REvoSim provides the user with control of many elements of the simulation. These are introduced herein, and can be modified within the the Simulation tab of the Settings dock, or from the command line.
6.4. Phylogeny settings
These radio buttons dictate the mode which by REvoSim tracks phylogeny.
|Off:||Does not track phylogenies and is thus the fastest mode (this could be useful for - as an example - studies focussing on changes in fitness).
| ||Identifies species in time slices to allow species to be coloured in the population view, and species diversity to be recorded.
|Phylogeny:||Identifies species, and then records their phylogeny, allowing a tree to be created at the end of a run.
|Phylogeny and metrics:|
| ||Does the same as Phylogeny, and also records a number of other metrics for each species, also output (when requested) at the end of a run.
Note: Moving between off and any form of tracking has a significant performance cost: there is little computational overhead moving between the different tracking options. Moving from basic to phylogeny to metrics does, however, come with an increasing memory overhead, as the trees and metrics are by necessity stored in RAM during a run, and written when the run completes. This could have implications for runs with a significant number of organisms and large numbers of iterations. See Running Log and Configuring Outputs and Run End Log for more details REvoSim outputs.
This is a capability introduced in v3.0.0 that links REvoSim variables to image maps (or each other, a functionality that has yet to be added, but is easily implemented on request). As default, REvoSim offers limited linked variables, however the system is designed so more can be added with ease. Please contact the authors if you would like one to be added - we will happily do so.
As currently coded, the image stack selected is used to spatially control a variable: specifically, for integer variables, the value of the R channel is multiplied by the value of the selected variable as defined in the settings docker. So, for example, if energy is set to 5 overall, for a pixel with an R value of 0 in the image map the energy will be set to 0 for that iteration. If the R value is set to 255, the energy level for that pixel will be 1275 (5x225). Note that this means that when using a linked integer variable it is likely that the default values will need to be changed. For boolean variables, an R channel value of zero is off, all other zero values (1-255) is on.
6.5.1. Create new linkage
To create a new linkage, use the push button labelled “Link a variable to an image mask”. This creates a pop up window with the following options:
|Variable:||This is the variable to which you would like to control using an image stack.
|Load Images:||Clicking this image loads a dialogue allowing you to load an image stack that controls the variable defined above, as described in the introduction to linkages.
|Mode:||This radio button defines the image mode for the stack controlling the variable. The modes are the same as used for the environment - see Environment settings.
| ||As with the environment settings, this defines whether REvoSim interpolates between images.
|Refresh rate:||The update rate of the image stacks controlling variables does not need to be the same as e.g. the environmental refresh rate: this spin box defines how often (in iterations) the next image in the stack is loaded.
6.5.2. Edit linkage
Once added, a linkage appears as a list item in the Current linkages text box on the bottom right of the simulation docker. To edit one double click on the linkage. Doing so will load a pre-filled dialogue with the same options as the add new linkage dialogue outlined above, all of which can be changed as required. The linkage can also be deleted using this dialogue box.