ticket summary component milestone severity owner created _changetime _description 1520 Add value per tonne as output Value Chain Ecopath 6: future version feature jeroens 2016-11-14T02:13:00-08:00 2016-11-14T02:13:00-08:00 It would be handy if Value Chain could produce value per tonne per unit in its outputs. 1521 Value Chain flow needs customization options Value Chain Ecopath 6: future version feature jeroens 2016-11-14T02:14:26-08:00 2016-11-14T02:14:26-08:00 Value Chain nodes need custom colours and images. Producer colours (and at some point images too) should be picked up from Ecopath 1522 Add Value Chain importer producers Value Chain Ecopath 6: future version feature jeroens 2016-11-14T02:17:30-08:00 2016-11-14T02:17:30-08:00 Just like having exporters, it might be necessary to add importer producers. Importer producers would not have an Ecopath fleet connection, but instead inject a fixed, user entered biomass into the system. 1493 AIC differences between EwE and Stepwise Fitting Stepwise fitting plug-in Ecopath 6: future version NOT SET jeroens 2016-06-13T10:35:49-07:00 2016-06-13T10:35:49-07:00 The AIC given by the stepwise fitting, and by the fit to time series (when using the same number of Vs to estimate) are different, although the SS is the same 1585 Show progress when exporting spatial temporal data Spatial temporal data framework Ecopath 6: Release 6.6 tweak jeroens 2018-07-19T07:16:15-07:00 2018-07-19T07:16:15-07:00 There is no way to know spatial temporal data export progress. The EwE status bar should show this information. 1076 Add means to manually add a plug-in that is not recognized Overall Plugins NOT SET feature jeroens 2012-01-14T09:18:36-08:00 2013-08-20T13:08:31-07:00 In some cases the EwE engine may not recognize a dll as a plug-in. It would be really if users can manually identify, update and integrate such a file in EwE 1102 Add BIGASC plug-in Overall Plugins NOT SET feature jeroens 2012-05-29T03:25:31-07:00 2012-05-29T03:25:31-07:00 "I retired with several algorithms that had been written, but which remained in a primitive state. (For example, BIGASC, which identifies the limiting elements and exchanges in a collection of multi-element networks (e.g., C, N, & P) describing an ecosystem. Ursula said she was going to try to enlist a mathematician/programmer to rehabilitate these programs into some contemporary language, like R. The thought came to me today that they might make useful ""plug-ins"" for ECOPATH?" 180 Auxillary data not copied when saving a scenario under a new name Overall GUI NOT SET major jeroens 2008-08-08T19:36:20-07:00 2010-11-01T06:46:08-07:00 "When saving an Ecosim or Ecospace scenario under a new name, existing remarks (Ecosim and Ecospace) and exsting visual styles (Ecospace layers) do not show up in the new scenario " 690 Show/hide groups settings are not saved with a model Overall GUI NOT SET feature villyc 2010-03-05T11:07:06-08:00 2010-11-01T11:59:53-07:00 Ecosim – show/ hide groups is not saved when a scenario is saved. 897 Have an 'undo' feature Overall GUI NOT SET tweak jeroens 2011-02-20T20:03:00-08:00 2011-02-20T20:03:00-08:00 Submitted at EwE25 conference. 898 Auto-backup of database Overall GUI NOT SET tweak jeroens 2011-02-20T20:04:40-08:00 2011-02-20T20:06:18-08:00 Submitted at EwE25 conference. Enable databases to be saved automatically at select intervals. 907 Add size shifted connectance plot Overall GUI NOT SET feature jeroens 2011-03-02T08:47:18-08:00 2011-03-02T08:47:18-08:00 The size shifted connectance plot in v5 (see attached) is not in the new version is it? Would be nice ... good way to look at the impact of fisheries vs predation 1088 Add ability to enter absolute Ecopath values (not corrected per area) Overall GUI NOT SET feature jeroens 2012-02-29T16:05:00-08:00 2012-02-29T16:05:00-08:00 It would be neat to have the option to enter values as absolute values or as values averaged per km². 1089 Add alternate names to groups, fleets, etc Overall GUI NOT SET feature jeroens 2012-02-29T17:18:53-08:00 2012-02-29T19:28:20-08:00 It would help to present a model to audiences from different languages if fleets, groups and possibly other entities could have multiple names such as common names, scientific names, Spanish names, etc. The user interface should have a way to choose what name to display. 1123 Toggle graph scales Overall GUI NOT SET tweak jeroens 2012-08-16T11:51:07-07:00 2016-07-06T15:10:28-07:00 It would be useful to add the ability to toggle graph display scales to Log 1313 Import Vulnerabilities does not seem to work Overall GUI Ecopath 6: future version minor jeroens 2013-11-30T02:09:18-08:00 2016-07-06T15:09:24-07:00 Tthe import vulnerabilities doesn’t seem to work 1408 Monte Carlo legend behaves strangely when running MC Overall GUI Ecopath 6: future version minor jeroens 2016-02-12T04:45:50-08:00 2016-07-06T15:07:28-07:00 The lines in the MC legend get reordered every time a new trial arrives in the graph 1594 Ecopath values not entering Overall GUI Ecopath 6: future version NOT SET jeroens 2018-09-27T13:25:02-07:00 2018-09-27T13:26:06-07:00 "on my computer, it is ok but on my colleague's: when we change a value in Ecopath Input, the new value is not taken into account in the calculation to balance the model, the old value stays. To get EwE to use the new value, Rohdi has to exit Ewe and re-enter. A nuisance. He works on an Acer laptop, Access 2016, 64bit. I do not know what this is about. Do you?" 1644 Value units are wrong in Ecopath > Fleet definitions Overall GUI 6.7 release tweak jeroens 2023-10-03T04:31:32-07:00 2023-10-03T04:31:32-07:00 The value fields are weighted by percentage, not in absolute terms 983 Cleanup incorrect use of CoreComponentType Overall NOT SET minor 2011-06-02T12:53:33-07:00 2012-10-13T21:39:59-07:00 "eCoreComponentType definitions are starting to approach eDataType granularity. Core Component flags are only meant for the UI, but usage is inconsistent (see for instance how shape changes are fired off in cCore.onChanged vs. the core component type of actual shapes and time series) A thorough assessment is needed to clean this up once and for all.," 1185 Add time series type to insert egg production function via time series Overall NOT SET feature jeroens 2012-10-30T10:09:55-07:00 2012-10-30T10:09:55-07:00 Add new time series type that imports a time series into an egg production forcing function. 1190 Add file templates for common import tasks to the samples folder Overall NOT SET feature jeroens 2012-11-02T18:35:00-07:00 2012-11-02T18:35:00-07:00 It would be really handy if EwE provided sample CSV files for the various import tasks, for instance for time series CSV files. 1247 EwE is fragile to mis-use when running Overall NOT SET major joeb 2013-06-19T09:09:38-07:00 2015-03-04T08:46:04-08:00 "When EwE is busy the interface allows users to take big and disastrous actions such as loading scenarios, etc. Both the user interface and the core should become more robust to this." 1359 Database dupliction fails Overall Ecopath 6: future version major jeroens 2014-09-30T01:30:25-07:00 2016-07-06T15:09:03-07:00 "In a few cases we have seen EwE failing to generate new databases, and internally !PrincipalServerDown exceptions are thrown. This exception is related to (lack of) user rights. The issue occurs in Ecopath model from Ecosim, for instance." 1396 0 should be a valid time series value Overall Ecopath 6: future version feature 2015-10-08T10:14:32-07:00 2015-10-08T10:14:32-07:00 "In every EwE version, 0 values are considered as no Time Series value. As a work-around, users can provide a very tiny number. This really needs to be changed: * empty CSV cells need to be converted to the internal NULL value * the core evaluates values >= 0 * the user interface must show empty cells for the internal NULL value" 1461 Overflow exception in MSE run NOT SET Ecopath 6: future version NOT SET 2016-05-31T07:37:19-07:00 2016-05-31T07:37:19-07:00 "When ”MSE Results” is selected after an MSE run, the window is blank with a red X across it, and a pop-up window appears reading “Unhandled exception has occurred in your application.” “Exception text: System.OverflowException: Value was either too large or too small at System.Decimal..ctor (Double Value)."" Exactly the same MSE simulation in the same model ran faultlessly in EwE 6.4." 1550 Change v's over time NOT SET NOT SET NOT SET 2017-12-09T05:42:38-08:00 2017-12-09T05:42:38-08:00 It would be great to be able to change the v's through time (ex. cod has a higher v when less abundant because they tend to aggregate and be more at risk of predation). 1576 Auqamaps import not showing x-axis data NOT SET NOT SET 2018-05-23T12:32:34-07:00 2018-05-23T12:32:34-07:00 I was importing Aquamaps HSPEN files in EwE 6.6 preparing a tutorial, and noticed that while the import works fine, the X-axis is not defined on the plot when opening them. They show default 0-1 range. When then clicking Change shape, the data are there, and closing the Change shape: all is good. But confusing if you don’t know it 1592 Ecospace should throw a warning when there are no water cells NOT SET NOT SET 2018-09-18T21:04:02-07:00 2018-09-18T21:04:02-07:00 Ecospace does not complain when all cells are excluded. It should, most certainly when a run is started 14 Network Analysis: Predator cycling index with detritus requested Network Analysis plug-in NOT SET tweak 2006-08-04T11:59:49-07:00 2013-08-20T13:16:31-07:00 "The Finn cycling index was not calculated in the Ecopath results - the predator cycling index is calculated, but it omits the throughput cycle including detritus and only uses predatory flows " 786 Network Analysis PPR values in .csv file not clear Network Analysis plug-in NOT SET minor villyc 2010-10-05T20:33:21-07:00 2013-08-20T13:06:28-07:00 I have been looking at the PPR estimated by Ecosim and Ecopath (for both EwE 5 and EwE6) and it is not clear to me what is being reproduced in the network.csv file. If you look at the value reproduced in the network.csv file for PPR it does not reproduce any of the values for PPR in the Ecopath model for the first year. Can you please check that? 844 Network Analysis export transfer efficiency in Ecosim CSV Network Analysis plug-in NOT SET feature 2010-11-15T20:21:01-08:00 2013-08-20T13:23:35-07:00 I would really really really really like to see all three Transfer Efficiency mean values (from PP, from Detritus, and total) included in the Network Analysis Ecosim results. Please? 1002 Add emergy calculations Network Analysis plug-in NOT SET feature 2011-06-14T18:54:52-07:00 2011-06-14T19:04:24-07:00 "it might be useful for my purposes to modify the program to allow the calculation of emergy flows on the pathways. If you are already able to calculate the pathway energy flows, it might not be too difficult to add in the emergy calculations. The key addition would be to get the emergy (calculated from the energy times the transformity or the emergy per unit energy of the food sources) values of the food sources (assuming they are the current fundamental inputs). The food sources themselves come from the physical energies supporting that system, which would be dynamic if put in as a time series for simulation. They could be put in as average values measured in the system or in similar systems to solve the matrix equations. This might not be practical, but take a look at the attached papers to see if you think it is feasible. If it is the code would have to be modified for this purpose or additional routines written. Of course it would be best for the person who wrote the code to do the modification, but alternatively if the code is open source someone else could write the add-on. In any case I will use EcoPath and EcoSim in there present form to start. Eventually, I will have to be able to make the emergy calculations using some platform. " 1075 Large models crashing when Network analysis runs Network Analysis plug-in NOT SET crash 2012-01-14T02:26:03-08:00 2013-08-20T13:08:09-07:00 In some cases, when the ecopath model is large or has some multi-stanzas, if you go to ecopath, tools, network analysis and run some analysis, the program starts computing but freezes and ends up crashing at the end. This happens with models that were originally build with v5 and were translated into 6. Some of these models are: ainsworth 5, ainsworth 6, Bullman 1, Bullman 2, Freire 1, Mohamed 2, Velasco 1 (all from the Biomass Regression database) and some models from Okey (2004, 2001) and Bundy (2005). I think this is only a problem for models that were translated from v5 to v6, but I am not sure. 1077 Ascendency and overhead (but not capacity) calculated on exports are wrong Network Analysis plug-in NOT SET major 2012-01-29T10:04:56-08:00 2013-08-20T13:08:50-07:00 "I have found this bug in the ascendency calculations in EwE (both version 5 and 6). Ascendency and overhead (but not capacity) calculated on exports are wrong. This bug is only present if your model has (not-negligible) emigration flows for one or more groups. To begin with, exports are calculated as the sum of catches and emigration, the latter includes exports from the system for detritus, which is = (1-EEdetritus)*(flow into detritus). Based on such flows, I have verified ascendency calculations based on equations found in Latham II (2006) Network flow analysis algorithms. Ecological Modelling 192: 586-600. Capacity (flowbits) is correctly calculated in EwE, but there is clearly a problem with calculation of ascendency, or overhead, or both: their sum is not equal to capacity (and can be very different), unlike it should be. I have not been able to find out where the calculations are wrong, but there is certainly a bug..." 1145 Network Analysis Ecosim nodes should be listed under Ecosim Tools Network Analysis plug-in NOT SET tweak jeroens 2012-10-04T09:21:33-07:00 2013-08-20T13:40:25-07:00 "I am running some scenarios and require output from the Network Analysis. I just installed the new version however am unable to get the Ecosim > Input > Tools function, nor the Ecosim > Output > Tools function to work. Nothing happens when I click on either of them. Any idea when theses tools will be added in?" 1224 Save MTI data with Network Analysis results Network Analysis plug-in NOT SET tweak jeroens 2013-02-13T09:15:07-08:00 2013-08-20T14:06:07-07:00 The MTI data is currently buried within the Network Analysis plug-in and is not provided in a raw form. This is necessary if users intend to produce their own plots 1320 cNetworkAnalysisManager.RunWithEcopath may not work when called from plugin Network Analysis plug-in Ecopath 6: future version minor 2014-01-08T11:32:40-08:00 2016-04-13T06:43:46-07:00 "The boolean flag cNetworkAnalysisManager.!RunWithEcopath is suppose to cause the !NetworkAnalysisPlugin to call !NetworkAnalysisManager.!RunMainNetwork() when an Ecopath run has completed. This runs the NA implicitly. The internal run state m_runstate will prevent this from working in its current configuration. This means you need to call !NetworkAnalysisManager.!RunMainNetwork() explicitly to get NA output" 1439 No network analysis stop option Network Analysis plug-in Ecopath 6: future version feature jeroens 2016-05-18T13:11:35-07:00 2016-05-26T04:10:32-07:00 There is no way to stop network analysis 1590 MTI slow Network Analysis plug-in major 2018-09-18T20:35:25-07:00 2018-09-18T20:35:25-07:00 "I’m running the North Sea model (Mackinson’s) in EwE6.6 and needed the Mixed Trophic Impact. First waited 30 minutes for the time out, then clicked MTI, thinking it would bypass the LIndeman calculations, but it started on a new 30 minutes trip to nowhere. I think we should change the default for time out to 1 minute, people get a warning and can extend. Also, the Lindeman is only needed for cycles and pathways, so we don’t need to invoke it for eg MTI" 1602 Separate Lindeman calculations from main ENA loop Network Analysis plug-in feature 2018-10-08T01:13:11-07:00 2018-10-08T01:13:11-07:00 The main ENA loop runs the Lindeman spine calculations, which are computationally expensive. The main ENA run loop could be split in two, where Lindeman is ran on demand. For some models this will dramatically speed up delivery of MTI indicators etc 1215 Multisim error checking Multi-sim plug-in NOT SET major jeroens 2013-01-10T23:50:54-08:00 2013-08-20T13:44:45-07:00 If you run Multisim without linking the PPA csv files to a properly named forcing function, EwE does not tell you that you screwed up until it has gone through all the multisim runs. That is, the name in the first row of the upload csv files does not match the name of a forcing function in your EwE model. think it would be better if EwE told you that there was a conflict between your input csv and the forcing function after the first trial. You also have to dismiss an equal number of error messages to the number of csv files with bad first rows. 1312 FMSY problems MSY Ecopath 6: future version major 2013-11-30T02:05:15-08:00 2013-11-30T02:05:15-08:00 "Well I thought I had this cracked but I've tried the Find Fmsys routine using V6.3 and V6.4 and with both versions the output gives fmsy==fbase often, even though FmsyFound claims to be 1...? strange behaviour - tempted to use Steve's output from V5 even though the model has been changed slightly since then. Anyone else found this issue.... there is no error or warning produced by the model so it looked like it was working is it just outputting the wrong data! The single group runs seem fine (so I've sorted the groups that have fmsyFound==0, However, I note there that the Value output are often on a very different scale to that from the all group Find Fmsys routine..." 912 MSE Best/B plot should only show groups that are being caught MSE NOT SET minor joeb 2011-03-09T14:40:50-08:00 2011-03-29T09:35:08-07:00 "Groups show being perturbed because MSE runs with default CV values for groups that are not caught, even though the user was unable to set CV values for these groups. A solution is two-fold: * Do not perturb groups that are not being caught * Do not show groups that are not being caught" 981 MSE effort inconsistent when fishing mortality TS loaded MSE NOT SET minor joeb 2011-06-01T11:05:55-07:00 2013-08-20T13:24:23-07:00 I load in forced fishing mortality time series in Ecosim. I then use MSE to run policy scenarios. If my start year in the MSE module overlaps with the period for which I've forced fishing mortality, MSE will set my effort for the fishery to zero regardless of control type. This makes sense. However, this only happens some of the time. Other times the effort will be positive. 1265 MSE plots should not display data before start year MSE Ecopath 6: future version minor joeb 2013-08-28T08:27:14-07:00 2016-07-06T15:09:44-07:00 "From the 2013 ICES course: When running the MSE start year past the first year, the MSE plots still reflect data before the start year. This is confusing." 1307 possible Monte Carlo bug Monte Carlo NOT SET NOT SET joeb 2013-11-30T01:56:48-08:00 2016-04-13T06:24:51-07:00 "I have hit a snag with Monte Carlo. The routine runs and produces properly formatted data files, but once you do the calculations, it turns out that the final biomass values for all groups are exactly the same in all trials - and identical to the baseline values. " 1533 Monte Carlo BA preturbation does not perturb BA rate Monte Carlo NOT SET NOT SET joeb 2017-06-06T03:23:10-07:00 2017-06-06T03:23:10-07:00 When I set MC to perturb BA, values with BA rates are not changed 1214 Add silent install option Installation NOT SET feature jeroens 2013-01-09T11:37:10-08:00 2013-01-09T11:37:10-08:00 "A user wrote: Is there a silent installation parameter that can be passed to the Ecopath installer ""EwE6_6.3.8634.0_setup.exe""? Other users have requested this feature too. Perhaps a good thing to add in the next release, even though the installer offers plenty of choices." 1584 flow scaling Flow diagram Ecopath 6: future version tweak jeroens 2018-07-18T05:11:36-07:00 2018-07-18T05:11:36-07:00 "During this week I have spent quite a few hours exploring the flow diagram thoroughly and particularly how flows are being presented therein: 1. The strength of a flow in the diagram to a prey corresponds to its proportion in the diet (consumption) of the predator. 2. For each predator - though - another conversion factor for the transformation from consumption data into flow strength is apparently being applied. Therefore, flows to a prey item are not comparable between predators. 3. Outgoing flows from a prey are still predator based, i.e. maintaining the flow strength to that respective prey in the consumption of the predator. The resulting assemblage of ""out-flows"" from a prey-box gives in my opinion a totally misleading impression of the outgoing flow of matter from a prey to its predators. This is also the reason why the outgoing flow from ""herring"" to ""seals"" in our model is much larger than the flow to the ""pelagic fleet"" although the pelagic fleet is extracting 200 times the amount that the seals are consuming (per m2 and year). Summarizing, it is now clear to me that ""the bug"" in the flow strengths of the fishing fleets to their ""prey"" is not a bug but basically in line with the allover concept of the flow diagram routine except maybe for the fact that flows are even less in proportion with their real size when comparing them to other top predators such as harbour porpoises and seals in our WBS model. I am not sure how time consuming it would be to modify the flow diagram routine and in what way it should be modified if at all (I am not the only user of course and the flow diagram in my understanding forms part of the core routine of EwE)" 1087 Fishing Policy iteration grid values are not intuitive Fishing Policy Search NOT SET major 2012-02-27T15:57:34-08:00 2013-08-20T13:09:11-07:00 William ran FPS with economic weight of 1, and ecological weight of 0. When he reversed these weights, economic weight of 0 and ecological weight of 1, he saw no difference 1310 Policy search interface problems Fishing Policy Search Ecopath 6: future version NOT SET 2013-11-30T02:02:49-08:00 2013-11-30T02:02:49-08:00 In the policy search, you should be able to colour several fleets using the same colour block, but when you run the opitmization you'll see that those fleets are being optimized independently and the colour of the output columns are all different (should reflect the colour codes you've entered in above). 1599 Extend policy optimization Fishing Policy Search feature 2018-10-07T22:08:39-07:00 2018-10-07T22:08:39-07:00 "Let's add a way in the policy optimization to consider energy use and environmental impact by fleet. There are two variable needed: !EnergyConsumption and !EnvironmentalImpact, and they need to occur in various disguises, i.e. as public variables in !EcopathData and as properties in cEcopathFleetInput. They are both relative values, so the user decides what to enter, any single goes, default is 1. We should add them to the fleet input screen. Next, add s new variable !FoodValue(fleet, group) to optimize for food security. Then, we’ll need to add these three variables to the policy optimization forms and also to the Ecosim/space output forms (not displayed by default) I think these additions add a simple way to capture something useful." 759 Ecoseed: Layout too cramped for lower resolution monitors. Ecospace NOT SET tweak jeroens 2010-07-16T13:21:12-07:00 2011-06-01T16:29:42-07:00 "Jacques.Moreau@ensat.fr Layout too small for Ecoseed output: bad for low resolution monitors. ""Ecoseed running properly (spatial optimization) but I cannot display the outputs on the screen (the screen is too small?) output appear incompletely on the lower part of the screen""" 1038 Ecospace leaking discards into non-fished habitat boxes Ecospace NOT SET NOT SET cathyb 2011-08-15T00:11:57-07:00 2013-08-20T13:07:28-07:00 Discards are occurring in all boxes even though there are no fleets fishing in them nor are there any fish assigned to them i.e they are in effect boundary boxes of water. 1128 Ecospace results should show a time series graph as well or instead of the summary data Ecospace NOT SET feature 2012-08-24T09:14:20-07:00 2013-08-20T13:30:29-07:00 The Ecospace results are shown in a grid for two summary periods set by the user. This data should also shown as a time series graph over all the time steps. Internally the data is stored for all the time steps then summarized into the time periods for display. 1132 Protect Ecospace from over-allocating habitats Ecospace NOT SET feature 2012-08-29T11:00:11-07:00 2013-08-20T13:33:16-07:00 New in version 6.3 is partial allocation of cells to habitats. The interface needs to prevent users to enter allocations > 1 1257 Ecospace IBM stops run due to Index out of bounds error Ecospace NOT SET crash joeb 2013-08-16T12:40:28-07:00 2016-07-06T15:10:03-07:00 The IBM model can try to put a packet into a cell that is out of the map bounds. Once it has done this it will continue trying to use the out of bounds cell. This is an intermittent issue because moving the packets has a random component. It should be fixable by checking the cell bounds when a packet is moved. 1395 More control needed for Ecospace fishery Ecospace Ecopath 6: future version feature jeroens 2015-10-02T02:18:37-07:00 2015-10-02T02:18:37-07:00 If Ecospace is to be used for management advise, users need better control to replicate historical fishing behaviour by entering fractions of habitat fishing instead of the current true/false implentation. 1400 Ecospace effort not distributing as expected Ecospace Ecopath 6: future version major joeb 2015-12-14T03:07:38-08:00 2016-07-06T15:07:55-07:00 "Just to specify what is not working: 1. The map of sailing costs is only based on distance from port, and not on the cost settings for the fleet in Ecopath. At least the map looks the same for all fleets, although the costs are all different. 2. The number of ports in the model affects how the sailing cost map looks like but not the effort distribution during the model run. Also, in Romagnoni et al. 2015 Appendix (section A.4.2.2) they make the same observation, no difference at all between having a few ports or ports everywhere." 1426 Ecospace results lost Ecospace Ecopath 6: future version minor jeroens 2016-04-12T01:20:42-07:00 2016-07-06T15:07:00-07:00 When one needs to check Ecospace results, has to do it immediately after the run, otherwise the “Ecospace results” option loses the ability of showing it and the model must be ran again. For instances, I check the results and I close the window afterwards. Whether I need to re-check the results, the window doesn’t open anymore and I have to run the model again. Since it takes 15/20 minutes to run the model you can imagine how frustrating it can be 1494 Ecopath migration in Ecospace Ecospace Ecopath 6: future version major 2016-06-13T23:35:14-07:00 2016-06-13T23:35:46-07:00 "There is a basic issue in moving from ecopath to ecospace. It is quite possible to have situations for small study areas where ecosystem support comes largely from dispersal of biomass into one or more trophic groups across the system boundary, which can be easily represented in ecopath by setting biomass import and export rates (immig and emig vectors in ecosim/space) for one or more groups high enough to support much higher biomasses of the groups that eat them than predicted by the PB values of the consumed groups. In Ecospace, immigration and emigration across the system boundary and among cells is represented explicitly by dispersal and advection rates. But the Derivtred in Ecospace still contains the immig, emig rates from Ecopath, representing biomass that enters every cell from outside the system, i.e. from nowhere. I tried just turning off immig, emig rates in a simple model where zooplankton needed algal import to support them, and this caused goofy ecospace behavior. Leaving the rates in also caused some misbehavior." 1505 Ecospace run - Catch plots are not drawing Ecospace Ecopath 6: future version minor jeroens 2016-06-24T02:52:12-07:00 2016-06-24T02:52:12-07:00 Run Ecospace > Map > Catch plots are flashing, and do rarely draw reliably. 1523 Ecospace does not distribute effort for fleets that only discard Ecospace Ecopath 6: future version minor joeb 2016-11-14T02:20:10-08:00 2016-11-14T02:20:10-08:00 To model the discards ban I have split a fleet into two: one fleet lands, the other only discards. The fleet that only discards is not fishing in Ecospace, but when I set a tiny landing (0.0000000001) the fleet suddenly becomes active in Ecospace. 1542 Add ability to auto-save Ecospace summaries Ecospace Ecopath 6: future version feature 2017-11-10T02:09:21-08:00 2017-11-14T02:54:19-08:00 One question I had to facilitate things in terms of extracting results:is there a way we could export to csv the whole Ecospace results? i.e., all time steps for all groups so instead of me typing in the timestep differences I want then copy pasting the results and doing this 3 times over per run (as I want 5 years, 10 years and 25 years past the 29 year time step) - I could run some R code to extract ot from the csv?? that would save a lot of time 1555 Advection direction is not obvious Ecospace Ecopath 6: Release 6.6 major 2018-02-13T12:58:31-08:00 2018-07-11T05:17:07-07:00 "EwE needs to provide explicit clarity, and import data control, stating how the x and y velocity are used in the model. Underneath, the directions are Horz: -1 = W, 1 = E Vert: -1 = N, 1 = S This is not intuitive, and most likely not standard" 403 Add Ecosim results stacked bar plot Ecosim NOT SET feature 2008-02-04T10:03:03-08:00 2010-11-01T06:45:51-07:00 "New output plot for Ecosim: display a form with a stacked bar plot with (1) volume of landings over time (2) value of landings over time " 445 Ecosim diagnostics: F-values Ecosim NOT SET feature 2008-04-02T11:14:21-07:00 2010-11-01T11:57:29-07:00 "I suggest we add a spreadsheet to the Ecosim tools: Diagnostics, F-value consistency. The spreadsheet should show for each group (or exploited group rather) the F-value calculated from Ecopath (F = catch / biomass) and the corresponding value in Ecosim (where it may be an input time series, e.g., if so it has to be consistent.)  In ewe5 we show this on the Fishing rate/Group display, where I added a tiny F from Ecopath before the first time step. Hence, if there was a discrepancy it would show up right away. It was however something one would have to know to find it, and it may be better making it an explicit diagnostics." 588 Apply mediation to effort Ecosim NOT SET feature jeroens 2009-03-18T15:35:01-07:00 2010-11-01T12:01:14-07:00 "We need one more option for Mediation, new subset: Apply mediation (effort). there should be spreadsheet that lists the fleets by row, and an option to use up to five mediation shapes to regulate the effort. Villy will help with the implementation, say when. We may be using this for the single player game to model effort of whale watchers. " 613 Monte Carlo biomass plot output Ecosim NOT SET feature 2009-05-20T10:24:16-07:00 2016-02-08T00:53:01-08:00 "Features needed for the Monte Carlo biomass plot. Once the trials have been run the biomass plot should be able to show all the runs, for selected groups, with the best fitting trial data highlighted. The user should be able to selected the combination of groups and trials. " 826 Handling of time series type 2 should be reconsidered Ecosim NOT SET tweak 2010-11-01T10:37:08-07:00 2010-11-01T11:13:25-07:00 "There is a fundamental difference between how EwE5 and EwE6 handle forcing time series, TS of type 2. These differences have been the subject of discussion in a few cases, most notably in issues #623 and #717. * In EwE5, TS 2 exist in memory and overwrite the data of a targeted forcing function when the TS is applied. If Ecosim scenario with such an altered forcing function is saved, the targeted forcing function is altered forever. * In EwE6, TS 2 are converted to forcing functions during time series import. TS 2 thus do NOT exist in memory in EwE6. Now, it needs to be assessed if this approach is correct." 990 Ecosim Plots multiple runs Ecosim NOT SET feature 2011-06-07T13:24:09-07:00 2011-09-04T07:01:21-07:00 When Multiple run are selected on the Run Ecosim form you could also view and selected from the multiple runs in the Ecosim Plots. 1024 Variable time steps in Ecosim Ecosim NOT SET feature 2011-07-12T10:58:40-07:00 2011-07-12T10:58:40-07:00 "Currently there is IN CODE functionality to set a variable time step in Ecosim. This can only be done via a Plugin. Port this over to work from the Scientific Interface. This will cause issues with plotting and time series data that will need to be sorted out." 1035 Ecosim effort time series not operating on model /creating own effort series Ecosim NOT SET NOT SET cathyb 2011-08-04T19:23:10-07:00 2013-08-20T13:07:10-07:00 I tried to run a scenario which has a time series of fishing efforts etc attached to itbut on running tThe fishing effort screen has suddenly changed to something else (i have no recollection of ever having a times series like these) and nothing I can do to alter effort now will work. I had “upgraded” the newer model a bit and deleted an Ecosim scenario I believe and from that time I’ve had this problem.perhaps the database has becme corrupted because I'm usingthe same software version on an older model with same sceanrio and the time series works properly. 1058 Add price to Ecosim plots Ecosim NOT SET feature 2011-11-18T13:46:19-08:00 2012-10-19T09:14:28-07:00 A small, no-rush thing for the ecosim group plots: add a plot with price (off-vessel price). With price elasticity the price can change, and this is an interesting plot to add. But no rush 1181 Discard Mortality rate dialogue should be moved to MSE Ecosim NOT SET major 2012-10-29T11:08:11-07:00 2013-08-20T13:42:06-07:00 "The Discard Mortality Rates were added as part of the MSE for the survival rate of the Selective Fishing Quota option. It sets the mortality rates of species that are discarded when the catch exceeds to quota. This only works correctly in the MSE.  Discard Mortality Rate is ignored completely in Ecopath.  In Ecosim it is only used correctly when the model is first loaded if the user edits Effort then it will be ignored and discard mortality is assumed to be 100% As a temporary measure the Discard Mortality form could be moved to the MSE tab. The next step would be to implement it correctly in Ecosim." 1186 Cannot leave remarks for forcing, egg prod and mediation assignments Ecosim NOT SET tweak jeroens 2012-11-01T06:24:40-07:00 2012-11-01T06:24:40-07:00 ...and it would be handy to be able to document specific assignments 1227 Show group breakdown by fleet catch Ecosim NOT SET feature 2013-02-19T00:42:18-08:00 2013-02-19T00:42:18-08:00 Group plots catch by fleets. It seems that your only a groups catch broken down in to fleets when the groups catch is dervied from relative effort series. In our case, all the key groups of intereset are driven by F series from assessment, and I cannot see that catch compositons by fleet. It would be really helpful if the breakdown can be displayed for these species. 1256 F in EwE6.3 Ecosim NOT SET major 2013-08-05T01:34:33-07:00 2013-08-05T01:35:57-07:00 "I am running test runs with the MSE procedure comparing them with a EwE run extended after my fitted period (1970-2008) to year 2070. To my surprise, EwE does not apply the F of the last year (0.73 for cod 7+) which appears in the EwE run window. It drops F inexplicably to roughly half of that (0.35) which appears in the group plot. Only when I import a time series that explicitly put in the F to be applied in the projected years, does EwE apply the right F. Is there something I do not understand here? I do not remember this behaviour, something must have changed" 1283 BA input is incorrectly ignored in calculating Ecosim rates Ecosim NOT SET major joeb 2013-09-30T00:44:52-07:00 2013-09-30T00:45:45-07:00 Ecosim assumes that each detritus pool is at equilibrium (dB/dt=0) at the Ecopath base. Its basic model for detritus biomass dynamics is dB/dt=Inputs-kB, where in most cases k represents decomposition rates due to microorganisms. So for dB/dt to equal 0 at the initial state, k has to satisfy dB/dt=0=inputs-kB, and from this we can calculate the decomposition (or export or whatever causes detritus loss) rate parameter k as k=inputs/B where B is the ecopath base detritus biomass. Note here that inputs is the sum of all flows to detritus from within the system, plus import rate. 1311 Ecosim 'All fleets' item missing from fishing mortalities Ecosim Ecopath 6: future version feature jeroens 2013-11-30T02:03:43-08:00 2018-05-09T04:45:49-07:00 "You used to be able to enter a comma-separated vector of fishing mortalities for all fleets via the 'set to value' button on run ecosim tab. that doesn't work now, you can only enter one fleet at a time. With the 'all fleets' item missing, these kind of bulk tasks cannot performed in Ecosim" 1486 Add ecosystem TL over time Ecosim Ecopath 6: future version feature 2016-06-09T10:38:12-07:00 2016-06-09T10:38:12-07:00 I was wondering if there is a way to extract the Trophic Level of the whole ecosystem with Ecosim. Indeed, I only found the TL of the ecosystem from the Ecopath model, TL of the catch through time, and the TL of the groups through time; but not the TL of the ecosystem through time. I think it would be an interesting indicator to have 1567 Apply shape dialog should show selected effect when row or col are clicked Ecosim Ecopath 6: Release 6.6 feature 2018-04-26T12:30:23-07:00 2018-05-09T04:56:38-07:00 When clicking a row or a column in the Ecosim apply forcing grids, users should be able to apply the same forcing function to the entire selected row or column. This does not work in 6.6 Beta 1589 Discard and landings TS in plots Ecosim Ecopath 6: Release 6.6 NOT SET 2018-09-18T20:22:52-07:00 2018-09-18T20:22:52-07:00 "On the group plots the total discards plot should show the modeled discard amount along with the reference data (somehow). The plots should be cumulative so we'll have to have colors stacked on top of each other, and the reference data in the same order as dots. Same for landing. and the total catch now shows cumulative catch, but not the cumulative sum of landings and discards. Presume discard survival should be cumulative as well" 1601 HRC in Ecosim Ecosim feature 2018-10-07T23:10:50-07:00 2021-05-16T14:21:24-07:00 "Today we briefly mentioned the possibility of implementing a Harvest Control Rule in the standard Ecosim fisheries. At present it can only be done by stetting up an MSE (either Carl's closed loop, or the more flexible Mackinson add on). For each ecosim fishery, we would be need to be able to specify a HCR with a cut off biomass below which F is zero (or a specified minimum F as needed for many european fisheries), and a one or two step jump to a max F, or a hockey stick F regime. What is the likely cost? I am willing kick in some funding if we can find someone to help with the funding." 1618 Applying fleet effort to pred/prey interactions does not seem to work Ecosim Ecopath 6: Release 6.6 major joeb 2018-12-04T02:06:11-08:00 2018-12-04T02:06:11-08:00 Applying fleet effort as a mediation driver to search rates (and likely other pred/prey interactions) does not seem to have an impact in the model 1638 Stored catchabilities can wreak havoc Ecosim 6.7 release major jeroens 2023-09-28T04:19:25-07:00 2023-09-28T04:21:10-07:00 "The EWE 6.6.* catchabilities can run totally out of sync with a model if one starts playing with run lengths and fishing effort. For EwE 6.7, catchabilities should no longer be stored but should be configurable via a time series instead. The catchabilities grid can be changed to show the Ecosim base catchabilities for building the time series upon" 1646 Loading Ecosim time series displays wrong number Ecosim 6.7 release minor 2024-01-26T09:57:17-08:00 2024-01-26T09:57:17-08:00 "Open the load Ecosim time series dialogue and look at the number of time series. Load a time series and close the dialogue. Reopen the dialog to load a different time series and look at the number, it will be the number in the currently load time series not the number in the group. " 1529 Add configurable time step to Model from Ecosim Ecopath from Ecosim plug-in Ecopath 6: future version feature jeroens 2017-01-19T02:44:07-08:00 2017-01-19T02:44:07-08:00 The Ecopath model from Ecosim logic writes values for month 6 by default. This should be configurable 1593 Time step not correctly used Ecopath from Ecosim plug-in Ecopath 6: Release 6.6 major 2018-09-27T13:22:35-07:00 2018-09-27T13:22:35-07:00 Attempting to generate Ecopath model from Ecosim for purposes of doing ecological network analysis at ecosim time slices. When specifying the “At time step” option, I noticed that the output model was not always referencing appropriate model timestep. Everything worked as expected for “At time step” = 1-6 (Jan-Jun), but no model was genearted when “At time step” = 7, and when “At time step” is 8-12 then it writes an Ecopath model at the model timestep minus 10. See status output below. In that example, the model begins in Jan 2009 and I am trying to write an Ecopath model for each month in 2010. So January 2010 would be time step 13, Feb2010=14, Mar2010=15, and so on. You can see that only 11 models were generated, because the July model “At time step=7” would not write, and after June (here timestep=18) it writes models for 10 timesteps previous. So it appears either the status output is incorrect or the “At time step” selection is not indexing properly. 924 Add new model wizard Ecopath NOT SET feature jeroens 2011-03-19T12:44:32-07:00 2012-10-13T21:37:32-07:00 Add a new model wizard where users can select a spatial area interactively on a map. This same map can be used to specify a cell size when creating an Ecospace scenario 1260 Add option to show Fleets in flow diagram Ecopath NOT SET feature jeroens 2013-08-28T03:11:20-07:00 2013-08-29T01:48:22-07:00 "From the ICES 2013 course: Policy makers like to see a fleet diagram. Perhaps this option can be added to the Flow diagram that currently shows groups?" 1328 Add detailed breakdown of exports Ecopath NOT SET feature 2014-03-31T04:15:40-07:00 2014-03-31T07:27:44-07:00 "Please can we get a “real flow” estimate of all exports in Ecopath – not just fisheries but also any detritus that might be exported. This will help with hypoxia, eutrophication, etc. Also if we can in get any changes calculated in Ecosim it would be very useful. " 1348 Possible bug in Omnivory Index Ecopath NOT SET minor 2014-06-20T07:44:59-07:00 2014-06-20T07:44:59-07:00 "I checked with Generic37, using Toothed Whale as target. The OI in the original model for this group is 0,325. When you add import (just adding 0.8 import and then ask to sum to 1 its diet) OI increases to 1.362. It seems to me that the problem is related to the fact that elements of DCij (diet matrix) but not the import (for which no TL estimate can be provided) are used to calculate the average TL of preys from which calculate the variance (OI). A consequence of this calculation is the implicit assumption that TL of import is equal to 0 . The fact a fraction of the diet is at TL so low (zero, indeed) increase a lot the variance of TL of preys, explaining the large OI for predators with import. A simple way to correct this is to assume that import have the TL of the average TL of the other preys. Is this, although small, a possible problem/bug?" 1357 Add ability to have non-feeding stanza life stages Ecopath Ecopath 6: future version feature 2014-09-24T10:43:09-07:00 2014-09-24T10:43:09-07:00 The stanza life-stage interface should be able to cater to non-feeding spawners. This requires in a check box in the Stanza interface, which would suppress respiration checks, and changes to Ecopath 1369 No warning when QB < PB Ecopath Ecopath 6: future version minor jeroens 2014-11-04T13:24:27-08:00 2014-11-04T13:24:27-08:00 Ecopath should produce a warning message when QB < PB. It does not say anything now. 1370 Make sure a model has all default pedigree levels Ecopath Ecopath 6: future version minor jeroens 2014-11-04T14:26:34-08:00 2016-04-13T07:16:15-07:00 Some new models do not have all default pedigree levels. They should. 1384 Possible bug(s) in the EwE6 Statistics calculations Ecopath Ecopath 6: future version minor 2015-03-01T06:26:25-08:00 2015-03-01T06:26:25-08:00 "I started checking that my code could replicate some of the ecosystem statistics that EwE6 reports (sum of consumption, exports, total system throughput, etc). I was having some trouble doing so, and I think I've traced the issue to an inconsistency in the way certain flows are categorized as either export or flow to detritus in EwE6. For ""Sum of all exports"", it looks like all fisheries catches are assumed to be exported from the system. However, for ""Sum of all flows to detritus"", fisheries discards to detritus are included again. In total system throughput, these flows are then counted twice, being both exported and recycled back to detritus. Also under the ""Export"" definition, I think exports related to non-predatory mortality and egestion (i.e. non-respiratory, non-predatory fluxes out of groups with detritus fate that includes export) are ignored. These issues might be related to ticket #1077, where ascendency and overhead are apparently off in groups with more complicated export terms." 1389 "Ecopath ""Habitat area fraction"" recalculates Biomass incorrectly for multi-stanza groups" Ecopath Ecopath 6: future version NOT SET jeroens 2015-06-10T06:42:38-07:00 2016-07-06T15:08:23-07:00 "When setting the Ecopath basic input ""Habitat area fraction"" for multi stanza groups the calculated biomass in Ecopath ""Basic estimates"" will be wrong. To recreate: For a multi stanza group set Habitat area fraction to a value(s) other than one In the multi stanza interface change leading biomass In the Basic estimates check the biomass values. " 471 EwE user's manual errors Documentation NOT SET minor villyc 2008-05-13T10:27:07-07:00 2013-08-20T13:22:47-07:00 "Subject Typos in help file? Date/Time 2008-03-28 08:32:41 Posted By Yu-Chun Kao I'm a beginner of EwE and learning EwE via the help files. I think there might be typos in EwE 6.0 help file. First, in section `3.2 Ecosim basic` equation 50, should the other mortality term be M0i instead of Mi? Then the notation will be more consistent. Second, in Ecopath document, 2.1 equation 11, gi is defined as gross food conversion efficiency, while in Ecosim, 3.2 equation 50, gi is the net growth efficiency. I'm wondering why they are different? Third, in Ecopath the suffix `ji` means group j prey on group i (i.e. DCji in equation 4) while in Ecosim, suffix `ji` means group i prey on group j (i.e. Qji in equation 50). It is very confusing to me but may not be a big problem as there always is explanation following those equations. From issue #577: manual proclaims Ecospace can be paused, but this feature does not yet exist in the code. The manual should be updated here. Posted by user on EwE support page....just a few typos for whomever is going to be working on the help files" 733 EwE manual equation 15 is wrong Documentation NOT SET minor villyc 2010-04-25T08:28:34-07:00 2010-11-01T11:59:06-07:00 "I noticed a mistake in the manual (made by me). Equation 15 should not be cgi =, it should just be gi =. Cheers Robyn" 1020 Appendixes missing from user manual Documentation NOT SET major 2011-07-06T21:24:55-07:00 2011-07-06T22:46:31-07:00 "Appendix 3 and Appendix 4 have been refereed in the introduction of the “User Guide” of Ecopath with Ecosim version 6. (at page #9 i.e., Technical details describing a number of ‘algorithms’, in which the equations used to estimate certain parameters are presented along with relevant comments and descriptions of special cases are given in Appendix 3 and Appendix 4.) Could you please tell me where I can get those ‘algorithms’ and Appendix 3 and Appendix 4?" 852 Add EwE5 'merge models' feature Database / Import NOT SET feature jeroens 2010-12-01T01:29:31-08:00 2010-12-01T01:29:31-08:00 "In EwE 5 we had a way of combining models, basically one would open a model, do a save as. Then point to another model, and ask for them to be combined. Operationally, it just needs to add the number of groups, and place the diet compositions and other information accordingly. The name of the added groups may have to be added to, e.g., by placing the first letter from the model and a space in front of the name. From Ecosim, we should import forcing functions and mediation functions. Time series can be entered again, so no need for them. Also, the habitat areas for the groups in each model need to be modified. We need to read the area (km2) for the model description in each model, then set the habitat area: New habitat area = old habitat area x model area / (sum of model areas) " 447 Primary producers as multi-stanza Core Computation NOT SET feature joeb 2008-04-04T14:07:46-07:00 2010-11-01T12:00:22-07:00 "the multi-stanza groups are presently for consumers only. Would be neat for terrestrial applications if they could be used for primary producers also. Trees for instance, or Colette's sea grass for that matter. We'll need to ignore the q/b calculations, and I think that's all the change that's needed. " 1551 Multiple contaminants in Ecotracer Contaminant tracing NOT SET feature 2018-01-04T14:38:46-08:00 2018-01-04T14:56:17-08:00 Can you include multiple environmental contaminant compartments (so that we can separate the environmental concentration from water and sediment) with their own direct uptake rates per species, and/or is there a direct uptake flow from the detritus concentration Cd possible? I’m looking at Figure 2 in Walters and Christensen (2018) and would like to replicate it in some form in the proposal. Would it be fair to draw an arrow from Cd to direct uptake in Figure 2? Or otherwise create two Co boxes and specify that one is sediment and one is water? 1645 Ecotracer banded results Contaminant tracing 6.7 release major joeb 2023-12-14T11:34:28-08:00 2023-12-14T11:54:46-08:00 "Ecotracer contaminant maps display bands when run on multiple threads. Version 6.7.0.18580 " 1425 Standardization of the number of decimal places assumed by the software Code Ecopath 6: future version tweak 2016-04-12T01:17:17-07:00 2016-04-12T01:17:17-07:00 "I downloaded Ecosim SS of each group via the new plug called Results extractor and noticed that in some cases, the SS shown in Ecosim plot assumes different decimal places (e.g.: for the single species group Beryx decadactylus, the value shown directly in Ecosim plot is 2,63 while the Ecosim extractor says the real value is 2,643238306. At the same time, for the group Mora moro, Ecosim plot shows an SS value of 0,0555 and the Ecosim extractor says it is 0,055480808. I know it seems insignificant but this incongruity might be a reason behind the fact we are not being able to exactly achieve the total Ecosim SS estimate manually. Additionally, in Ecospace, when I input the 1200 values that will define a group environmental response, the decimal places assumed by the program are not constant in every point. Also, in the foraging area response form - for instances, if I fill the X min with the value 0,1432 it changes the value to 0,143199995160103. A bit weird, no?"