Closed skycolt closed 5 years ago
Happy to help but I need a bit more information.
How did you attempt to retrieve the simulation data?
Following your code:
# access the state data for trial 1
julia> result.simulation_data[1].xdata
2×41 Array{Int64,2}:
10 9 8 8 8 8 8 8 8 8 7 … 8 6 7 6 7 8 8 8 7 7
0 1 2 2 2 2 2 2 2 2 3 2 4 3 4 3 2 2 2 3 3
# access the saved time points
julia> result.simulation_data[1].tdata
41-element Array{Float64,1}:
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
⋮
3.4
3.5
3.6
3.7
3.8
3.9
4.0
Alternative we discussed before:
julia> using DataFrames
julia> DataFrame(result)
41×4 DataFrame
│ Row │ trial │ time │ A │ B │
│ │ Int64 │ Float64 │ Int64 │ Int64 │
├─────┼───────┼─────────┼───────┼───────┤
│ 1 │ 1 │ 0.0 │ 10 │ 0 │
│ 2 │ 1 │ 0.1 │ 9 │ 1 │
│ 3 │ 1 │ 0.2 │ 8 │ 2 │
│ 4 │ 1 │ 0.3 │ 8 │ 2 │
│ 5 │ 1 │ 0.4 │ 8 │ 2 │
⋮
│ 36 │ 1 │ 3.5 │ 7 │ 3 │
│ 37 │ 1 │ 3.6 │ 8 │ 2 │
│ 38 │ 1 │ 3.7 │ 8 │ 2 │
│ 39 │ 1 │ 3.8 │ 8 │ 2 │
│ 40 │ 1 │ 3.9 │ 7 │ 3 │
│ 41 │ 1 │ 4.0 │ 7 │ 3 │
Thanks for the fast response. I used the most simple way:
result.simulation_data[n].xdata
julia> result.simulation_data[1].xdata 2×41 Array{Int64,2}: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
this is what I got...
I start to think will there be some version difference between your code and the code on GitHub. Because the code I installed has a weird behavior that the last mod(totalnumber, 4) traces are all 0s. I tried it on several computer and it's consistent.
I restarted the Atom and the problem seems to have been solved. I still don't know what's going wrong but anyway, sorry about the false alarm
That is strange behavior. I tend to use a REPL outside of Atom but I'll keep this on my radar. Thanks for reporting this.
Hello,
I am trying to use the package to do some simulation. I started with a very simple model
model = Network("test")
species definitions
model <= Species("A", 10) model <= Species("B", 0)
reaction definitions
model <= Reaction("R1", 1., "A --> B") model <= Reaction("R2", 1., "B --> A")
result = simulate(model, Direct(), time = 4.0, epochs = 40, trials = 1)
The behavior of the model is that A and B interconvert to each other and their total will always be 10. But the simulation result is very wired. If I set trials number to be 1. I consistently get all 0s for both A and B. If I set trial number to be 2 or 3, all 0s. If trial number is 4, the result seems to be OK. If I set trials to be 10, the last two runs always give me all 0s. I don't know what's really going on but there are definitely something wrong. Please help me with this.
Thanks Wenzhe