Release COMOKIT 1.0.1

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,38 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

COMOKIT Template Project/templates/Case Studies Comparison.template

@@ -12,6 +12,12 @@ model $TITLE$
 import "All COMOKIT.gaml"
 
 global {
+
+	// Parameter file folder
+	// by default parameter files are placed in Parameters/ folder of COMOKIT
+	// if you decide to redefine the path to that folder identify the place COMOKIT can find your parameter files
+	string parameter_folder_path <- "../../COMOKIT/Parameters/";
+
 	string POLICY_NAME <- "your_policy"; // Not mandatory but will be used in GUI
 }
 

COMOKIT Template Project/templates/Policy Comparison.template

@@ -13,6 +13,11 @@ import "All COMOKIT.gaml"
 
 global {
 
+	// Parameter file folder
+	// by default parameter files are placed in Parameters/ folder of COMOKIT
+	// if you decide to redefine the path to that folder identify the place COMOKIT can find your parameter files
+	string parameter_folder_path <- "../../COMOKIT/Parameters/";
+
 	string dataset_path <- "../Datasets/Case Study/"; // Relative path to the folder containing the boundary.shp, buildings.shp, satellite.png, etc. datafiles. 
 	string POLICY_NAME <- "your_policy"; // Not mandatory but will be used in GUI
 

COMOKIT Template Project/templates/Possible visualisations.template

@@ -12,6 +12,12 @@ model $TITLE$
 import "All COMOKIT.gaml"
 
 global {
+
+	// Parameter file folder
+	// by default parameter files are placed in Parameters/ folder of COMOKIT
+	// if you decide to redefine the path to that folder identify the place COMOKIT can find your parameter files
+	string parameter_folder_path <- "../../COMOKIT/Parameters/";
+
 	string dataset_path <- "../Datasets/Case Study/"; // Relative path to the folder containing the boundary.shp, buildings.shp, satellite.png, etc. datafiles. 		
 
 	action define_policy{  

COMOKIT Template Project/templates/Simple Policy.template

@@ -13,9 +13,13 @@ import "All COMOKIT.gaml"
 
 global {
 
+	// Parameter file folder
+	// by default parameter files are placed in Parameters/ folder of COMOKIT
+	// if you decide to redefine the path to that folder identify the place COMOKIT can find your parameter files
+	string parameter_folder_path <- "../../COMOKIT/Parameters/";
+
 	string dataset_path <- "../Datasets/Case Study/"; // Relative path to the folder containing the boundary.shp, buildings.shp, satellite.png, etc. datafiles. 
 
-
 	action define_policy{  
 		// ***************************************************************************
 		// SEE Model/Entities/Authority.gaml for built-in functions to create policies

COMOKIT/Experiments/Abstract Experiment.gaml

@@ -30,9 +30,11 @@ global {
 	 * Gloabl three steps initialization of a any simulation
 	 */
 	init {
+		do before_init;
 		do init_epidemiological_parameters;
 		do global_init;
 		do create_authority;
+		do after_init;
 	}
 
 }
@@ -158,6 +160,36 @@ experiment "Abstract Experiment" virtual: true {
 			}
 
 		}
+
+		// DEMOGRAPHICS
+
+		display "demographics_age" virtual: true {
+			chart "Ages" type: histogram {
+				loop i from: 0 to: max_age { data ""+i value: Individual count(each.age = i); }
+			}
+		}
+
+		display "demographics_sex" virtual: true {
+			chart "sex" type: pie {
+				data "Male" value: Individual count (each.sex=0);
+				data "Female" value: Individual count (each.sex=1);
+			}
+		}
+
+		display "demographics_employed" virtual: true {
+			chart "unemployed" type: pie {
+				data "Employed" value: Individual count not(each.is_unemployed);
+				data "Unemployed" value: Individual count each.is_unemployed;
+			}
+		}
+
+		display "demographics_household_size" virtual: true {
+			chart "Household size" type:histogram {
+				loop i from: 0 to:max(Individual collect (length(each.relatives))) { 
+					data string(i) value: Individual count (length(each.relatives)=i);
+				}
+			}
+		}	 
 
 	}
 

COMOKIT/Experiments/Baseline/No containment.gaml

@@ -31,5 +31,10 @@ experiment "No Containment" parent: "Abstract Experiment" autorun: true {
 
 		display "Main" parent: default_display {}
 		display "Plot" parent: states_evolution_chart {}	
+
+		display "Population age" parent: demographics_age { }
+		display "Population gender" parent: demographics_sex { }
+		display "Population employment status" parent: demographics_employed { }
+		display "Household size" parent: demographics_household_size { }
 	}
 }

COMOKIT/Experiments/Sensitivity Analysis/Comparison With and Without Environmental Transmission.gaml

@@ -20,7 +20,12 @@
 model CoVid19
 
 import "../../Model/Global.gaml"
-import "../Abstract Experiment.gaml"
+import "../Abstract Batch Experiment.gaml"
+
+global{
+
+	list<string> force_parameters <- list(epidemiological_transmission_building,epidemiological_basic_viral_decrease,epidemiological_basic_viral_release);
+}
 
 experiment "Comparison" parent: "Abstract Experiment" autorun: true {
 
@@ -84,3 +89,10 @@ experiment "Comparison" parent: "Abstract Experiment" autorun: true {
 		display "Main" parent: default_display {}
 	}
 }
+
+experiment HeadlessComparison parent: "Abstract Headless"  {
+	parameter "Allow Transmission Building" var: allow_transmission_building init: true; 
+
+	parameter "Basic Viral Release" var: basic_viral_release init: 0.01 min: 0.01 max: 0.1 step: 0.01; // if: [allow_transmission_building,true]
+	parameter "Basic Viral Decrease" var: basic_viral_decrease init: 0.02 min: 0.02 max: 0.2 step: 0.02; // if: [allow_transmission_building,true]
+}

COMOKIT/Experiments/Sensitivity Analysis/Sensitivity Analysis.gaml

@@ -23,6 +23,7 @@ import "../Abstract Batch Experiment.gaml"
 
 global {
 	int cycle_limit <- 5000 const:true; 
+	list<string> force_parameters <- list(epidemiological_successful_contact_rate_human);
 }
 
 experiment Sensitivity parent: "Abstract Batch" 
@@ -50,3 +51,8 @@ experiment Sensitivity parent: "Abstract Batch"
 }
 
 experiment SensitivityHeadless parent: "Abstract Headless"  {}
+
+
+experiment ContactRateHumanHeadless parent: "Abstract Headless"  {
+	parameter "Init All Ages Successful Contact Rate Human" var: init_all_ages_successful_contact_rate_human init: 0.01529959 among: [0.01529959, 0.02236774, 0.02993250, 0.03034067, 0.03319786, 0.034014,  0.03673534, 0.04043608, 0.04854507, 0.07120533];
+}

COMOKIT/Model/Constants.gaml

@@ -53,6 +53,12 @@ global {
 	string gravity <- "gravity";
 	string closest <- "closest";
 
+	//List of demogrphic attributes
+	string AGE <- "age";
+	string SEX <- "sex";
+	string EMP <- "is_unemployed";
+	string HID <- "household_id";
+	string IID <- "individual_id";
 
 	//number of the column for the epidemiological parameters CSV file
 	int epidemiological_csv_column_name <- 0; //Name of the parameter
@@ -91,5 +97,7 @@ global {
 	string epidemiological_proportion_death_symptomatic <- "Proportion_death_symptomatic";
 	string epidemiological_infectious_period_symptomatic <- "Infectious_period_symptomatic";
 	string epidemiological_infectious_period_asymptomatic <- "Infectious_period_asymptomatic";
+	string epidemiological_allow_viral_individual_factor <- "Allow_viral_individual_factor";
+	string epidemiological_viral_individual_factor <- "Viral_individual_factor";
 
 }

COMOKIT/Model/Entities/Biological Entity.gaml

@@ -57,6 +57,8 @@ species BiologicalEntity control:fsm{
 	int last_test <- 0;
 	//Age of the entity
 	int age;
+	//Factor for the beta and the basic viral release
+	float viral_factor;
 	//Factor of the contact rate for asymptomatic and presymptomatic individuals (might be age-dependent, hence its presence here)
 	float factor_contact_rate_asymptomatic;
 	//Basic viral release of the agent (might be age-dependent, hence its presence here)
@@ -75,6 +77,7 @@ species BiologicalEntity control:fsm{
 		factor_contact_rate_asymptomatic <- world.get_factor_contact_rate_asymptomatic(age);
 		basic_viral_release <- world.get_basic_viral_release(age);
 		contact_rate <- world.get_contact_rate_human(age);
+		viral_factor <- world.get_viral_factor(age);
 	}
 
 	//Action to call when performing a test on a individual

COMOKIT/Model/Entities/Building.gaml

@@ -67,4 +67,6 @@ species Building {
 
 }
 
-species outside parent: Building ;
+species outside parent: Building{
+	string type <- "Outside";
+}

COMOKIT/Model/Entities/Hospital.gaml

@@ -19,16 +19,13 @@ import "Building.gaml"
 global{
 	//Number of hospital in the city
 	int number_hospital <- 1;
-	//Capacity of hospitalisation per hospital (this should be initialised by data, but we don't have any :))
-	int capacity_hospitalisation_per_hospital <- 10000;
-	//Capacity of ICU per hospital (this should be initialised by data, but we don't have any :))
-	int capacity_ICU_per_hospital <- 1000;
 
 	//Action to create a hospital TO CHANGE WHEN DATA ARE AVAILABLE (which building to chose, what capacity)
 	action create_hospital{
 		create Hospital number:number_hospital{
-			capacity_hospitalisation <- capacity_hospitalisation_per_hospital;
-			capacity_ICU <- capacity_ICU_per_hospital;
+			type <- "Hospital";
+			capacity_hospitalisation <- hospitalisation_capacity;
+			capacity_ICU <- ICU_capacity;
 		}
 	}
 }

COMOKIT/Model/Entities/Individual.gaml

@@ -44,6 +44,8 @@ species Individual parent: BiologicalEntity schedules: shuffle(Individual where
 	int sex; //0 M 1 F
 	//employement status of the individual
 	bool is_unemployed; 
+	//COMOKIT identifier
+	string individual_id;
 
 	//Bool to consider only once the death
 	bool is_counted_dead <- false;
@@ -147,22 +149,20 @@ species Individual parent: BiologicalEntity schedules: shuffle(Individual where
 		basic_viral_release <- world.get_basic_viral_release(age);
 		contact_rate <- world.get_contact_rate_human(age);
 		proba_wearing_mask <- world.get_proba_wearing_mask(age);
+		viral_factor <- world.get_viral_factor(age);
 	}
 
 	//Action to call to define a new case, obtaining different time to key events
 	action define_new_case
 	{
 		//Add the new case to the total number of infected (not mandatorily known)
 		total_number_of_infected <- total_number_of_infected +1;
+
 		//Add the infection to the infections having been caused in the building
 		if(building_infections.keys contains(current_place.type))
 		{
 			building_infections[current_place.type] <- building_infections[current_place.type] +1;
 		}
-		else
-		{
-			add 1 to: building_infections at: current_place.type;
-		}
 		//Add the infection to the infections of the same age
 		if(total_incidence_age.keys contains(self.age))
 		{
@@ -260,7 +260,7 @@ species Individual parent: BiologicalEntity schedules: shuffle(Individual where
 	reflex infect_others when: not is_outside and is_infectious
 	{
 		//Computation of the reduction of the transmission when being asymptomatic/presymptomatic and/or wearing mask
-		float reduction_factor <- 1.0;
+		float reduction_factor <- viral_factor;
 		if(is_asymptomatic)
 		{
 			reduction_factor <- reduction_factor * factor_contact_rate_asymptomatic;

COMOKIT/Model/Functions.gaml

@@ -86,6 +86,21 @@ global
 		}
 	}
 
+
+	//Basic viral release in the environment of an infectious individual of a given age MUST BE A DISTRIBUTION
+	float get_viral_factor(int age)
+	{
+		if(allow_viral_individual_factor=false)
+		{
+			//No difference between individuals
+			return 1.0;
+		}
+		else
+		{
+			return get_rnd_from_distribution(map_epidemiological_parameters[age][epidemiological_viral_individual_factor][0],float(map_epidemiological_parameters[age][epidemiological_viral_individual_factor][1]),float(map_epidemiological_parameters[age][epidemiological_viral_individual_factor][2]));
+		}
+	}
+
 	//Time between exposure and symptom onset of an individual of a given age
 	float get_incubation_period_symptomatic(int age)
 	{