Essentially you can use an advanced feature called spatial multipliers to constrain the transition probabilities over space and time in any way you like. In the limit you can generate one multiplier raster for each transition and timestep. This raster then scales (i.e. multiplies) your base transition probabilities up and down over space and time. So the effect of any spatial layer (i.e. roads, rivers, zoning regulations etc.) can be either positive or negative. You can now also generate these multiplier files dynamically (i.e. as you run your simulation) so that they can be responsive to changes in your landscape. All this is pretty advanced work with our software and really is best done with a scripting language to generate the multiplier files. We recommend R as we have an R package to help but you could also other languages like Python. There are some shortcut ways to generate the spatial multipliers directly in ST-Sim without scripting, as was used in the Daniel et al (2016) paper, however the bottom line is you can do pretty much anything you like in terms of modifying transition probabilities if you are willing and able to venture into R.
I just tried it and you are right the Daniel et al (2016) supplementary files aren’t working with the latest version of our software. We’ll try to get a fix for this shortly and post it on the forum.
Note that we have an online course coming up in March that would probably cover a lot of your questions – see http://www.apexrms.com/training. We are actually also updating our videos this week in preparation for another course in February. If you subscribe to our newsfeed on the apexrms.com homepage you’ll get notifications about both the videos and the course.