parametrize workhours and add inf. distribution

disease_SLIR.lua

@@ -9,6 +9,8 @@ local conf
 local lib
 local ds_model
 
+local workhours
+
 local function w_states ( t )
   --w_states('t', 'L', 'P', 'I', 'R', 'quarantined')
   conf.w_states(t, ' ', M.state_count.L, ' ', M.state_count.P, ' ',
@@ -49,7 +51,8 @@ local states_mt = {
 }
 
 
-local function compute_beta_SLIR (d)
+local function compute_beta_SLIR (p)
+  local d = p.disease
   local beta
   if d.state == 'I' then
     if d.symptomatic then
@@ -60,6 +63,16 @@ local function compute_beta_SLIR (d)
   elseif d.state == 'P' then
     beta = ds_model.k * ds_model.R0 / ds_model._mu 
   end
+
+  if not beta then return end -- not infective
+
+  local beta_h = beta * 24 / ( 24+workhours*(conf.mobility.ws-1) )
+  if p.in_zone == p.home_zone then
+    beta = beta_h
+  elseif p.in_zone == p.work_zone then
+    beta = conf.mobility.ws * beta_h
+  end
+
   return beta
 end
 
@@ -70,7 +83,7 @@ M.infector = function (person, to_t)
   local infgen = d.infgen + 1
   d.infgen = infgen
 
-  local beta = compute_beta_SLIR(d)
+  local beta = compute_beta_SLIR(person)
   if not beta then
     return lib.esim.sleep_to(to_t)
   end
@@ -85,7 +98,7 @@ M.infector = function (person, to_t)
     and not d.quarantined then
       lib.agents.create_exposed(zone, person)
     end
-    local beta = compute_beta_SLIR(d)
+    local beta = compute_beta_SLIR(person)
     if not beta then
       return lib.esim.sleep_to(to_t)
     end
@@ -161,6 +174,10 @@ M.initialize = function ( c )
   conf = assert(c)
   ds_model = c.disease
   lib = conf.lib
+  workhours = conf.mobility.random_bus_day.end_hour - 
+    conf.mobility.random_bus_day.start_hour
+  conf.mobility.ws = conf.mobility.ws or 1
+  
   M.state_count = {L=0, P=0, I=0, R=0, quarantined=0}
 
   w_states('t', 'L', 'P', 'I', 'R', 'quarantined')

mobility.lua

@@ -78,44 +78,45 @@ end
 M.process.random_bus_day = function ( person )
   local f = function ()
     local t = lib.esim.now
-    local home, work
-    local next_go = next_hour_of_day(t, 7)
-    local next_ret = next_hour_of_day(t, 17)
+    local next_go = next_hour_of_day(t, conf.mobility.random_bus_day.start_hour)
+    local next_ret = next_hour_of_day(t, conf.mobility.random_bus_day.end_hour)
     local trip = 0.2 + 0.8 * math.random()
 
     if next_ret<next_go then -- started at work
-      work = person.in_zone
+      person.work_zone = person.in_zone
       lib.disease.infector(person, next_ret)
       if person.disease.state=='R' then return end
       t = esim.sleep_to(next_ret)
 
-      home = pick_random_source( person, t )  -- ponderated source of workers for work
+      -- ponderated source of workers for work
+      person.home_zone = pick_random_source( person, t )
       person.in_zone = nil
       t = esim.sleep_to(t+trip)
-      person.in_zone = home
+      person.in_zone = person.home_zone
     else
-      home = person.in_zone
+      person.home_zone = person.in_zone
     end
 
     while true do
 
-      local next_go = next_hour_of_day(t, 7)
+      local next_go = next_hour_of_day(t, conf.mobility.random_bus_day.start_hour)
       t = lib.disease.infector(person, next_go)
       if person.disease.state=='R' then return end
 
-      work = work or pick_random_destination( person, t )
+      person.work_zone = person.work_zone or pick_random_destination( person, t )
       --person.in_zone = nil
       --t = esim.sleep_to(t+trip)
-      person.in_zone = work
+      person.in_zone = person.work_zone
 
-      local next_ret = next_hour_of_day(t, 17)
+      local next_ret = next_hour_of_day(t, conf.mobility.random_bus_day.end_hour)
       t = lib.disease.infector(person, next_ret)
       if person.state=='R' then return end
 
-      home = home or pick_random_source( person, t )  -- ponderated source of workers for work
+      -- ponderated source of workers for work
+      person.home_zone = person.home_zone or pick_random_source( person, t )  
       --person.in_zone = nil
       --t = esim.sleep_to(t+trip)
-      person.in_zone = home
+      person.in_zone = person.home_zone
     end
   end
   return f
@@ -133,8 +134,8 @@ M.pick_mobility_model = function ( t, zone, exposed_from )
   local trabajan_aca = zone.trabajacasa + zone.trabajaloc
   local trabajan_remoto
 
-  local next_go = next_hour_of_day(t, 7)
-  local next_ret = next_hour_of_day(t, 17)
+  local next_go = next_hour_of_day(t, conf.mobility.random_bus_day.start_hour)
+  local next_ret = next_hour_of_day(t, conf.mobility.random_bus_day.end_hour)
   if next_ret<next_go then -- work hour
     trabajan_remoto = zone.trabajar_viene 
   else

sample.conf

@@ -50,6 +50,16 @@ disease = {
   q_coop = 1, -- probability of entering self quarantine
 }, 
 
+-- mobility related parameters
+mobility = {
+  random_bus_day = {
+    start_hour = 7, -- working hours
+    end_hour = 17,
+  },
+  ws = 1.0, -- infective power at work / infective power at home
+},
+
+
 -- contact tracers behavior
 ct_count = 0,  -- number if contact tracers working
 ct_hit_t =  1, -- time to hitting an exposed