R/malrates.R
In slphyx/MEEM: MEEM
# ************************************************************************************* #
# Function to calculate transition rates, given variables and parameters
# ************************************************************************************* #
MM_Malrates <- function(x, input, parmal, t, ti) {
# tempfile1<-input$tempfile1
# tempfile2<-input$tempfile2
# tmp1<-read.csv(tempfile1)
# tmp2<-read.csv(tempfile2)
# for(n in names(tmp1)){
# txt<-paste0(n,"<-","tmp1$",n)
# eval(parse(text = txt))
# }
# for(n in names(tmp2)){
# txt<-paste0(n,"<-","tmp2$",n)
# eval(parse(text = txt))
# }
N<-input$N
B<-input$B
A<-input$A
V<-input$V
L<-input$L
startyear<-input$startyear
dtout<-input$dtout
tsteps<-input$tsteps
tyears<-input$tyears
pvxy<-input$pvxy
yrprim<-input$yrprim
g6pDd<-input$g6pDd
varind<-matrix(0,nrow=B,ncol=N)
traind<-matrix(0,nrow=A,ncol=N)
for (n in 1:N){
for (b in 1:B){
varind[b,n]<-(n-1)*B+b
}
for (a in 1:A){
traind[a,n]<-(n-1)*A+a
}
}
###########################
falpop<-1:10
vivpop<-11:23
############################
t_internal<-(ti-1)*dtout+t+startyear
#Set up matrices
seas<-c(rep(1,N)) # seasonality
popf<-c(rep(0,N)) # population sizes
popv<-c(rep(0,N)) # population sizes
foif<-c(rep(0,N)) # forces of infection falciparum
foiv<-c(rep(0,N)) # forces of infection vivax
tranrate<-matrix(0,nrow=N,ncol=A) # transition rate matrix
itn<-c(rep(0,N)) #ITN coverage
c_vmw<-c(rep(0,N)) #VMW coverage
veff<-c(rep(0,N)) #VMW effect decline
tau<-c(rep(0,N)) #Treatment probabilty
tauo<-c(rep(0,N)) #Treatment with other
tauh<-c(rep(0,N)) #Treatment with HIS
tauv<-c(rep(0,N)) #Treatment with VMW
eln<-approx(input$eln_t,input$eln_inp,xout=t_internal)$y
for (n in 1:N){
seas[n]<-1+eln*parmal$amp[n]*cos(2*pi*(t_internal-parmal$phi[n])) # seasonal forcing signal
popf[n]<-sum(x[varind[falpop,n]]) # list of the variable indices for the human population
popv[n]<-sum(x[varind[vivpop,n]]) # list of the variable indices for the human population
itn[n]<-approx(input$itn_time,input$c_itn[,n],xout=t_internal)$y
foif[n]<-sum(input$connect[n,]*seas[n]*((((1-itn[n])*parmal$bites)^2*parmal$prob_m*parmal$prob_h*(parmal$Pmaxf[n])/popf[n]*(parmal$zeta_n*x[varind[2,n]]+parmal$zeta_a*x[varind[3,n]]+x[varind[4,n]]+x[varind[5,n]])/sum(input$connect[n,]*popf))/((1-itn[n])*parmal$bites*parmal$prob_h*parmal$Pmaxf[n]/popf[n]+parmal$delta_m)*(parmal$gamma_m/(parmal$gamma_m+parmal$delta_m))))
foiv[n]<-sum(input$connect[n,]*seas[n]*((((1-itn[n])*parmal$bites)^2*parmal$prob_m*parmal$vprob_h*(parmal$Pmaxv[n])/popv[n]*(parmal$vzeta_n*x[varind[12,n]]+parmal$vzeta_a*x[varind[13,n]]+x[varind[14,n]]+x[varind[15,n]])/sum(input$connect[n,]*popv))/((1-itn[n])*parmal$bites*parmal$vprob_h*parmal$Pmaxv[n]/popv[n]+parmal$delta_m)*(parmal$vgamma_m/(parmal$vgamma_m+parmal$delta_m))))
foifa<-(1/(1/(foif[n])+1/parmal$gamma_h+1/parmal$gamma_m))
foiva<-(1/(1/(foiv[n])+1/parmal$vgamma_h+1/parmal$vgamma_m))
c_vmw[n]<-approx(input$vmw_time,input$cov_vmw[,n],xout=t_internal)$y
veff[n]<-approx(input$vmw_time,input$vmw_eff[,n],xout=t_internal)$y
tau[n]<-c_vmw[n]*input$sens_vmw*veff[n]+(1-c_vmw[n]*veff[n])*input$sens_his*parmal$eff_his+(1-c_vmw[n]*veff[n]-(1-c_vmw[n]*veff[n])*parmal$eff_his)*input$sens_oth*parmal$eff_oth #prob of treatment
tauo[n]<-(1-c_vmw[n]*veff[n]-(1-c_vmw[n]*veff[n])*parmal$eff_his)*input$sens_oth*parmal$eff_oth #Prob treated by Other
tauh[n]<-(1-c_vmw[n]*veff[n])*input$sens_his*parmal$eff_his #Prob treated by HIS
tauv[n]<-c_vmw[n]*veff[n]*input$sens_vmw #Prob treated by VMW
t3=0
if (t_internal>yrprim[n]){t3=1} #start radical cure from policy start date
tranrate[n,]<-c( #falciparum
parmal$demog*popf[n]+(1-parmal$tausev)*parmal$pmort*parmal$nuq*x[varind[5,n]]+parmal$tausev*parmal$nuq*parmal$pmortt*x[varind[5,n]], # rate of birth 1
parmal$demog*x[varind[1,n]], # rate of death of S 2
parmal$demog*x[varind[2,n]], # rate of death of In 3
parmal$demog*x[varind[3,n]], # rate of death of Ia 4
parmal$demog*x[varind[4,n]], # rate of death of Ic 5
parmal$demog*x[varind[5,n]], # rate of death of Is 6
parmal$demog*x[varind[6,n]], # rate of death of To 7
parmal$demog*x[varind[7,n]], # rate of death of Tv 8
parmal$demog*x[varind[8,n]], # rate of death of Th 9
parmal$demog*x[varind[9,n]], # rate of death of R 10
parmal$demog*x[varind[10,n]], # rate of death of H 11
parmal$psn*(1-parmal$ps)*foifa*x[varind[1,n]], #incidence S to In 12
(1-parmal$psn)*(1-parmal$ps)*foifa*x[varind[1,n]], # incidence S to Ia 13
(1-tau[n])*parmal$ps*foifa*x[varind[1,n]], # incidence S to Ic 14
tauo[n]*parmal$ps*foifa*x[varind[1,n]], # incidence S to To 15
tauv[n]*parmal$ps*foifa*x[varind[1,n]], # incidence S to Tv 16
tauh[n]*parmal$ps*foifa*x[varind[1,n]], # incidence S to Th 17
(1-parmal$tausev)*(1-parmal$pmort)*parmal$nuq*x[varind[5,n]], #recovery Is to Ic 18
(1-parmal$psev)*parmal$nuc*x[varind[4,n]], # recovery Ic to Ia 19
parmal$nua*x[varind[3,n]], # recovery Ia to In 20
input$nun*x[varind[2,n]], # recovery In to R 21
(1-parmal$ptf)*parmal$nut*x[varind[6,n]], # recovery To to H 22
(1-parmal$ptf)*parmal$nut*x[varind[7,n]], # recovery Tv to H 23
(1-parmal$ptf)*parmal$nut*x[varind[8,n]], # recovery Th to H 24
parmal$tausev*parmal$nuq*(1-parmal$pmortt)*x[varind[5,n]], # recovery Is to H 25
(1-parmal$prn)*(1-parmal$pr)*foifa*x[varind[2,n]], # incidence In to Ia 26
parmal$pr*(1-tau[n])*foifa*x[varind[3,n]], # incidence Ia to Ic 27
parmal$pr*tauo[n]*foifa*x[varind[3,n]], # incidence Ia to To 28
parmal$pr*tauv[n]*foifa*x[varind[3,n]], # incidence Ia to Tv 29
parmal$pr*tauh[n]*foifa*x[varind[3,n]], # incidence Ia to Th 30
parmal$psev*parmal$nuc*x[varind[4,n]], # incidence Ic to Is 31
parmal$pr*(1-tau[n])*foifa*x[varind[2,n]], # incidence In to Ic 32
parmal$pr*tauo[n]*foifa*x[varind[2,n]], # incidence In to To 33
parmal$pr*tauv[n]*foifa*x[varind[2,n]], # incidence In to Tv 34
parmal$pr*tauh[n]*foifa*x[varind[2,n]], # incidence In to Th 35
parmal$prn*(1-parmal$pr)*foifa*x[varind[9,n]], # incidence R to In 36
(1-parmal$prn)*(1-parmal$pr)*foifa*x[varind[9,n]], # incidence R to Ia 37
(1-tau[n])*parmal$pr*foifa*x[varind[9,n]], # incidence R to Ic 38
tauo[n]*parmal$pr*foifa*x[varind[9,n]], # incidence R to To 39
tauv[n]*parmal$pr*foifa*x[varind[9,n]], # incidence R to Tv 40
tauh[n]*parmal$pr*foifa*x[varind[9,n]], # incidence R to Th 41
parmal$omega*x[varind[9,n]], # loss of immunity from R to S 42
parmal$prn*(1-parmal$pr)*foifa*x[varind[10,n]], # incidence H to In 43
(1-parmal$prn)*(1-parmal$pr)*foifa*x[varind[10,n]], # incidence H to Ia 44
(1-tau[n])*parmal$pr*foifa*x[varind[10,n]], # incidence H to Ic 45
tauo[n]*parmal$pr*foifa*x[varind[10,n]], # incidence H to To 46
tauv[n]*parmal$pr*foifa*x[varind[10,n]], # incidence H to Tv 47
tauh[n]*parmal$pr*foifa*x[varind[10,n]], # incidence H to Th 48
parmal$chi*x[varind[10,n]], # loss HRP2 H to R 49
(1-parmal$tausev)*parmal$pmort*parmal$nuq*x[varind[5,n]]+parmal$tausev*parmal$nuq*parmal$pmortt*x[varind[5,n]], # death untreated+treated Is 50
(1-parmal$ptfc)*parmal$ptf*parmal$nut*x[varind[6,n]], # failure To to Ia 51
parmal$ptfc*(1-parmal$ptftr)*parmal$ptf*parmal$nut*x[varind[6,n]], # failure To to Ic 52
parmal$ptfc*parmal$ptftr*parmal$ptf*parmal$nut*x[varind[6,n]], # failure To to Th 53
(1-parmal$ptfc)*parmal$ptf*parmal$nut*x[varind[7,n]], # failure Tv to Ia 54
parmal$ptfc*(1-parmal$ptftr)*parmal$ptf*parmal$nut*x[varind[7,n]], # failure Tv to Ic 55
parmal$ptfc*parmal$ptftr*parmal$ptf*parmal$nut*x[varind[7,n]], # failure Tv to Tv 56
(1-parmal$ptfc)*parmal$ptf*parmal$nut*x[varind[8,n]], # failure Th to Ia 57
parmal$ptfc*(1-parmal$ptftr)*parmal$ptf*parmal$nut*x[varind[8,n]], # failure Th to Ic 58
parmal$ptfc*parmal$ptftr*parmal$ptf*parmal$nut*x[varind[8,n]], # failure Th to Th 59
#vivax
parmal$demog*popv[n]+(1-parmal$vtausev)*parmal$vpmort*parmal$vnuq*x[varind[15,n]]+parmal$vtausev*parmal$vpmortt*parmal$vnuq*x[varind[15,n]], # rate of birth 60
parmal$demog*x[varind[11,n]], # rate of death of S 61
parmal$demog*x[varind[12,n]], # rate of death of In 62
parmal$demog*x[varind[13,n]], # rate of death of Ia 63
parmal$demog*x[varind[14,n]], # rate of death of Ic 64
parmal$demog*x[varind[15,n]], # rate of death of Is 65
parmal$demog*x[varind[16,n]], # rate of death of To 66
parmal$demog*x[varind[17,n]], # rate of death of Tv 67
parmal$demog*x[varind[18,n]], # rate of death of Th 68
parmal$demog*x[varind[19,n]], # rate of death of R 69
parmal$demog*x[varind[20,n]], # rate of death of L 70
parmal$demog*x[varind[21,n]], # rate of death of Togd 71
parmal$demog*x[varind[22,n]], # rate of death of Tvgd 72
parmal$demog*x[varind[23,n]], # rate of death of Thgd 73
parmal$vpsn*((1-parmal$vps)*(1-parmal$propgd[n])+(1-parmal$pgd)*parmal$propgd[n])*foiva*x[varind[11,n]], #incidence S to In 74
(1-parmal$vpsn)*((1-parmal$vps)*(1-parmal$propgd[n])+(1-parmal$pgd)*parmal$propgd[n])*foiva*x[varind[11,n]], # incidence S to Ia 75
(1-tau[n])*(parmal$vps*(1-parmal$propgd[n])+parmal$pgd*parmal$propgd[n])*foiva*x[varind[11,n]], # incidence S to Ic 76
(1-parmal$propgd[n])*parmal$vps*tauo[n]*foiva*x[varind[11,n]], # incidence S to To 77
(1-parmal$propgd[n])*tauv[n]*parmal$vps*foiva*x[varind[11,n]], # incidence S to Tv 78
(1-parmal$propgd[n])*tauh[n]*parmal$vps*foiva*x[varind[11,n]], # incidence S to Th 79
parmal$propgd[n]*parmal$pgd*tauo[n]*foiva*x[varind[11,n]], # incidence S to Togd 80
parmal$propgd[n]*parmal$pgd*tauv[n]*foiva*x[varind[11,n]], # incidence S to Tvgd 81
parmal$propgd[n]*parmal$pgd*tauh[n]*foiva*x[varind[11,n]], # incidence S to Thgd 82
(1-parmal$tausev)*(1-parmal$vpmort)*parmal$vnuq*x[varind[15,n]], # recovery Is to Ic 83
(1-parmal$vpsev)*parmal$vnuc*x[varind[14,n]], # recovery Ic to Ia 84
parmal$vnua*x[varind[13,n]], # recovery Ia to In 85
(1-parmal$vph)*input$vnun*x[varind[12,n]], # recovery In to R 86
parmal$vph*input$vnun*x[varind[12,n]], # recovery In to L 87
(1-t3)*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[16,n]], # recovery To to R 88
(1-t3)*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[17,n]], # recovery Tv to R 89
(1-t3)*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[18,n]], # recovery Th to R 90
(1-t3)*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[21,n]], # recovery Togd to R 91
(1-t3)*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[22,n]], # recovery Tvgd to R 92
(1-t3)*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[23,n]], # recovery Thgd to R 93
(1-parmal$vph)*parmal$vtausev*(1-parmal$vpmortt)*parmal$vnuq*x[varind[15,n]], # recovery Is to R 94
(1-t3)*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[16,n]], # recovery To to L 95
(1-t3)*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[17,n]], # recovery Tv to L 96
(1-t3)*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[18,n]], # recovery Th to L 97
(1-t3)*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[21,n]], # recovery Togd to L 98
(1-t3)*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[22,n]], # recovery Tvgd to L 99
(1-t3)*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[23,n]], # recovery Thgd to L 100
parmal$vph*parmal$vtausev*(1-parmal$vpmortt)*parmal$vnuq*x[varind[15,n]], # recovery Is to L 101
(1-parmal$vprn)*(1-parmal$vpr)*foiva*x[varind[12,n]], # incidence In to Ia 102
parmal$vpr*(1-tau[n])*foiva*x[varind[12,n]], # incidence In to Ic 103
(1-parmal$propgd[n])*parmal$vpr*tauo[n]*foiva*x[varind[12,n]], # incidence In to To 104
(1-parmal$propgd[n])*parmal$vpr*tauv[n]*foiva*x[varind[12,n]], # incidence In to Tv 105
(1-parmal$propgd[n])*parmal$vpr*tauh[n]*foiva*x[varind[12,n]], # incidence In to Th 106
parmal$propgd[n]*parmal$vpr*tauo[n]*foiva*x[varind[12,n]], # incidence In to Togd 107
parmal$propgd[n]*parmal$vpr*tauv[n]*foiva*x[varind[12,n]], # incidence In to Tvgd 108
parmal$propgd[n]*parmal$vpr*tauh[n]*foiva*x[varind[12,n]], # incidence In to Thgd 109
parmal$vpr*(1-tau[n])*foiva*x[varind[13,n]], # incidence Ia to Ic 110
(1-parmal$propgd[n])*parmal$vpr*tauo[n]*foiva*x[varind[13,n]], # incidence Ia to To 111
(1-parmal$propgd[n])*parmal$vpr*tauv[n]*foiva*x[varind[13,n]], # incidence Ia to Tv 112
(1-parmal$propgd[n])*parmal$vpr*tauh[n]*foiva*x[varind[13,n]], # incidence Ia to Th 113
parmal$propgd[n]*parmal$vpr*tauo[n]*foiva*x[varind[13,n]], # incidence Ia to Togd 114
parmal$propgd[n]*parmal$vpr*tauv[n]*foiva*x[varind[13,n]], # incidence Ia to Tvgd 115
parmal$propgd[n]*parmal$vpr*tauh[n]*foiva*x[varind[13,n]], # incidence Ia to Thgd 116
parmal$vpsev*parmal$vnuc*x[varind[14,n]], # incidence Ic to Is 117
parmal$vprn*(1-parmal$vpr)*foiva*x[varind[19,n]], # incidence R to In 118
(1-parmal$vprn)*(1-parmal$vpr)*foiva*x[varind[19,n]], # incidence R to Ia 119
(1-tau[n])*parmal$vpr*foiva*x[varind[19,n]], # incidence R to Ic 120
(1-parmal$propgd[n])*tauo[n]*parmal$vpr*foiva*x[varind[19,n]], # incidence R to To 121
(1-parmal$propgd[n])*tauv[n]*parmal$vpr*foiva*x[varind[19,n]], # incidence R to Tv 122
(1-parmal$propgd[n])*tauh[n]*parmal$vpr*foiva*x[varind[19,n]], # incidence R to Th 123
parmal$propgd[n]*tauo[n]*parmal$vpr*foiva*x[varind[19,n]], # incidence R to Togd 124
parmal$propgd[n]*tauv[n]*parmal$vpr*foiva*x[varind[19,n]], # incidence R to Tvgd 125
parmal$propgd[n]*tauh[n]*parmal$vpr*foiva*x[varind[19,n]], # incidence R to Thgd 126
parmal$vomega*x[varind[19,n]], # loss of immunity from R to S 127
parmal$vprn*(1-parmal$vpr)*(foiva)*x[varind[20,n]], # incidence L to In 128
(1-parmal$vprn)*(1-parmal$vpr)*(foiva)*x[varind[20,n]], # incidence L to Ia 129
(1-tau[n])*parmal$vpr*(foiva)*x[varind[20,n]], # incidence L to Ic 130
(1-parmal$propgd[n])*tauo[n]*parmal$vpr*(foiva)*x[varind[20,n]], # incidence L to To 131
(1-parmal$propgd[n])*tauv[n]*parmal$vpr*(foiva)*x[varind[20,n]], # incidence L to Tv 132
(1-parmal$propgd[n])*tauh[n]*parmal$vpr*(foiva)*x[varind[20,n]], # incidence L to Th 133
parmal$propgd[n]*tauo[n]*parmal$vpr*(foiva)*x[varind[20,n]], # incidence L to Togd 134
parmal$propgd[n]*tauv[n]*parmal$vpr*(foiva)*x[varind[20,n]], # incidence L to Tvgd 135
parmal$propgd[n]*tauh[n]*parmal$vpr*(foiva)*x[varind[20,n]], # incidence L to Thgd 136
parmal$vprn*(1-parmal$vpr)*parmal$vprel*parmal$vrel*x[varind[10,n]], # relapse L to In 137
(1- parmal$t2)*(1-parmal$vprn)*(1-parmal$vpr)*parmal$vprel*parmal$vrel*x[varind[10,n]], # relapse L to Ia 138
(1- parmal$t2)*(1-tau[n])*parmal$vpr*parmal$vprel*parmal$vrel*x[varind[10,n]], # relapse L to Ic 139
(1- parmal$t2)*(1-parmal$propgd[n])*tauo[n]*parmal$vpr*parmal$vprel*parmal$vrel*x[varind[10,n]], # relapse L to To 140
(1- parmal$t2)*(1-parmal$propgd[n])*tauv[n]*parmal$vpr*parmal$vprel*parmal$vrel*x[varind[10,n]], # relapse L to Tv 141
(1- parmal$t2)*(1-parmal$propgd[n])*tauh[n]*parmal$vpr*parmal$vprel*parmal$vrel*x[varind[10,n]], # relapse L to Th 142
(1- parmal$t2)*parmal$propgd[n]*tauo[n]*parmal$vpr*parmal$vprel*parmal$vrel*x[varind[10,n]], # relapse L to Togd 143
(1- parmal$t2)*parmal$propgd[n]*tauv[n]*parmal$vpr*parmal$vprel*parmal$vrel*x[varind[10,n]], # relapse L to Tvgd 144
(1- parmal$t2)*parmal$propgd[n]*tauh[n]*parmal$vpr*parmal$vprel*parmal$vrel*x[varind[10,n]], # relapse L to Thgd 145
parmal$vkappa*x[varind[10,n]], # death of hypnozoites L to S 146
(1-parmal$vtausev)*parmal$vpmort*parmal$vnuq*x[varind[15,n]]+parmal$vtausev*parmal$vpmortt*parmal$vnuq*x[varind[15,n]], # death untreated+treated Is 147
(1-t3)*(1-parmal$vptfc)*parmal$vptf*parmal$vnut*x[varind[16,n]], # failed trt To to Ia 148
(1-t3)*(1-parmal$vptftr)*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[16,n]], # failed trt To to Ic 149
(1-t3)*parmal$vptftr*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[16,n]], # failed trt To to Th 150
(1-t3)*(1-parmal$vptfc)*parmal$vptf*parmal$vnut*x[varind[17,n]], # failed trt Tv to Ia 151
(1-t3)*(1-parmal$vptftr)*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[17,n]], # failed trt Tv to Ic 152
(1-t3)*parmal$vptftr*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[17,n]], # failed trt Tv to Tv 153
(1-t3)*(1-parmal$vptfc)*parmal$vptf*parmal$vnut*x[varind[18,n]], # failed trt Th to Ia 154
(1-t3)*(1-parmal$vptftr)*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[18,n]], # failed trt Th to Ic 155
(1-t3)*parmal$vptftr*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[18,n]], # failed trt Th to Th 156
(1-t3)*(1-parmal$vptfc)*parmal$vptf*parmal$vnut*x[varind[21,n]], # failed trt Togd to Ia 157
(1-t3)*(1-parmal$vptftr)*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[21,n]], # failed trt Togd to Ic 158
(1-t3)*parmal$vptftr*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[21,n]], # failed trt Togd to Thgd 159
(1-t3)*(1-parmal$vptfc)*parmal$vptf*parmal$vnut*x[varind[22,n]], # failed trt Tvgd to Ia 160
(1-t3)*(1-parmal$vptftr)*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[22,n]], # failed trt Tvgd to Ic 161
(1-t3)*parmal$vptftr*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[22,n]], # failed trt Tvgd to Tvgd 162
(1-t3)*(1-parmal$vptfc)*parmal$vptf*parmal$vnut*x[varind[23,n]], # failed trt Thgd to Ia 163
(1-t3)*(1-parmal$vptftr)*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[23,n]], # failed trt Thgd to Ic 164
(1-t3)*parmal$vptftr*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[23,n]], # failed trt Thgd to Thgd 165
#Entanglements (dual treat)
parmal$t1*(1-parmal$ptf)*parmal$nut*x[varind[2,n]]*(x[varind[16,n]]+x[varind[17,n]]+x[varind[18,n]]+x[varind[21,n]]+x[varind[22,n]]+x[varind[23,n]])/popv[n], # dual trt Fal In to H 166
parmal$t1*(1-parmal$ptf)*parmal$nut*x[varind[3,n]]*(x[varind[16,n]]+x[varind[17,n]]+x[varind[18,n]]+x[varind[21,n]]+x[varind[22,n]]+x[varind[23,n]])/popv[n], # dual trt Fal Ia to H 167
parmal$t1*(1-parmal$ptf)*parmal$nut*x[varind[4,n]]*(x[varind[16,n]]+x[varind[17,n]]+x[varind[18,n]]+x[varind[21,n]]+x[varind[22,n]]+x[varind[23,n]])/popv[n], # dual trt Fal Ic to H 168
parmal$t1*(1-parmal$ptf)*parmal$nut*x[varind[5,n]]*(x[varind[16,n]]+x[varind[17,n]]+x[varind[18,n]]+x[varind[21,n]]+x[varind[22,n]]+x[varind[23,n]])/popv[n], # dual trt Fal Is to H 169
parmal$t1*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[12,n]]*(x[varind[6,n]]+x[varind[7,n]]+x[varind[8,n]])/popf[n], # dual trt Viv In to R 170
parmal$t1*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[13,n]]*(x[varind[6,n]]+x[varind[7,n]]+x[varind[8,n]])/popf[n], # dual trt Viv Ia to R 171
parmal$t1*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[14,n]]*(x[varind[6,n]]+x[varind[7,n]]+x[varind[8,n]])/popf[n], # dual trt Viv Ic to R 172
parmal$t1*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[15,n]]*(x[varind[6,n]]+x[varind[7,n]]+x[varind[8,n]])/popf[n], # dual trt Viv Is to R 173
parmal$t1*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[12,n]]*(x[varind[6,n]]+x[varind[7,n]]+x[varind[8,n]])/popf[n], # dual trt Viv In to L 174
parmal$t1*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[13,n]]*(x[varind[6,n]]+x[varind[7,n]]+x[varind[8,n]])/popf[n], # dual trt Viv Ia to L 175
parmal$t1*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[14,n]]*(x[varind[6,n]]+x[varind[7,n]]+x[varind[8,n]])/popf[n], # dual trt Viv Ic to L 176
parmal$t1*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[15,n]]*(x[varind[6,n]]+x[varind[7,n]]+x[varind[8,n]])/popf[n], # dual trt Viv Is to L 177
t3*(1-parmal$mask)*(1-parmal$vphprim)*(1-parmal$vptfp)*parmal$vnup*x[varind[16,n]], # primaquine recovery To to R 178
t3*(1-parmal$mask)*(1-parmal$vphprim)*(1-parmal$vptfp)*parmal$vnup*x[varind[17,n]], #primaquine recovery Tv to R 179
t3*(1-parmal$mask)*(1-parmal$vphprim)*(1-parmal$vptfp)*parmal$vnup*x[varind[18,n]], #primaquine recovery Th to R 180
t3*(1-parmal$mask)*parmal$vphprim*(1-parmal$vptfp)*parmal$vnup*x[varind[16,n]], # primaquine recovery To to L 181
t3*(1-parmal$mask)*parmal$vphprim*(1-parmal$vptfp)*parmal$vnup*x[varind[17,n]], #primaquine recovery Tv to L 182
t3*(1-parmal$mask)*parmal$vphprim*(1-parmal$vptfp)*parmal$vnup*x[varind[18,n]], #primaquine recovery Th to L 183
t3*(1-parmal$mask)*(parmal$sensgd*parmal$vnut*(1-parmal$vph)*(1-parmal$vptf))*x[varind[21,n]], # test + act recovery Togd to R 184
t3*(1-parmal$mask)*(parmal$sensgd*parmal$vnut*(1-parmal$vph)*(1-parmal$vptf))*x[varind[22,n]], #test + act recovery Tvgd to R 185
t3*(1-parmal$mask)*(parmal$sensgd*parmal$vnut*(1-parmal$vph)*(1-parmal$vptf))*x[varind[23,n]], #test + act recovery Thgd to R 186
t3*(1-parmal$mask)*(parmal$sensgd*parmal$vnut*parmal$vph*(1-parmal$vptf))*x[varind[21,n]], # test + act recovery of GDef Togd to L 187
t3*(1-parmal$mask)*(parmal$sensgd*parmal$vnut*parmal$vph*(1-parmal$vptf))*x[varind[22,n]], #test + act recovery of GDef Tvgd to L 188
t3*(1-parmal$mask)*(parmal$sensgd*parmal$vnut*parmal$vph*(1-parmal$vptf))*x[varind[23,n]], #test + act recovery of GDef Thgd to L 189
t3*(1-parmal$mask)*((1-parmal$sensgd)*(1-parmal$vptfp)*(1-parmal$vphprim)*parmal$vnup)*x[varind[21,n]], # test - primaquine recovery Togd to R 190
t3*(1-parmal$mask)*((1-parmal$sensgd)*(1-parmal$vptfp)*(1-parmal$vphprim)*parmal$vnup)*x[varind[22,n]], # test - primaquine recovery Tvgd to R 191
t3*(1-parmal$mask)*((1-parmal$sensgd)*(1-parmal$vptfp)*(1-parmal$vphprim)*parmal$vnup)*x[varind[23,n]], #test - primaquine recovery Thgd to R 192
t3*(1-parmal$mask)*((1-parmal$sensgd)*parmal$vphprim*(1-parmal$vptfp)*parmal$vnup)*x[varind[21,n]], # test - primaquine recovery of GDef Togd to L 193
t3*(1-parmal$mask)*((1-parmal$sensgd)*parmal$vphprim*(1-parmal$vptfp)*parmal$vnup)*x[varind[22,n]], #test - primaquine recovery of GDef Tvgd to L 194
t3*(1-parmal$mask)*((1-parmal$sensgd)*parmal$vphprim*(1-parmal$vptfp)*parmal$vnup)*x[varind[23,n]], #test - primaquine recovery of GDef Thgd to L 195
t3*parmal$mask*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[16,n]], # masked act recovery To to R 196
t3*parmal$mask*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[17,n]], #masked act recovery Tv to R 197
t3*parmal$mask*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[18,n]], #masked act recovery Th to R 198
t3*parmal$mask*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[16,n]], # masked act recovery To to L 199
t3*parmal$mask*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[17,n]], #masked act recovery Tv to L 200
t3*parmal$mask*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[18,n]], #masked act recovery Th to L 201
t3*parmal$mask*parmal$vnut*(1-parmal$vph)*(1-parmal$vptf)*x[varind[21,n]], # masked act recovery Togd to R 202
t3*parmal$mask*parmal$vnut*(1-parmal$vph)*(1-parmal$vptf)*x[varind[22,n]], #masked act recovery Tvgd to R 203
t3*parmal$mask*parmal$vnut*(1-parmal$vph)*(1-parmal$vptf)*x[varind[23,n]], #masked act recovery Thgd to R 204
t3*parmal$mask*parmal$vnut*parmal$vph*(1-parmal$vptf)*x[varind[21,n]], # masked act recovery of GDef Togd to L 205
t3*parmal$mask*parmal$vnut*parmal$vph*(1-parmal$vptf)*x[varind[22,n]], #masked act recovery of GDef Tvgd to L 206
t3*parmal$mask*parmal$vnut*parmal$vph*(1-parmal$vptf)*x[varind[23,n]], #masked act recovery of GDef Thgd to L 207
parmal$t2*parmal$vprn*(1-parmal$vpr)*(parmal$vprel*((popf[n]-x[varind[9,n]]-x[varind[10,n]])/popf[n])+parmal$vincprel*((x[varind[9,n]]+x[varind[10,n]])/popf[n]))*parmal$vrel*x[varind[20,n]], # relapse L to In +triggering 208
parmal$t2*(1-parmal$vprn)*(1-parmal$vpr)*(parmal$vprel*((popf[n]-x[varind[9,n]]-x[varind[10,n]])/popf[n])+parmal$vincprel*((x[varind[9,n]]+x[varind[10,n]])/popf[n]))*parmal$vrel*x[varind[20,n]], # relapse L to Ia +triggering 209
parmal$t2*(1-tau[n])*parmal$vpr*(parmal$vprel*((popf[n]-x[varind[9,n]]-x[varind[10,n]])/popf[n])+parmal$vincprel*((x[varind[9,n]]+x[varind[10,n]])/popf[n]))*parmal$vrel*x[varind[20,n]], # relapse L to Ic+triggering 210
parmal$t2*(1-parmal$propgd[n])*tauo[n]*parmal$vpr*(parmal$vprel*((popf[n]-x[varind[9,n]]-x[varind[10,n]])/popf[n])+parmal$vincprel*((x[varind[9,n]]+x[varind[10,n]])/popf[n]))*parmal$vrel*x[varind[20,n]], # relapse L to To +triggering 211
parmal$t2*(1-parmal$propgd[n])*tauv[n]*parmal$vpr*(parmal$vprel*((popf[n]-x[varind[9,n]]-x[varind[10,n]])/popf[n])+parmal$vincprel*((x[varind[9,n]]+x[varind[10,n]])/popf[n]))*parmal$vrel*x[varind[20,n]], # relapse L to Tv+triggering 212
parmal$t2*(1-parmal$propgd[n])*tauh[n]*parmal$vpr*(parmal$vprel*((popf[n]-x[varind[9,n]]-x[varind[10,n]])/popf[n])+parmal$vincprel*((x[varind[9,n]]+x[varind[10,n]])/popf[n]))*parmal$vrel*x[varind[20,n]], # relapse L to Th +triggering 213
parmal$t2*parmal$propgd[n]*tauo[n]*parmal$vpr*(parmal$vprel*((popf[n]-x[varind[9,n]]-x[varind[10,n]])/popf[n])+parmal$vincprel*((x[varind[9,n]]+x[varind[10,n]])/popf[n]))*parmal$vrel*x[varind[20,n]], # relapse L to Togd +triggering 214
parmal$t2*parmal$propgd[n]*tauv[n]*parmal$vpr*(parmal$vprel*((popf[n]-x[varind[9,n]]-x[varind[10,n]])/popf[n])+parmal$vincprel*((x[varind[9,n]]+x[varind[10,n]])/popf[n]))*parmal$vrel*x[varind[20,n]], # relapse L to Tvgd+triggering 215
parmal$t2*parmal$propgd[n]*tauh[n]*parmal$vpr*(parmal$vprel*((popf[n]-x[varind[9,n]]-x[varind[10,n]])/popf[n])+parmal$vincprel*((x[varind[9,n]]+x[varind[10,n]])/popf[n]))*parmal$vrel*x[varind[20,n]], # relapse L to Thgd +triggering 216
#Failed treatments
t3*(1-parmal$mask)*(1-parmal$vptfc)*parmal$vptfp*parmal$vnup*x[varind[16,n]], # primaquine failed trt To to Ia 217
t3*(1-parmal$mask)*(1-parmal$vptftr)*parmal$vptfc*parmal$vptfp*parmal$vnup*x[varind[16,n]], # primaquine failed trt To to Ic 218
t3*(1-parmal$mask)*parmal$vptftr*parmal$vptfc*parmal$vptfp*parmal$vnup*x[varind[16,n]], # primaquine failed trt To to Th 219
t3*(1-parmal$mask)*(1-parmal$vptfc)*parmal$vptfp*parmal$vnup*x[varind[17,n]], #primaquine failed trt Tv to Ia 220
t3*(1-parmal$mask)*(1-parmal$vptftr)*parmal$vptfc*parmal$vptfp*parmal$vnup*x[varind[17,n]], #primaquine failed trt Tv to Ic 221
t3*(1-parmal$mask)*parmal$vptftr*parmal$vptfc*parmal$vptfp*parmal$vnup*x[varind[17,n]], #primaquine failed trt Tv to Tv 222
t3*(1-parmal$mask)*(1-parmal$vptfc)*parmal$vptfp*parmal$vnup*x[varind[18,n]], #primaquine failed trt Th to Ia 223
t3*(1-parmal$mask)*(1-parmal$vptftr)*parmal$vptfc*parmal$vptfp*parmal$vnup*x[varind[18,n]], #primaquine failed trt Th to Ic 224
t3*(1-parmal$mask)*parmal$vptftr*parmal$vptfc*parmal$vptfp*parmal$vnup*x[varind[18,n]], #primaquine failed trt Th to Th 225
t3*parmal$mask*(1-parmal$vptfc)*parmal$vptf*parmal$vnut*x[varind[16,n]], # masked act failed trt To to Ia 226
t3*parmal$mask*(1-parmal$vptftr)*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[16,n]], # masked act failed trt To to Ic 227
t3*parmal$mask*parmal$vptftr*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[16,n]], # masked act failed trt To to Th 228
t3*parmal$mask*(1-parmal$vptfc)*parmal$vptf*parmal$vnut*x[varind[17,n]], #masked act failed trt Tv to Ia 229
t3*parmal$mask*(1-parmal$vptftr)*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[17,n]], #masked act failed trt Tv to Ic 230
t3*parmal$mask*parmal$vptftr*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[17,n]], #masked act failed trt Tv to Tv 231
t3*parmal$mask*(1-parmal$vptfc)*parmal$vptf*parmal$vnut*x[varind[18,n]], #masked act failed trt Th to Ia 232
t3*parmal$mask*(1-parmal$vptftr)*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[18,n]], #masked act failed trt Th to Ic 233
t3*parmal$mask*parmal$vptftr*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[18,n]], #masked act failed trt Th to Th 234
t3*parmal$mask*(1-parmal$vptfc)*parmal$vnut*parmal$vptf*x[varind[21,n]], # masked act failed trt Togd to Ia 235
t3*parmal$mask*(1-parmal$vptftr)*parmal$vptfc*parmal$vnut*parmal$vptf*x[varind[21,n]], # masked act failed trt Togd to Ic 236
t3*parmal$mask*parmal$vptftr*parmal$vptfc*parmal$vnut*parmal$vptf*x[varind[21,n]], # masked act failed trt Togd to Thgd 237
t3*parmal$mask*(1-parmal$vptfc)*parmal$vnut*parmal$vptf*x[varind[22,n]], #masked act failed trt Tvgd to Ia 238
t3*parmal$mask*(1-parmal$vptftr)*parmal$vptfc*parmal$vnut*parmal$vptf*x[varind[22,n]], #masked act failed trt Tvgd to Ic 239
t3*parmal$mask*parmal$vptftr*parmal$vptfc*parmal$vnut*parmal$vptf*x[varind[22,n]], #masked act failed trt Tvgd to Tvgd 240
t3*parmal$mask*(1-parmal$vptfc)*parmal$vnut*parmal$vptf*x[varind[23,n]], #masked act failed trt Thgd to Ia 241
t3*parmal$mask*(1-parmal$vptftr)*parmal$vptfc*parmal$vnut*parmal$vptf*x[varind[23,n]], #masked act failed trt Thgd to Ic 242
t3*parmal$mask*parmal$vptftr*parmal$vptfc*parmal$vnut*parmal$vptf*x[varind[23,n]], #masked act failed trt Thgd to Thgd 243
t3*(1-parmal$mask)*(1-parmal$vptfc)*parmal$sensgd*parmal$vnut*parmal$vptf*x[varind[21,n]], # test + act failed trt Togd to Ia 244
t3*(1-parmal$mask)*(1-parmal$vptftr)*parmal$vptfc*parmal$sensgd*parmal$vnut*parmal$vptf*x[varind[21,n]], # test + act failed trt Togd to Ic 245
t3*(1-parmal$mask)*parmal$vptftr*parmal$vptfc*parmal$sensgd*parmal$vnut*parmal$vptf*x[varind[21,n]], # test + act failed trt Togd to Thgd 246
t3*(1-parmal$mask)*(1-parmal$vptfc)*parmal$sensgd*parmal$vnut*parmal$vptf*x[varind[22,n]], #test + act failed trt Tvgd to Ia 247
t3*(1-parmal$mask)*(1-parmal$vptftr)*parmal$vptfc*parmal$sensgd*parmal$vnut*parmal$vptf*x[varind[22,n]], #test + act failed trt Tvgd to Ic 248
t3*(1-parmal$mask)*parmal$vptftr*parmal$vptfc*parmal$sensgd*parmal$vnut*parmal$vptf*x[varind[22,n]], #test + act failed trt Tvgd to Tvgd 249
t3*(1-parmal$mask)*(1-parmal$vptfc)*parmal$sensgd*parmal$vnut*parmal$vptf*x[varind[23,n]], #test + act failed trt Thgd to Ia 250
t3*(1-parmal$mask)*(1-parmal$vptftr)*parmal$vptfc*parmal$sensgd*parmal$vnut*parmal$vptf*x[varind[23,n]], #test + act failed trt Thgd to Ic 251
t3*(1-parmal$mask)*parmal$vptftr*parmal$vptfc*parmal$sensgd*parmal$vnut*parmal$vptf*x[varind[23,n]], #test + act failed trt Thgd to Thgd 252
t3*(1-parmal$mask)*(1-parmal$vptfc)*(1-parmal$sensgd)*parmal$vptfp*parmal$vnup*x[varind[21,n]], # test - primaquine failed trt Togd to Ia 253
t3*(1-parmal$mask)*(1-parmal$vptftr)*parmal$vptfc*(1-parmal$sensgd)*parmal$vptfp*parmal$vnup*x[varind[21,n]], # test - primaquine failed trt Togd to Ic 254
t3*(1-parmal$mask)*parmal$vptftr*parmal$vptfc*(1-parmal$sensgd)*parmal$vptfp*parmal$vnup*x[varind[21,n]], # test - primaquine failed trt Togd to Thgd 255
t3*(1-parmal$mask)*(1-parmal$vptfc)*(1-parmal$sensgd)*parmal$vptfp*parmal$vnup*x[varind[22,n]], # test - primaquine failed trt Tvgd to Ia 256
t3*(1-parmal$mask)*(1-parmal$vptftr)*parmal$vptfc*(1-parmal$sensgd)*parmal$vptfp*parmal$vnup*x[varind[22,n]], # test - primaquine failed trt Tvgd to Ic 257
t3*(1-parmal$mask)*parmal$vptftr*parmal$vptfc*(1-parmal$sensgd)*parmal$vptfp*parmal$vnup*x[varind[22,n]], # test - primaquine failed trt Tvgd to Tvgd 258
t3*(1-parmal$mask)*(1-parmal$vptfc)*(1-parmal$sensgd)*parmal$vptfp*parmal$vnup*x[varind[23,n]], #test - primaquine failed trt Thgd to Ia 259
t3*(1-parmal$mask)*(1-parmal$vptftr)*parmal$vptfc*(1-parmal$sensgd)*parmal$vptfp*parmal$vnup*x[varind[23,n]], #test - primaquine failed trt Thgd to Ic 260
t3*(1-parmal$mask)*parmal$vptftr*parmal$vptfc*(1-parmal$sensgd)*parmal$vptfp*parmal$vnup*x[varind[23,n]] #test - primaquine failed trt Thgd to Thgd 261
)
}
return(c(t(tranrate)))
}
slphyx/MEEM documentation built on May 30, 2019, 3:06 a.m.
R Package Documentation
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# ************************************************************************************* #
# Function to calculate transition rates, given variables and parameters
# ************************************************************************************* #
MM_Malrates <- function(x, input, parmal, t, ti) {
# tempfile1<-input$tempfile1
# tempfile2<-input$tempfile2
# tmp1<-read.csv(tempfile1)
# tmp2<-read.csv(tempfile2)
# for(n in names(tmp1)){
# txt<-paste0(n,"<-","tmp1$",n)
# eval(parse(text = txt))
# }
# for(n in names(tmp2)){
# txt<-paste0(n,"<-","tmp2$",n)
# eval(parse(text = txt))
# }
N<-input$N
B<-input$B
A<-input$A
V<-input$V
L<-input$L
startyear<-input$startyear
dtout<-input$dtout
tsteps<-input$tsteps
tyears<-input$tyears
pvxy<-input$pvxy
yrprim<-input$yrprim
g6pDd<-input$g6pDd
varind<-matrix(0,nrow=B,ncol=N)
traind<-matrix(0,nrow=A,ncol=N)
for (n in 1:N){
for (b in 1:B){
varind[b,n]<-(n-1)*B+b
}
for (a in 1:A){
traind[a,n]<-(n-1)*A+a
}
}
###########################
falpop<-1:10
vivpop<-11:23
############################
t_internal<-(ti-1)*dtout+t+startyear
#Set up matrices
seas<-c(rep(1,N)) # seasonality
popf<-c(rep(0,N)) # population sizes
popv<-c(rep(0,N)) # population sizes
foif<-c(rep(0,N)) # forces of infection falciparum
foiv<-c(rep(0,N)) # forces of infection vivax
tranrate<-matrix(0,nrow=N,ncol=A) # transition rate matrix
itn<-c(rep(0,N)) #ITN coverage
c_vmw<-c(rep(0,N)) #VMW coverage
veff<-c(rep(0,N)) #VMW effect decline
tau<-c(rep(0,N)) #Treatment probabilty
tauo<-c(rep(0,N)) #Treatment with other
tauh<-c(rep(0,N)) #Treatment with HIS
tauv<-c(rep(0,N)) #Treatment with VMW
eln<-approx(input$eln_t,input$eln_inp,xout=t_internal)$y
for (n in 1:N){
seas[n]<-1+eln*parmal$amp[n]*cos(2*pi*(t_internal-parmal$phi[n])) # seasonal forcing signal
popf[n]<-sum(x[varind[falpop,n]]) # list of the variable indices for the human population
popv[n]<-sum(x[varind[vivpop,n]]) # list of the variable indices for the human population
itn[n]<-approx(input$itn_time,input$c_itn[,n],xout=t_internal)$y
foif[n]<-sum(input$connect[n,]*seas[n]*((((1-itn[n])*parmal$bites)^2*parmal$prob_m*parmal$prob_h*(parmal$Pmaxf[n])/popf[n]*(parmal$zeta_n*x[varind[2,n]]+parmal$zeta_a*x[varind[3,n]]+x[varind[4,n]]+x[varind[5,n]])/sum(input$connect[n,]*popf))/((1-itn[n])*parmal$bites*parmal$prob_h*parmal$Pmaxf[n]/popf[n]+parmal$delta_m)*(parmal$gamma_m/(parmal$gamma_m+parmal$delta_m))))
foiv[n]<-sum(input$connect[n,]*seas[n]*((((1-itn[n])*parmal$bites)^2*parmal$prob_m*parmal$vprob_h*(parmal$Pmaxv[n])/popv[n]*(parmal$vzeta_n*x[varind[12,n]]+parmal$vzeta_a*x[varind[13,n]]+x[varind[14,n]]+x[varind[15,n]])/sum(input$connect[n,]*popv))/((1-itn[n])*parmal$bites*parmal$vprob_h*parmal$Pmaxv[n]/popv[n]+parmal$delta_m)*(parmal$vgamma_m/(parmal$vgamma_m+parmal$delta_m))))
foifa<-(1/(1/(foif[n])+1/parmal$gamma_h+1/parmal$gamma_m))
foiva<-(1/(1/(foiv[n])+1/parmal$vgamma_h+1/parmal$vgamma_m))
c_vmw[n]<-approx(input$vmw_time,input$cov_vmw[,n],xout=t_internal)$y
veff[n]<-approx(input$vmw_time,input$vmw_eff[,n],xout=t_internal)$y
tau[n]<-c_vmw[n]*input$sens_vmw*veff[n]+(1-c_vmw[n]*veff[n])*input$sens_his*parmal$eff_his+(1-c_vmw[n]*veff[n]-(1-c_vmw[n]*veff[n])*parmal$eff_his)*input$sens_oth*parmal$eff_oth #prob of treatment
tauo[n]<-(1-c_vmw[n]*veff[n]-(1-c_vmw[n]*veff[n])*parmal$eff_his)*input$sens_oth*parmal$eff_oth #Prob treated by Other
tauh[n]<-(1-c_vmw[n]*veff[n])*input$sens_his*parmal$eff_his #Prob treated by HIS
tauv[n]<-c_vmw[n]*veff[n]*input$sens_vmw #Prob treated by VMW
t3=0
if (t_internal>yrprim[n]){t3=1} #start radical cure from policy start date
tranrate[n,]<-c( #falciparum
parmal$demog*popf[n]+(1-parmal$tausev)*parmal$pmort*parmal$nuq*x[varind[5,n]]+parmal$tausev*parmal$nuq*parmal$pmortt*x[varind[5,n]], # rate of birth 1
parmal$demog*x[varind[1,n]], # rate of death of S 2
parmal$demog*x[varind[2,n]], # rate of death of In 3
parmal$demog*x[varind[3,n]], # rate of death of Ia 4
parmal$demog*x[varind[4,n]], # rate of death of Ic 5
parmal$demog*x[varind[5,n]], # rate of death of Is 6
parmal$demog*x[varind[6,n]], # rate of death of To 7
parmal$demog*x[varind[7,n]], # rate of death of Tv 8
parmal$demog*x[varind[8,n]], # rate of death of Th 9
parmal$demog*x[varind[9,n]], # rate of death of R 10
parmal$demog*x[varind[10,n]], # rate of death of H 11
parmal$psn*(1-parmal$ps)*foifa*x[varind[1,n]], #incidence S to In 12
(1-parmal$psn)*(1-parmal$ps)*foifa*x[varind[1,n]], # incidence S to Ia 13
(1-tau[n])*parmal$ps*foifa*x[varind[1,n]], # incidence S to Ic 14
tauo[n]*parmal$ps*foifa*x[varind[1,n]], # incidence S to To 15
tauv[n]*parmal$ps*foifa*x[varind[1,n]], # incidence S to Tv 16
tauh[n]*parmal$ps*foifa*x[varind[1,n]], # incidence S to Th 17
(1-parmal$tausev)*(1-parmal$pmort)*parmal$nuq*x[varind[5,n]], #recovery Is to Ic 18
(1-parmal$psev)*parmal$nuc*x[varind[4,n]], # recovery Ic to Ia 19
parmal$nua*x[varind[3,n]], # recovery Ia to In 20
input$nun*x[varind[2,n]], # recovery In to R 21
(1-parmal$ptf)*parmal$nut*x[varind[6,n]], # recovery To to H 22
(1-parmal$ptf)*parmal$nut*x[varind[7,n]], # recovery Tv to H 23
(1-parmal$ptf)*parmal$nut*x[varind[8,n]], # recovery Th to H 24
parmal$tausev*parmal$nuq*(1-parmal$pmortt)*x[varind[5,n]], # recovery Is to H 25
(1-parmal$prn)*(1-parmal$pr)*foifa*x[varind[2,n]], # incidence In to Ia 26
parmal$pr*(1-tau[n])*foifa*x[varind[3,n]], # incidence Ia to Ic 27
parmal$pr*tauo[n]*foifa*x[varind[3,n]], # incidence Ia to To 28
parmal$pr*tauv[n]*foifa*x[varind[3,n]], # incidence Ia to Tv 29
parmal$pr*tauh[n]*foifa*x[varind[3,n]], # incidence Ia to Th 30
parmal$psev*parmal$nuc*x[varind[4,n]], # incidence Ic to Is 31
parmal$pr*(1-tau[n])*foifa*x[varind[2,n]], # incidence In to Ic 32
parmal$pr*tauo[n]*foifa*x[varind[2,n]], # incidence In to To 33
parmal$pr*tauv[n]*foifa*x[varind[2,n]], # incidence In to Tv 34
parmal$pr*tauh[n]*foifa*x[varind[2,n]], # incidence In to Th 35
parmal$prn*(1-parmal$pr)*foifa*x[varind[9,n]], # incidence R to In 36
(1-parmal$prn)*(1-parmal$pr)*foifa*x[varind[9,n]], # incidence R to Ia 37
(1-tau[n])*parmal$pr*foifa*x[varind[9,n]], # incidence R to Ic 38
tauo[n]*parmal$pr*foifa*x[varind[9,n]], # incidence R to To 39
tauv[n]*parmal$pr*foifa*x[varind[9,n]], # incidence R to Tv 40
tauh[n]*parmal$pr*foifa*x[varind[9,n]], # incidence R to Th 41
parmal$omega*x[varind[9,n]], # loss of immunity from R to S 42
parmal$prn*(1-parmal$pr)*foifa*x[varind[10,n]], # incidence H to In 43
(1-parmal$prn)*(1-parmal$pr)*foifa*x[varind[10,n]], # incidence H to Ia 44
(1-tau[n])*parmal$pr*foifa*x[varind[10,n]], # incidence H to Ic 45
tauo[n]*parmal$pr*foifa*x[varind[10,n]], # incidence H to To 46
tauv[n]*parmal$pr*foifa*x[varind[10,n]], # incidence H to Tv 47
tauh[n]*parmal$pr*foifa*x[varind[10,n]], # incidence H to Th 48
parmal$chi*x[varind[10,n]], # loss HRP2 H to R 49
(1-parmal$tausev)*parmal$pmort*parmal$nuq*x[varind[5,n]]+parmal$tausev*parmal$nuq*parmal$pmortt*x[varind[5,n]], # death untreated+treated Is 50
(1-parmal$ptfc)*parmal$ptf*parmal$nut*x[varind[6,n]], # failure To to Ia 51
parmal$ptfc*(1-parmal$ptftr)*parmal$ptf*parmal$nut*x[varind[6,n]], # failure To to Ic 52
parmal$ptfc*parmal$ptftr*parmal$ptf*parmal$nut*x[varind[6,n]], # failure To to Th 53
(1-parmal$ptfc)*parmal$ptf*parmal$nut*x[varind[7,n]], # failure Tv to Ia 54
parmal$ptfc*(1-parmal$ptftr)*parmal$ptf*parmal$nut*x[varind[7,n]], # failure Tv to Ic 55
parmal$ptfc*parmal$ptftr*parmal$ptf*parmal$nut*x[varind[7,n]], # failure Tv to Tv 56
(1-parmal$ptfc)*parmal$ptf*parmal$nut*x[varind[8,n]], # failure Th to Ia 57
parmal$ptfc*(1-parmal$ptftr)*parmal$ptf*parmal$nut*x[varind[8,n]], # failure Th to Ic 58
parmal$ptfc*parmal$ptftr*parmal$ptf*parmal$nut*x[varind[8,n]], # failure Th to Th 59
#vivax
parmal$demog*popv[n]+(1-parmal$vtausev)*parmal$vpmort*parmal$vnuq*x[varind[15,n]]+parmal$vtausev*parmal$vpmortt*parmal$vnuq*x[varind[15,n]], # rate of birth 60
parmal$demog*x[varind[11,n]], # rate of death of S 61
parmal$demog*x[varind[12,n]], # rate of death of In 62
parmal$demog*x[varind[13,n]], # rate of death of Ia 63
parmal$demog*x[varind[14,n]], # rate of death of Ic 64
parmal$demog*x[varind[15,n]], # rate of death of Is 65
parmal$demog*x[varind[16,n]], # rate of death of To 66
parmal$demog*x[varind[17,n]], # rate of death of Tv 67
parmal$demog*x[varind[18,n]], # rate of death of Th 68
parmal$demog*x[varind[19,n]], # rate of death of R 69
parmal$demog*x[varind[20,n]], # rate of death of L 70
parmal$demog*x[varind[21,n]], # rate of death of Togd 71
parmal$demog*x[varind[22,n]], # rate of death of Tvgd 72
parmal$demog*x[varind[23,n]], # rate of death of Thgd 73
parmal$vpsn*((1-parmal$vps)*(1-parmal$propgd[n])+(1-parmal$pgd)*parmal$propgd[n])*foiva*x[varind[11,n]], #incidence S to In 74
(1-parmal$vpsn)*((1-parmal$vps)*(1-parmal$propgd[n])+(1-parmal$pgd)*parmal$propgd[n])*foiva*x[varind[11,n]], # incidence S to Ia 75
(1-tau[n])*(parmal$vps*(1-parmal$propgd[n])+parmal$pgd*parmal$propgd[n])*foiva*x[varind[11,n]], # incidence S to Ic 76
(1-parmal$propgd[n])*parmal$vps*tauo[n]*foiva*x[varind[11,n]], # incidence S to To 77
(1-parmal$propgd[n])*tauv[n]*parmal$vps*foiva*x[varind[11,n]], # incidence S to Tv 78
(1-parmal$propgd[n])*tauh[n]*parmal$vps*foiva*x[varind[11,n]], # incidence S to Th 79
parmal$propgd[n]*parmal$pgd*tauo[n]*foiva*x[varind[11,n]], # incidence S to Togd 80
parmal$propgd[n]*parmal$pgd*tauv[n]*foiva*x[varind[11,n]], # incidence S to Tvgd 81
parmal$propgd[n]*parmal$pgd*tauh[n]*foiva*x[varind[11,n]], # incidence S to Thgd 82
(1-parmal$tausev)*(1-parmal$vpmort)*parmal$vnuq*x[varind[15,n]], # recovery Is to Ic 83
(1-parmal$vpsev)*parmal$vnuc*x[varind[14,n]], # recovery Ic to Ia 84
parmal$vnua*x[varind[13,n]], # recovery Ia to In 85
(1-parmal$vph)*input$vnun*x[varind[12,n]], # recovery In to R 86
parmal$vph*input$vnun*x[varind[12,n]], # recovery In to L 87
(1-t3)*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[16,n]], # recovery To to R 88
(1-t3)*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[17,n]], # recovery Tv to R 89
(1-t3)*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[18,n]], # recovery Th to R 90
(1-t3)*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[21,n]], # recovery Togd to R 91
(1-t3)*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[22,n]], # recovery Tvgd to R 92
(1-t3)*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[23,n]], # recovery Thgd to R 93
(1-parmal$vph)*parmal$vtausev*(1-parmal$vpmortt)*parmal$vnuq*x[varind[15,n]], # recovery Is to R 94
(1-t3)*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[16,n]], # recovery To to L 95
(1-t3)*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[17,n]], # recovery Tv to L 96
(1-t3)*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[18,n]], # recovery Th to L 97
(1-t3)*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[21,n]], # recovery Togd to L 98
(1-t3)*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[22,n]], # recovery Tvgd to L 99
(1-t3)*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[23,n]], # recovery Thgd to L 100
parmal$vph*parmal$vtausev*(1-parmal$vpmortt)*parmal$vnuq*x[varind[15,n]], # recovery Is to L 101
(1-parmal$vprn)*(1-parmal$vpr)*foiva*x[varind[12,n]], # incidence In to Ia 102
parmal$vpr*(1-tau[n])*foiva*x[varind[12,n]], # incidence In to Ic 103
(1-parmal$propgd[n])*parmal$vpr*tauo[n]*foiva*x[varind[12,n]], # incidence In to To 104
(1-parmal$propgd[n])*parmal$vpr*tauv[n]*foiva*x[varind[12,n]], # incidence In to Tv 105
(1-parmal$propgd[n])*parmal$vpr*tauh[n]*foiva*x[varind[12,n]], # incidence In to Th 106
parmal$propgd[n]*parmal$vpr*tauo[n]*foiva*x[varind[12,n]], # incidence In to Togd 107
parmal$propgd[n]*parmal$vpr*tauv[n]*foiva*x[varind[12,n]], # incidence In to Tvgd 108
parmal$propgd[n]*parmal$vpr*tauh[n]*foiva*x[varind[12,n]], # incidence In to Thgd 109
parmal$vpr*(1-tau[n])*foiva*x[varind[13,n]], # incidence Ia to Ic 110
(1-parmal$propgd[n])*parmal$vpr*tauo[n]*foiva*x[varind[13,n]], # incidence Ia to To 111
(1-parmal$propgd[n])*parmal$vpr*tauv[n]*foiva*x[varind[13,n]], # incidence Ia to Tv 112
(1-parmal$propgd[n])*parmal$vpr*tauh[n]*foiva*x[varind[13,n]], # incidence Ia to Th 113
parmal$propgd[n]*parmal$vpr*tauo[n]*foiva*x[varind[13,n]], # incidence Ia to Togd 114
parmal$propgd[n]*parmal$vpr*tauv[n]*foiva*x[varind[13,n]], # incidence Ia to Tvgd 115
parmal$propgd[n]*parmal$vpr*tauh[n]*foiva*x[varind[13,n]], # incidence Ia to Thgd 116
parmal$vpsev*parmal$vnuc*x[varind[14,n]], # incidence Ic to Is 117
parmal$vprn*(1-parmal$vpr)*foiva*x[varind[19,n]], # incidence R to In 118
(1-parmal$vprn)*(1-parmal$vpr)*foiva*x[varind[19,n]], # incidence R to Ia 119
(1-tau[n])*parmal$vpr*foiva*x[varind[19,n]], # incidence R to Ic 120
(1-parmal$propgd[n])*tauo[n]*parmal$vpr*foiva*x[varind[19,n]], # incidence R to To 121
(1-parmal$propgd[n])*tauv[n]*parmal$vpr*foiva*x[varind[19,n]], # incidence R to Tv 122
(1-parmal$propgd[n])*tauh[n]*parmal$vpr*foiva*x[varind[19,n]], # incidence R to Th 123
parmal$propgd[n]*tauo[n]*parmal$vpr*foiva*x[varind[19,n]], # incidence R to Togd 124
parmal$propgd[n]*tauv[n]*parmal$vpr*foiva*x[varind[19,n]], # incidence R to Tvgd 125
parmal$propgd[n]*tauh[n]*parmal$vpr*foiva*x[varind[19,n]], # incidence R to Thgd 126
parmal$vomega*x[varind[19,n]], # loss of immunity from R to S 127
parmal$vprn*(1-parmal$vpr)*(foiva)*x[varind[20,n]], # incidence L to In 128
(1-parmal$vprn)*(1-parmal$vpr)*(foiva)*x[varind[20,n]], # incidence L to Ia 129
(1-tau[n])*parmal$vpr*(foiva)*x[varind[20,n]], # incidence L to Ic 130
(1-parmal$propgd[n])*tauo[n]*parmal$vpr*(foiva)*x[varind[20,n]], # incidence L to To 131
(1-parmal$propgd[n])*tauv[n]*parmal$vpr*(foiva)*x[varind[20,n]], # incidence L to Tv 132
(1-parmal$propgd[n])*tauh[n]*parmal$vpr*(foiva)*x[varind[20,n]], # incidence L to Th 133
parmal$propgd[n]*tauo[n]*parmal$vpr*(foiva)*x[varind[20,n]], # incidence L to Togd 134
parmal$propgd[n]*tauv[n]*parmal$vpr*(foiva)*x[varind[20,n]], # incidence L to Tvgd 135
parmal$propgd[n]*tauh[n]*parmal$vpr*(foiva)*x[varind[20,n]], # incidence L to Thgd 136
parmal$vprn*(1-parmal$vpr)*parmal$vprel*parmal$vrel*x[varind[10,n]], # relapse L to In 137
(1- parmal$t2)*(1-parmal$vprn)*(1-parmal$vpr)*parmal$vprel*parmal$vrel*x[varind[10,n]], # relapse L to Ia 138
(1- parmal$t2)*(1-tau[n])*parmal$vpr*parmal$vprel*parmal$vrel*x[varind[10,n]], # relapse L to Ic 139
(1- parmal$t2)*(1-parmal$propgd[n])*tauo[n]*parmal$vpr*parmal$vprel*parmal$vrel*x[varind[10,n]], # relapse L to To 140
(1- parmal$t2)*(1-parmal$propgd[n])*tauv[n]*parmal$vpr*parmal$vprel*parmal$vrel*x[varind[10,n]], # relapse L to Tv 141
(1- parmal$t2)*(1-parmal$propgd[n])*tauh[n]*parmal$vpr*parmal$vprel*parmal$vrel*x[varind[10,n]], # relapse L to Th 142
(1- parmal$t2)*parmal$propgd[n]*tauo[n]*parmal$vpr*parmal$vprel*parmal$vrel*x[varind[10,n]], # relapse L to Togd 143
(1- parmal$t2)*parmal$propgd[n]*tauv[n]*parmal$vpr*parmal$vprel*parmal$vrel*x[varind[10,n]], # relapse L to Tvgd 144
(1- parmal$t2)*parmal$propgd[n]*tauh[n]*parmal$vpr*parmal$vprel*parmal$vrel*x[varind[10,n]], # relapse L to Thgd 145
parmal$vkappa*x[varind[10,n]], # death of hypnozoites L to S 146
(1-parmal$vtausev)*parmal$vpmort*parmal$vnuq*x[varind[15,n]]+parmal$vtausev*parmal$vpmortt*parmal$vnuq*x[varind[15,n]], # death untreated+treated Is 147
(1-t3)*(1-parmal$vptfc)*parmal$vptf*parmal$vnut*x[varind[16,n]], # failed trt To to Ia 148
(1-t3)*(1-parmal$vptftr)*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[16,n]], # failed trt To to Ic 149
(1-t3)*parmal$vptftr*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[16,n]], # failed trt To to Th 150
(1-t3)*(1-parmal$vptfc)*parmal$vptf*parmal$vnut*x[varind[17,n]], # failed trt Tv to Ia 151
(1-t3)*(1-parmal$vptftr)*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[17,n]], # failed trt Tv to Ic 152
(1-t3)*parmal$vptftr*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[17,n]], # failed trt Tv to Tv 153
(1-t3)*(1-parmal$vptfc)*parmal$vptf*parmal$vnut*x[varind[18,n]], # failed trt Th to Ia 154
(1-t3)*(1-parmal$vptftr)*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[18,n]], # failed trt Th to Ic 155
(1-t3)*parmal$vptftr*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[18,n]], # failed trt Th to Th 156
(1-t3)*(1-parmal$vptfc)*parmal$vptf*parmal$vnut*x[varind[21,n]], # failed trt Togd to Ia 157
(1-t3)*(1-parmal$vptftr)*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[21,n]], # failed trt Togd to Ic 158
(1-t3)*parmal$vptftr*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[21,n]], # failed trt Togd to Thgd 159
(1-t3)*(1-parmal$vptfc)*parmal$vptf*parmal$vnut*x[varind[22,n]], # failed trt Tvgd to Ia 160
(1-t3)*(1-parmal$vptftr)*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[22,n]], # failed trt Tvgd to Ic 161
(1-t3)*parmal$vptftr*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[22,n]], # failed trt Tvgd to Tvgd 162
(1-t3)*(1-parmal$vptfc)*parmal$vptf*parmal$vnut*x[varind[23,n]], # failed trt Thgd to Ia 163
(1-t3)*(1-parmal$vptftr)*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[23,n]], # failed trt Thgd to Ic 164
(1-t3)*parmal$vptftr*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[23,n]], # failed trt Thgd to Thgd 165
#Entanglements (dual treat)
parmal$t1*(1-parmal$ptf)*parmal$nut*x[varind[2,n]]*(x[varind[16,n]]+x[varind[17,n]]+x[varind[18,n]]+x[varind[21,n]]+x[varind[22,n]]+x[varind[23,n]])/popv[n], # dual trt Fal In to H 166
parmal$t1*(1-parmal$ptf)*parmal$nut*x[varind[3,n]]*(x[varind[16,n]]+x[varind[17,n]]+x[varind[18,n]]+x[varind[21,n]]+x[varind[22,n]]+x[varind[23,n]])/popv[n], # dual trt Fal Ia to H 167
parmal$t1*(1-parmal$ptf)*parmal$nut*x[varind[4,n]]*(x[varind[16,n]]+x[varind[17,n]]+x[varind[18,n]]+x[varind[21,n]]+x[varind[22,n]]+x[varind[23,n]])/popv[n], # dual trt Fal Ic to H 168
parmal$t1*(1-parmal$ptf)*parmal$nut*x[varind[5,n]]*(x[varind[16,n]]+x[varind[17,n]]+x[varind[18,n]]+x[varind[21,n]]+x[varind[22,n]]+x[varind[23,n]])/popv[n], # dual trt Fal Is to H 169
parmal$t1*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[12,n]]*(x[varind[6,n]]+x[varind[7,n]]+x[varind[8,n]])/popf[n], # dual trt Viv In to R 170
parmal$t1*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[13,n]]*(x[varind[6,n]]+x[varind[7,n]]+x[varind[8,n]])/popf[n], # dual trt Viv Ia to R 171
parmal$t1*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[14,n]]*(x[varind[6,n]]+x[varind[7,n]]+x[varind[8,n]])/popf[n], # dual trt Viv Ic to R 172
parmal$t1*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[15,n]]*(x[varind[6,n]]+x[varind[7,n]]+x[varind[8,n]])/popf[n], # dual trt Viv Is to R 173
parmal$t1*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[12,n]]*(x[varind[6,n]]+x[varind[7,n]]+x[varind[8,n]])/popf[n], # dual trt Viv In to L 174
parmal$t1*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[13,n]]*(x[varind[6,n]]+x[varind[7,n]]+x[varind[8,n]])/popf[n], # dual trt Viv Ia to L 175
parmal$t1*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[14,n]]*(x[varind[6,n]]+x[varind[7,n]]+x[varind[8,n]])/popf[n], # dual trt Viv Ic to L 176
parmal$t1*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[15,n]]*(x[varind[6,n]]+x[varind[7,n]]+x[varind[8,n]])/popf[n], # dual trt Viv Is to L 177
t3*(1-parmal$mask)*(1-parmal$vphprim)*(1-parmal$vptfp)*parmal$vnup*x[varind[16,n]], # primaquine recovery To to R 178
t3*(1-parmal$mask)*(1-parmal$vphprim)*(1-parmal$vptfp)*parmal$vnup*x[varind[17,n]], #primaquine recovery Tv to R 179
t3*(1-parmal$mask)*(1-parmal$vphprim)*(1-parmal$vptfp)*parmal$vnup*x[varind[18,n]], #primaquine recovery Th to R 180
t3*(1-parmal$mask)*parmal$vphprim*(1-parmal$vptfp)*parmal$vnup*x[varind[16,n]], # primaquine recovery To to L 181
t3*(1-parmal$mask)*parmal$vphprim*(1-parmal$vptfp)*parmal$vnup*x[varind[17,n]], #primaquine recovery Tv to L 182
t3*(1-parmal$mask)*parmal$vphprim*(1-parmal$vptfp)*parmal$vnup*x[varind[18,n]], #primaquine recovery Th to L 183
t3*(1-parmal$mask)*(parmal$sensgd*parmal$vnut*(1-parmal$vph)*(1-parmal$vptf))*x[varind[21,n]], # test + act recovery Togd to R 184
t3*(1-parmal$mask)*(parmal$sensgd*parmal$vnut*(1-parmal$vph)*(1-parmal$vptf))*x[varind[22,n]], #test + act recovery Tvgd to R 185
t3*(1-parmal$mask)*(parmal$sensgd*parmal$vnut*(1-parmal$vph)*(1-parmal$vptf))*x[varind[23,n]], #test + act recovery Thgd to R 186
t3*(1-parmal$mask)*(parmal$sensgd*parmal$vnut*parmal$vph*(1-parmal$vptf))*x[varind[21,n]], # test + act recovery of GDef Togd to L 187
t3*(1-parmal$mask)*(parmal$sensgd*parmal$vnut*parmal$vph*(1-parmal$vptf))*x[varind[22,n]], #test + act recovery of GDef Tvgd to L 188
t3*(1-parmal$mask)*(parmal$sensgd*parmal$vnut*parmal$vph*(1-parmal$vptf))*x[varind[23,n]], #test + act recovery of GDef Thgd to L 189
t3*(1-parmal$mask)*((1-parmal$sensgd)*(1-parmal$vptfp)*(1-parmal$vphprim)*parmal$vnup)*x[varind[21,n]], # test - primaquine recovery Togd to R 190
t3*(1-parmal$mask)*((1-parmal$sensgd)*(1-parmal$vptfp)*(1-parmal$vphprim)*parmal$vnup)*x[varind[22,n]], # test - primaquine recovery Tvgd to R 191
t3*(1-parmal$mask)*((1-parmal$sensgd)*(1-parmal$vptfp)*(1-parmal$vphprim)*parmal$vnup)*x[varind[23,n]], #test - primaquine recovery Thgd to R 192
t3*(1-parmal$mask)*((1-parmal$sensgd)*parmal$vphprim*(1-parmal$vptfp)*parmal$vnup)*x[varind[21,n]], # test - primaquine recovery of GDef Togd to L 193
t3*(1-parmal$mask)*((1-parmal$sensgd)*parmal$vphprim*(1-parmal$vptfp)*parmal$vnup)*x[varind[22,n]], #test - primaquine recovery of GDef Tvgd to L 194
t3*(1-parmal$mask)*((1-parmal$sensgd)*parmal$vphprim*(1-parmal$vptfp)*parmal$vnup)*x[varind[23,n]], #test - primaquine recovery of GDef Thgd to L 195
t3*parmal$mask*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[16,n]], # masked act recovery To to R 196
t3*parmal$mask*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[17,n]], #masked act recovery Tv to R 197
t3*parmal$mask*(1-parmal$vph)*(1-parmal$vptf)*parmal$vnut*x[varind[18,n]], #masked act recovery Th to R 198
t3*parmal$mask*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[16,n]], # masked act recovery To to L 199
t3*parmal$mask*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[17,n]], #masked act recovery Tv to L 200
t3*parmal$mask*parmal$vph*(1-parmal$vptf)*parmal$vnut*x[varind[18,n]], #masked act recovery Th to L 201
t3*parmal$mask*parmal$vnut*(1-parmal$vph)*(1-parmal$vptf)*x[varind[21,n]], # masked act recovery Togd to R 202
t3*parmal$mask*parmal$vnut*(1-parmal$vph)*(1-parmal$vptf)*x[varind[22,n]], #masked act recovery Tvgd to R 203
t3*parmal$mask*parmal$vnut*(1-parmal$vph)*(1-parmal$vptf)*x[varind[23,n]], #masked act recovery Thgd to R 204
t3*parmal$mask*parmal$vnut*parmal$vph*(1-parmal$vptf)*x[varind[21,n]], # masked act recovery of GDef Togd to L 205
t3*parmal$mask*parmal$vnut*parmal$vph*(1-parmal$vptf)*x[varind[22,n]], #masked act recovery of GDef Tvgd to L 206
t3*parmal$mask*parmal$vnut*parmal$vph*(1-parmal$vptf)*x[varind[23,n]], #masked act recovery of GDef Thgd to L 207
parmal$t2*parmal$vprn*(1-parmal$vpr)*(parmal$vprel*((popf[n]-x[varind[9,n]]-x[varind[10,n]])/popf[n])+parmal$vincprel*((x[varind[9,n]]+x[varind[10,n]])/popf[n]))*parmal$vrel*x[varind[20,n]], # relapse L to In +triggering 208
parmal$t2*(1-parmal$vprn)*(1-parmal$vpr)*(parmal$vprel*((popf[n]-x[varind[9,n]]-x[varind[10,n]])/popf[n])+parmal$vincprel*((x[varind[9,n]]+x[varind[10,n]])/popf[n]))*parmal$vrel*x[varind[20,n]], # relapse L to Ia +triggering 209
parmal$t2*(1-tau[n])*parmal$vpr*(parmal$vprel*((popf[n]-x[varind[9,n]]-x[varind[10,n]])/popf[n])+parmal$vincprel*((x[varind[9,n]]+x[varind[10,n]])/popf[n]))*parmal$vrel*x[varind[20,n]], # relapse L to Ic+triggering 210
parmal$t2*(1-parmal$propgd[n])*tauo[n]*parmal$vpr*(parmal$vprel*((popf[n]-x[varind[9,n]]-x[varind[10,n]])/popf[n])+parmal$vincprel*((x[varind[9,n]]+x[varind[10,n]])/popf[n]))*parmal$vrel*x[varind[20,n]], # relapse L to To +triggering 211
parmal$t2*(1-parmal$propgd[n])*tauv[n]*parmal$vpr*(parmal$vprel*((popf[n]-x[varind[9,n]]-x[varind[10,n]])/popf[n])+parmal$vincprel*((x[varind[9,n]]+x[varind[10,n]])/popf[n]))*parmal$vrel*x[varind[20,n]], # relapse L to Tv+triggering 212
parmal$t2*(1-parmal$propgd[n])*tauh[n]*parmal$vpr*(parmal$vprel*((popf[n]-x[varind[9,n]]-x[varind[10,n]])/popf[n])+parmal$vincprel*((x[varind[9,n]]+x[varind[10,n]])/popf[n]))*parmal$vrel*x[varind[20,n]], # relapse L to Th +triggering 213
parmal$t2*parmal$propgd[n]*tauo[n]*parmal$vpr*(parmal$vprel*((popf[n]-x[varind[9,n]]-x[varind[10,n]])/popf[n])+parmal$vincprel*((x[varind[9,n]]+x[varind[10,n]])/popf[n]))*parmal$vrel*x[varind[20,n]], # relapse L to Togd +triggering 214
parmal$t2*parmal$propgd[n]*tauv[n]*parmal$vpr*(parmal$vprel*((popf[n]-x[varind[9,n]]-x[varind[10,n]])/popf[n])+parmal$vincprel*((x[varind[9,n]]+x[varind[10,n]])/popf[n]))*parmal$vrel*x[varind[20,n]], # relapse L to Tvgd+triggering 215
parmal$t2*parmal$propgd[n]*tauh[n]*parmal$vpr*(parmal$vprel*((popf[n]-x[varind[9,n]]-x[varind[10,n]])/popf[n])+parmal$vincprel*((x[varind[9,n]]+x[varind[10,n]])/popf[n]))*parmal$vrel*x[varind[20,n]], # relapse L to Thgd +triggering 216
#Failed treatments
t3*(1-parmal$mask)*(1-parmal$vptfc)*parmal$vptfp*parmal$vnup*x[varind[16,n]], # primaquine failed trt To to Ia 217
t3*(1-parmal$mask)*(1-parmal$vptftr)*parmal$vptfc*parmal$vptfp*parmal$vnup*x[varind[16,n]], # primaquine failed trt To to Ic 218
t3*(1-parmal$mask)*parmal$vptftr*parmal$vptfc*parmal$vptfp*parmal$vnup*x[varind[16,n]], # primaquine failed trt To to Th 219
t3*(1-parmal$mask)*(1-parmal$vptfc)*parmal$vptfp*parmal$vnup*x[varind[17,n]], #primaquine failed trt Tv to Ia 220
t3*(1-parmal$mask)*(1-parmal$vptftr)*parmal$vptfc*parmal$vptfp*parmal$vnup*x[varind[17,n]], #primaquine failed trt Tv to Ic 221
t3*(1-parmal$mask)*parmal$vptftr*parmal$vptfc*parmal$vptfp*parmal$vnup*x[varind[17,n]], #primaquine failed trt Tv to Tv 222
t3*(1-parmal$mask)*(1-parmal$vptfc)*parmal$vptfp*parmal$vnup*x[varind[18,n]], #primaquine failed trt Th to Ia 223
t3*(1-parmal$mask)*(1-parmal$vptftr)*parmal$vptfc*parmal$vptfp*parmal$vnup*x[varind[18,n]], #primaquine failed trt Th to Ic 224
t3*(1-parmal$mask)*parmal$vptftr*parmal$vptfc*parmal$vptfp*parmal$vnup*x[varind[18,n]], #primaquine failed trt Th to Th 225
t3*parmal$mask*(1-parmal$vptfc)*parmal$vptf*parmal$vnut*x[varind[16,n]], # masked act failed trt To to Ia 226
t3*parmal$mask*(1-parmal$vptftr)*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[16,n]], # masked act failed trt To to Ic 227
t3*parmal$mask*parmal$vptftr*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[16,n]], # masked act failed trt To to Th 228
t3*parmal$mask*(1-parmal$vptfc)*parmal$vptf*parmal$vnut*x[varind[17,n]], #masked act failed trt Tv to Ia 229
t3*parmal$mask*(1-parmal$vptftr)*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[17,n]], #masked act failed trt Tv to Ic 230
t3*parmal$mask*parmal$vptftr*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[17,n]], #masked act failed trt Tv to Tv 231
t3*parmal$mask*(1-parmal$vptfc)*parmal$vptf*parmal$vnut*x[varind[18,n]], #masked act failed trt Th to Ia 232
t3*parmal$mask*(1-parmal$vptftr)*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[18,n]], #masked act failed trt Th to Ic 233
t3*parmal$mask*parmal$vptftr*parmal$vptfc*parmal$vptf*parmal$vnut*x[varind[18,n]], #masked act failed trt Th to Th 234
t3*parmal$mask*(1-parmal$vptfc)*parmal$vnut*parmal$vptf*x[varind[21,n]], # masked act failed trt Togd to Ia 235
t3*parmal$mask*(1-parmal$vptftr)*parmal$vptfc*parmal$vnut*parmal$vptf*x[varind[21,n]], # masked act failed trt Togd to Ic 236
t3*parmal$mask*parmal$vptftr*parmal$vptfc*parmal$vnut*parmal$vptf*x[varind[21,n]], # masked act failed trt Togd to Thgd 237
t3*parmal$mask*(1-parmal$vptfc)*parmal$vnut*parmal$vptf*x[varind[22,n]], #masked act failed trt Tvgd to Ia 238
t3*parmal$mask*(1-parmal$vptftr)*parmal$vptfc*parmal$vnut*parmal$vptf*x[varind[22,n]], #masked act failed trt Tvgd to Ic 239
t3*parmal$mask*parmal$vptftr*parmal$vptfc*parmal$vnut*parmal$vptf*x[varind[22,n]], #masked act failed trt Tvgd to Tvgd 240
t3*parmal$mask*(1-parmal$vptfc)*parmal$vnut*parmal$vptf*x[varind[23,n]], #masked act failed trt Thgd to Ia 241
t3*parmal$mask*(1-parmal$vptftr)*parmal$vptfc*parmal$vnut*parmal$vptf*x[varind[23,n]], #masked act failed trt Thgd to Ic 242
t3*parmal$mask*parmal$vptftr*parmal$vptfc*parmal$vnut*parmal$vptf*x[varind[23,n]], #masked act failed trt Thgd to Thgd 243
t3*(1-parmal$mask)*(1-parmal$vptfc)*parmal$sensgd*parmal$vnut*parmal$vptf*x[varind[21,n]], # test + act failed trt Togd to Ia 244
t3*(1-parmal$mask)*(1-parmal$vptftr)*parmal$vptfc*parmal$sensgd*parmal$vnut*parmal$vptf*x[varind[21,n]], # test + act failed trt Togd to Ic 245
t3*(1-parmal$mask)*parmal$vptftr*parmal$vptfc*parmal$sensgd*parmal$vnut*parmal$vptf*x[varind[21,n]], # test + act failed trt Togd to Thgd 246
t3*(1-parmal$mask)*(1-parmal$vptfc)*parmal$sensgd*parmal$vnut*parmal$vptf*x[varind[22,n]], #test + act failed trt Tvgd to Ia 247
t3*(1-parmal$mask)*(1-parmal$vptftr)*parmal$vptfc*parmal$sensgd*parmal$vnut*parmal$vptf*x[varind[22,n]], #test + act failed trt Tvgd to Ic 248
t3*(1-parmal$mask)*parmal$vptftr*parmal$vptfc*parmal$sensgd*parmal$vnut*parmal$vptf*x[varind[22,n]], #test + act failed trt Tvgd to Tvgd 249
t3*(1-parmal$mask)*(1-parmal$vptfc)*parmal$sensgd*parmal$vnut*parmal$vptf*x[varind[23,n]], #test + act failed trt Thgd to Ia 250
t3*(1-parmal$mask)*(1-parmal$vptftr)*parmal$vptfc*parmal$sensgd*parmal$vnut*parmal$vptf*x[varind[23,n]], #test + act failed trt Thgd to Ic 251
t3*(1-parmal$mask)*parmal$vptftr*parmal$vptfc*parmal$sensgd*parmal$vnut*parmal$vptf*x[varind[23,n]], #test + act failed trt Thgd to Thgd 252
t3*(1-parmal$mask)*(1-parmal$vptfc)*(1-parmal$sensgd)*parmal$vptfp*parmal$vnup*x[varind[21,n]], # test - primaquine failed trt Togd to Ia 253
t3*(1-parmal$mask)*(1-parmal$vptftr)*parmal$vptfc*(1-parmal$sensgd)*parmal$vptfp*parmal$vnup*x[varind[21,n]], # test - primaquine failed trt Togd to Ic 254
t3*(1-parmal$mask)*parmal$vptftr*parmal$vptfc*(1-parmal$sensgd)*parmal$vptfp*parmal$vnup*x[varind[21,n]], # test - primaquine failed trt Togd to Thgd 255
t3*(1-parmal$mask)*(1-parmal$vptfc)*(1-parmal$sensgd)*parmal$vptfp*parmal$vnup*x[varind[22,n]], # test - primaquine failed trt Tvgd to Ia 256
t3*(1-parmal$mask)*(1-parmal$vptftr)*parmal$vptfc*(1-parmal$sensgd)*parmal$vptfp*parmal$vnup*x[varind[22,n]], # test - primaquine failed trt Tvgd to Ic 257
t3*(1-parmal$mask)*parmal$vptftr*parmal$vptfc*(1-parmal$sensgd)*parmal$vptfp*parmal$vnup*x[varind[22,n]], # test - primaquine failed trt Tvgd to Tvgd 258
t3*(1-parmal$mask)*(1-parmal$vptfc)*(1-parmal$sensgd)*parmal$vptfp*parmal$vnup*x[varind[23,n]], #test - primaquine failed trt Thgd to Ia 259
t3*(1-parmal$mask)*(1-parmal$vptftr)*parmal$vptfc*(1-parmal$sensgd)*parmal$vptfp*parmal$vnup*x[varind[23,n]], #test - primaquine failed trt Thgd to Ic 260
t3*(1-parmal$mask)*parmal$vptftr*parmal$vptfc*(1-parmal$sensgd)*parmal$vptfp*parmal$vnup*x[varind[23,n]] #test - primaquine failed trt Thgd to Thgd 261
)
}
return(c(t(tranrate)))
}
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