From 0c6b3c3f854d0c0019eff21add7bf6e1644371f8 Mon Sep 17 00:00:00 2001 From: Jack Chaillet Date: Tue, 12 Apr 2022 15:59:14 -0400 Subject: [PATCH] NEW GEN IMMUNITY CHANGES --- batchRuns/ODESGeneralizedImmunity.R | 26 ++++++++++++-------------- 1 file changed, 12 insertions(+), 14 deletions(-) diff --git a/batchRuns/ODESGeneralizedImmunity.R b/batchRuns/ODESGeneralizedImmunity.R index 8e943ef..e51265c 100644 --- a/batchRuns/ODESGeneralizedImmunity.R +++ b/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)