diff --git a/.DS_Store b/.DS_Store index b0134f0..a6a193a 100644 Binary files a/.DS_Store and b/.DS_Store differ diff --git a/ODESImmunity_v11.R b/ODESImmunity_v11.R deleted file mode 100644 index 78ccd25..0000000 --- a/ODESImmunity_v11.R +++ /dev/null @@ -1,1257 +0,0 @@ -require(deSolve) -library(tidyverse) -args <- commandArgs(trailingOnly = TRUE) -print(args) -paramFile<-args[1] -No<-as.integer(args[2]) -resultsFolder <-args[3] -jobid<-as.integer(args[4]) -#paramFile<-"v11_param.csv" -#No<-267 -#resultsFolder<-"~/Dropbox/research/current/resistance/MalariaResistance-old/batchRuns" -#resultsFolder<-"./" -outFile<-paste(resultsFolder,"/",strsplit(paramFile,split="[.]")[[1]][1],"_",No,"_results.csv",sep="") - -SEAI_p<-function(t,y,p){ - - with(as.list(c(y,p)),{ - # total host population size - #print(t) - N = NU+ND+SU+SD+AU+AD - # total parasite population size - #PW = PW_NU+PW_ND+PW_SU+PW_SD+PW_AU+PW_AD - #PR = PR_NU+PR_ND+PR_SU+PR_SD+PR_AU+PR_AD - #P = PW+PR - - # parasite/host ratio - rNU <- (PW_NU+PR_NU)/(NU+1e-6) - rND <- (PW_ND+PR_ND)/(ND+1e-6) - rSU <- (PW_SU+PR_SU)/(SU+1e-6) - rSD <- (PW_SD+PR_SD)/(SD+1e-6) - rAU <- (PW_AU+PR_AU)/(AU+1e-6) - rAD <- (PW_AD+PR_AD)/(AD+1e-6) - - # prevalence - I_NU = 1-exp(-rNU) - I_ND = 1-exp(-rND) - I_SU = 1-exp(-rSU) - I_SD = 1-exp(-rSD) - I_AU = 1-exp(-rAU) - I_AD = 1-exp(-rAD) - - # proportion of hosts that have no parasites from W or R respectively - p0_NU <- c(exp(-rNU*PW_NU/(PW_NU+PR_NU+1e-6)), exp(-rNU*PR_NU/(PW_NU+PR_NU+1e-6))) - p0_ND <- c(exp(-rND*PW_ND/(PW_ND+PR_ND+1e-6)), exp(-rND*PR_ND/(PW_ND+PR_ND+1e-6))) - p0_SU <- c(exp(-rSU*PW_SU/(PW_SU+PR_SU+1e-6)), exp(-rSU*PR_SU/(PW_SU+PR_SU+1e-6))) - p0_SD <- c(exp(-rSD*PW_SD/(PW_SD+PR_SD+1e-6)), exp(-rSD*PR_SD/(PW_SD+PR_SD+1e-6))) - p0_AU <- c(exp(-rAU*PW_AU/(PW_AU+PR_AU+1e-6)), exp(-rAU*PR_AU/(PW_AU+PR_AU+1e-6))) - p0_AD <- c(exp(-rAD*PW_AD/(PW_AD+PR_AD+1e-6)), exp(-rAD*PR_AD/(PW_AD+PR_AD+1e-6))) - - # contributions of wild strain clones, wild strain in mixed, resistant clone and resistant mix in a bite - ctr_NU <- c((1-p0_NU[1])*p0_NU[2], (1-p0_NU[1])*(1-p0_NU[2])*PW_NU/(PW_NU+PR_NU+1e-6), (1-p0_NU[2])*p0_NU[1], (1-p0_NU[1])*(1-p0_NU[2])*PR_NU/(PW_NU+PR_NU+1e-6)) - ctr_ND <- c((1-p0_ND[1])*p0_ND[2], (1-p0_ND[1])*(1-p0_ND[2])*PW_ND/(PW_ND+PR_ND+1e-6), (1-p0_ND[2])*p0_ND[1], (1-p0_ND[1])*(1-p0_ND[2])*PR_ND/(PW_ND+PR_ND+1e-6)) - ctr_SU <- c((1-p0_SU[1])*p0_SU[2], (1-p0_SU[1])*(1-p0_SU[2])*PW_SU/(PW_SU+PR_SU+1e-6), (1-p0_SU[2])*p0_SU[1], (1-p0_SU[1])*(1-p0_SU[2])*PR_SU/(PW_SU+PR_SU+1e-6)) - ctr_SD <- c((1-p0_SD[1])*p0_SD[2], (1-p0_SD[1])*(1-p0_SD[2])*PW_SD/(PW_SD+PR_SD+1e-6), (1-p0_SD[2])*p0_SD[1], (1-p0_SD[1])*(1-p0_SD[2])*PR_SD/(PW_SD+PR_SD+1e-6)) - ctr_AU <- c((1-p0_AU[1])*p0_AU[2], (1-p0_AU[1])*(1-p0_AU[2])*PW_AU/(PW_AU+PR_AU+1e-6), (1-p0_AU[2])*p0_AU[1], (1-p0_AU[1])*(1-p0_AU[2])*PR_AU/(PW_AU+PR_AU+1e-6)) - ctr_AD <- c((1-p0_AD[1])*p0_AD[2], (1-p0_AD[1])*(1-p0_AD[2])*PW_AD/(PW_AD+PR_AD+1e-6), (1-p0_AD[2])*p0_AD[1], (1-p0_AD[1])*(1-p0_AD[2])*PR_AD/(PW_AD+PR_AD+1e-6)) - - - # converted contribution of W or R with mixed infection cos---- - h_NU = c(ctr_NU[1]+ctr_NU[2]+ctr_NU[4]*(mixCost), ctr_NU[3]*(1-cloneCost)+ctr_NU[4]*(1-mixCost)) - h_ND = c(ctr_ND[1]+ctr_ND[2]+ctr_ND[4]*(mixCost), ctr_ND[3]*(1-cloneCost)+ctr_ND[4]*(1-mixCost)) - h_SU = c(ctr_SU[1]+ctr_SU[2]+ctr_SU[4]*(mixCost), ctr_SU[3]*(1-cloneCost)+ctr_SU[4]*(1-mixCost)) - h_SD = c(ctr_SD[1]+ctr_SD[2]+ctr_SD[4]*(mixCost), ctr_SD[3]*(1-cloneCost)+ctr_SD[4]*(1-mixCost)) - h_AU = c(ctr_AU[1]+ctr_AU[2]+ctr_AU[4]*(mixCost), ctr_AU[3]*(1-cloneCost)+ctr_AU[4]*(1-mixCost)) - h_AD = c(ctr_AD[1]+ctr_AD[2]+ctr_AD[4]*(mixCost), ctr_AD[3]*(1-cloneCost)+ctr_AD[4]*(1-mixCost)) - - #transmissibility is reduced to the number of infected hosts, - #receiving hosts needs to have open "resource room" for accepting new strains - B_PW = b*( - h_NU[1]*NU + - h_ND[1]*ND + - h_SU[1]*SU + - h_SD[1]*SD + - h_AU[1]*AU + - h_AD[1]*AD - )/N - - - B_PR = b*( - h_NU[2]*NU+ - h_ND[2]*ND+ - h_SU[2]*SU+ - h_SD[2]*SD+ - h_AU[2]*AU+ - h_AD[2]*AD - )/N - - - - # per capita biting rate for hosts who are not treated - Bu = (B_PW+B_PR) - # per capita biting rate for hosts who are drug treated - Bd = B_PR - #print(B) - - # pop size +1 is to prevent N = 0 for undefined scenario - fracN = P_acc_N/(NU+ND+1e-6) - fracS = P_acc_S/(SU+SD+1e-6) - fracA = P_acc_A/(AU+AD+1e-6) - - # probability that the infected strain has not been seen by the adaptive immune system - infN = (1-1/nstrains)^fracN - infS = (1-1/nstrains)^fracS - infA = (1-1/nstrains)^fracA - #print(infN) - - - #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*(1-infN))+rNU*muWU*rho1 - - #naive U class die from infections - NUInfDie = rNU*muWU*muNU - - #naive D class getting enough # of infections to move to SD - ND2SD = (Bd*(1-rND/capacity)*rho1*(1-infN)) + rND*rho1*muRD - - #naive D class die from infections - NDInfDie = rND*muRD*muND - - #SU class getting infected, show symptoms, and treated - SU2SD = (Bu*(1-rSU/capacity)*infS*d2) - - #SU class getting enough # of infections to move to AU - SU2AU = Bu*(1-rSU/capacity)*rho2*(1-infS) + rSU*rho2*muWU - - #SD class getting enough # of new infections to move to AD - SD2AD = (Bd*(1-rSD/capacity)*rho2*(1-infS)) + rSD*rho2*muRD - - #AU class getting infected, show symptoms, and treated - AU2AD = (Bu*(1-rAU/capacity)*infA*omega*d3) - - #lose immunity----- - #SU back to NU due to loss of immune memory - hsu = (Bu*(1-rSU/capacity)) + SU2SD+SU2AU+att - SU2NU = hsu*exp(-hsu/ImmLost)/(1-exp(-hsu/ImmLost)) - - #SD back to ND due to loss of immune memory - hsd = (Bd*(1-rSD/capacity)) +1/Tau+att - SD2ND = hsd*exp(-hsd/ImmLost)/(1-exp(-hsd/ImmLost)) - - #AU back to SU due to loss of immune memory - hau = (Bu*(1-rAU/capacity)) + AU2AD + att - AU2SU = hau*exp(-hau/ImmLost)/(1-exp(-hau/ImmLost)) - - #AD back to SD due to loss of immune memory - had = (Bd*(1-rAD/capacity)) + 1/Tau + att - AD2SD = had*exp(-had/ImmLost)/(1-exp(-had/ImmLost)) - - # Parasite pop ODE------ - ## sensitive------- - dPW_NU.dt = B_PW*NU*infN*(1-rNU/capacity) + #new infections - PW_SU*SU2NU + # SU lose immunity back to NU - (PW_ND/Tau)- # drug loose effectiveness - (PW_NU*NU2ND) - #naive class getting infected, and treated - (PW_NU*NU2SU) - #naive class getting enough # of infections to move to S - (PW_NU*NUInfDie)- #naive class die from infections - (PW_NU*att)- #normal death rate - (PW_NU*muWU)#clearance of infection - - - #print(dNU.dt) - - dPW_ND.dt = 0 + # no new infections - PW_SD*SD2ND + # SD lose immunity back to ND - (PW_NU*NU2ND) - #naive class getting infected, and treated - (PW_ND/Tau) - # drug loose effectiveness - (PW_ND*ND2SD) -#naive class getting enough # of infections to move to S - (PW_ND*NDInfDie) -#naive class die from infections - (PW_ND*att)- #normal death rate - (PW_ND*muWD)#clearance from drug - - #print(dND.dt) - - dPW_SU.dt = B_PW*SU*infS*(1-rSU/capacity) + #new infections - (PW_NU*NU2SU) +#naive class getting enough # of infections to move to S - (PW_AU*AU2SU) + #AU moves back to SU due to immunity loss - (PW_SD/Tau)- # drug loose effectiveness - (PW_SU*SU2SD)- #symptomatic class getting infected, show symptoms, and treated - (PW_SU*SU2AU) -#symptomatic class getting enough # of infections to move to AU - (PW_SU*SU2NU) - # lose immunity back to NU - (PW_SU*att)- #normal death rate - (PW_SU*muWU)#clearance of infection - - dPW_SD.dt = 0 + # no new infections - (PW_ND*ND2SD)+ #naive class getting enough # of infections to move to S - (PW_AD*AD2SD) + #AD moves back to SU due to immunity loss - (PW_SU*SU2SD)- #symptomatic class getting infected, show symptoms, and treated - (PW_SD/Tau) - # drug loose effectiveness - (PW_SD*SD2AD)- #symptomatic class getting enough # of infections to move to AD - (PW_SD*SD2ND) - # lose immunity back to ND - (PW_SD*att)- #normal death rate - (PW_SD*muWD)#clearance from drug - - dPW_AU.dt = B_PW*AU*infA*(1-rAU/capacity) + #new infections - (PW_SU*SU2AU)+ #symptomatic class getting enough # of infections to move to AU - (PW_AD/Tau)- # drug loose effectiveness - (PW_AU*AU2AD)- #asymptomatic class getting infected, show symptoms, and treated - (PW_AU*att)- #normal death rate - (PW_AU*AU2SU) - #AU moves back to SU due to immunity loss - (PW_AU*muWU)#clearance from infection - - dPW_AD.dt = 0 + # no new infections - (PW_SD*SD2AD) + #symptomatic class getting enough # of infections to move to AD - (PW_AU*AU2AD)- #asymptomatic class getting infected, show symptoms, and treated - (PW_AD/Tau)- # drug loose effectiveness - (PW_AD*att)- #normal death rate - (PW_AD*AD2SD) - #AD moves back to SU due to immunity loss - (PW_AD*muWD)#clearance from drug - - ## resistant------- - dPR_NU.dt = B_PR*NU*infN*(1-rNU/capacity) + #new infections - PR_SU*SU2NU + # lose immunity from SU to NU - (PR_ND/Tau)- # drug loose effectiveness - (PR_NU*NU2ND) - #naive class getting infected, and treated - (PR_NU*NU2SU) - #naive class getting enough # of infections to move to S - (PR_NU*NUInfDie)- #naive class die from infections - (PR_NU*att)- #normal death rate - (PR_NU*muRU)#clearance of infection - - #print(dNU.dt) - - dPR_ND.dt = B_PR*ND*infN*(1-rND/capacity) + #new infections - PR_SD*SD2ND + # lose immunity from SD to ND - (PR_NU*NU2ND) - #naive class getting infected, and treated - (PR_ND/Tau) - # drug loose effectiveness - (PR_ND*ND2SD) -#naive class getting enough # of infections to move to S - (PR_ND*NDInfDie) -#naive class die from infections - (PR_ND*att)- #normal death rate - (PR_ND*muRD)#clearance from drug - - #print(dND.dt) - - dPR_SU.dt = B_PR*SU*infS*(1-rSU/capacity) + #new infections - (PR_NU*NU2SU) +#naive class getting enough # of infections to move to S - (PR_AU*AU2SU) + #AU moves back to SU due to immunity loss - (PR_SD/Tau)- # drug loose effectiveness - (PR_SU*SU2SD)- #symptomatic class getting infected, show symptoms, and treated - (PR_SU*SU2AU) -#symptomatic class getting enough # of infections to move to AU - PR_SU*SU2NU - # lose immunity to NU - (PR_SU*att)- #normal death rate - (PR_SU*muRU)#clearance of infection - - dPR_SD.dt = B_PR*SD*infS*(1-rSD/capacity) + #new infections - (PR_ND*ND2SD)+ #naive class getting enough # of infections to move to S - (PR_AD*AD2SD) + #AD moves back to SD due to immunity loss - (PR_SU*SU2SD)- #symptomatic class getting infected, show symptoms, and treated - (PR_SD/Tau) - # drug loose effectiveness - (PR_SD*SD2AD)- #symptomatic class getting enough # of infections to move to AD - PR_SD*SD2ND- # lose immunity to ND - (PR_SD*att)- #normal death rate - (PR_SD*muRD)#clearance from drug - - dPR_AU.dt = B_PR*AU*infA*(1-rAU/capacity) + #new infections - (PR_SU*SU2AU)+ #symptomatic class getting enough # of infections to move to AU - (PR_AD/Tau)- # drug loose effectiveness - (PR_AU*AU2AD)- #asymptomatic class getting infected, show symptoms, and treated - (PR_AU*att)- #normal death rate - (PR_AU*AU2SU) - #AU moves back to SU due to immunity loss - (PR_AU*muRU)#clearance from infection - - dPR_AD.dt = B_PR*AD*infA*(1-rAD/capacity) + #new infections - (PR_SD*SD2AD) + #symptomatic class getting enough # of infections to move to AD - (PR_AU*AU2AD)- #asymptomatic class getting infected, show symptoms, and treated - (PR_AD/Tau)- # drug loose effectiveness - (PR_AD*att)- #normal death rate - (PR_AD*AD2SD) - #AD moves back to SD due to immunity loss - (PR_AD*muRD)#clearance from drug - - # Generalized immunity ODE------ - dNU.dt = birth + - SU*SU2NU + # lose immunity - (ND/Tau)- # drug loose effectiveness - NU*NU2ND - #naive class getting infected, and treated - NU*NU2SU - #naive class getting enough # of infections to move to S - NU*NUInfDie- #naive class die from infections - (NU*att)#normal death rate - - - #print(dNU.dt) - - dND.dt = NU*NU2ND + #naive class getting infected, and treated - SD*SD2ND - # lose immunity - (ND/Tau) - # drug loose effectiveness - ND*ND2SD -#naive class getting enough # of infections to move to S - ND*NDInfDie -#naive class die from infections - (ND*att) #normal death rate - #print(dND.dt) - - dSU.dt = NU*NU2SU +#naive class getting enough # of infections to move to S - (AU*AU2SU) + #AU moves back to SU due to immunity loss - (SD/Tau)- # drug loose effectiveness - SU*SU2SD- #symptomatic class getting infected, show symptoms, and treated - SU*SU2AU -#symptomatic class getting enough # of infections to move to AU - SU*SU2NU - # lose immunity - (SU*att) #normal death rate - - dSD.dt = ND*ND2SD+ #naive class getting enough # of infections to move to S - (AD*AD2SD) + #AD moves back to SD due to immunity loss - SU*SU2SD- #symptomatic class getting infected, show symptoms, and treated - (SD/Tau) - # drug loose effectiveness - SD*SD2AD- #symptomatic class getting enough # of infections to move to AD - SD*SD2ND - # lose immunity - (SD*att) #normal death rate - - dAU.dt = SU*SU2AU+ #symptomatic class getting enough # of infections to move to AS - (AD/Tau)- # drug loose effectiveness - AU*AU2AD- #asymptomatic class getting infected, show symptoms, and treated - (AU*AU2SU) - #AU moves back to SU due to immunity loss - (AU*att) #normal death rate - - dAD.dt = SD*SD2AD + #symptomatic class getting enough # of infections to move to AS - AU*AU2AD- #asymptomatic class getting infected, show symptoms, and treated - (AD/Tau)- # drug loose effectiveness - (AD*AD2SD) - #AD moves back to SD due to immunity loss - (AD*att) #normal death rate - - #sprintf("%.0f, %.0f,%.0f,%.0f,%.0f,%.0f",dNU.dt,dND.dt,dSU.dt,dSD.dt,dAU.dt,dAD.dt) - - # track the mean number of times infected per immunity class------ - dP_acc_N.dt = NU*NU2SU/rho1 + ND*ND2SD/rho1- # total number of infections received - (NU*(NUInfDie))*fracN- #when naive U class die how many infections deducted - (ND*(NDInfDie))*fracN- #when naive D class die many infections deducted - (NU*NU2SU+ND*ND2SD)*fracN- #when naive class leave to S - (att+ImmLost)*P_acc_N+ - (SU*SU2NU+SD*SD2ND)*fracS #immune loss back to N - - dP_acc_S.dt = (NU*NU2SU+ND*ND2SD)*fracN+ #when naive class leave to S - SU*SU2AU/rho2 + - SD*SD2AD/rho2 + #total number of new infections - (AU*AU2SU+AD*AD2SD)*fracA- #immune loss from A - (att+ImmLost)*P_acc_S- # normal death+immune loss - (SU*SU2AU+SD*SD2AD)*fracS- #Symptomatic move to Asymptomatic - (SU*SU2NU+SD*SD2ND)*fracS #immune loss back to N - - dP_acc_A.dt = (SU*SU2AU+SD*SD2AD)*fracS+ #Symptomatic move to Asymptomatic - AU*(Bu*(1-rAU/capacity)*(1-infA)+rAU*muWU) + - AD*(Bd*(1-rAD/capacity)*(1-infA)+rAD*muRD)- #total number of new infections - (att+ImmLost)*P_acc_A- # normal death - (AU*AU2SU+AD*AD2SD)*fracA #immune loss from A - - a <- 365/(2*pi) - db.dt = bavgnull * seasonality / a *(1- dryWidth *cos(phase+t/a))*sin(phase+t/a-dryWidth*sin(phase+t/a)) - - return(list(c(dPW_NU.dt,dPW_ND.dt,dPW_SU.dt,dPW_SD.dt,dPW_AU.dt,dPW_AD.dt, - dPR_NU.dt,dPR_ND.dt,dPR_SU.dt,dPR_SD.dt,dPR_AU.dt,dPR_AD.dt, - dNU.dt,dND.dt,dSU.dt,dSD.dt,dAU.dt,dAD.dt, - dP_acc_N.dt, dP_acc_S.dt, dP_acc_A.dt, db.dt))) - }) -} - -SEAI_resOnly<-function(t,y,p){ - - with(as.list(c(y,p)),{ - # total host population size - N = NU+ND+SU+SD+AU+AD - # total parasite population size - #PW = PW_NU+PW_ND+PW_SU+PW_SD+PW_AU+PW_AD - #PR = PR_NU+PR_ND+PR_SU+PR_SD+PR_AU+PR_AD - #P = PW+PR - - # parasite/host ratio - rNU <- (PW_NU+PR_NU)/(NU+1e-6) - rND <- (PW_ND+PR_ND)/(ND+1e-6) - rSU <- (PW_SU+PR_SU)/(SU+1e-6) - rSD <- (PW_SD+PR_SD)/(SD+1e-6) - rAU <- (PW_AU+PR_AU)/(AU+1e-6) - rAD <- (PW_AD+PR_AD)/(AD+1e-6) - - # prevalence - I_NU = 1-exp(-rNU) - I_ND = 1-exp(-rND) - I_SU = 1-exp(-rSU) - I_SD = 1-exp(-rSD) - I_AU = 1-exp(-rAU) - I_AD = 1-exp(-rAD) - - # proportion of hosts that have no parasites from W or R - p0_NU <- c(exp(-rNU*PW_NU/(PW_NU+PR_NU+1e-6)), exp(-rNU*PR_NU/(PW_NU+PR_NU+1e-6))) - p0_ND <- c(exp(-rND*PW_ND/(PW_ND+PR_ND+1e-6)), exp(-rND*PR_ND/(PW_ND+PR_ND+1e-6))) - p0_SU <- c(exp(-rSU*PW_SU/(PW_SU+PR_SU+1e-6)), exp(-rSU*PR_SU/(PW_SU+PR_SU+1e-6))) - p0_SD <- c(exp(-rSD*PW_SD/(PW_SD+PR_SD+1e-6)), exp(-rSD*PR_SD/(PW_SD+PR_SD+1e-6))) - p0_AU <- c(exp(-rAU*PW_AU/(PW_AU+PR_AU+1e-6)), exp(-rAU*PR_AU/(PW_AU+PR_AU+1e-6))) - p0_AD <- c(exp(-rAD*PW_AD/(PW_AD+PR_AD+1e-6)), exp(-rAD*PR_AD/(PW_AD+PR_AD+1e-6))) - - # contributions of wild strain clones, wild strain in mixed, resistant clone and resistant mix in a bite - ctr_NU <- c((1-p0_NU[1])*p0_NU[2], (1-p0_NU[1])*(1-p0_NU[2])*PW_NU/(PW_NU+PR_NU+1e-6), (1-p0_NU[2])*p0_NU[1], (1-p0_NU[1])*(1-p0_NU[2])*PR_NU/(PW_NU+PR_NU+1e-6)) - ctr_ND <- c((1-p0_ND[1])*p0_ND[2], (1-p0_ND[1])*(1-p0_ND[2])*PW_ND/(PW_ND+PR_ND+1e-6), (1-p0_ND[2])*p0_ND[1], (1-p0_ND[1])*(1-p0_ND[2])*PR_ND/(PW_ND+PR_ND+1e-6)) - ctr_SU <- c((1-p0_SU[1])*p0_SU[2], (1-p0_SU[1])*(1-p0_SU[2])*PW_SU/(PW_SU+PR_SU+1e-6), (1-p0_SU[2])*p0_SU[1], (1-p0_SU[1])*(1-p0_SU[2])*PR_SU/(PW_SU+PR_SU+1e-6)) - ctr_SD <- c((1-p0_SD[1])*p0_SD[2], (1-p0_SD[1])*(1-p0_SD[2])*PW_SD/(PW_SD+PR_SD+1e-6), (1-p0_SD[2])*p0_SD[1], (1-p0_SD[1])*(1-p0_SD[2])*PR_SD/(PW_SD+PR_SD+1e-6)) - ctr_AU <- c((1-p0_AU[1])*p0_AU[2], (1-p0_AU[1])*(1-p0_AU[2])*PW_AU/(PW_AU+PR_AU+1e-6), (1-p0_AU[2])*p0_AU[1], (1-p0_AU[1])*(1-p0_AU[2])*PR_AU/(PW_AU+PR_AU+1e-6)) - ctr_AD <- c((1-p0_AD[1])*p0_AD[2], (1-p0_AD[1])*(1-p0_AD[2])*PW_AD/(PW_AD+PR_AD+1e-6), (1-p0_AD[2])*p0_AD[1], (1-p0_AD[1])*(1-p0_AD[2])*PR_AD/(PW_AD+PR_AD+1e-6)) - - # converted contribution of W or R with mixed infection cos---- - h_NU = c(ctr_NU[1]+ctr_NU[2]+ctr_NU[4]*(mixCost), ctr_NU[3]*(1-cloneCost)+ctr_NU[4]*(1-mixCost)) - h_ND = c(ctr_ND[1]+ctr_ND[2]+ctr_ND[4]*(mixCost), ctr_ND[3]*(1-cloneCost)+ctr_ND[4]*(1-mixCost)) - h_SU = c(ctr_SU[1]+ctr_SU[2]+ctr_SU[4]*(mixCost), ctr_SU[3]*(1-cloneCost)+ctr_SU[4]*(1-mixCost)) - h_SD = c(ctr_SD[1]+ctr_SD[2]+ctr_SD[4]*(mixCost), ctr_SD[3]*(1-cloneCost)+ctr_SD[4]*(1-mixCost)) - h_AU = c(ctr_AU[1]+ctr_AU[2]+ctr_AU[4]*(mixCost), ctr_AU[3]*(1-cloneCost)+ctr_AU[4]*(1-mixCost)) - h_AD = c(ctr_AD[1]+ctr_AD[2]+ctr_AD[4]*(mixCost), ctr_AD[3]*(1-cloneCost)+ctr_AD[4]*(1-mixCost)) - - #transmissibility is reduced to the number of infected hosts, - #receiving hosts needs to have open "resource room" for accepting new strains - B_PW = b*( - h_NU[1]*NU + - h_ND[1]*ND + - h_SU[1]*SU + - h_SD[1]*SD + - h_AU[1]*AU + - h_AD[1]*AD - )/N - - - B_PR = b*( - h_NU[2]*NU+ - h_ND[2]*ND+ - h_SU[2]*SU+ - h_SD[2]*SD+ - h_AU[2]*AU+ - h_AD[2]*AD - )/N - - - # per capita biting rate for hosts who are not treated - Bu = (B_PW+B_PR) - # per capita biting rate for hosts who are drug treated - Bd = B_PR - #print(B) - - # pop size +1 is to prevent N = 0 for undefined scenario - fracN = P_acc_N/(NU+ND+1e-6) - fracS = P_acc_S/(SU+SD+1e-6) - fracA = P_acc_A/(AU+AD+1e-6) - - # probability that the infected strain has not been seen by the adaptive immune system - infN = (1-1/nstrains)^fracN - infS = (1-1/nstrains)^fracS - infA = (1-1/nstrains)^fracA - - #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*(1-infN))+rNU*muWU*rho1 - - #naive U class die from infections - NUInfDie = rNU*muWU*muNU - - #naive D class getting enough # of infections to move to SD - ND2SD = (Bd*(1-rND/capacity)*rho1*(1-infN)) + rND*rho1*muRD - - #naive D class die from infections - NDInfDie = rND*muRD*muND - - #SU class getting infected, show symptoms, and treated - SU2SD = (Bu*(1-rSU/capacity)*infS*d2) - - #SU class getting enough # of infections to move to AU - SU2AU = Bu*(1-rSU/capacity)*rho2*(1-infS) + rSU*rho2*muWU - - #SD class getting enough # of new infections to move to AD - SD2AD = (Bd*(1-rSD/capacity)*rho2*(1-infS)) + rSD*rho2*muRD - - #AU class getting infected, show symptoms, and treated - AU2AD = (Bu*(1-rAU/capacity)*infA*omega*d3) - - #lose immunity----- - #SU back to NU due to loss of immune memory - hsu = (Bu*(1-rSU/capacity)) + SU2SD+SU2AU+att - SU2NU = hsu*exp(-hsu/ImmLost)/(1-exp(-hsu/ImmLost)) - - #SD back to ND due to loss of immune memory - hsd = (Bd*(1-rSD/capacity)) +1/Tau+att - SD2ND = hsd*exp(-hsd/ImmLost)/(1-exp(-hsd/ImmLost)) - - #AU back to SU due to loss of immune memory - hau = (Bu*(1-rAU/capacity)) + AU2AD + att - AU2SU = hau*exp(-hau/ImmLost)/(1-exp(-hau/ImmLost)) - - #AD back to SD due to loss of immune memory - had = (Bd*(1-rAD/capacity)) + 1/Tau + att - AD2SD = had*exp(-had/ImmLost)/(1-exp(-had/ImmLost)) - - # Parasite pop ODE------ - ## sensitive------- - dPW_NU.dt = 0 - - #print(dNU.dt) - - dPW_ND.dt = 0 - - #print(dND.dt) - - dPW_SU.dt = 0 - - dPW_SD.dt = 0 - - dPW_AU.dt = 0 - - dPW_AD.dt = 0 - - ## resistant------- - dPR_NU.dt = B_PR*NU*infN*(1-rNU/capacity) + #new infections - PR_SU*SU2NU + # lose immunity from SU to NU - (PR_ND/Tau)- # drug loose effectiveness - (PR_NU*NU2ND) - #naive class getting infected, and treated - (PR_NU*NU2SU) - #naive class getting enough # of infections to move to S - (PR_NU*NUInfDie)- #naive class die from infections - (PR_NU*att)- #normal death rate - (PR_NU*muRU)#clearance of infection - - #print(dNU.dt) - - dPR_ND.dt = B_PR*ND*infN*(1-rND/capacity) + #new infections - PR_SD*SD2ND + # lose immunity from SD to ND - (PR_NU*NU2ND) - #naive class getting infected, and treated - (PR_ND/Tau) - # drug loose effectiveness - (PR_ND*ND2SD) -#naive class getting enough # of infections to move to S - (PR_ND*NDInfDie) -#naive class die from infections - (PR_ND*att)- #normal death rate - (PR_ND*muRD)#clearance from drug - - #print(dND.dt) - - dPR_SU.dt = B_PR*SU*infS*(1-rSU/capacity) + #new infections - (PR_NU*NU2SU) +#naive class getting enough # of infections to move to S - (PR_AU*AU2SU) + #AU moves back to SU due to immunity loss - (PR_SD/Tau)- # drug loose effectiveness - (PR_SU*SU2SD)- #symptomatic class getting infected, show symptoms, and treated - (PR_SU*SU2AU) -#symptomatic class getting enough # of infections to move to AU - PR_SU*SU2NU - # lose immunity to NU - (PR_SU*att)- #normal death rate - (PR_SU*muRU)#clearance of infection - - dPR_SD.dt = B_PR*SD*infS*(1-rSD/capacity) + #new infections - (PR_ND*ND2SD)+ #naive class getting enough # of infections to move to S - (PR_AD*AD2SD) + #AD moves back to SD due to immunity loss - (PR_SU*SU2SD)- #symptomatic class getting infected, show symptoms, and treated - (PR_SD/Tau) - # drug loose effectiveness - (PR_SD*SD2AD)- #symptomatic class getting enough # of infections to move to AD - PR_SD*SD2ND- # lose immunity to ND - (PR_SD*att)- #normal death rate - (PR_SD*muRD)#clearance from drug - - dPR_AU.dt = B_PR*AU*infA*(1-rAU/capacity) + #new infections - (PR_SU*SU2AU)+ #symptomatic class getting enough # of infections to move to AU - (PR_AD/Tau)- # drug loose effectiveness - (PR_AU*AU2AD)- #asymptomatic class getting infected, show symptoms, and treated - (PR_AU*att)- #normal death rate - (PR_AU*AU2SU) - #AU moves back to SU due to immunity loss - (PR_AU*muRU)#clearance from infection - - dPR_AD.dt = B_PR*AD*infA*(1-rAD/capacity) + #new infections - (PR_SD*SD2AD) + #symptomatic class getting enough # of infections to move to AD - (PR_AU*AU2AD)- #asymptomatic class getting infected, show symptoms, and treated - (PR_AD/Tau)- # drug loose effectiveness - (PR_AD*att)- #normal death rate - (PR_AD*AD2SD) - #AD moves back to SD due to immunity loss - (PR_AD*muRD)#clearance from drug - - # Generalized immunity ODE------ - dNU.dt = birth + - SU*SU2NU + # lose immunity - (ND/Tau)- # drug loose effectiveness - NU*NU2ND - #naive class getting infected, and treated - NU*NU2SU - #naive class getting enough # of infections to move to S - NU*NUInfDie- #naive class die from infections - (NU*att)#normal death rate - - - #print(dNU.dt) - - dND.dt = NU*NU2ND + #naive class getting infected, and treated - SD*SD2ND - # lose immunity - (ND/Tau) - # drug loose effectiveness - ND*ND2SD -#naive class getting enough # of infections to move to S - ND*NDInfDie -#naive class die from infections - (ND*att) #normal death rate - #print(dND.dt) - - dSU.dt = NU*NU2SU +#naive class getting enough # of infections to move to S - (AU*AU2SU) + #AU moves back to SU due to immunity loss - (SD/Tau)- # drug loose effectiveness - SU*SU2SD- #symptomatic class getting infected, show symptoms, and treated - SU*SU2AU -#symptomatic class getting enough # of infections to move to AU - SU*SU2NU - # lose immunity - (SU*att) #normal death rate - - dSD.dt = ND*ND2SD+ #naive class getting enough # of infections to move to S - (AD*AD2SD) + #AD moves back to SD due to immunity loss - SU*SU2SD- #symptomatic class getting infected, show symptoms, and treated - (SD/Tau) - # drug loose effectiveness - SD*SD2AD- #symptomatic class getting enough # of infections to move to AD - SD*SD2ND - # lose immunity - (SD*att) #normal death rate - - dAU.dt = SU*SU2AU+ #symptomatic class getting enough # of infections to move to AS - (AD/Tau)- # drug loose effectiveness - AU*AU2AD- #asymptomatic class getting infected, show symptoms, and treated - (AU*AU2SU) - #AU moves back to SU due to immunity loss - (AU*att) #normal death rate - - dAD.dt = SD*SD2AD + #symptomatic class getting enough # of infections to move to AS - AU*AU2AD- #asymptomatic class getting infected, show symptoms, and treated - (AD/Tau)- # drug loose effectiveness - (AD*AD2SD) - #AD moves back to SD due to immunity loss - (AD*att) #normal death rate - - #sprintf("%.0f, %.0f,%.0f,%.0f,%.0f,%.0f",dNU.dt,dND.dt,dSU.dt,dSD.dt,dAU.dt,dAD.dt) - - # track the mean number of times infected per immunity class------ - dP_acc_N.dt = NU*NU2SU/rho1 + ND*ND2SD/rho1- # total number of infections received - (NU*(NUInfDie))*fracN- #when naive U class die how many infections deducted - (ND*(NDInfDie))*fracN- #when naive D class die many infections deducted - (NU*NU2SU+ND*ND2SD)*fracN- #when naive class leave to S - (att+ImmLost)*P_acc_N+ - (SU*SU2NU+SD*SD2ND)*fracS #immune loss back to N - - dP_acc_S.dt = (NU*NU2SU+ND*ND2SD)*fracN+ #when naive class leave to S - SU*SU2AU/rho2 + - SD*SD2AD/rho2 + #total number of new infections - (AU*AU2SU+AD*AD2SD)*fracA- #immune loss from A - (att+ImmLost)*P_acc_S- # normal death+immune loss - (SU*SU2AU+SD*SD2AD)*fracS- #Symptomatic move to Asymptomatic - (SU*SU2NU+SD*SD2ND)*fracS #immune loss back to N - - dP_acc_A.dt = (SU*SU2AU+SD*SD2AD)*fracS+ #Symptomatic move to Asymptomatic - AU*(Bu*(1-rAU/capacity)*(1-infA)+rAU*muWU) + - AD*(Bd*(1-rAD/capacity)*(1-infA)+rAD*muRD)- #total number of new infections - (att+ImmLost)*P_acc_A- # normal death - (AU*AU2SU+AD*AD2SD)*fracA #immune loss from A - - a <- 365/(2*pi) - db.dt = bavgnull * seasonality / a *(1- dryWidth *cos(phase+t/a))*sin(phase+t/a-dryWidth*sin(phase+t/a)) - - return(list(c(dPW_NU.dt,dPW_ND.dt,dPW_SU.dt,dPW_SD.dt,dPW_AU.dt,dPW_AD.dt, - dPR_NU.dt,dPR_ND.dt,dPR_SU.dt,dPR_SD.dt,dPR_AU.dt,dPR_AD.dt, - dNU.dt,dND.dt,dSU.dt,dSD.dt,dAU.dt,dAD.dt, - dP_acc_N.dt, dP_acc_S.dt, dP_acc_A.dt, db.dt))) - }) -} - -SEAI_wildOnly<-function(t,y,p){ - - with(as.list(c(y,p)),{ - # total host population size - N = NU+ND+SU+SD+AU+AD - # total parasite population size - #PW = PW_NU+PW_ND+PW_SU+PW_SD+PW_AU+PW_AD - #PR = PR_NU+PR_ND+PR_SU+PR_SD+PR_AU+PR_AD - #P = PW+PR - # parasite/host ratio - rNU <- (PW_NU+PR_NU)/(NU+1e-6) - rND <- (PW_ND+PR_ND)/(ND+1e-6) - rSU <- (PW_SU+PR_SU)/(SU+1e-6) - rSD <- (PW_SD+PR_SD)/(SD+1e-6) - rAU <- (PW_AU+PR_AU)/(AU+1e-6) - rAD <- (PW_AD+PR_AD)/(AD+1e-6) - - # prevalence - I_NU = 1-exp(-rNU) - I_ND = 1-exp(-rND) - I_SU = 1-exp(-rSU) - I_SD = 1-exp(-rSD) - I_AU = 1-exp(-rAU) - I_AD = 1-exp(-rAD) - - # proportion of hosts that have no parasites from W or - p0_NU <- c(exp(-rNU*PW_NU/(PW_NU+PR_NU+1e-6)), exp(-rNU*PR_NU/(PW_NU+PR_NU+1e-6))) - p0_ND <- c(exp(-rND*PW_ND/(PW_ND+PR_ND+1e-6)), exp(-rND*PR_ND/(PW_ND+PR_ND+1e-6))) - p0_SU <- c(exp(-rSU*PW_SU/(PW_SU+PR_SU+1e-6)), exp(-rSU*PR_SU/(PW_SU+PR_SU+1e-6))) - p0_SD <- c(exp(-rSD*PW_SD/(PW_SD+PR_SD+1e-6)), exp(-rSD*PR_SD/(PW_SD+PR_SD+1e-6))) - p0_AU <- c(exp(-rAU*PW_AU/(PW_AU+PR_AU+1e-6)), exp(-rAU*PR_AU/(PW_AU+PR_AU+1e-6))) - p0_AD <- c(exp(-rAD*PW_AD/(PW_AD+PR_AD+1e-6)), exp(-rAD*PR_AD/(PW_AD+PR_AD+1e-6))) - - # contributions of wild strain clones, wild strain in mixed, resistant clone and resistant mix in a bite - ctr_NU <- c((1-p0_NU[1])*p0_NU[2], (1-p0_NU[1])*(1-p0_NU[2])*PW_NU/(PW_NU+PR_NU+1e-6), (1-p0_NU[2])*p0_NU[1], (1-p0_NU[1])*(1-p0_NU[2])*PR_NU/(PW_NU+PR_NU+1e-6)) - ctr_ND <- c((1-p0_ND[1])*p0_ND[2], (1-p0_ND[1])*(1-p0_ND[2])*PW_ND/(PW_ND+PR_ND+1e-6), (1-p0_ND[2])*p0_ND[1], (1-p0_ND[1])*(1-p0_ND[2])*PR_ND/(PW_ND+PR_ND+1e-6)) - ctr_SU <- c((1-p0_SU[1])*p0_SU[2], (1-p0_SU[1])*(1-p0_SU[2])*PW_SU/(PW_SU+PR_SU+1e-6), (1-p0_SU[2])*p0_SU[1], (1-p0_SU[1])*(1-p0_SU[2])*PR_SU/(PW_SU+PR_SU+1e-6)) - ctr_SD <- c((1-p0_SD[1])*p0_SD[2], (1-p0_SD[1])*(1-p0_SD[2])*PW_SD/(PW_SD+PR_SD+1e-6), (1-p0_SD[2])*p0_SD[1], (1-p0_SD[1])*(1-p0_SD[2])*PR_SD/(PW_SD+PR_SD+1e-6)) - ctr_AU <- c((1-p0_AU[1])*p0_AU[2], (1-p0_AU[1])*(1-p0_AU[2])*PW_AU/(PW_AU+PR_AU+1e-6), (1-p0_AU[2])*p0_AU[1], (1-p0_AU[1])*(1-p0_AU[2])*PR_AU/(PW_AU+PR_AU+1e-6)) - ctr_AD <- c((1-p0_AD[1])*p0_AD[2], (1-p0_AD[1])*(1-p0_AD[2])*PW_AD/(PW_AD+PR_AD+1e-6), (1-p0_AD[2])*p0_AD[1], (1-p0_AD[1])*(1-p0_AD[2])*PR_AD/(PW_AD+PR_AD+1e-6)) - - # converted contribution of W or R with mixed infection cos---- - h_NU = c(ctr_NU[1]+ctr_NU[2]+ctr_NU[4]*(mixCost), ctr_NU[3]*(1-cloneCost)+ctr_NU[4]*(1-mixCost)) - h_ND = c(ctr_ND[1]+ctr_ND[2]+ctr_ND[4]*(mixCost), ctr_ND[3]*(1-cloneCost)+ctr_ND[4]*(1-mixCost)) - h_SU = c(ctr_SU[1]+ctr_SU[2]+ctr_SU[4]*(mixCost), ctr_SU[3]*(1-cloneCost)+ctr_SU[4]*(1-mixCost)) - h_SD = c(ctr_SD[1]+ctr_SD[2]+ctr_SD[4]*(mixCost), ctr_SD[3]*(1-cloneCost)+ctr_SD[4]*(1-mixCost)) - h_AU = c(ctr_AU[1]+ctr_AU[2]+ctr_AU[4]*(mixCost), ctr_AU[3]*(1-cloneCost)+ctr_AU[4]*(1-mixCost)) - h_AD = c(ctr_AD[1]+ctr_AD[2]+ctr_AD[4]*(mixCost), ctr_AD[3]*(1-cloneCost)+ctr_AD[4]*(1-mixCost)) - - #transmissibility is reduced to the number of infected hosts, - #receiving hosts needs to have open "resource room" for accepting new strains - B_PW = b*( - h_NU[1]*NU + - h_ND[1]*ND + - h_SU[1]*SU + - h_SD[1]*SD + - h_AU[1]*AU + - h_AD[1]*AD - )/N - - - B_PR = b*( - h_NU[2]*NU+ - h_ND[2]*ND+ - h_SU[2]*SU+ - h_SD[2]*SD+ - h_AU[2]*AU+ - h_AD[2]*AD - )/N - - - - # per capita biting rate for hosts who are not treated - Bu = (B_PW+B_PR) - # per capita biting rate for hosts who are drug treated - Bd = B_PR - #print(B) - - # pop size +1 is to prevent N = 0 for undefined scenario - fracN = P_acc_N/(NU+ND+1e-6) - fracS = P_acc_S/(SU+SD+1e-6) - fracA = P_acc_A/(AU+AD+1e-6) - - # probability that the infected strain has not been seen by the adaptive immune system - infN = (1-1/nstrains)^fracN - infS = (1-1/nstrains)^fracS - infA = (1-1/nstrains)^fracA - - - #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*(1-infN))+rNU*muWU*rho1 - - #naive U class die from infections - NUInfDie = rNU*muWU*muNU - - #naive D class getting enough # of infections to move to SD - ND2SD = (Bd*(1-rND/capacity)*rho1*(1-infN)) + rND*rho1*muRD - - #naive D class die from infections - NDInfDie = rND*muRD*muND - - #SU class getting infected, show symptoms, and treated - SU2SD = (Bu*(1-rSU/capacity)*infS*d2) - - #SU class getting enough # of infections to move to AU - SU2AU = Bu*(1-rSU/capacity)*rho2*(1-infS) + rSU*rho2*muWU - - #SD class getting enough # of new infections to move to AD - SD2AD = (Bd*(1-rSD/capacity)*rho2*(1-infS)) + rSD*rho2*muRD - - #AU class getting infected, show symptoms, and treated - AU2AD = (Bu*(1-rAU/capacity)*infA*omega*d3) - - #lose immunity----- - #SU back to NU due to loss of immune memory - hsu = (Bu*(1-rSU/capacity)) + SU2SD+SU2AU+att - SU2NU = hsu*exp(-hsu/ImmLost)/(1-exp(-hsu/ImmLost)) - - #SD back to ND due to loss of immune memory - hsd = (Bd*(1-rSD/capacity)) +1/Tau+att - SD2ND = hsd*exp(-hsd/ImmLost)/(1-exp(-hsd/ImmLost)) - - #AU back to SU due to loss of immune memory - hau = (Bu*(1-rAU/capacity)) + AU2AD + att - AU2SU = hau*exp(-hau/ImmLost)/(1-exp(-hau/ImmLost)) - - #AD back to SD due to loss of immune memory - had = (Bd*(1-rAD/capacity)) + 1/Tau + att - AD2SD = had*exp(-had/ImmLost)/(1-exp(-had/ImmLost)) - - # Parasite pop ODE------ - ## sensitive------- - dPW_NU.dt = B_PW*NU*infN*(1-rNU/capacity) + #new infections - PW_SU*SU2NU + # SU lose immunity back to NU - (PW_ND/Tau)- # drug loose effectiveness - (PW_NU*NU2ND) - #naive class getting infected, and treated - (PW_NU*NU2SU) - #naive class getting enough # of infections to move to S - (PW_NU*NUInfDie)- #naive class die from infections - (PW_NU*att)- #normal death rate - (PW_NU*muWU)#clearance of infection - - - #print(dNU.dt) - - dPW_ND.dt = 0 + # no new infections - PW_SD*SD2ND + # SD lose immunity back to ND - (PW_NU*NU2ND) - #naive class getting infected, and treated - (PW_ND/Tau) - # drug loose effectiveness - (PW_ND*ND2SD) -#naive class getting enough # of infections to move to S - (PW_ND*NDInfDie) -#naive class die from infections - (PW_ND*att)- #normal death rate - (PW_ND*muWD)#clearance from drug - - #print(dND.dt) - - dPW_SU.dt = B_PW*SU*infS*(1-rSU/capacity) + #new infections - (PW_NU*NU2SU) +#naive class getting enough # of infections to move to S - (PW_AU*AU2SU) + #AU moves back to SU due to immunity loss - (PW_SD/Tau)- # drug loose effectiveness - (PW_SU*SU2SD)- #symptomatic class getting infected, show symptoms, and treated - (PW_SU*SU2AU) -#symptomatic class getting enough # of infections to move to AU - (PW_SU*SU2NU) - # lose immunity back to NU - (PW_SU*att)- #normal death rate - (PW_SU*muWU)#clearance of infection - - dPW_SD.dt = 0 + # no new infections - (PW_ND*ND2SD)+ #naive class getting enough # of infections to move to S - (PW_AD*AD2SD) + #AD moves back to SU due to immunity loss - (PW_SU*SU2SD)- #symptomatic class getting infected, show symptoms, and treated - (PW_SD/Tau) - # drug loose effectiveness - (PW_SD*SD2AD)- #symptomatic class getting enough # of infections to move to AD - (PW_SD*SD2ND) - # lose immunity back to ND - (PW_SD*att)- #normal death rate - (PW_SD*muWD)#clearance from drug - - dPW_AU.dt = B_PW*AU*infA*(1-rAU/capacity) + #new infections - (PW_SU*SU2AU)+ #symptomatic class getting enough # of infections to move to AU - (PW_AD/Tau)- # drug loose effectiveness - (PW_AU*AU2AD)- #asymptomatic class getting infected, show symptoms, and treated - (PW_AU*att)- #normal death rate - (PW_AU*AU2SU) - #AU moves back to SU due to immunity loss - (PW_AU*muWU)#clearance from infection - - dPW_AD.dt = 0 + # no new infections - (PW_SD*SD2AD) + #symptomatic class getting enough # of infections to move to AD - (PW_AU*AU2AD)- #asymptomatic class getting infected, show symptoms, and treated - (PW_AD/Tau)- # drug loose effectiveness - (PW_AD*att)- #normal death rate - (PW_AD*AD2SD) - #AD moves back to SU due to immunity loss - (PW_AD*muWD)#clearance from drug - - ## resistant------- - dPR_NU.dt = 0 - - #print(dNU.dt) - - dPR_ND.dt = 0 - - #print(dND.dt) - - dPR_SU.dt = 0 - - dPR_SD.dt = 0 - - dPR_AU.dt = 0 - - dPR_AD.dt = 0 - - # Generalized immunity ODE------ - dNU.dt = birth + - SU*SU2NU + # lose immunity - (ND/Tau)- # drug loose effectiveness - NU*NU2ND - #naive class getting infected, and treated - NU*NU2SU - #naive class getting enough # of infections to move to S - NU*NUInfDie- #naive class die from infections - (NU*att)#normal death rate - - - #print(dNU.dt) - - dND.dt = NU*NU2ND + #naive class getting infected, and treated - SD*SD2ND - # lose immunity - (ND/Tau) - # drug loose effectiveness - ND*ND2SD -#naive class getting enough # of infections to move to S - ND*NDInfDie -#naive class die from infections - (ND*att) #normal death rate - #print(dND.dt) - - dSU.dt = NU*NU2SU +#naive class getting enough # of infections to move to S - (AU*AU2SU) + #AU moves back to SU due to immunity loss - (SD/Tau)- # drug loose effectiveness - SU*SU2SD- #symptomatic class getting infected, show symptoms, and treated - SU*SU2AU -#symptomatic class getting enough # of infections to move to AU - SU*SU2NU - # lose immunity - (SU*att) #normal death rate - - dSD.dt = ND*ND2SD+ #naive class getting enough # of infections to move to S - (AD*AD2SD) + #AD moves back to SD due to immunity loss - SU*SU2SD- #symptomatic class getting infected, show symptoms, and treated - (SD/Tau) - # drug loose effectiveness - SD*SD2AD- #symptomatic class getting enough # of infections to move to AD - SD*SD2ND - # lose immunity - (SD*att) #normal death rate - - dAU.dt = SU*SU2AU+ #symptomatic class getting enough # of infections to move to AS - (AD/Tau)- # drug loose effectiveness - AU*AU2AD- #asymptomatic class getting infected, show symptoms, and treated - (AU*AU2SU) - #AU moves back to SU due to immunity loss - (AU*att) #normal death rate - - dAD.dt = SD*SD2AD + #symptomatic class getting enough # of infections to move to AS - AU*AU2AD- #asymptomatic class getting infected, show symptoms, and treated - (AD/Tau)- # drug loose effectiveness - (AD*AD2SD) - #AD moves back to SD due to immunity loss - (AD*att) #normal death rate - - #sprintf("%.0f, %.0f,%.0f,%.0f,%.0f,%.0f",dNU.dt,dND.dt,dSU.dt,dSD.dt,dAU.dt,dAD.dt) - - # track the mean number of times infected per immunity class------ - dP_acc_N.dt = NU*NU2SU/rho1 + ND*ND2SD/rho1- # total number of infections received - (NU*(NUInfDie))*fracN- #when naive U class die how many infections deducted - (ND*(NDInfDie))*fracN- #when naive D class die many infections deducted - (NU*NU2SU+ND*ND2SD)*fracN- #when naive class leave to S - (att+ImmLost)*P_acc_N+ - (SU*SU2NU+SD*SD2ND)*fracS #immune loss back to N - - dP_acc_S.dt = (NU*NU2SU+ND*ND2SD)*fracN+ #when naive class leave to S - SU*SU2AU/rho2 + - SD*SD2AD/rho2 + #total number of new infections - (AU*AU2SU+AD*AD2SD)*fracA- #immune loss from A - (att+ImmLost)*P_acc_S- # normal death+immune loss - (SU*SU2AU+SD*SD2AD)*fracS- #Symptomatic move to Asymptomatic - (SU*SU2NU+SD*SD2ND)*fracS #immune loss back to N - - dP_acc_A.dt = (SU*SU2AU+SD*SD2AD)*fracS+ #Symptomatic move to Asymptomatic - AU*(Bu*(1-rAU/capacity)*(1-infA)+rAU*muWU) + - AD*(Bd*(1-rAD/capacity)*(1-infA)+rAD*muRD)- #total number of new infections - (att+ImmLost)*P_acc_A- # normal death - (AU*AU2SU+AD*AD2SD)*fracA #immune loss from A - - a <- 365/(2*pi) - db.dt = bavgnull * seasonality / a *(1- dryWidth *cos(phase+t/a))*sin(phase+t/a-dryWidth*sin(phase+t/a)) - - return(list(c(dPW_NU.dt,dPW_ND.dt,dPW_SU.dt,dPW_SD.dt,dPW_AU.dt,dPW_AD.dt, - dPR_NU.dt,dPR_ND.dt,dPR_SU.dt,dPR_SD.dt,dPR_AU.dt,dPR_AD.dt, - dNU.dt,dND.dt,dSU.dt,dSD.dt,dAU.dt,dAD.dt, - dP_acc_N.dt, dP_acc_S.dt, dP_acc_A.dt, db.dt))) - }) -} - -allPara<-read.csv(paramFile,sep=",",header=T) - -currentPara<-allPara[allPara$No==No,] - -# Step 1 get no drug treating intensity, wildOnly----- - -currentPara$d1<-0 -currentPara$d2<-0 -currentPara$d3<-0 - -t2 = seq(from=0,to=30*365,by=1) -N0 = c(PW_NU=100,PW_ND=0,PW_SU=0,PW_SD=0,PW_AU=0,PW_AD=0, - PR_NU=0,PR_ND=0,PR_SU=0,PR_SD=0,PR_AU=0,PR_AD=0, - NU=10000,ND=0,SU=0,SD=0,AU=0,AD=0, - P_acc_N=0,P_acc_S=0,P_acc_A=0, - b=currentPara$bavgnull*(1-currentPara$seasonality)) -print(N0) -out2 = ode(y=N0,times=t2,func=SEAI_wildOnly,parms=currentPara) - -out2<-as_tibble(out2) -sumOut2<-out2%>%mutate(year = floor(time/365),PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, - PR = PR_NU+PR_SU+PR_AU+PR_ND+PR_SD+PR_AD,P=PW+PR, N = NU+ND+SU+SD+AU+AD)%>% - group_by(year)%>%summarise(meanP=mean(P),meanN=mean(N)) -print(tail(sumOut2)) - -print(abs(sumOut2[20,"meanP"]-sumOut2[30,"meanP"])/(sumOut2[30,"meanP"]+0.0001)) -print(abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)) - -while((abs(sumOut2[20,"meanP"]-sumOut2[30,"meanP"])/(sumOut2[30,"meanP"]+0.0001)>0.001 )| - (abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)>0.001)){ - print(out2[30*365,2:23]) - t2<-t2+30*365 - N0 = as.numeric(out2[30*365+1,2:23]) - names(N0)<-colnames(out2[,2:23]) - out2 = ode(y=N0,times=t2,func=SEAI_wildOnly,parms=currentPara) - out2<-as_tibble(out2) - sumOut2<-out2%>%mutate(year = floor(time/365),PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, - PR = PR_NU+PR_SU+PR_AU+PR_ND+PR_SD+PR_AD,P=PW+PR, N = NU+ND+SU+SD+AU+AD)%>% - group_by(year)%>%summarise(meanP=mean(P),meanN=mean(N)) -} -out2<-as.data.frame(out2) -out2<-out2%>%mutate(m_N = P_acc_N/(NU+ND),m_S =P_acc_S/(SU+SD), m_A = P_acc_A/(AU+AD), - PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, - PR = PR_NU+PR_SU+PR_AU+PR_ND+PR_SD+PR_AD, - P=PW+PR,N = NU+ND+SU+SD+AU+AD, prev = 1-exp(-P/N)) - -##you can check the output through this graph -#out2.melt<-reshape2::melt(out2%>%filter(time%%10==0,time>1000), id.vars=1) -#ggplot(out2.melt, aes(time,value ))+geom_line()+ylim(0,NA)+ -# facet_wrap(.~variable,scales="free_y") -outData<-as.data.frame(cbind(jobid=jobid,wildOnly=1,currentPara,tail(out2,1))) -if(No!=1){ - write.table(outData, - file = outFile, row.names=F, col.names=F,sep=",", - quote=F,append=T) -}else{ - write.csv(outData, - file = outFile, row.names=F, - quote=F) - -} - -storeOut<-tail(out2,1)[,2:23] -# Step 2 treat occasionally, wildOnly----- - -currentPara$d1<-0.5 -currentPara$d2<-0.5 -currentPara$d3<-0.5 - -t2 = seq(from=0,to=30*365,by=1) -N0 = c(PW_NU=100,PW_ND=0,PW_SU=0,PW_SD=0,PW_AU=0,PW_AD=0, - PR_NU=0,PR_ND=0,PR_SU=0,PR_SD=0,PR_AU=0,PR_AD=0, - NU=10000,ND=0,SU=0,SD=0,AU=0,AD=0, - P_acc_N=0,P_acc_S=0,P_acc_A=0, - b=currentPara$bavgnull*(1-currentPara$seasonality)) -print(N0) -out2 = ode(y=N0,times=t2,func=SEAI_wildOnly,parms=currentPara) - -out2<-as_tibble(out2) -sumOut2<-out2%>%mutate(year = floor(time/365),PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, - PR = PR_NU+PR_SU+PR_AU+PR_ND+PR_SD+PR_AD,P=PW+PR, N = NU+ND+SU+SD+AU+AD)%>% - group_by(year)%>%summarise(meanP=mean(P),meanN=mean(N)) -print(tail(sumOut2)) - -print(abs(sumOut2[20,"meanP"]-sumOut2[30,"meanP"])/(sumOut2[30,"meanP"]+0.0001)) -print(abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)) - -while((abs(sumOut2[20,"meanP"]-sumOut2[30,"meanP"])/(sumOut2[30,"meanP"]+0.0001)>0.001 )| - (abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)>0.001)){ - print(out2[30*365,2:23]) - t2<-t2+30*365 - N0 = as.numeric(out2[30*365+1,2:23]) - names(N0)<-colnames(out2[,2:23]) - out2 = ode(y=N0,times=t2,func=SEAI_wildOnly,parms=currentPara) - out2<-as_tibble(out2) - sumOut2<-out2%>%mutate(year = floor(time/365),PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, - PR = PR_NU+PR_SU+PR_AU+PR_ND+PR_SD+PR_AD,P=PW+PR, N = NU+ND+SU+SD+AU+AD)%>% - group_by(year)%>%summarise(meanP=mean(P),meanN=mean(N)) -} -out2<-as.data.frame(out2) -out2<-out2%>%mutate(m_N = P_acc_N/(NU+ND),m_S =P_acc_S/(SU+SD), m_A = P_acc_A/(AU+AD), - PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, - PR = PR_NU+PR_SU+PR_AU+PR_ND+PR_SD+PR_AD, - P=PW+PR,N = NU+ND+SU+SD+AU+AD, prev = 1-exp(-P/N)) - -##you can check the output through this graph -#out2.melt<-reshape2::melt(out2%>%filter(time%%10==0,time>10), id.vars=1) -#ggplot(out2.melt, aes(time,value ))+geom_line()+ylim(0,NA)+ -# facet_wrap(.~variable,scales="free_y") -outData<-as.data.frame(cbind(jobid=jobid,wildOnly=1,currentPara,tail(out2,1))) -#if(file.exists(outFile)){ -write.table(outData, - file = outFile, row.names=F, col.names=F,sep=",", - quote=F,append=T) -#}else{ -# write.csv(outData, -# file = outFile, row.names=F, -# quote=F) -# -#} - -storeOut<-rbind(storeOut,tail(out2,1)[,2:23]) -# Step 3 full treatment, wildOnly----- - -currentPara$d1<-1 -currentPara$d2<-1 -currentPara$d3<-1 - -t2 = seq(from=0,to=30*365,by=1) -N0 = c(PW_NU=100,PW_ND=0,PW_SU=0,PW_SD=0,PW_AU=0,PW_AD=0, - PR_NU=0,PR_ND=0,PR_SU=0,PR_SD=0,PR_AU=0,PR_AD=0, - NU=10000,ND=0,SU=0,SD=0,AU=0,AD=0, - P_acc_N=0,P_acc_S=0,P_acc_A=0, - b=currentPara$bavgnull*(1-currentPara$seasonality)) -print(N0) -out2 = ode(y=N0,times=t2,func=SEAI_wildOnly,parms=currentPara) - -out2<-as_tibble(out2) -sumOut2<-out2%>%mutate(year = floor(time/365),PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, - PR = PR_NU+PR_SU+PR_AU+PR_ND+PR_SD+PR_AD,P=PW+PR, N = NU+ND+SU+SD+AU+AD)%>% - group_by(year)%>%summarise(meanP=mean(P),meanN=mean(N)) -print(tail(sumOut2)) - -print(abs(sumOut2[20,"meanP"]-sumOut2[30,"meanP"])/(sumOut2[30,"meanP"]+0.0001)) -print(abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)) - -while((abs(sumOut2[20,"meanP"]-sumOut2[30,"meanP"])/(sumOut2[30,"meanP"]+0.0001)>0.001 )| - (abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)>0.001)){ - print(out2[30*365,2:23]) - t2<-t2+30*365 - N0 = as.numeric(out2[30*365+1,2:23]) - names(N0)<-colnames(out2[,2:23]) - out2 = ode(y=N0,times=t2,func=SEAI_wildOnly,parms=currentPara) - out2<-as_tibble(out2) - sumOut2<-out2%>%mutate(year = floor(time/365),PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, - PR = PR_NU+PR_SU+PR_AU+PR_ND+PR_SD+PR_AD,P=PW+PR, N = NU+ND+SU+SD+AU+AD)%>% - group_by(year)%>%summarise(meanP=mean(P),meanN=mean(N)) -} -out2<-as.data.frame(out2) -out2<-out2%>%mutate(m_N = P_acc_N/(NU+ND),m_S =P_acc_S/(SU+SD), m_A = P_acc_A/(AU+AD), - PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, - PR = PR_NU+PR_SU+PR_AU+PR_ND+PR_SD+PR_AD, - P=PW+PR,N = NU+ND+SU+SD+AU+AD, prev = 1-exp(-P/N)) - -##you can check the output through this graph -#out2.melt<-reshape2::melt(out2%>%filter(time%%10==0,time>10), id.vars=1) -#ggplot(out2.melt, aes(time,value ))+geom_line()+ylim(0,NA)+ -# facet_wrap(.~variable,scales="free_y") -outData<-as.data.frame(cbind(jobid=jobid,wildOnly=1,currentPara,tail(out2,1))) -#if(file.exists(outFile)){ -write.table(outData, - file = outFile, row.names=F, col.names=F,sep=",", - quote=F,append=T) -#}else{ -# write.csv(outData, -# file = outFile, row.names=F, -# quote=F) -# -#} - -storeOut<-rbind(storeOut,tail(out2,1)[,2:23]) - -# Step 4 resistant strains only, no treatment ------ -currentPara$d1<-0 -currentPara$d2<-0 -currentPara$d3<-0 - -t2 = seq(from=0,to=30*365,by=1) -N0 = c(PW_NU=0,PW_ND=0,PW_SU=0,PW_SD=0,PW_AU=0,PW_AD=0, - PR_NU=100,PR_ND=0,PR_SU=0,PR_SD=0,PR_AU=0,PR_AD=0, - NU=10000,ND=0,SU=0,SD=0,AU=0,AD=0, - P_acc_N=0,P_acc_S=0,P_acc_A=0, - b=currentPara$bavgnull*(1-currentPara$seasonality)) -print(N0) -out2 = ode(y=N0,times=t2,func=SEAI_resOnly,parms=currentPara) - -out2<-as_tibble(out2) -sumOut2<-out2%>%mutate(year = floor(time/365),PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, - PR = PR_NU+PR_SU+PR_AU+PR_ND+PR_SD+PR_AD,P=PW+PR, N = NU+ND+SU+SD+AU+AD)%>% - group_by(year)%>%summarise(meanP=mean(P),meanN=mean(N)) -print(tail(sumOut2)) - -print(abs(sumOut2[20,"meanP"]-sumOut2[30,"meanP"])/(sumOut2[30,"meanP"]+0.0001)) -print(abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)) - -while((abs(sumOut2[20,"meanP"]-sumOut2[30,"meanP"])/(sumOut2[30,"meanP"]+0.0001)>0.001 )| - (abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)>0.001)){ - print(out2[30*365,2:23]) - t2<-t2+30*365 - N0 = as.numeric(out2[30*365+1,2:23]) - names(N0)<-colnames(out2[,2:23]) - out2 = ode(y=N0,times=t2,func=SEAI_resOnly,parms=currentPara) - out2<-as_tibble(out2) - sumOut2<-out2%>%mutate(year = floor(time/365),PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, - PR = PR_NU+PR_SU+PR_AU+PR_ND+PR_SD+PR_AD,P=PW+PR, N = NU+ND+SU+SD+AU+AD)%>% - group_by(year)%>%summarise(meanP=mean(P),meanN=mean(N)) -} -out2<-as.data.frame(out2) -out2<-out2%>%mutate(m_N = P_acc_N/(NU+ND),m_S =P_acc_S/(SU+SD), m_A = P_acc_A/(AU+AD), - PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, - PR = PR_NU+PR_SU+PR_AU+PR_ND+PR_SD+PR_AD, - P=PW+PR,N = NU+ND+SU+SD+AU+AD, prev = 1-exp(-P/N)) - -##you can check the output through this graph -#out2.melt<-reshape2::melt(out2%>%filter(time%%10==0,time>10), id.vars=1) -#ggplot(out2.melt, aes(time,value ))+geom_line()+ylim(0,NA)+ -# facet_wrap(.~variable,scales="free_y") -outData<-as.data.frame(cbind(jobid=jobid,wildOnly=0,currentPara,tail(out2,1))) -#if(file.exists(outFile)){ -write.table(outData, - file = outFile, row.names=F, col.names=F,sep=",", - quote=F,append=T) -#}else{ -# write.csv(outData, -# file = outFile, row.names=F, -# quote=F) -# -#} - -# Step 5 treat occasionally, wildOnly + resistant----- - -currentPara$d1<-0.5 -currentPara$d2<-0.5 -currentPara$d3<-0.5 - -t2 = seq(from=0,to=50*365,by=1) -N0 = unlist(storeOut[2,]) - -N0["PR_NU"]<-min(10,as.numeric(currentPara["capacity"]*N0["NU"]-N0["PW_NU"])) -N0["PR_ND"]<-min(10,as.numeric(currentPara["capacity"]*N0["ND"]-N0["PW_ND"])) -N0["PR_SU"]<-min(10,as.numeric(currentPara["capacity"]*N0["SU"]-N0["PW_SU"])) -N0["PR_SD"]<-min(10,as.numeric(currentPara["capacity"]*N0["SD"]-N0["PW_SD"])) -N0["PR_AU"]<-min(10,as.numeric(currentPara["capacity"]*N0["AU"]-N0["PW_AU"])) -N0["PR_AD"]<-min(10,as.numeric(currentPara["capacity"]*N0["AD"]-N0["PW_AD"])) -print(N0) -out2 = ode(y=N0,times=t2,func=SEAI_p,parms=currentPara) - -out2<-as.data.frame(out2) -out2<-out2%>%mutate(m_N = P_acc_N/(NU+ND),m_S =P_acc_S/(SU+SD), m_A = P_acc_A/(AU+AD), - PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, - PR = PR_NU+PR_SU+PR_AU+PR_ND+PR_SD+PR_AD, - P=PW+PR,N = NU+ND+SU+SD+AU+AD, prev = 1-exp(-P/N)) - -##you can check the output through this graph -#out2.melt<-reshape2::melt(out2%>%filter(time%%10==0,time>1000), id.vars=1) -#ggplot(out2.melt, aes(time,value ))+geom_line()+ylim(0,NA)+ -# facet_wrap(.~variable,scales="free_y") -outData<-as.data.frame(cbind(jobid=jobid,wildOnly=0,currentPara,tail(out2,1))) -#if(file.exists(outFile)){ -write.table(outData, - file = outFile, row.names=F, col.names=F,sep=",", - quote=F,append=T) -#}else{ -# write.csv(outData, -# file = outFile, row.names=F, -# quote=F) -# -#} - -# Step 6 treat fully, wildOnly + resistant----- - -currentPara$d1<-1 -currentPara$d2<-1 -currentPara$d3<-1 - -t2 = seq(from=0,to=50*365,by=1) -N0 = unlist(storeOut[3,]) -N0["PR_NU"]<-min(10,as.numeric(currentPara["capacity"]*N0["NU"]-N0["PW_NU"])) -N0["PR_ND"]<-min(10,as.numeric(currentPara["capacity"]*N0["ND"]-N0["PW_ND"])) -N0["PR_SU"]<-min(10,as.numeric(currentPara["capacity"]*N0["SU"]-N0["PW_SU"])) -N0["PR_SD"]<-min(10,as.numeric(currentPara["capacity"]*N0["SD"]-N0["PW_SD"])) -N0["PR_AU"]<-min(10,as.numeric(currentPara["capacity"]*N0["AU"]-N0["PW_AU"])) -N0["PR_AD"]<-min(10,as.numeric(currentPara["capacity"]*N0["AD"]-N0["PW_AD"])) -print(N0) -out2 = ode(y=N0,times=t2,func=SEAI_p,parms=currentPara) -out2<-as.data.frame(out2) -out2<-out2%>%mutate(m_N = P_acc_N/(NU+ND),m_S =P_acc_S/(SU+SD), m_A = P_acc_A/(AU+AD), - PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, - PR = PR_NU+PR_SU+PR_AU+PR_ND+PR_SD+PR_AD, - P=PW+PR,N = NU+ND+SU+SD+AU+AD, prev = 1-exp(-P/N)) - -##you can check the output through this graph -#out2.melt<-reshape2::melt(out2%>%filter(time%%10==0,time>10), id.vars=1) -#ggplot(out2.melt, aes(time,value ))+geom_line()+ylim(0,NA)+ -# facet_wrap(.~variable,scales="free_y") -outData<-as.data.frame(cbind(jobid=jobid,wildOnly=0,currentPara,tail(out2,1))) -#if(file.exists(outFile)){ -write.table(outData, - file = outFile, row.names=F, col.names=F,sep=",", - quote=F,append=T) -#}else{ -# write.csv(outData, -# file = outFile, row.names=F, -# quote=F) -# -#} -#out2.melt<-reshape2::melt(out2%>%filter(time%%10==0,time>10), id.vars=1) -#ggplot(out2.melt, aes(time,value ))+geom_line()+ylim(0,NA)+ -# facet_wrap(.~variable,scales="free_y") - diff --git a/ODESImmunity_v13.R b/ODESImmunity_v13.R old mode 100755 new mode 100644 index 23a0ed4..bcdd8b6 --- a/ODESImmunity_v13.R +++ b/ODESImmunity_v13.R @@ -1,7 +1,8 @@ require(deSolve) library(tidyverse) -paramFile<-"v11_param.csv" -No<-267 +paramFile<-"v13_param.csv" +No<-3354 +No<-1506 jobid<-1 #resultsFolder<-"~/Dropbox/research/current/resistance/MalariaResistance-old/batchRuns" resultsFolder<-"./" @@ -153,7 +154,8 @@ SEAI_p<-function(t,y,p){ SD2ADnew = rSD*rho2*muRD SD2AD = SD2ADrepeat + SD2ADnew #AU class getting infected, show symptoms, and treated - AU2AD = rAU*omega*d3 + AU2AD = rAU*omega/nstrains*d3 + P_AU2AD = omega/nstrains*d3 #lose immunity----- #SU back to NU due to loss of immune memory @@ -227,7 +229,7 @@ SEAI_p<-function(t,y,p){ (PW_SU*SU2AUrepeat) +#symptomatic class getting enough # of infections to move to AU (PW_SU*rho2*muWU*(1+rSU_PW)) + #symptomatic class getting enough # of infections to move (PW_AD/Tau)- # drug loose effectiveness - (PW_AU*omega*d3*(1+rAU_PW))- #asymptomatic class getting infected, show symptoms, and treated + (PW_AU*P_AU2AD*(1+rAU_PW))- #asymptomatic class getting infected, show symptoms, and treated (PW_AU*att)- #normal death rate (PW_AU*AU2SU) - #AU moves back to SU due to immunity loss (PW_AU*muWU)#clearance from infection @@ -235,7 +237,7 @@ SEAI_p<-function(t,y,p){ dPW_AD.dt = 0 + # no new infections (PW_SD*SD2ADrepeat)+ #symptomatic class getting enough # of infections to move to AD (PW_SD*rho2*muRD*(1+rSD_PW))+ #symptomatic class getting enough # of infections to move - (PW_AU*omega*d3*(1+rAU_PW))- #asymptomatic class getting infected, show symptoms, and treated + (PW_AU*P_AU2AD*(1+rAU_PW))- #asymptomatic class getting infected, show symptoms, and treated (PW_AD/Tau)- # drug loose effectiveness (PW_AD*att)- #normal death rate (PW_AD*AD2SD) - #AD moves back to SU due to immunity loss @@ -294,7 +296,7 @@ SEAI_p<-function(t,y,p){ (PR_SU*SU2AUrepeat) +#symptomatic class getting enough # of infections to move to AU (PR_SU*rho2*muWU*(1+rSU_PR)) +#symptomatic class getting enough # of infections to move (PR_AD/Tau)- # drug loose effectiveness - (PR_AU*omega*d3*(1+rAU_PR))- #asymptomatic class getting infected, show symptoms, and treated + (PR_AU*P_AU2AD*(1+rAU_PR))- #asymptomatic class getting infected, show symptoms, and treated (PR_AU*att)- #normal death rate (PR_AU*AU2SU) - #AU moves back to SU due to immunity loss (PR_AU*muRU)#clearance from infection @@ -302,7 +304,7 @@ SEAI_p<-function(t,y,p){ dPR_AD.dt = B_PR*AD*infA*(1-rAD/capacity) + #new infections (PR_SD*SD2ADrepeat)+ #symptomatic class getting enough # of infections to move to AD (PR_SD*rho2*muRD*(1+rSD_PR))+ #symptomatic class getting enough # of infections to move - (PR_AU*omega*d3*(1+rAU_PR))- #asymptomatic class getting infected, show symptoms, and treated + (PR_AU*P_AU2AD*(1+rAU_PR))- #asymptomatic class getting infected, show symptoms, and treated (PR_AD/Tau)- # drug loose effectiveness (PR_AD*att)- #normal death rate (PR_AD*AD2SD) - #AD moves back to SD due to immunity loss @@ -525,8 +527,8 @@ SEAI_resOnly<-function(t,y,p){ SD2ADnew = rSD*rho2*muRD SD2AD = SD2ADrepeat + SD2ADnew #AU class getting infected, show symptoms, and treated - AU2AD = rAU*omega*d3 - + AU2AD = rAU*omega/nstrains*d3 + P_AU2AD = omega/nstrains*d3 #lose immunity----- #SU back to NU due to loss of immune memory hsu = (Bu*(1-rSU/capacity)) + att @@ -615,7 +617,7 @@ SEAI_resOnly<-function(t,y,p){ (PR_SU*SU2AUrepeat) +#symptomatic class getting enough # of infections to move to AU (PR_SU*rho2*muWU*(1+rSU_PR)) +#symptomatic class getting enough # of infections to move (PR_AD/Tau)- # drug loose effectiveness - (PR_AU*omega*d3*(1+rAU_PR))- #asymptomatic class getting infected, show symptoms, and treated + (PR_AU*P_AU2AD*(1+rAU_PR))- #asymptomatic class getting infected, show symptoms, and treated (PR_AU*att)- #normal death rate (PR_AU*AU2SU) - #AU moves back to SU due to immunity loss (PR_AU*muRU)#clearance from infection @@ -623,7 +625,7 @@ SEAI_resOnly<-function(t,y,p){ dPR_AD.dt = B_PR*AD*infA*(1-rAD/capacity) + #new infections (PR_SD*SD2ADrepeat)+ #symptomatic class getting enough # of infections to move to AD (PR_SD*rho2*muRD*(1+rSD_PR))+ #symptomatic class getting enough # of infections to move - (PR_AU*omega*d3*(1+rAU_PR))- #asymptomatic class getting infected, show symptoms, and treated + (PR_AU*P_AU2AD*(1+rAU_PR))- #asymptomatic class getting infected, show symptoms, and treated (PR_AD/Tau)- # drug loose effectiveness (PR_AD*att)- #normal death rate (PR_AD*AD2SD) - #AD moves back to SD due to immunity loss @@ -846,8 +848,8 @@ SEAI_wildOnly<-function(t,y,p){ SD2ADnew = rSD*rho2*muRD SD2AD = SD2ADrepeat + SD2ADnew #AU class getting infected, show symptoms, and treated - AU2AD = rAU*omega*d3 - + AU2AD = rAU*omega/nstrains*d3 + P_AU2AD = omega/nstrains*d3 #lose immunity----- #SU back to NU due to loss of immune memory hsu = (Bu*(1-rSU/capacity)) + att @@ -920,7 +922,7 @@ SEAI_wildOnly<-function(t,y,p){ (PW_SU*SU2AUrepeat) +#symptomatic class getting enough # of infections to move to AU (PW_SU*rho2*muWU*(1+rSU_PW)) + #symptomatic class getting enough # of infections to move (PW_AD/Tau)- # drug loose effectiveness - (PW_AU*omega*d3*(1+rAU_PW))- #asymptomatic class getting infected, show symptoms, and treated + (PW_AU*P_AU2AD*(1+rAU_PW))- #asymptomatic class getting infected, show symptoms, and treated (PW_AU*att)- #normal death rate (PW_AU*AU2SU) - #AU moves back to SU due to immunity loss (PW_AU*muWU)#clearance from infection @@ -928,7 +930,7 @@ SEAI_wildOnly<-function(t,y,p){ dPW_AD.dt = 0 + # no new infections (PW_SD*SD2ADrepeat)+ #symptomatic class getting enough # of infections to move to AD (PW_SD*rho2*muRD*(1+rSD_PW))+ #symptomatic class getting enough # of infections to move - (PW_AU*omega*d3*(1+rAU_PW))- #asymptomatic class getting infected, show symptoms, and treated + (PW_AU*P_AU2AD*(1+rAU_PW))- #asymptomatic class getting infected, show symptoms, and treated (PW_AD/Tau)- # drug loose effectiveness (PW_AD*att)- #normal death rate (PW_AD*AD2SD) - #AD moves back to SU due to immunity loss @@ -1038,7 +1040,7 @@ allPara<-read.csv(paramFile,sep=",",header=T) currentPara<-allPara[allPara$No==No,] # Step 1 get no drug treating intensity, wildOnly----- - +print("step1") currentPara$d1<-0 currentPara$d2<-0 currentPara$d3<-0 @@ -1097,6 +1099,7 @@ if(No!=1){ storeOut<-tail(out2,1)[,2:23] # Step 2 treat occasionally, wildOnly----- +print("step2") currentPara$d1<-0.2 currentPara$d2<-0.2 @@ -1117,16 +1120,16 @@ print(abs(sumOut2[20,"meanP"]-sumOut2[30,"meanP"])/(sumOut2[30,"meanP"]+0.0001)) print(abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)) -#while((abs(sumOut2[20,"meanP"]-sumOut2[30,"meanP"])/(sumOut2[30,"meanP"]+0.0001#)>0.001 )| -# (abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001#)>0.001)){ +#while((abs(sumOut2[20,"meanP"]-sumOut2[30,"meanP"])/(sumOut2[30,"meanP"]+0.0001)>0.001 )| +# (abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)>0.001)){ # print(out2[30*365,2:23]) # t2<-t2+30*365 # N0 = as.numeric(out2[30*365+1,2:23]) # names(N0)<-colnames(out2[,2:23]) # out2 = ode(y=N0,times=t2,func=SEAI_wildOnly,parms=currentPara) # out2<-as_tibble(out2) -# sumOut2<-out2%>%mutate(year = floor(time/365),PW = PW_NU+PW_SU+PW_AU+PW_ND#+PW_SD+PW_AD, -# PR = PR_NU+PR_SU+PR_AU+PR_ND+PR_SD+PR_AD,P=PW+PR, N = #NU+ND+SU+SD+AU+AD)%>% +# sumOut2<-out2%>%mutate(year = floor(time/365),PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, +# PR = PR_NU+PR_SU+PR_AU+PR_ND+PR_SD+PR_AD,P=PW+PR, N = NU+ND+SU+SD+AU+AD)%>% # group_by(year)%>%summarise(meanP=mean(P),meanN=mean(N)) #} out2<-as.data.frame(out2) @@ -1153,7 +1156,7 @@ write.table(outData, storeOut<-rbind(storeOut,tail(out2,1)[,2:23]) # Step 3 full treatment, wildOnly----- - +print("step3") currentPara$d1<-0.05 currentPara$d2<-0.05 currentPara$d3<-0.05 @@ -1172,16 +1175,16 @@ print(tail(sumOut2)) print(abs(sumOut2[20,"meanP"]-sumOut2[30,"meanP"])/(sumOut2[30,"meanP"]+0.0001)) print(abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)) -#while((abs(sumOut2[20,"meanP"]-sumOut2[30,"meanP"])/(sumOut2[30,"meanP"]+0.0001#)>0.001 )| -# (abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001#)>0.001)){ +#while((abs(sumOut2[20,"meanP"]-sumOut2[30,"meanP"])/(sumOut2[30,"meanP"]+0.0001)>0.001 )| +# (abs(sumOut2[20,"meanN"]-sumOut2[30,"meanN"])/(sumOut2[30,"meanN"]+0.0001)>0.001)){ # print(out2[30*365,2:23]) # t2<-t2+30*365 # N0 = as.numeric(out2[30*365+1,2:23]) # names(N0)<-colnames(out2[,2:23]) # out2 = ode(y=N0,times=t2,func=SEAI_wildOnly,parms=currentPara) # out2<-as_tibble(out2) -# sumOut2<-out2%>%mutate(year = floor(time/365),PW = PW_NU+PW_SU+PW_AU+PW_ND#+PW_SD+PW_AD, -# PR = PR_NU+PR_SU+PR_AU+PR_ND+PR_SD+PR_AD,P=PW+PR, N = #NU+ND+SU+SD+AU+AD)%>% +# sumOut2<-out2%>%mutate(year = floor(time/365),PW = PW_NU+PW_SU+PW_AU+PW_ND+PW_SD+PW_AD, +# PR = PR_NU+PR_SU+PR_AU+PR_ND+PR_SD+PR_AD,P=PW+PR, N = NU+ND+SU+SD+AU+AD)%>% # group_by(year)%>%summarise(meanP=mean(P),meanN=mean(N)) #} out2<-as.data.frame(out2) @@ -1209,6 +1212,7 @@ write.table(outData, storeOut<-rbind(storeOut,tail(out2,1)[,2:23]) # Step 4 resistant strains only, no treatment ------ +print("step4") currentPara$d1<-0 currentPara$d2<-0 currentPara$d3<-0 @@ -1250,9 +1254,9 @@ out2<-out2%>%mutate(m_N = P_acc_N/(NU+ND),m_S =P_acc_S/(SU+SD), m_A = P_acc_A/(A P=PW+PR,N = NU+ND+SU+SD+AU+AD, prev = 1-exp(-P/N)) ##you can check the output through this graph -#out2.melt<-reshape2::melt(out2%>%filter(time%%10==0,time>10), id.vars=1) -#ggplot(out2.melt, aes(time,value ))+geom_line()+ylim(0,NA)+ -# facet_wrap(.~variable,scales="free_y") +out2.melt<-reshape2::melt(out2%>%filter(time%%10==0,time>10), id.vars=1) +ggplot(out2.melt, aes(time,value ))+geom_line()+ylim(0,NA)+ + facet_wrap(.~variable,scales="free_y") outData<-as.data.frame(cbind(jobid=jobid,wildOnly=0,currentPara,tail(out2,1))) #if(file.exists(outFile)){ write.table(outData, @@ -1266,7 +1270,7 @@ write.table(outData, #} # Step 5 treat occasionally, wildOnly + resistant----- - +print("step5") currentPara$d1<-0.2 currentPara$d2<-0.2 currentPara$d3<-0.2 @@ -1280,6 +1284,7 @@ N0["PR_SU"]<-min(10,as.numeric(currentPara["capacity"]*N0["SU"]-N0["PW_SU"])) N0["PR_SD"]<-min(10,as.numeric(currentPara["capacity"]*N0["SD"]-N0["PW_SD"])) N0["PR_AU"]<-min(10,as.numeric(currentPara["capacity"]*N0["AU"]-N0["PW_AU"])) N0["PR_AD"]<-min(10,as.numeric(currentPara["capacity"]*N0["AD"]-N0["PW_AD"])) + print(N0) out2 = ode(y=N0,times=t2,func=SEAI_p,parms=currentPara) @@ -1290,9 +1295,9 @@ out2<-out2%>%mutate(m_N = P_acc_N/(NU+ND),m_S =P_acc_S/(SU+SD), m_A = P_acc_A/(A P=PW+PR,N = NU+ND+SU+SD+AU+AD, prev = 1-exp(-P/N)) ##you can check the output through this graph -#out2.melt<-reshape2::melt(out2%>%filter(time%%10==0,time>1000), id.vars=1) -#ggplot(out2.melt, aes(time,value ))+geom_line()+ylim(0,NA)+ -# facet_wrap(.~variable,scales="free_y") +out2.melt<-reshape2::melt(out2%>%filter(time%%10==0,time>1000), id.vars=1) +ggplot(out2.melt, aes(time,value ))+geom_line()+ylim(0,NA)+ + facet_wrap(.~variable,scales="free_y") outData<-as.data.frame(cbind(jobid=jobid,wildOnly=0,currentPara,tail(out2,1))) #if(file.exists(outFile)){ write.table(outData, @@ -1306,7 +1311,7 @@ write.table(outData, #} # Step 6 treat fully, wildOnly + resistant----- - +print("step6") currentPara$d1<-0.05 currentPara$d2<-0.05 currentPara$d3<-0.05 @@ -1320,6 +1325,7 @@ N0["PR_SD"]<-min(10,as.numeric(currentPara["capacity"]*N0["SD"]-N0["PW_SD"])) N0["PR_AU"]<-min(10,as.numeric(currentPara["capacity"]*N0["AU"]-N0["PW_AU"])) N0["PR_AD"]<-min(10,as.numeric(currentPara["capacity"]*N0["AD"]-N0["PW_AD"])) print(N0) + out2 = ode(y=N0,times=t2,func=SEAI_p,parms=currentPara) out2<-as.data.frame(out2) out2<-out2%>%mutate(m_N = P_acc_N/(NU+ND),m_S =P_acc_S/(SU+SD), m_A = P_acc_A/(AU+AD), @@ -1328,9 +1334,9 @@ out2<-out2%>%mutate(m_N = P_acc_N/(NU+ND),m_S =P_acc_S/(SU+SD), m_A = P_acc_A/(A P=PW+PR,N = NU+ND+SU+SD+AU+AD, prev = 1-exp(-P/N)) ##you can check the output through this graph -#out2.melt<-reshape2::melt(out2%>%filter(time%%10==0,time>10), id.vars=1) -#ggplot(out2.melt, aes(time,value ))+geom_line()+ylim(0,NA)+ -# facet_wrap(.~variable,scales="free_y") +out2.melt<-reshape2::melt(out2%>%filter(time%%10==0), id.vars=1) +ggplot(out2.melt, aes(time,value ))+geom_line()+ylim(0,NA)+ + facet_wrap(.~variable,scales="free_y") outData<-as.data.frame(cbind(jobid=jobid,wildOnly=0,currentPara,tail(out2,1))) #if(file.exists(outFile)){ write.table(outData, @@ -1346,3 +1352,9 @@ write.table(outData, #ggplot(out2.melt, aes(time,value ))+geom_line()+ylim(0,NA)+ # facet_wrap(.~variable,scales="free_y") +ggplot(out2.melt, aes(time,value ))+geom_line()+ylim(0,NA)+ + facet_wrap(.~variable,scales="free_y") + +write.csv(out2.melt, file=paste("v13_param_",No,"_ResisInvTimeSeries.csv",sep=""),row.names=F,col.names=T, quote=F,append=F) + + diff --git a/policy_change.R b/policy_change.R index 9cbd0cc..7935a9e 100644 --- a/policy_change.R +++ b/policy_change.R @@ -1,18 +1,21 @@ ## this script is designed for generating trajectory of resistance changes after policy changes require(deSolve) library(tidyverse) +paramFile<-"v13_results_filtered.csv" +No<-209 +jobid<-1 +resultsFolder<-"./" args <- commandArgs(trailingOnly = TRUE) print(args) -paramFile<-args[1] -No<-as.integer(args[2]) -resultsFolder <-args[3] -jobid<-as.integer(args[4]) -#paramFile<-"v10_param_combined.csv" -#No<-178 -#resultsFolder<-"./" +if (length(args)>1){ + paramFile<-args[1] + No<-as.integer(args[2]) + resultsFolder <-args[3] + jobid<-as.integer(args[4]) +} outFile<-paste(resultsFolder,"/",strsplit(paramFile,split="[.]")[[1]][1],"_",No,"_policy.csv",sep="") -#v11 +#v13 SEAI_p<-function(t,y,p){ @@ -24,7 +27,18 @@ SEAI_p<-function(t,y,p){ #PW = PW_NU+PW_ND+PW_SU+PW_SD+PW_AU+PW_AD #PR = PR_NU+PR_ND+PR_SU+PR_SD+PR_AU+PR_AD #P = PW+PR - + PW_NU = max(0,PW_NU) + PW_ND = max(0,PW_ND) + PW_SU = max(0,PW_SU) + PW_SD = max(0,PW_SD) + PW_AU = max(0,PW_AU) + PW_AD = max(0,PW_AD) + PR_NU = max(0,PR_NU) + PR_ND = max(0,PR_ND) + PR_SU = max(0,PR_SU) + PR_SD = max(0,PR_SD) + PR_AU = max(0,PR_AU) + PR_AD = max(0,PR_AD) # parasite/host ratio rNU <- (PW_NU+PR_NU)/(NU+1e-6) rND <- (PW_ND+PR_ND)/(ND+1e-6) @@ -32,6 +46,18 @@ SEAI_p<-function(t,y,p){ rSD <- (PW_SD+PR_SD)/(SD+1e-6) rAU <- (PW_AU+PR_AU)/(AU+1e-6) rAD <- (PW_AD+PR_AD)/(AD+1e-6) + rNU_PW <- (PW_NU)/(NU+1e-6) + rND_PW <- (PW_ND)/(ND+1e-6) + rSU_PW <- (PW_SU)/(SU+1e-6) + rSD_PW <- (PW_SD)/(SD+1e-6) + rAU_PW <- (PW_AU)/(AU+1e-6) + rAD_PW <- (PW_AD)/(AD+1e-6) + rNU_PR <- (PR_NU)/(NU+1e-6) + rND_PR <- (PR_ND)/(ND+1e-6) + rSU_PR <- (PR_SU)/(SU+1e-6) + rSD_PR <- (PR_SD)/(SD+1e-6) + rAU_PR <- (PR_AU)/(AU+1e-6) + rAD_PR <- (PR_AD)/(AD+1e-6) # prevalence I_NU = 1-exp(-rNU) @@ -59,12 +85,12 @@ SEAI_p<-function(t,y,p){ # converted contribution of W or R with mixed infection cos---- - h_NU = c(ctr_NU[1]+ctr_NU[2]+ctr_NU[4]*(mixCost), ctr_NU[3]*(1-cloneCost)+ctr_NU[4]*(1-mixCost)) - h_ND = c(ctr_ND[1]+ctr_ND[2]+ctr_ND[4]*(mixCost), ctr_ND[3]*(1-cloneCost)+ctr_ND[4]*(1-mixCost)) - h_SU = c(ctr_SU[1]+ctr_SU[2]+ctr_SU[4]*(mixCost), ctr_SU[3]*(1-cloneCost)+ctr_SU[4]*(1-mixCost)) - h_SD = c(ctr_SD[1]+ctr_SD[2]+ctr_SD[4]*(mixCost), ctr_SD[3]*(1-cloneCost)+ctr_SD[4]*(1-mixCost)) - h_AU = c(ctr_AU[1]+ctr_AU[2]+ctr_AU[4]*(mixCost), ctr_AU[3]*(1-cloneCost)+ctr_AU[4]*(1-mixCost)) - h_AD = c(ctr_AD[1]+ctr_AD[2]+ctr_AD[4]*(mixCost), ctr_AD[3]*(1-cloneCost)+ctr_AD[4]*(1-mixCost)) + h_NU = c(ctr_NU[1]+ctr_NU[2]+ctr_NU[4]*(mixCost)*(varyCost), ctr_NU[3]*(1-cloneCost)+ctr_NU[4]*(1-mixCost)) + h_ND = c(ctr_ND[1]+ctr_ND[2]+ctr_ND[4]*(mixCost)*(varyCost), ctr_ND[3]*(1-cloneCost)+ctr_ND[4]*(1-mixCost)) + h_SU = c(ctr_SU[1]+ctr_SU[2]+ctr_SU[4]*(mixCost)*(varyCost), ctr_SU[3]*(1-cloneCost)+ctr_SU[4]*(1-mixCost)) + h_SD = c(ctr_SD[1]+ctr_SD[2]+ctr_SD[4]*(mixCost)*(varyCost), ctr_SD[3]*(1-cloneCost)+ctr_SD[4]*(1-mixCost)) + h_AU = c(ctr_AU[1]+ctr_AU[2]+ctr_AU[4]*(mixCost)*(varyCost), ctr_AU[3]*(1-cloneCost)+ctr_AU[4]*(1-mixCost)) + h_AD = c(ctr_AD[1]+ctr_AD[2]+ctr_AD[4]*(mixCost)*(varyCost), ctr_AD[3]*(1-cloneCost)+ctr_AD[4]*(1-mixCost)) #transmissibility is reduced to the number of infected hosts, #receiving hosts needs to have open "resource room" for accepting new strains @@ -106,59 +132,69 @@ SEAI_p<-function(t,y,p){ infA = (1-1/nstrains)^fracA #print(infN) + #naive class getting treated because of infection + NU2ND = rNU*(d1) - #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*(1-infN))+rNU*muWU*rho1 + # naive U class getting enough # of infections to move to SU + # because the strain has been seen + NU2SUrepeat = Bu*(1-rNU/capacity)*(1-infN)*rho1 + #naive U class getting enough # of new infections to move to SU + NU2SUnew = rNU*muWU*rho1 + NU2SU = NU2SUrepeat + NU2SUnew #naive U class die from infections NUInfDie = rNU*muWU*muNU #naive D class getting enough # of infections to move to SD - ND2SD = (Bd*(1-rND/capacity)*rho1*(1-infN)) + rND*rho1*muRD - + ND2SDrepeat = (Bd*(1-rND/capacity)*rho1*(1-infN)) + #naive D class getting enough # of infections to move to SD + ND2SDnew = rND*rho1*muRD + ND2SD = ND2SDrepeat + ND2SDnew #naive D class die from infections NDInfDie = rND*muRD*muND #SU class getting infected, show symptoms, and treated - SU2SD = (Bu*(1-rSU/capacity)*infS*d2) + SU2SD = rSU*d2 #SU class getting enough # of infections to move to AU - SU2AU = Bu*(1-rSU/capacity)*rho2*(1-infS) + rSU*rho2*muWU + SU2AUrepeat = Bu*(1-rSU/capacity)*rho2*(1-infS) + SU2AUnew = rSU*rho2*muWU + SU2AU = SU2AUrepeat + SU2AUnew #SD class getting enough # of new infections to move to AD - SD2AD = (Bd*(1-rSD/capacity)*rho2*(1-infS)) + rSD*rho2*muRD - + SD2ADrepeat = (Bd*(1-rSD/capacity)*rho2*(1-infS)) + SD2ADnew = rSD*rho2*muRD + SD2AD = SD2ADrepeat + SD2ADnew #AU class getting infected, show symptoms, and treated - AU2AD = (Bu*(1-rAU/capacity)*infA*omega*d3) + AU2AD = rAU*omega/nstrains*d3 + P_AU2AD = omega/nstrains*d3 #lose immunity----- #SU back to NU due to loss of immune memory - hsu = (Bu*(1-rSU/capacity)) + SU2SD+SU2AU+att + hsu = (Bu*(1-rSU/capacity)) + att SU2NU = hsu*exp(-hsu/ImmLost)/(1-exp(-hsu/ImmLost)) #SD back to ND due to loss of immune memory - hsd = (Bd*(1-rSD/capacity)) +1/Tau+att + hsd = (Bd*(1-rSD/capacity)) +att SD2ND = hsd*exp(-hsd/ImmLost)/(1-exp(-hsd/ImmLost)) #AU back to SU due to loss of immune memory - hau = (Bu*(1-rAU/capacity)) + AU2AD + att + hau = (Bu*(1-rAU/capacity)) + att AU2SU = hau*exp(-hau/ImmLost)/(1-exp(-hau/ImmLost)) #AD back to SD due to loss of immune memory - had = (Bd*(1-rAD/capacity)) + 1/Tau + att + had = (Bd*(1-rAD/capacity)) + att AD2SD = had*exp(-had/ImmLost)/(1-exp(-had/ImmLost)) # Parasite pop ODE------ ## sensitive------- - dPW_NU.dt = B_PW*NU*infN*(1-rNU/capacity) + #new infections + dPW_NU.dt = B_PW*NU*(1-rNU/capacity)*infN + #new infections PW_SU*SU2NU + # SU lose immunity back to NU (PW_ND/Tau)- # drug loose effectiveness - (PW_NU*NU2ND) - #naive class getting infected, and treated - (PW_NU*NU2SU) - #naive class getting enough # of infections to move to S - (PW_NU*NUInfDie)- #naive class die from infections + (PW_NU*d1*(1+rNU_PW)) - #naive class getting infected, and treated + (PW_NU*muWU*rho1*(1+rNU_PW)) - #naive class getting enough # of infections to move to S + (PW_NU*NU2SUrepeat) - #naive class getting enough # of infections to move to S + (PW_NU*muWU*muNU*(1+rNU_PW))- #naive class die from infections (PW_NU*att)- #normal death rate (PW_NU*muWU)#clearance of infection @@ -167,46 +203,53 @@ SEAI_p<-function(t,y,p){ dPW_ND.dt = 0 + # no new infections PW_SD*SD2ND + # SD lose immunity back to ND - (PW_NU*NU2ND) - #naive class getting infected, and treated + (PW_NU*d1*(1+rNU_PW)) - #naive class getting infected, and treated (PW_ND/Tau) - # drug loose effectiveness - (PW_ND*ND2SD) -#naive class getting enough # of infections to move to S - (PW_ND*NDInfDie) -#naive class die from infections + (PW_ND*ND2SDrepeat) -#naive class getting enough # of infections to move to S + (PW_ND*rho1*muRD*(1+rND_PW)) -#naive class getting enough # of infections to move to S + (PW_ND*muRD*muND*(1+rND_PW)) -#naive class die from infections (PW_ND*att)- #normal death rate (PW_ND*muWD)#clearance from drug #print(dND.dt) dPW_SU.dt = B_PW*SU*infS*(1-rSU/capacity) + #new infections - (PW_NU*NU2SU) +#naive class getting enough # of infections to move to S + (PW_NU*muWU*rho1*(1+rNU_PW)) + #naive class getting enough # of infections to move to S + (PW_NU*NU2SUrepeat) + #naive class getting enough # of infections to move to S (PW_AU*AU2SU) + #AU moves back to SU due to immunity loss (PW_SD/Tau)- # drug loose effectiveness - (PW_SU*SU2SD)- #symptomatic class getting infected, show symptoms, and treated - (PW_SU*SU2AU) -#symptomatic class getting enough # of infections to move to AU + (PW_SU*d2*(1+rSU_PW))- #symptomatic class getting infected, show symptoms, and treated + (PW_SU*SU2AUrepeat) -#symptomatic class getting enough # of infections to move to AU + (PW_SU*rho2*muWU*(1+rSU_PW)) -#symptomatic class getting enough # of infections to move to AU (PW_SU*SU2NU) - # lose immunity back to NU (PW_SU*att)- #normal death rate (PW_SU*muWU)#clearance of infection dPW_SD.dt = 0 + # no new infections - (PW_ND*ND2SD)+ #naive class getting enough # of infections to move to S + (PW_ND*ND2SDrepeat) +#naive class getting enough # of infections to move to S + (PW_ND*rho1*muRD*(1+rND_PW)) +#naive class getting enough # of infections to move to S (PW_AD*AD2SD) + #AD moves back to SU due to immunity loss - (PW_SU*SU2SD)- #symptomatic class getting infected, show symptoms, and treated + (PW_SU*d2*(1+rSU_PW))- #symptomatic class getting infected, show symptoms, and treated (PW_SD/Tau) - # drug loose effectiveness - (PW_SD*SD2AD)- #symptomatic class getting enough # of infections to move to AD + (PW_SD*SD2ADrepeat)- #symptomatic class getting enough # of infections to move to AD + (PW_SD*rho2*muRD*(1+rSD_PW))- #symptomatic class getting enough # of infections to move to AD (PW_SD*SD2ND) - # lose immunity back to ND (PW_SD*att)- #normal death rate (PW_SD*muWD)#clearance from drug dPW_AU.dt = B_PW*AU*infA*(1-rAU/capacity) + #new infections - (PW_SU*SU2AU)+ #symptomatic class getting enough # of infections to move to AU + (PW_SU*SU2AUrepeat) +#symptomatic class getting enough # of infections to move to AU + (PW_SU*rho2*muWU*(1+rSU_PW)) + #symptomatic class getting enough # of infections to move (PW_AD/Tau)- # drug loose effectiveness - (PW_AU*AU2AD)- #asymptomatic class getting infected, show symptoms, and treated + (PW_AU*P_AU2AD*(1+rAU_PW))- #asymptomatic class getting infected, show symptoms, and treated (PW_AU*att)- #normal death rate (PW_AU*AU2SU) - #AU moves back to SU due to immunity loss (PW_AU*muWU)#clearance from infection dPW_AD.dt = 0 + # no new infections - (PW_SD*SD2AD) + #symptomatic class getting enough # of infections to move to AD - (PW_AU*AU2AD)- #asymptomatic class getting infected, show symptoms, and treated + (PW_SD*SD2ADrepeat)+ #symptomatic class getting enough # of infections to move to AD + (PW_SD*rho2*muRD*(1+rSD_PW))+ #symptomatic class getting enough # of infections to move + (PW_AU*P_AU2AD*(1+rAU_PW))- #asymptomatic class getting infected, show symptoms, and treated (PW_AD/Tau)- # drug loose effectiveness (PW_AD*att)- #normal death rate (PW_AD*AD2SD) - #AD moves back to SU due to immunity loss @@ -216,9 +259,10 @@ SEAI_p<-function(t,y,p){ dPR_NU.dt = B_PR*NU*infN*(1-rNU/capacity) + #new infections PR_SU*SU2NU + # lose immunity from SU to NU (PR_ND/Tau)- # drug loose effectiveness - (PR_NU*NU2ND) - #naive class getting infected, and treated - (PR_NU*NU2SU) - #naive class getting enough # of infections to move to S - (PR_NU*NUInfDie)- #naive class die from infections + (PR_NU*d1*(1+rNU_PR)) - #naive class getting infected, and treated + (PR_NU*muWU*rho1*(1+rNU_PR)) - #naive class getting enough # of infections to move to S + (PR_NU*NU2SUrepeat) - #naive class getting enough # of infections to move to S + (PR_NU*muWU*muNU*(1+rNU_PR))- #naive class die from infections (PR_NU*att)- #normal death rate (PR_NU*muRU)#clearance of infection @@ -226,46 +270,53 @@ SEAI_p<-function(t,y,p){ dPR_ND.dt = B_PR*ND*infN*(1-rND/capacity) + #new infections PR_SD*SD2ND + # lose immunity from SD to ND - (PR_NU*NU2ND) - #naive class getting infected, and treated + (PR_NU*d1*(1+rNU_PR)) - #naive class getting infected, and treated (PR_ND/Tau) - # drug loose effectiveness - (PR_ND*ND2SD) -#naive class getting enough # of infections to move to S - (PR_ND*NDInfDie) -#naive class die from infections + (PR_ND*ND2SDrepeat) -#naive class getting enough # of infections to move to S + (PR_ND*rho1*muRD*(1+rND_PR)) -#naive class getting enough # of infections to move to S + (PR_ND*muRD*muND*(1+rND_PR)) -#naive class die from infections (PR_ND*att)- #normal death rate (PR_ND*muRD)#clearance from drug #print(dND.dt) dPR_SU.dt = B_PR*SU*infS*(1-rSU/capacity) + #new infections - (PR_NU*NU2SU) +#naive class getting enough # of infections to move to S + (PR_NU*muWU*rho1*(1+rNU_PR)) + #naive class getting enough # of infections to move to S + (PR_NU*NU2SUrepeat) + #naive class getting enough # of infections to move to S (PR_AU*AU2SU) + #AU moves back to SU due to immunity loss (PR_SD/Tau)- # drug loose effectiveness - (PR_SU*SU2SD)- #symptomatic class getting infected, show symptoms, and treated - (PR_SU*SU2AU) -#symptomatic class getting enough # of infections to move to AU + (PR_SU*d2*(1+rSU_PR))- #symptomatic class getting infected, show symptoms, and treated + (PR_SU*SU2AUrepeat) -#symptomatic class getting enough # of infections to move to AU + (PR_SU*rho2*muWU*(1+rSU_PR)) -#symptomatic class getting enough # of infections to move to AU PR_SU*SU2NU - # lose immunity to NU (PR_SU*att)- #normal death rate (PR_SU*muRU)#clearance of infection dPR_SD.dt = B_PR*SD*infS*(1-rSD/capacity) + #new infections - (PR_ND*ND2SD)+ #naive class getting enough # of infections to move to S + (PR_ND*ND2SDrepeat) +#naive class getting enough # of infections to move to S + (PR_ND*rho1*muRD*(1+rND_PR)) +#naive class getting enough # of infections to move to S (PR_AD*AD2SD) + #AD moves back to SD due to immunity loss - (PR_SU*SU2SD)- #symptomatic class getting infected, show symptoms, and treated + (PR_SU*d2*(1+rSU_PR))- #symptomatic class getting infected, show symptoms, and treated (PR_SD/Tau) - # drug loose effectiveness - (PR_SD*SD2AD)- #symptomatic class getting enough # of infections to move to AD + (PR_SD*SD2ADrepeat)- #symptomatic class getting enough # of infections to move to AD + (PR_SD*rho2*muRD*(1+rSD_PR))- #symptomatic class getting enough # of infections to move to AD PR_SD*SD2ND- # lose immunity to ND (PR_SD*att)- #normal death rate (PR_SD*muRD)#clearance from drug dPR_AU.dt = B_PR*AU*infA*(1-rAU/capacity) + #new infections - (PR_SU*SU2AU)+ #symptomatic class getting enough # of infections to move to AU + (PR_SU*SU2AUrepeat) +#symptomatic class getting enough # of infections to move to AU + (PR_SU*rho2*muWU*(1+rSU_PR)) +#symptomatic class getting enough # of infections to move (PR_AD/Tau)- # drug loose effectiveness - (PR_AU*AU2AD)- #asymptomatic class getting infected, show symptoms, and treated + (PR_AU*P_AU2AD*(1+rAU_PR))- #asymptomatic class getting infected, show symptoms, and treated (PR_AU*att)- #normal death rate (PR_AU*AU2SU) - #AU moves back to SU due to immunity loss (PR_AU*muRU)#clearance from infection dPR_AD.dt = B_PR*AD*infA*(1-rAD/capacity) + #new infections - (PR_SD*SD2AD) + #symptomatic class getting enough # of infections to move to AD - (PR_AU*AU2AD)- #asymptomatic class getting infected, show symptoms, and treated + (PR_SD*SD2ADrepeat)+ #symptomatic class getting enough # of infections to move to AD + (PR_SD*rho2*muRD*(1+rSD_PR))+ #symptomatic class getting enough # of infections to move + (PR_AU*P_AU2AD*(1+rAU_PR))- #asymptomatic class getting infected, show symptoms, and treated (PR_AD/Tau)- # drug loose effectiveness (PR_AD*att)- #normal death rate (PR_AD*AD2SD) - #AD moves back to SD due to immunity loss @@ -357,10 +408,11 @@ allPara<-read.csv(paramFile,sep=",",header=T) currentPara<-allPara%>%filter(No==(!!No), wildOnly==0, d1>0) # Step 1 getting ------------ -CQvec = c(0.54,0.54,0.54,0.54,0.5,0.5,0.5,0.5,0.18,0.18,0.18,0.18,0.01,0.01,0.01,0.01) - +d1List <- unique(currentPara$d1) +#CQvec = c(0.54,0.54,0.54,0.54,0.5,0.5,0.5,0.5,0.18,0.18,0.18,0.18,0.01,0.01,0.01,0.01) +CQvec = c(0.52,0.52,0.52,0.52,0.21,0.21,0.21,0.21,0,0,0,0,0,0,0,0) outData<-c() -for (d1 in c(0.5,1)){ +for (d1 in d1List){ cut_inp<-currentPara%>%filter(d1==(!!d1)) N0<-as.numeric(cut_inp[30:51]) N0[1] <- N0[1] + 1 @@ -369,7 +421,7 @@ for (d1 in c(0.5,1)){ for (tend in 1:length(CQvec)){ t2 = seq(from=(tend-1)*365,to=tend*365,by=1) cut_inp$muRD<-cut_inp$muRU*(CQvec[tend])+cut_inp$muWD*(1-CQvec[tend]) - out2 = ode(y=N0,times=t2,func=SEAI_p,parms=cut_inp[2:27]) + out2 = ode(y=N0,times=t2,func=SEAI_p,parms=cut_inp[2:28]) out2<-as.data.frame(out2) outData<-rbind(outData,c(jobid=jobid,cut_inp[1,2:28],tail(out2,1))) N0<-as.numeric(tail(out2,1)[2:23]) diff --git a/v11_1020_results.csv b/v11_1020_results.csv deleted file mode 100755 index 321774e..0000000 --- a/v11_1020_results.csv +++ /dev/null @@ -1,30251 +0,0 @@ -jobid,wildOnly,No,birth,att,muND,muNU,nstrains,rho1,rho2,omega,cloneCost,mixCost,ImmLost,capacity,muWU,muWD,muRD,muRU,Tau,d1,d2,d3,bavgnull,seasonality,dryWidth,phase,modelType,time,PW_NU,PW_ND,PW_SU,PW_SD,PW_AU,PW_AD,PR_NU,PR_ND,PR_SU,PR_SD,PR_AU,PR_AD,NU,ND,SU,SD,AU,AD,P_acc_N,P_acc_S,P_acc_A,b,m_N,m_S,m_A,PW,PR,P,N,prev -20610011,1,1,1,9.13e-05,0.1,0.1,6,0.5,0.05,0.01,0,0.3,0.000273973,10,0.00666666666666667,0.99,0.00666666666666667,0.00666666666666667,20,0,0,0,0.0125892541179417,0.95,1,0,onelocus_0,21900,140.923414957413,0,36.8991084240048,0,0.9475325666828,0,0,0,0,0,0,0,7759.40198181642,0,2013.56474571032,0,52.055438410708,0,2809.98901754144,891.80694077822,25.1533717247889,0.000629556831375965,0.362139894817467,0.442899560432869,0.483203532478842,178.770055948101,0,178.770055948101,9825.02216593745,0.0180308479298869 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