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Very cool – nice start on the module!
Our plan with the packages is to simplify the interaction with ST-Sim model inputs so as to avoid intermediate CSV files – pretty much as you suggest for the initial conditions. Same would be true for outputs. As for the connected graph, that’s not something we’ve ever come across before – perhaps at some point you could show us an example of how you use this? Colin
Hi Taylor – good question about working with Python. We have in fact begun developing a pair of packages for interacting with ST-Sim – our plan is to develop a package for each of Python and R. Our initial focus will be on post-processing output, but we will eventually be adding a full suite of functionality for setting up and running models also. We are hoping to have a first version of at least one of these packages by the end of the calendar year – which language will come first is still a matter of debate!
For now my suggestion would be for you to wrap your command-line calls in whatever language you prefer – Python or R would be my suggestion, as then you might be able to take advantage of the packages once they come online. The more people we have working in these 2 languages, the better! We have others doing the same – both in Python and R – and it is these initial scripts that are forming the basis for our packages. If you are interested in sharing your scripts at some point – or even what functionality you are interested in – then it could possibly help us shape the direction and scope of the initial package – we are always interested in learning what features and functionality are important to others.
Regards, Colin.
Thanks for the feedback. It seems like perhaps we should be posting a warning to the Run Log in the future when model parameters are supplied that are outside of the bounds of the Run Control timesteps. We’ll see if we can’t add that to an upcoming release. Colin.
Thanks for the feedback. It seems like perhaps we should be posting a warning to the Run Log in the future when model parameters are supplied that are outside of the bounds of the Run Control timesteps. We’ll see if we can’t add that to an upcoming release. Colin.
Short answer is no… you can leave all those fields blank. I suggest you strip them out of your ST-Sim models (in Excel) if they came across from VDDT, as they will only get in the way if you are not using them. To do this simply display all of your Probabilistic Transitions together under the “Probabilistic Transitions” tab (under Pathways property), right click and select “Export All” from the context menu. Remove the unwanted values in your Excel file and then reimport the edits using the “Import” option from the same context menu.
Unlike VDDT any fields in ST-Sim that are optional do not need to be specified. All of the fields to the right of Prob are in fact optional. Their default values are those that you would expect in order to make them have no effect – you have identified all of the default values correctly in your post except for Age Reset, which is set to Yes by default (as this is the most common behaviour for most transitions).
The behaviour or these functions in VDDT was always confusing to users and so it was modified in ST-Sim to make it consistent and simpler to use. Best to forget about VDDT syntax and look at the online help at:
http://wiki.syncrosim.com/index.php?title=Probabilistic_transitionsNeither feature ever “trumps” the other – they do slightly different things and so now work together. Age Reset if calculated first, followed by the Age Shift.
First thing is to determine the effect of the Age Reset – this says whether or not to reset the age of a cell after a transition. Default is yes (which is what happens when it is left blank). If yes then the new age of a cell is set to the start age of the post-transition state class; otherwise the cell maintains its pre-transition age after the transition.
The age shift is then applied to whatever age is first calculated using the Age Reset for a transition. Default is 0 (i.e. no shift if left blank). An age shift of +20 would add 20 to whatever age was first determined using the Age Reset.
Note that the age of a cell can never be beyond the bounds of its state class min and max ages.
So you are correct in that the -15 for Age Shift is redundant. In fact the Age Reset= Yes is also redundant. Leaving both fields blank invokes the default behaviours for both: resetting the age (in this case to 0) and having no shift.
You turn on the multi-process capability for ST-Sim using the menu option File-Library Definitions. We suggest setting the number of jobs to be at most the number of cores on your machine (for overnight runs); alternatively you might want to save one core for doing other things while the runs are underway. This will break up your simulations into jobs according to scenarios and iterations. You can determine the number of cores on you machine by opening the Performance tab under the Windows Task Manager and counting the number of panels under "CPU Usage History".
Note that you can further divide your simulations into jobs according to secondary strata using the Advanced-Processing scenario property. In general this latter option would only make sense if you had more cores available than the product of scenarios X iterations, and your secondary strata are independent of each other during the simulations.
Hope this helps – Colin.
That first line was just to caution you against inserting your own new fields in Excel. If you follow either steps 1 or 2 above then your formerly hidden fields will be validated the same as any other fields when imported.
Good question – it’s not recommended to add fields to the Excel export files before re-importing, as most fields have built-in validation. Instead there are two solutions to working with any fields that are hidden in ST-Sim:
1. As you noted you can unhide the fields in ST-Sim before exporting by right-clicking on the table of values for the property and selecting the hidden field name. Note that any fields for which there are no data are automatically hidden in ST-Sim.
2. The hidden ST-Sim fields are actually exported to excel. You can see this by looking at the Excel column title letters (ie columns A, B, C, etc.).. If there are hidden columns then Excel will skip letters for the column names. To unhide a column in Excel, select one or more entire columns on either side of the hidden column(s), right-click and select “Unhide”. You can unhide all the hidden columns at once by selecting all columns in the Excel worksheet before selecting “Unhide”.
Hope this helps!
Here are my suggestions. The first citation for the actual software, the second for the approach.
Apex Resource Management Solutions (2014). ST-Sim state-and-transition simulation model software. Retrieved from http://www.apexrms.com/stsm
Daniel, Colin J.; Frid, Leonardo. 2012. Predicting landscape vegetation dynamics using state-and-transition simulation models. In: Kerns, Becky K.; Shlisky, Ayn J.; Daniel, Colin J., tech. eds. Proceedings of the First Landscape State-and-Transition Simulation Modeling Conference, June 14–16, 2011, Portland, Oregon. Gen. Tech. Rep. PNW-GTR-869. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station: 5-22.
At present there is only a Windows version of ST-Sim. However we do have plans to release a Linux version – hopefully in early 2014 – assuming we can secure the necessary funding.
While we haven’t tried it yet, there is no reason to believe it wouldn’t work. However as a fallback you can always run legacy applications in compatibility mode – see http://www.dummies.com/how-to/content/how-to-run-older-programs-under-windows-8.html
If you do try it under Windows 8 please let us know how it goes.
We do not have a formal policy for end of support. Note that this is free software provided to our consulting clients as a service; as such our software support policy is outlined at http://www.apexrms.com/support . For those users that enter into a support arrangement with us, each support request is dealt with on a case-by-case basis.
