Merge pull request #11 from pedro-andrade-inpe/master

update to beta-5

description.lua

@@ -1,4 +1,4 @@
-version = "0.6.5"
+version = "0.7.3"
 license = "GPL"
 package = "sysdyn"
 depends = "terrame (>= 2.0), sci (>= 0.3)"

images/yeast.lua

@@ -0,0 +1,12 @@
+
+Random{seed = 12345}
+
+import("sysdyn")
+
+y = Yeast{}
+
+y:run()
+
+y.chart:save("yeast.bmp")
+clean()
+

lua/RandomWalk.lua

@@ -10,6 +10,7 @@ RandomWalk = Model{
 	value = 0,
 	prob  = Choice{0, 0.3, 0.5, 0.7, 0.95, 1, default = 0.5},
 	finalTime = Choice{min = 10, default = 100},
+	random = true,
 	execute = function(model)
 		if Random():number(0, 1) <= model.prob then
 			model.value = model.value + 1

lua/SIR.lua

@@ -4,19 +4,23 @@
 -- @arg data.infected The initial indected population. The default value is 2.
 -- @arg data.recovered The initial recovered population. The default value is 0.
 -- @arg data.duration The duration of the disease in days. The default value is 2.
+-- @arg data.contacts The number of contacts each infected has each time step. The default value is 6.
 -- @arg data.finalTime The final simulation time, in days. The default value is 30.
 -- @arg data.probability The probability of a susceptible person getting infected after
--- a contact with an infected one.
+-- a contact with an infected one. The default value is 0.25.
 -- @arg data.maximum A threshold of infected people that activates a public policy. The
 -- policy asks people to start leaving their houses, which cuts the contacts
 -- between people by half.
 -- @image sir.bmp
+-- @output maxInfected The maximum number of infected individuals along the simulation.
+-- @output finalInfected A table with number of infected individuals in each simulation step.
 SIR = Model{
 	susceptible = 9998,
 	infected = 2,
 	recovered = 0,
 	duration = 2,
 	finalTime = 30,
+	contacts = 6,
 	maximum = math.huge,
 	probability = 0.25,
 	init = function(model)
@@ -26,20 +30,27 @@ SIR = Model{
 			color = {"green", "red", "blue"}
 		}
 
-		model.contacts = 6
+		model.maxInfected = model.infected
+		model.finalInfected = {model.infected}
 
 		model.timer = Timer{
 			Event{action = function()
-				 local proportion = model.susceptible / 
-					 (model.susceptible + model.infected + model.recovered)
+				local proportion = model.susceptible / 
+					(model.susceptible + model.infected + model.recovered)
 
-				 local newInfected = model.infected * model.contacts * model.probability * proportion
+				local newInfected = model.infected * model.contacts * model.probability * proportion
 
-				 local newRecovered = model.infected / model.duration
+				local newRecovered = model.infected / model.duration
 
-				 model.susceptible = model.susceptible - newInfected
-				 model.recovered = model.recovered + newRecovered
-				 model.infected = model.infected + newInfected - newRecovered
+				model.susceptible = model.susceptible - newInfected
+				model.recovered = model.recovered + newRecovered
+				model.infected = model.infected + newInfected - newRecovered
+
+				if model.maxInfected < model.infected then
+					model.maxInfected = model.infected
+				end
+
+				table.insert(model.finalInfected, model.infected)
 			end},
 			Event{action = function()
 				if model.infected >= model.maximum then

lua/Yeast.lua

@@ -0,0 +1,35 @@
+--- A yeast growth model.
+-- @arg data.cells The initial number of cells. The default value is 9.6.
+-- @arg data.capacity The total capacity of the environment. The default value is 665.
+-- @arg data.rate The growth rate of the cells. The default value is 1.1.
+-- @arg data.finalTime The final simulation time. The default value is 9.
+-- @output finalCells A vector with the quantity of cells in each time step.
+-- @image yeast.bmp
+Yeast = Model{
+	cells     = 9.6,
+	capacity  = 665.0,
+	rate      = Choice{min = 0, max = 3.5, default = 1.1},
+	finalTime = 9,
+	init = function(model)
+		model.chart = Chart{
+			target = model,
+			select = {"cells"}
+		}
+
+		model.finalCells = {[0] = model.cells}
+
+		model.timer = Timer{
+			Event{action = function()
+				model.cells = model.cells + model.cells * model.rate * (1 - model.cells / model.capacity)
+
+				if model.cells > model.capacity then
+					model.cells = model.capacity
+				end
+
+				table.insert(model.finalCells, model.cells)
+			end},
+			Event{action = model.chart}
+		}
+	end
+}
+

tests/Daisyworld.lua

@@ -3,7 +3,7 @@
 
 return{
 	Daisyworld = function(unitTest)
-		local model = Daisyworld{}
+		local model = Daisyworld{finalTime = 40}
 
 		model:run()
 

tests/PredatorPrey.lua

@@ -3,10 +3,10 @@
 
 return{
 	PredatorPrey = function(unitTest)
-		local p = PredatorPrey{}
+		local p = PredatorPrey{finalTime = 200}
 		p:run()
 
-		unitTest:assertEquals(p.predator, 41, 0.1)
+		unitTest:assertEquals(p.predator, 65.6, 0.1)
 		unitTest:assertSnapshot(p.chart1, "predator-prey-1.png", 0.1)
 		unitTest:assertSnapshot(p.chart2, "predator-prey-2.png", 0.1)
 	end,

tests/Yeast.lua

@@ -0,0 +1,13 @@
+-- Test file for Yeast.lua
+-- Author: Gilberto Camara and Pedro R. Andrade
+
+return{
+	Yeast = function(unitTest)
+		local model = Yeast{}
+
+		model:run()
+
+		unitTest:assertSnapshot(model.chart, "Yeast-chart-1.bmp", 0.05)
+	end,
+}
+