | Merge | 20 January 2015, 02:17:19 UTC |
| 7ac46a9 | Andreas Raue | 20 January 2015, 02:15:32 UTC | Merge | 20 January 2015, 02:15:32 UTC |
| 4e1cd11 | Andreas Raue | 20 January 2015, 02:10:59 UTC | Finished first implementation. The functionality should correspond to the old function, however, the code is much cleaner now. I implemented transparency in the plots, which is pretty nice... The new plots are disable by default for now. If you want to use them, set ar.config.useNewPlots = true | 20 January 2015, 02:10:59 UTC |
| 45c1dbb | Andreas Raue | 18 January 2015, 14:55:29 UTC | improved function, prepared to plot also X and V | 18 January 2015, 14:55:29 UTC |
| acf8edc | Andreas Raue | 17 January 2015, 02:26:51 UTC | implemented new plot for time course and dose response data. | 17 January 2015, 02:26:51 UTC |
| 9c9a65e | Andreas Raue | 16 January 2015, 22:47:07 UTC | small bug fixed | 16 January 2015, 22:47:07 UTC |
| 34825f0 | Andreas Raue | 16 January 2015, 22:25:01 UTC | There was a major bug in the arCompress / arUncompress and arSimu function. I think this resulted in some of the crashes that were reported. Also, there were scenarios where the model was simulate uncomplete... please update your code! | 16 January 2015, 22:25:01 UTC |
| 2a809b6 | Andreas Raue | 16 January 2015, 15:23:08 UTC | Merge | 16 January 2015, 15:23:08 UTC |
| b3dd94b | Andreas Raue | 16 January 2015, 15:14:59 UTC | Backout changeset 7d531eb86a3a98d8e2af061ceab4baec580ff38f | 16 January 2015, 15:14:59 UTC |
| 260d3b1 | Andreas Raue | 16 January 2015, 15:14:45 UTC | Merge | 16 January 2015, 15:14:45 UTC |
| 5bd4e8c | Andreas Raue | 16 January 2015, 15:13:34 UTC | Backout changeset 90fc9da17e3ac944b28015fa6129e9bb9e0270e2 | 16 January 2015, 15:13:34 UTC |
| a714b80 | Andreas Raue | 16 January 2015, 14:50:35 UTC | This is a first test. I cleaned up the file and introduced transparency. | 16 January 2015, 14:50:35 UTC |
| 800b8a3 | Bernhard Steiert | 16 January 2015, 11:18:56 UTC | Fix issue #27 | 16 January 2015, 11:18:56 UTC |
| 3557df3 | Andreas Raue | 16 January 2015, 04:37:45 UTC | Plot function factoring: bug fix | 16 January 2015, 04:37:45 UTC |
| f97b33f | Andreas Raue | 16 January 2015, 03:26:29 UTC | Plot function refactored: removed redundant myColsAndRows functions | 16 January 2015, 03:26:29 UTC |
| 9d138a8 | Andreas Raue | 16 January 2015, 03:16:43 UTC | Plot function refactored: Unified usage of arRaiseFigure | 16 January 2015, 03:16:43 UTC |
| f013fa8 | Andreas Raue | 16 January 2015, 02:35:36 UTC | deleted old arMLE... functions | 16 January 2015, 02:35:36 UTC |
| 4ac4486 | Andreas Raue | 16 January 2015, 02:35:15 UTC | Plot functions refactored: arSaveFigure used consistently | 16 January 2015, 02:35:15 UTC |
| e3e4ee8 | Andreas Raue | 16 January 2015, 02:19:29 UTC | Plot function refactored: unified use of arLineMarkersAndColors function, some nicer colors added as well | 16 January 2015, 02:19:29 UTC |
| 0473f5f | Andreas Raue | 16 January 2015, 01:20:35 UTC | Plot function refactored: consistent use of arSpaceAxisLimits | 16 January 2015, 01:20:35 UTC |
| 25f5847 | Andreas Raue | 16 January 2015, 01:12:42 UTC | Plot functions refactored: arNameTrafo and arPathConvert and arSubplotStyle | 16 January 2015, 01:12:42 UTC |
| b263209 | Andreas Raue | 16 January 2015, 00:24:09 UTC | Refactored plot functions: separated arSubplotStyle | 16 January 2015, 00:24:09 UTC |
| 9b053b4 | Andreas Raue | 15 January 2015, 19:40:21 UTC | suppress function output | 15 January 2015, 19:40:21 UTC |
