remove inbounds checks, fix bug in edge sampling

CovidAlertVaccinationModel/src/ABM/mixing_graphs.jl

@@ -36,7 +36,7 @@ Resample all the weights in `mixing_graph`
 function sample_mixing_graph!(mixing_graph)
     mixing_edges = mixing_graph.mixing_edges
     for i in 1:size(mixing_edges.contact_array)[1], j in 1:i  #diagonal            
-            rand!(RNG, mixing_edges.sampler_matrix[demo_i,demo_j],mixing_edges.sample_cache[i,j])
+            rand!(RNG, mixing_edges.sampler_matrix[i,j],mixing_edges.sample_cache[i,j])
             for k in 1:length(mixing_edges.contact_array[i,j][1])
                 kth_node_i = mixing_edges.contact_array[i,j][1][k]
                 kth_node_j = mixing_edges.contact_array[i,j][2][k]

CovidAlertVaccinationModel/src/ABM/solve.jl

@@ -2,7 +2,7 @@
 function contact_weight(p, contact_time) 
     return 1 - (1-p)^contact_time
 end
-function update_alert_durations!(t,modelsol)  
+Base.@propagate_inbounds @views function update_alert_durations!(t,modelsol)  
     @unpack notification_parameter = modelsol.params
     @unpack time_of_last_alert, app_user_index,inf_network,covid_alert_times,app_user = modelsol
     for (i,node) in enumerate(modelsol.app_user_index), mixing_graph in modelsol.inf_network.graph_list[t]
@@ -21,7 +21,7 @@ function update_alert_durations!(t,modelsol)
     end
 end
 
-function update_infection_state!(t,modelsol)
+Base.@propagate_inbounds @views function update_infection_state!(t,modelsol)
     @unpack base_transmission_probability,immunization_loss_prob,recovery_rate = modelsol.params
     @unpack u_inf,u_vac,u_next_inf,u_next_vac,demographics,inf_network,status_totals = modelsol
     
@@ -64,7 +64,7 @@ function update_infection_state!(t,modelsol)
     end
     # display(u_next_inf)
 end
-function update_vaccination_opinion_state!(t,modelsol,total_infections)
+Base.@propagate_inbounds @views function update_vaccination_opinion_state!(t,modelsol,total_infections)
     
     @unpack π_base, η,γ, κ, ω, ρ, ω_en,ρ_en,γ,β = modelsol.params
     @unpack demographics,time_of_last_alert, nodes, soc_network,u_vac,u_next_vac,app_user,app_user_list = modelsol
@@ -116,7 +116,7 @@ function agents_step!(t,modelsol)
     remake!(modelsol.inf_network,modelsol.index_vectors,modelsol.ws_matrix_tuple.daily)
     remake!(modelsol.soc_network,modelsol.index_vectors,modelsol.rest_matrix_tuple.daily)
     for network in modelsol.inf_network.graph_list[t]
-        sample_mixing_graph!(network,modelsol.demographics) #get new contact weights
+        sample_mixing_graph!(network) #get new contact weights
     end
 
     update_alert_durations!(t,modelsol)