1. 01 Dec, 2020 1 commit
    • Bentriou Mahmoud's avatar
      Test of distance G automaton passes! · f4c41acb
      Bentriou Mahmoud authored
      The two Cosmos tests checks the statistical correctness of estimated
      distance value for R1,R2,R3,R5 experiments. Also, they test that all
      trajectories are accepted.
      A bunch of errors were fixed in automata files (Cosmos .lha and julia
      ./automata files) and simulation function that introduced statistical
      bias, i.e. approximated values that were closed but not in the
      confidence interval. The general structure of simulation and was
      reworked in order to suits well te behavior of Cosmos.
  2. 30 Nov, 2020 1 commit
    • Bentriou Mahmoud's avatar
      A major fix in simulation was done, side effect issue, an efficient · c095bee4
      Bentriou Mahmoud authored
      copyto! is implemented for LHA states.
      Automaton G works almost well, a bias in the distance is identified
      compared to Cosmos when one of the model parameters is zero.
      Implementation of volatile_simulate, which simulates SynchronizedModel
      without saving values: it only returns the last LHA state of the
      Implementation of distributed computations of variable automata with
      Tests passed.
  3. 29 Nov, 2020 2 commits
  4. 27 Nov, 2020 2 commits
  5. 26 Nov, 2020 2 commits
  6. 25 Nov, 2020 1 commit
  7. 24 Nov, 2020 3 commits
  8. 23 Nov, 2020 2 commits
    • Bentriou Mahmoud's avatar
      Change of Trajectory.values type from Matrix to Vector of Vector in · 5b7fc78f
      Bentriou Mahmoud authored
      order to replace vcat by push!.
      The benchmarks are at least equal, and better when the buffer size is
      small. However, no significative difference of performance with adequate
      buffer size.
      My opinion the gain can be seen when simulations are going to be very
      long with more complicated models than we have implemented for now.
      All tests passed.
    • Bentriou Mahmoud's avatar
      Forgot the notebook in the last commit. · 27d56ab9
      Bentriou Mahmoud authored
      Automaton G is implemented and runs OK. Not tested with Cosmos call.
      The next step of development is the restruction of data collection for
      From now on: Trajectory.values::Matrix{Float64}, it will be
      According to small performance tests I've made, it will increase the
      performance of the package.
  9. 22 Nov, 2020 2 commits
    • Bentriou Mahmoud's avatar
      Small restruction in Cosmos tests. · fadb5929
      Bentriou Mahmoud authored
      Add of set_time_bound!
      Add of a first notebook example to explain the package.
    • Bentriou Mahmoud's avatar
      Add of a function in models that creates new model objects + tests. · 2a9d3b72
      Bentriou Mahmoud authored
      Add of a major test based on Cosmos: tests/cosmos/distance_F/ER_1D.jl
      The LHA distance F of this package is tested with Cosmos.
      For several parameters in R1, R2, R3 experiments (see Bentriou,
      Ballarini, Cournede 2018), Cosmos is called to
      compute an average distance. Then we collect the number of simulations
      and the estimated value computed by Cosmos.
      We compute an average distance by the package methods with the same
      number of simulations done by Cosmos
      Then the two average distances are compared to each others with
      regard to the width of the confidence interval set in Cosmos.
      Test passed.
  10. 21 Nov, 2020 2 commits
  11. 20 Nov, 2020 2 commits
  12. 19 Nov, 2020 1 commit
  13. 18 Nov, 2020 3 commits
  14. 17 Nov, 2020 5 commits
  15. 16 Nov, 2020 5 commits
  16. 15 Nov, 2020 4 commits
    • Bentriou Mahmoud's avatar
      Improvement of memory allocation. · d690d6b9
      Bentriou Mahmoud authored
      In fine I give the Abstract and Static arrays types up.
    • Bentriou Mahmoud's avatar
      Fix of type instability in SIR model: · 384b4ad7
      Bentriou Mahmoud authored
      - Real => Float64 for better performance (Real is an abstract type)
      - Should not create a type inside the model because the compiler fails
      at estimating the type of the output of the f function (detected with
      - Intentionaly ER is not as well improved as SIR in order to check the
      differences of performance.
    • Bentriou Mahmoud's avatar
      - Add of ER model + tests · 06dca928
      Bentriou Mahmoud authored
      - Add of benchmark scripts that compares perf wrt pygmalion.
      => As expected it is bad in terms of reading cost (because of row by row
      matrix read) but it is also not good in terms of simulation cost.
      hcat seems to perform badly, should investigate.
    • Bentriou Mahmoud's avatar
      Commit that implement the essentials for the lauch of a simulation of a · 2f7fea8f
      Bentriou Mahmoud authored
      SIR model.
      - Evolution of the ContinuousTimeModel type
      - simulate, easy access to Trajectory fields
      - fix of several errors
  17. 14 Nov, 2020 2 commits