altered transition rates in Gen Immunity script

GeneralizedImmunityExp1.R

@@ -6,9 +6,9 @@ paramFile<-args[1]
 No<-as.integer(args[2])
 resultsFolder <-args[3]
 jobid<-as.integer(args[4])
-paramFile<-"ParamListGen.csv"
-No<-3
-resultsFolder<-"./"
+#paramFile<-"ParamListGen.csv"
+#No<-3
+#resultsFolder<-"./"
 outFile<-paste(resultsFolder,"/",strsplit(paramFile,split="[.]")[[1]][1],"_results.csv",sep="")
 
 SEAI_p<-function(t,y,p){
@@ -65,22 +65,22 @@ SEAI_p<-function(t,y,p){
     #transmissibility is reduced to the number of infected hosts, 
     #receiving hosts needs to have open "resource room" for accepting new strains
     B_PW = b*(
-      eN*h_NU[1] +
-        eN*h_ND[1] + 
-        eS*h_SU[1] +
-        eS*h_SD[1] +
-        eA*h_AU[1] +
-        eA*h_AD[1] 
+      h_NU[1] +
+        h_ND[1] + 
+        h_SU[1] +
+        h_SD[1] +
+        h_AU[1] +
+        h_AD[1] 
     )
 
 
     B_PR = b*(
-      eN*h_NU[2]+
-        eN*h_ND[2]+ 
-        eS*h_SU[2]+
-        eS*h_SD[2]+
-        eA*h_AU[2]+
-        eA*h_AD[2]
+      h_NU[2]+
+        h_ND[2]+ 
+        h_SU[2]+
+        h_SD[2]+
+        h_AU[2]+
+        h_AD[2]
     )
 
 
@@ -121,24 +121,24 @@ SEAI_p<-function(t,y,p){
     infA = 1
     #print(infN)
     #naive class getting infected, and treated
-    NU2ND = (Bu*(1-rNU/capacity)*infN*d1)
+    NU2ND = rNU*(1/8)*d1
 
     #naive U class getting enough # of infections to move to SU
     #NU2SU = (Bu*(1-rNU/capacity)*rho1*1/((infN/(muWU_gen_N))+((1-infN))))
     NU2SU = (rNU*muRU_gen_N)*rho1
 
     #naive U class die from infections
-    NUInfDie = (Bu*(1-rNU/capacity)*infN*muWU_gen_N*muNU)
+    NUInfDie = rNU*muWU_gen_N*muNU
 
     #naive D class getting enough # of infections to move to SD
     #ND2SD = (Bd*(1-rND/capacity)*rho1*1/((infN/(muRU_gen_N))+((1-infN))))
     ND2SD = (rND*muRD_gen_N)*rho1
 
     #naive D class die from infections
-    NDInfDie = (Bd*(1-rND/capacity)*infN*muRD_gen_N*muND)
+    NDInfDie = rND*muRD_gen_N*muND
 
     #SU class getting infected, show symptoms, and treated
-    SU2SD = (Bu*(1-rSU/capacity)*infS*d2)
+    SU2SD = (rSU*(1/8)*d2)
 
     #SU class getting enough # of infections to move to AU
     #SU2AU = (Bu*(1-rSU/capacity)*rho2*1/((infS/(muWU_gen_S))+((1-infS))))
@@ -149,7 +149,7 @@ SEAI_p<-function(t,y,p){
     SD2AD = (rSD*muWD_gen_S)*rho2
 
     #AU class getting infected, show symptoms, and treated
-    AU2AD = (Bu*(1-rAU/capacity)*infA*omega*d3)
+    AU2AD = (rAU*(1/8)*d3)
 
 
 
@@ -442,24 +442,24 @@ SEAI_resOnly<-function(t,y,p){
     infA = 1
     #print(infN)
     #naive class getting infected, and treated
-    NU2ND = (Bu*(1-rNU/capacity)*infN*d1)
+    NU2ND = rNU*(1/8)*d1
 
     #naive U class getting enough # of infections to move to SU
     #NU2SU = (Bu*(1-rNU/capacity)*rho1*1/((infN/(muWU_gen_N))+((1-infN))))
     NU2SU = (rNU*muRU_gen_N)*rho1
 
     #naive U class die from infections
-    NUInfDie = (Bu*(1-rNU/capacity)*infN*muWU_gen_N*muNU)
+    NUInfDie = rNU*muWU_gen_N*muNU
 
     #naive D class getting enough # of infections to move to SD
     #ND2SD = (Bd*(1-rND/capacity)*rho1*1/((infN/(muRU_gen_N))+((1-infN))))
     ND2SD = (rND*muRD_gen_N)*rho1
 
     #naive D class die from infections
-    NDInfDie = (Bd*(1-rND/capacity)*infN*muRD_gen_N*muND)
+    NDInfDie = rND*muRD_gen_N*muND
 
     #SU class getting infected, show symptoms, and treated
-    SU2SD = (Bu*(1-rSU/capacity)*infS*d2)
+    SU2SD = (rSU*(1/8)*d2)
 
     #SU class getting enough # of infections to move to AU
     #SU2AU = (Bu*(1-rSU/capacity)*rho2*1/((infS/(muWU_gen_S))+((1-infS))))
@@ -470,7 +470,7 @@ SEAI_resOnly<-function(t,y,p){
     SD2AD = (rSD*muWD_gen_S)*rho2
 
     #AU class getting infected, show symptoms, and treated
-    AU2AD = (Bu*(1-rAU/capacity)*infA*omega*d3)    
+    AU2AD = (rAU*(1/8)*d3)
 
     # Parasite pop ODE------
     ## sensitive-------
@@ -726,24 +726,24 @@ SEAI_wildOnly<-function(t,y,p){
     infA = 1
     #print(infN)
     #naive class getting infected, and treated
-    NU2ND = (Bu*(1-rNU/capacity)*infN*d1)
+    NU2ND = rNU*(1/8)*d1
 
     #naive U class getting enough # of infections to move to SU
     #NU2SU = (Bu*(1-rNU/capacity)*rho1*1/((infN/(muWU_gen_N))+((1-infN))))
     NU2SU = (rNU*muRU_gen_N)*rho1
 
     #naive U class die from infections
-    NUInfDie = (Bu*(1-rNU/capacity)*infN*muWU_gen_N*muNU)
+    NUInfDie = rNU*muWU_gen_N*muNU
 
     #naive D class getting enough # of infections to move to SD
     #ND2SD = (Bd*(1-rND/capacity)*rho1*1/((infN/(muRU_gen_N))+((1-infN))))
     ND2SD = (rND*muRD_gen_N)*rho1
 
     #naive D class die from infections
-    NDInfDie = (Bd*(1-rND/capacity)*infN*muRD_gen_N*muND)
+    NDInfDie = rND*muRD_gen_N*muND
 
     #SU class getting infected, show symptoms, and treated
-    SU2SD = (Bu*(1-rSU/capacity)*infS*d2)
+    SU2SD = (rSU*(1/8)*d2)
 
     #SU class getting enough # of infections to move to AU
     #SU2AU = (Bu*(1-rSU/capacity)*rho2*1/((infS/(muWU_gen_S))+((1-infS))))
@@ -754,7 +754,7 @@ SEAI_wildOnly<-function(t,y,p){
     SD2AD = (rSD*muWD_gen_S)*rho2
 
     #AU class getting infected, show symptoms, and treated
-    AU2AD = (Bu*(1-rAU/capacity)*infA*omega*d3)    
+    AU2AD = (rAU*(1/8)*d3)
 
     # Parasite pop ODE------
     ## sensitive-------