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Washington's updates to calibration 0.3 and 0.4 - part 1 #200

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merged 11 commits into from
Dec 16, 2017
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Merged

Washington's updates to calibration 0.3 and 0.4 - part 1 #200

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a6c23ed
Close #164 - Fix multiple runs to enable the model to read files in c…
wsenafranca Dec 6, 2017
90fddab
Close #172 - Remove MultipleRuns:output.
wsenafranca Dec 6, 2017
18f3b03
Fix to remove MultipleRuns:output for sample strategy.
wsenafranca Dec 6, 2017
fafdb8f
Close #48 - Redirect every print from models to log files in Multiple…
wsenafranca Dec 7, 2017
082407e
Close #189 - Add MultipleRuns:free to remove unnecessary memory
wsenafranca Dec 12, 2017
c80cf02
Review the message shown for output function error #172
wsenafranca Dec 13, 2017
674db42
Review the function to redirect output #48
wsenafranca Dec 13, 2017
6643053
Remove internal call to run model in randomModel #164
wsenafranca Dec 13, 2017
b6dd657
Remove freeModel function #164
wsenafranca Dec 13, 2017
7ee24fb
Close #159 - Remove graphics from multiLevel
wsenafranca Dec 13, 2017
eb72097
Remove skipRun from doc
wsenafranca Dec 13, 2017
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3 changes: 1 addition & 2 deletions examples/daisy.lua
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Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,7 @@ local m = MultipleRuns{
model = Daisyworld,
parameters = {
sunLuminosity = Choice{min = 0.4, max = 1.6, step = 0.01},
},
output = {"blackArea", "whiteArea", "emptyArea"}
}
}

chart = Chart{
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3 changes: 1 addition & 2 deletions examples/sir-mr-campaign.lua
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Expand Up @@ -10,8 +10,7 @@ runs = MultipleRuns{
model = SIR,
parameters = {
maximum = Choice{min = 100, max = 4000, step = 10}
},
output = {"maxInfected", "susceptible"}
}
}

chart = Chart{
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1 change: 0 additions & 1 deletion examples/sir-mr-probability.lua
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Expand Up @@ -12,7 +12,6 @@ runs = MultipleRuns{
probability = Choice{min = 0.05, max = 0.3, step = 0.001}
},
--output = {"infected", "probability"} -- error!
output = {"susceptible", "maxInfected"}
}

chart = Chart{
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32 changes: 10 additions & 22 deletions lua/GoodnessOfFit.lua
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Expand Up @@ -259,47 +259,35 @@ multiLevel = function(data)
end

local fitnessSum = pixelByPixel(data.cs1, data.cs2, data.attribute, data.attribute, data.continuous)
local fitChart = Cell{sqrFit = fitnessSum}
if data.graphics == true then
Chart{ --SKIP
title = "MultiLevel Results", --SKIP
target = fitChart, --SKIP
select = {"sqrFit"} --SKIP
} --SKIP
fitChart:notify(0) --SKIP
end

local fitSquareTable = {}
local resolutionTable = {}
table.insert(fitSquareTable, fitnessSum)
table.insert(resolutionTable, 0)
if data.continuous == true then
for i = 1, (largerSquare) do
-- increase the square size and calculate fitness for each square.
local fitSquare = continuousSquareBySquare(i, data.cs1, data.cs2, data.attribute)
if fitSquare ~= -1 then
if data.graphics == true then
fitChart.sqrFit = fitSquare --SKIP
fitChart:notify(i) --SKIP
end

table.insert(fitSquareTable, fitSquare)
table.insert(resolutionTable, i)
fitnessSum = fitnessSum + (fitSquare * math.exp(-k * 2 ^ (i - 1)))
exp = exp + math.exp(-k * 2 ^ (i - 1))
end
end

else
for i = 1, (largerSquare) do
-- increase the square size and calculate fitness for each square.
local fitSquare = newDiscreteSquareBySquare(i, data.cs1, data.cs2, data.attribute)
if fitSquare ~= -1 then
if data.graphics == true then
fitChart.sqrFit = fitSquare --SKIP
fitChart:notify(i) --SKIP
end

table.insert(fitSquareTable, fitSquare)
table.insert(resolutionTable, i)
fitnessSum = fitnessSum + (fitSquare * math.exp(-k * 2 ^ (i - 1)))
exp = exp + math.exp(-k * 2 ^ (i - 1))
end
end
end

local fitness = fitnessSum / exp
return fitness
local df = DataFrame{fit = fitSquareTable, resolution = resolutionTable}
return fitness, df
end
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