fast map-based example by petrelharp · Pull Request #35 · kr-colab/spatial_sims_standard

petrelharp · 2024-10-04T23:12:24Z

I realized I never put this in!

bhaller

Some perhaps useful comments...

bhaller · 2024-10-07T15:00:04Z

minimal_high_density.md

+
+**code:** [minimal_high_density.slim](minimal_high_density.slim); on [github](https://github.com/kr-colab/spatial_sims_standard/blob/main/minimal_high_density.slim)
+
+This code implements the same model as [`minimal.slim`](minimal.html),


what is "minimal.html" here? I don't see that file in the repo...

bhaller · 2024-10-07T15:02:55Z

minimal_high_density.md

+(i.e., quadratic in the parameter `K`): local density computation, and mate choice.
+The two methods can be used independently - for instance, maybe your simulation
+has small interaction neighborhood size but large mating neighborhood size,
+so you'd use these methods for mating but not density computations.


A little vague what "these methods" refers to. Maybe it would be helpful to actually give the method shown in this example a name, so you can refer to it? Otherwise, "the alternative method shown here" instead of "these methods", I guess.

Or just plop down the method/function names here to clarify the important differences? smooth and sampleNearbyPoint, maybe others?

Something like "The main changes from the minimal.slim example are use of the SpatialMap methods smooth and sampleNearbyPoint, which are described in more detail below."

bhaller · 2024-10-07T15:04:42Z

minimal_high_density.md

+has small interaction neighborhood size but large mating neighborhood size,
+so you'd use these methods for mating but not density computations.
+
+Both methods are linear because they rely on a pre-computed map of local density.


And now "both methods" is also vague/confusing here. I thought at first that it referred to both the "standard" method and the "alternative" method, but that didn't make sense, so I guess the "alternative" method is actually two methods? Anyhow, the usage of this vague term "method" needs to be cleaned up.

bhaller · 2024-10-07T15:05:29Z

minimal_high_density.md

+Well, we'd like these to be as big as is reasonable,
+because computation will scale with the number of these squares.
+But, this grid is the source of any discretization artifacts:
+the smaller the grid squares are, the closer this model is to `minimal.slim`.


or even worse, potentially! could be much worse if you make them really small!

bhaller · 2024-10-07T15:20:45Z

minimal_high_density.md

+with a certain characteristic scale: `SX` for local density (for "interactions") and `SM` for mating.
+So, as long as our grid squares are sufficiently smaller than these,
+any discretization will be smoothed out by those operations.
+So, we set the size of the grid cells to be approximately `min(SX,SM)/2`:


perhaps i will be obvious to most readers but of course if you're only using the method for one or the other purpose, you could customize the grid to either SX or SM; and you could conceivably make two different grids, too, if SX and SM are very different, right?

bhaller · 2024-10-07T15:30:03Z

minimal_high_density.md

+```
+initializeInteractionType(2, "xy", reciprocal=T, maxDistance=5/sqrt(K));
+```
+to have maximum interaction distance `5/sqrt(K)`.


This last sentence, "Since...", is a sentence fragment.

Also, it needs explanation why the max distance is "5/sqrt(K)" – where does that come from?

bhaller · 2024-10-07T15:33:35Z

minimal_high_density.md

+If the density is roughly $K$, this means there should be around 25 individuals in each circle of that radius;
+however, if density is sufficiently nonuniform, or if you are simulating some nonequilibrium situation,
+then this may fail.
+The code is robust to this:


How about "The code in this example handles this issue, by doing:". I misread "The code is robust to this:" as saying "The code in the model is robust to the following two lines of code:" which had me scratching my head for a good thirty seconds! As usual, "this" creates ambiguity and confusion. :->

bhaller · 2024-10-07T15:35:04Z

minimal_high_density.md

+```
+means that if an individual has no neighbors, they will not reproduce,
+but this is over a much smaller distance than our nominal mating distance, `SM`,
+so we don't want this to happen very much.


This needs a bit of rewriting. "means that..." seems like it starts a sentence in the middle, and "this is over" and "we don't want this" both use "this" in an ambiguous way that I am honestly unable to puzzle out.

bhaller · 2024-10-07T15:36:08Z

minimal_high_density.md

+but this is over a much smaller distance than our nominal mating distance, `SM`,
+so we don't want this to happen very much.
+(Indeed, if `SM` was not much larger than `5/sqrt(K)` then we wouldn't be saving any computation at all.)
+


Ends rather abruptly; some kind of closing sentence, a conclusion, a take-home point?

bhaller · 2024-10-07T15:47:00Z

minimal_high_density.slim

@@ -0,0 +1,130 @@
+initialize() {


I didn't try actually running the model, but I don't see any problems. :->

Runs fine on my end!

silastittes · 2024-10-07T17:27:05Z

This is great! The grid set up at the beginning is a nice way to make the grid computation behind the scenes more explicit. Definitely a very helpful addition to the repo.

silastittes · 2024-10-07T16:50:05Z

minimal_high_density.md

+
+**code:** [minimal_high_density.slim](minimal_high_density.slim); on [github](https://github.com/kr-colab/spatial_sims_standard/blob/main/minimal_high_density.slim)
+
+This code implements the same model as [`minimal.slim`](minimal.html),


Suggested change

This code implements the same model as [`minimal.slim`](minimal.html),

This code implements the same model as [`minimal.slim`](https://github.com/kr-colab/spatial_sims_standard/blob/main/minimal.slim),

silastittes · 2024-10-07T16:50:55Z

minimal_high_density.md

+(i.e., quadratic in the parameter `K`): local density computation, and mate choice.
+The two methods can be used independently - for instance, maybe your simulation
+has small interaction neighborhood size but large mating neighborhood size,
+so you'd use these methods for mating but not density computations.


Or just plop down the method/function names here to clarify the important differences? smooth and sampleNearbyPoint, maybe others?

Something like "The main changes from the minimal.slim example are use of the SpatialMap methods smooth and sampleNearbyPoint, which are described in more detail below."

silastittes · 2024-10-07T17:25:59Z

minimal_high_density.slim

@@ -0,0 +1,130 @@
+initialize() {


Runs fine on my end!

fast map-based example

d5b7211

petrelharp requested review from bhaller and silastittes October 4, 2024 23:12

bhaller reviewed Oct 7, 2024

View reviewed changes

silastittes reviewed Oct 7, 2024

View reviewed changes


		code: [minimal_high_density.slim](minimal_high_density.slim); on [github](https://github.com/kr-colab/spatial_sims_standard/blob/main/minimal_high_density.slim)

		This code implements the same model as [`minimal.slim`](minimal.html),

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petrelharp commented Oct 4, 2024

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silastittes commented Oct 7, 2024

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