corrected age to account for each node’s spawn date

3 files changed, 24 insertions, 20 deletions

diff --git a/R Scripts/generate-dag-dat.R b/R Scripts/generate-dag-dat.R
index 660a503..b5f2c3a 100755
--- a/R Scripts/generate-dag-dat.R
+++ b/R Scripts/generate-dag-dat.R
@@ -35,25 +35,12 @@ print(proc.time()-ptm) #3.5 hours
 colnames(dag_dat_all) = c('from','to','t1','t2','dist','w1','w2','w3')
 rownames(dag_dat_all) = NULL
 
+dag_dat_all$spawn1 = hyp_lcc_verts$spawn.date[dag_dat_all$from]
+dag_dat_all$spawn2 = hyp_lcc_verts$spawn.date[dag_dat_all$to]
+
 save(dag_dat_all, file='Results/dag_dat_all.RData')
 write.csv(dag_dat_all, file='Results/dag_dat_all.csv')
 
 dag_dat_vics = dag_dat_all[!is.na(dag_dat_all$t2),]
 save(dag_dat_vics, file='Results/dag_dat_vics.RData')
 write.csv(dag_dat_vics, file='Results/dag_dat_vics.csv')
-
-# analyze min possible infection time
-i = 1
-min_time = 0#rep(Inf,length(unique(dag_dat_vics$to)))
-min_time_dist = 0#rep(Inf,length(unique(dag_dat_vics$to)))
-for(to in unique(dag_dat_vics$to)){
-  rows = which(dag_dat_vics$to==to & dag_dat_vics$dist<2)
-  if(length(rows)>0){
-    min_time[i] = min(dag_dat_vics$t2[rows]-dag_dat_vics$t1[rows])
-    min_time_dist[i] = dag_dat_vics$dist[rows[which.min(dag_dat_vics$t2[rows]-dag_dat_vics$t1[rows])]]
-    i = i + 1
-  }
-}
-median(min_time)
-mean(min_time<100)
-save(min_time_1,min_time_2,min_time_3,file='Results/min_inf_time.RData')
diff --git a/R Scripts/min_inf_time.R b/R Scripts/min_inf_time.R
new file mode 100644
index 0000000..914af61
--- /dev/null
+++ b/R Scripts/min_inf_time.R
@@ -0,0 +1,15 @@
+# analyze min possible infection time
+i = 1
+min_time = 0#rep(Inf,length(unique(dag_dat_vics$to)))
+min_time_dist = 0#rep(Inf,length(unique(dag_dat_vics$to)))
+for(to in unique(dag_dat_vics$to)){
+  rows = which(dag_dat_vics$to==to & dag_dat_vics$dist<2)
+  if(length(rows)>0){
+    min_time[i] = min(dag_dat_vics$t2[rows]-dag_dat_vics$t1[rows])
+    min_time_dist[i] = dag_dat_vics$dist[rows[which.min(dag_dat_vics$t2[rows]-dag_dat_vics$t1[rows])]]
+    i = i + 1
+  }
+}
+median(min_time)
+mean(min_time<100)
+save(min_time_1,min_time_2,min_time_3,file='Results/min_inf_time.RData')
diff --git a/experiments/build_network.py b/experiments/build_network.py
index 8eb17ec..23b958f 100644
--- a/experiments/build_network.py
+++ b/experiments/build_network.py
@@ -11,6 +11,7 @@ def build_network(filename):
     with open(filename) as fh:
         reader = DictReader(fh)
         for row in reader:
+            print age
             from_, to = int(float(row["from"])), int(float(row["to"]))
             dist = int(row["dist"])
             if int(float(row["dist"])) > 2:
@@ -20,28 +21,29 @@ def build_network(filename):
                 dt = int(row["t2"]) - int(row["t1"])
                 parent = (dist, dt)
                 if to not in victims:
-                    age += int(row["t2"])
+                    age += int(row["t2"]) - int(row["spawn2"])
                     victims[to] = []
                 victims[to].append(parent)
                 if from_ not in victims:
-                    age += int(row["t1"])
+                    age += int(row["t1"]) - int(row["spawn1"])
                     victims[from_] = []
             # 'to' is not a victim
             else:
                 dt = 3012 - int(row["t1"])
                 parent = (dist, dt)
                 if to not in non_victims:
-                    age += 3012
+                    age += 3012 - int(row["spawn2"])
                     non_victims[to] = []
                 non_victims[to].append(parent)
                 if from_ not in victims:
-                    age += int(row["t1"])
+                    age += int(row["t1"]) - int(row["spawn1"])
                     victims[from_] = []
     root_victims = {}
     for victim in victims.keys():
         if not victims[victim]:
             del victims[victim]
             root_victims[victim] = []
+    print age
     return root_victims, victims, non_victims, age