From f57e872d153499042f64218b9a42f22bba453e02 Mon Sep 17 00:00:00 2001
From: Mahmoud Bentriou <mahmoud.bentriou@centralesupelec.fr>
Date: Fri, 11 Dec 2020 23:58:50 +0100
Subject: [PATCH] fix of syntaxes in first notebook
---
examples/notebooks/1_Simulation.ipynb | 139 +++++++++++++++-----------
1 file changed, 83 insertions(+), 56 deletions(-)
diff --git a/examples/notebooks/1_Simulation.ipynb b/examples/notebooks/1_Simulation.ipynb
index f4e50b3..b00d02e 100644
--- a/examples/notebooks/1_Simulation.ipynb
+++ b/examples/notebooks/1_Simulation.ipynb
@@ -15,7 +15,16 @@
"cell_type": "code",
"execution_count": 2,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "┌ Info: Precompiling MarkovProcesses [top-level]\n",
+ "â”” @ Base loading.jl:1260\n"
+ ]
+ }
+ ],
"source": [
"using MarkovProcesses"
]
@@ -40,7 +49,7 @@
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
@@ -56,22 +65,33 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 6,
"metadata": {},
"outputs": [
{
- "data": {
- "text/plain": [
- "ContinuousTimeModel(3, 2, Dict(\"S\" => 1,\"I\" => 2,\"R\" => 3), Dict(\"I\" => 1), Dict(\"kr\" => 2,\"ki\" => 1), Union{Nothing, String}[\"R1\", \"R2\"], [0.0012, 0.05], [95, 5, 0], 0.0, MarkovProcesses.SIR_f!, [\"I\"], [2], MarkovProcesses.isabsorbing_SIR, Inf, 10)"
- ]
- },
- "execution_count": 3,
- "metadata": {},
- "output_type": "execute_result"
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "SIR SSA pkg model (ContinuousTimeModel)\n",
+ "- variables :\n",
+ "* I (index = 2 in state space)\n",
+ "* R (index = 3 in state space)\n",
+ "* S (index = 1 in state space)\n",
+ "- parameters :\n",
+ "* ki (index = 1 in parameter space)\n",
+ "* kr (index = 2 in parameter space)\n",
+ "- transitions : R1,R2\n",
+ "- observed variables :\n",
+ "* I (index = 1 in observed state space, index = 2 in state space)\n",
+ "p = [0.02, 0.07]\n",
+ "x0 = [95, 5, 0]\n",
+ "t0 = 0.0\n",
+ "time bound = Inf\n"
+ ]
}
],
"source": [
- "SIR"
+ "println(SIR)"
]
},
{
@@ -147,7 +167,7 @@
}
],
"source": [
- "set_param!(SIR, \"ki\", 0.015)\n",
+ "set_param!(SIR, :ki, 0.015)\n",
"@show SIR.p\n",
"set_param!(SIR, [0.02, 0.07])\n",
"@show SIR.p"
@@ -164,16 +184,21 @@
},
{
"cell_type": "code",
- "execution_count": 6,
+ "execution_count": 7,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
- "Trajectory(ContinuousTimeModel(3, 2, Dict(\"S\" => 1,\"I\" => 2,\"R\" => 3), Dict(\"I\" => 1), Dict(\"kr\" => 2,\"ki\" => 1), Union{Nothing, String}[\"R1\", \"R2\"], [0.02, 0.07], [95, 5, 0], 0.0, MarkovProcesses.SIR_f!, [\"I\"], [2], MarkovProcesses.isabsorbing_SIR, Inf, 10), [5; 6; … ; 1; 0], [0.0, 0.0002090421844976379, 0.026738149867351305, 0.1546747797181483, 0.1670337962687422, 0.1864041143902683, 0.22499455696452758, 0.2609816573473689, 0.26211457357364876, 0.34981665245812765 … 28.156954777152635, 29.8789510639123, 31.349526365163364, 31.418132567003155, 43.3115664747499, 49.84826982651157, 50.582546017297425, 51.33856085518521, 55.25637949865968, 63.081159577787396], Union{Nothing, String}[nothing, \"R1\", \"R1\", \"R1\", \"R1\", \"R1\", \"R1\", \"R1\", \"R1\", \"R1\" … \"R2\", \"R2\", \"R2\", \"R2\", \"R2\", \"R2\", \"R2\", \"R2\", \"R2\", \"R2\"])"
+ "Trajectory\n",
+ "- Model name: SIR SSA pkg \n",
+ "- Variable trajectories:\n",
+ "* I: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 46, 47, 48, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 79, 78, 79, 80, 81, 82, 83, 82, 81, 82, 83, 84, 85, 86, 87, 86, 87, 86, 87, 88, 87, 86, 85, 84, 85, 86, 87, 86, 85, 84, 83, 82, 81, 80, 79, 78, 77, 76, 75, 74, 73, 72, 71, 70, 69, 68, 67, 66, 65, 64, 63, 62, 61, 60, 59, 58, 57, 56, 55, 54, 53, 52, 51, 50, 49, 48, 47, 46, 45, 44, 43, 42, 41, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0]\n",
+ "- times = [0.0, 0.24577855621552194, 0.2478149161565589, 0.2853150202535163, 0.4573465669300486, 0.5156802507122017, 0.5488713853151262, 0.5694106885211497, 0.5788872503885709, 0.6245912291868114, 0.6566121315415033, 0.7931283435353416, 0.83270020199368, 0.8386998075002131, 0.8417042952608857, 0.8427551376647552, 0.8701999554468036, 0.8951256292071661, 0.9077288218029982, 0.9376622319229073, 0.9827229649909012, 0.9953032576765457, 0.9986177826032556, 1.0153848291967649, 1.0447914188625567, 1.0492014122265003, 1.070524783103734, 1.0726269740951375, 1.072967138802752, 1.0943818500991553, 1.116489485084964, 1.1285735695980215, 1.1723375316129172, 1.213845977572097, 1.2286687178948017, 1.2295093483811073, 1.2312638191767724, 1.2325709282468362, 1.244481593691647, 1.2624870979965666, 1.2834145939861266, 1.285764796090055, 1.310972419324214, 1.324617274813682, 1.3451928372043, 1.390603165691919, 1.4116004938074227, 1.4505176830738031, 1.4547213579879592, 1.4624171730488276, 1.4632236357632131, 1.4702808868992607, 1.4742187030030112, 1.4754940369410445, 1.4755237349411963, 1.4797055276946836, 1.4822125736745166, 1.5234583191077604, 1.5472145358013738, 1.5643622279323768, 1.587883934525096, 1.6060487480766195, 1.6719097587058893, 1.692707314337466, 1.697088843328341, 1.7073061626597648, 1.710582536000933, 1.7131112181403199, 1.7241992997835416, 1.7634968816756837, 1.78550991157585, 1.8672533491313623, 1.868775294555033, 1.8780308579480804, 1.9271595351999966, 1.9433721804249033, 2.0115414023682696, 2.0307236004972524, 2.0331919769914935, 2.111600134727418, 2.129193253114897, 2.13941932331246, 2.1802017796212882, 2.203441732414025, 2.21058492861084, 2.2181127678095187, 2.2382137733157794, 2.269453289860572, 2.273242781280825, 2.3235086535004847, 2.354182479039521, 2.3687838068308014, 2.394257920516965, 2.4510845536452797, 2.5223982640674647, 2.5811289105807145, 2.6021582222564925, 2.7226222986870483, 2.7910197312036473, 2.9425350009980282, 3.02055077757811, 3.039594333770209, 3.133377977116126, 3.1817075376142987, 3.4147235863411423, 3.539782357009317, 3.587084899226989, 3.620447160024518, 3.6274441686043883, 3.8364757218525587, 3.8391673517442046, 3.915668148051359, 4.013608159662592, 4.153708574532225, 4.181307293785593, 4.383741529594886, 4.755130254057704, 5.4036065556424635, 5.410621801836842, 5.4330236196083534, 5.7776665099328985, 5.802258390336277, 5.953384202813328, 5.9957703036539165, 6.006366484766268, 6.033378984272586, 6.1441075669762135, 6.157705333270836, 6.212908365173471, 6.252648412582357, 6.392052855060355, 6.4025853260551, 6.518930517440784, 6.592596845941982, 6.7164258553402245, 7.132577546602882, 7.1635240737101045, 7.786486929175749, 7.801298892611052, 7.880452010019803, 8.023739641544415, 8.194073072136348, 8.227854219758548, 8.389105633271651, 8.997315201732246, 9.49806435329397, 9.684927150070815, 9.757433953477268, 10.384896097233423, 10.412553909276932, 10.482340218974503, 10.72193174545675, 10.729699137569275, 10.934608965950016, 11.11917441898455, 11.20446838592195, 11.446224333854014, 11.803183235069083, 12.468580993540257, 12.681442546818868, 13.245705889763494, 13.256101393479387, 14.089151139720176, 14.155401738255222, 14.177565343853095, 14.357063891191089, 14.894584527602456, 16.417373253382813, 16.43496115585706, 16.676589190572557, 17.44669462094279, 17.466179493638776, 18.621869021895897, 19.519031289839436, 20.33698130395561, 21.012241021922648, 22.94396170910104, 24.779124484090048, 25.904276533056056, 26.291353569941716, 26.757984872221343, 27.572970488225828, 28.090717842386944, 28.3914382857189, 30.188892511626793, 31.083610922646052, 31.275510714328856, 33.987557235729874, 36.0759352242401, 43.47952103086246, 43.64008186023434, 45.106699045418154, 46.59516722084342, 49.974791679941056, 65.89654404976704, 114.54035862296453]\n",
+ "- transitions = Union{Nothing, Symbol}[nothing, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R2, :R1, :R1, :R2, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R2, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R1, :R2, :R2, :R1, :R1, :R1, :R1, :R1, :R2, :R2, :R1, :R1, :R1, :R1, :R1, :R1, :R2, :R1, :R2, :R1, :R1, :R2, :R2, :R2, :R2, :R1, :R1, :R1, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2, :R2]"
]
},
- "execution_count": 6,
+ "execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
@@ -191,7 +216,7 @@
},
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": 8,
"metadata": {},
"outputs": [
{
@@ -200,18 +225,19 @@
"text": [
"σ[3] = [7]\n",
"length_states(σ) = 196\n",
- "σ[\"I\", 4] = 8\n",
- "get_state_from_time(σ, 2.3) = [76]\n"
+ "σ[:I, 4] = 8\n",
+ "σ.I[4] = 8\n",
+ "get_state_from_time(σ, 2.3) = [83]\n"
]
},
{
"data": {
"text/plain": [
- "1-element view(::Array{Int64,2}, 84, :) with eltype Int64:\n",
- " 76"
+ "1-element Array{Int64,1}:\n",
+ " 83"
]
},
- "execution_count": 7,
+ "execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
@@ -219,7 +245,8 @@
"source": [
"@show σ[3] # the third state of the trajectory\n",
"@show length_states(σ) # number of states\n",
- "@show σ[\"I\", 4] # Fourth value of the variable I\n",
+ "@show σ[:I, 4] # Fourth value of the variable I\n",
+ "@show σ.I[4] # Fourth value of the variable I\n",
"@show get_state_from_time(σ, 2.3)"
]
},
@@ -232,25 +259,25 @@
},
{
"cell_type": "code",
- "execution_count": 8,
+ "execution_count": 9,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
- "SIR.map_var_idx = Dict(\"S\" => 1,\"I\" => 2,\"R\" => 3)\n",
- "SIR.g = [\"I\"]\n",
- "(size(σ.values), length(σ[\"I\"])) = ((196, 1), 196)\n"
+ "SIR.map_var_idx = Dict(:I => 2,:R => 3,:S => 1)\n",
+ "SIR.g = [:I]\n",
+ "(size(σ.values), length(σ[:I])) = ((1,), 196)\n"
]
},
{
"data": {
"text/plain": [
- "((196, 1), 196)"
+ "((1,), 196)"
]
},
- "execution_count": 8,
+ "execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
@@ -258,7 +285,7 @@
"source": [
"@show SIR.map_var_idx\n",
"@show SIR.g\n",
- "@show size(σ.values), length(σ[\"I\"]) # Only one column which corresponds to the I variable"
+ "@show size(σ.values), length(σ[:I]) # Only one column which corresponds to the I variable"
]
},
{
@@ -270,7 +297,7 @@
},
{
"cell_type": "code",
- "execution_count": 9,
+ "execution_count": 10,
"metadata": {},
"outputs": [
{
@@ -287,7 +314,7 @@
"false"
]
},
- "execution_count": 9,
+ "execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
@@ -306,7 +333,7 @@
},
{
"cell_type": "code",
- "execution_count": 10,
+ "execution_count": 11,
"metadata": {},
"outputs": [
{
@@ -320,10 +347,10 @@
{
"data": {
"text/plain": [
- "20.942860320770663"
+ "31.26273873394255"
]
},
- "execution_count": 10,
+ "execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
@@ -341,7 +368,7 @@
},
{
"cell_type": "code",
- "execution_count": 11,
+ "execution_count": 12,
"metadata": {},
"outputs": [
{
@@ -350,7 +377,7 @@
"120.0"
]
},
- "execution_count": 11,
+ "execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
@@ -368,7 +395,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "dist_lp(simulate(SIR), simulate(SIR)) = 270.22871331339087\n",
+ "dist_lp(simulate(SIR), simulate(SIR)) = 164.33150971327115\n",
"isbounded(SIR) = true\n",
"isbounded(simulate(SIR)) = true\n"
]
@@ -401,7 +428,7 @@
},
{
"cell_type": "code",
- "execution_count": 13,
+ "execution_count": 18,
"metadata": {},
"outputs": [
{
@@ -409,21 +436,21 @@
"output_type": "stream",
"text": [
"ER.buffer_size = 10\n",
- " 0.070949 seconds (130.66 k allocations: 7.141 MiB)\n",
- "elapsed time (ns): 70948721\n",
- "bytes allocated: 7488324\n",
- "pool allocs: 130585\n",
- "non-pool GC allocs:73\n",
- "length_states(σ) = 407\n"
+ " 0.036003 seconds (54.02 k allocations: 2.972 MiB)\n",
+ "elapsed time (ns): 36002718\n",
+ "bytes allocated: 3115887\n",
+ "pool allocs: 53998\n",
+ "non-pool GC allocs:18\n",
+ "length_states(σ) = 385\n"
]
},
{
"data": {
"text/plain": [
- "407"
+ "385"
]
},
- "execution_count": 13,
+ "execution_count": 18,
"metadata": {},
"output_type": "execute_result"
}
@@ -444,28 +471,28 @@
},
{
"cell_type": "code",
- "execution_count": 15,
+ "execution_count": 19,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
- " 0.000232 seconds (3.02 k allocations: 212.000 KiB)\n",
- "elapsed time (ns): 231641\n",
- "bytes allocated: 217088\n",
- "pool allocs: 3004\n",
- "non-pool GC allocs:11\n",
- "length_states(σ2) = 425\n"
+ " 0.000154 seconds (411 allocations: 59.938 KiB)\n",
+ "elapsed time (ns): 153854\n",
+ "bytes allocated: 61376\n",
+ "pool allocs: 399\n",
+ "non-pool GC allocs:12\n",
+ "length_states(σ2) = 379\n"
]
},
{
"data": {
"text/plain": [
- "425"
+ "379"
]
},
- "execution_count": 15,
+ "execution_count": 19,
"metadata": {},
"output_type": "execute_result"
}
--
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