Enhance "bag of clocks", migrate examples to docs and build #55
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…thin width on screen
docs/src/distributions-11.png
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Would it work if we didn't check in the pngs and the markdown that are created by Literate.jl? That way they aren't part of what we distribute, and they will be made on the fly, just when docs are created.
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So do you mean add those to the .gitignore? I wonder if there's any better solution, as then we need to manually add a lot of individual files to the gitignore.
docs/src/distributions.md
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The same goes for the markdowns generated. Could we get away with non committing these?
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| All these sets are visualized in the figure below, reproduced from "Stochastic petri nets: Modelling, stability, simulation" by Peter J. Haas (2002). | ||
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Thank you for putting in this section and especially this diagram. Really helpful.
| @@ -48,4 +48,4 @@ For a continuous-time simulation, each event happens at a distinct time. Right a | |||
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| 2. A clock may be enabled. For instance, once a person is infected, they can now infect all neighboring people. | |||
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| 3. The rate of a clock may change. We discussed moves on a chessboard earlier. Maybe there's now a breeze so that the right to move right is greater than the rate to move left. The Exponential distributions would change accordingly. | |||
| a linear space and the latter works by accumulating survival of a distribution | ||
| in a log space. | ||
| ["Efficient Exact Stochastic Simulation of Chemical Systems with Many Species | ||
| and Many Channels"](https://doi.org/10.1021/jp993732q). |
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Now I feel like I was lazy. I had that paper in front of me.
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@adolgert I resolved the SIR state comment. As for the Literate.jl output, I am not sure what is the best solution to avoid committing stuff produced when running make.jl locally to check changes. I guess we could add them manually to the gitignore but that seems brittle, especially those .pngs. After you advise on that as for the best solution, I'm happy to merge this PR. |
… into a literate subdirectory to simplify the gitignore
This PR:
I am going to do the PDMP example (#45) in a different PR as it is somewhat complex. Please ignore docs/pdmp.jl for now. Also note the issue #54, for some reason lots of stuff is being dumped into docs/src, I am not sure why.
When merged, this will close #50 and #43