NEW GEN IMMUNITY CHANGES

batchRuns/ODESGeneralizedImmunity.R

@@ -108,12 +108,12 @@ SEAI_p<-function(t,y,p){
     NU2ND = (Bu*(1-rNU/capacity)*infN*d1)
 
     #naive U class getting enough # of infections to move to SU
-    NU2SU = (Bu*(1-rNU/capacity)*rho1*(infN*muWU+(1-infN)))
+    NU2SU = (Bu*(1-rNU/capacity)*rho1*1/((1/(infN*muWU))+(1/(1-infN))))
     #naive U class die from infections
     NUInfDie = (Bu*(1-rNU/capacity)*infN*muWU*muNU)
 
     #naive D class getting enough # of infections to move to SD
-    ND2SD = (Bd*(1-rND/capacity)*rho1*(infN*muRD+(1-infN)))
+    ND2SD = (Bd*(1-rND/capacity)*rho1*1/((1/(infN*muRU))+(1/(1-infN))))
 
     #naive D class die from infections
     NDInfDie = (Bd*(1-rND/capacity)*infN*muRD*muND)
@@ -122,10 +122,10 @@ SEAI_p<-function(t,y,p){
     SU2SD = (Bu*(1-rSU/capacity)*infS*d2)
 
     #SU class getting enough # of infections to move to AU
-    SU2AU = (Bu*(1-rSU/capacity)*rho2*(infS*muWU+(1-infS)))
+    SU2AU = (Bu*(1-rSU/capacity)*rho2*1/((1/(infS*muWU))+(1/(1-infS))))
 
     #SD class getting enough # of infections to move to AD
-    SD2AD = (Bd*(1-rSD/capacity)*rho2*(infS*muRD+(1-infS)))
+    SD2AD = (Bd*(1-rSD/capacity)*rho2*1/((1/(infS*muRD))+(1/(1-infS))))
 
     #AU class getting infected, show symptoms, and treated
     AU2AD = (Bu*(1-rAU/capacity)*infA*omega*d3)
@@ -379,17 +379,16 @@ SEAI_resOnly<-function(t,y,p){
     infS = 1 - (red) #red is the reduction in infectivity due to generalized immunity and is between 0 and 0.5
     #infA = (1-1/nstrains)^fracA
     infA = 1 - (2*red)
-
     #naive class getting infected, and treated
     NU2ND = (Bu*(1-rNU/capacity)*infN*d1)
 
     #naive U class getting enough # of infections to move to SU
-    NU2SU = (Bu*(1-rNU/capacity)*rho1*(infN*muWU+(1-infN)))
+    NU2SU = (Bu*(1-rNU/capacity)*rho1*1/((1/(infN*muWU))+(1/(1-infN))))
     #naive U class die from infections
     NUInfDie = (Bu*(1-rNU/capacity)*infN*muWU*muNU)
 
     #naive D class getting enough # of infections to move to SD
-    ND2SD = (Bd*(1-rND/capacity)*rho1*(infN*muRD+(1-infN)))
+    ND2SD = (Bd*(1-rND/capacity)*rho1*1/((1/(infN*muRU))+(1/(1-infN))))
 
     #naive D class die from infections
     NDInfDie = (Bd*(1-rND/capacity)*infN*muRD*muND)
@@ -398,14 +397,13 @@ SEAI_resOnly<-function(t,y,p){
     SU2SD = (Bu*(1-rSU/capacity)*infS*d2)
 
     #SU class getting enough # of infections to move to AU
-    SU2AU = (Bu*(1-rSU/capacity)*rho2*(infS*muWU+(1-infS)))
+    SU2AU = (Bu*(1-rSU/capacity)*rho2*1/((1/(infS*muWU))+(1/(1-infS))))
 
     #SD class getting enough # of infections to move to AD
-    SD2AD = (Bd*(1-rSD/capacity)*rho2*(infS*muRD+(1-infS)))
+    SD2AD = (Bd*(1-rSD/capacity)*rho2*1/((1/(infS*muRD))+(1/(1-infS))))
 
     #AU class getting infected, show symptoms, and treated
     AU2AD = (Bu*(1-rAU/capacity)*infA*omega*d3)
-
     # Parasite pop ODE------
     ## sensitive-------
     dPW_NU.dt = 0
@@ -621,12 +619,12 @@ SEAI_wildOnly<-function(t,y,p){
     NU2ND = (Bu*(1-rNU/capacity)*infN*d1)
 
     #naive U class getting enough # of infections to move to SU
-    NU2SU = (Bu*(1-rNU/capacity)*rho1*(infN*muWU+(1-infN)))
+    NU2SU = (Bu*(1-rNU/capacity)*rho1*1/((1/(infN*muWU))+(1/(1-infN))))
     #naive U class die from infections
     NUInfDie = (Bu*(1-rNU/capacity)*infN*muWU*muNU)
 
     #naive D class getting enough # of infections to move to SD
-    ND2SD = (Bd*(1-rND/capacity)*rho1*(infN*muRD+(1-infN)))
+    ND2SD = (Bd*(1-rND/capacity)*rho1*1/((1/(infN*muRU))+(1/(1-infN))))
 
     #naive D class die from infections
     NDInfDie = (Bd*(1-rND/capacity)*infN*muRD*muND)
@@ -635,10 +633,10 @@ SEAI_wildOnly<-function(t,y,p){
     SU2SD = (Bu*(1-rSU/capacity)*infS*d2)
 
     #SU class getting enough # of infections to move to AU
-    SU2AU = (Bu*(1-rSU/capacity)*rho2*(infS*muWU+(1-infS)))
+    SU2AU = (Bu*(1-rSU/capacity)*rho2*1/((1/(infS*muWU))+(1/(1-infS))))
 
     #SD class getting enough # of infections to move to AD
-    SD2AD = (Bd*(1-rSD/capacity)*rho2*(infS*muRD+(1-infS)))
+    SD2AD = (Bd*(1-rSD/capacity)*rho2*1/((1/(infS*muRD))+(1/(1-infS))))
 
     #AU class getting infected, show symptoms, and treated
     AU2AD = (Bu*(1-rAU/capacity)*infA*omega*d3)