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9_sweep_setup.R
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sweep0<-readRDS("1_main/0_sweep_sero.RDS")
sweep<- readRDS("1_main/0_sweep_imm4.RDS")
sweep_r0 <- sweep0%>%group_by(sweep_unique)%>%slice(1)
sweep<- sweep%>%
filter(omega2_pc==1/180)%>%
filter(kappa3%in%c(1/1000,1/1500,1/2000,1/2500))%>%
filter(sero_thresh==0)
sweep <- rbind(sweep,sweep,sweep,sweep,sweep)
sweep <- sweep%>%mutate(
foi_sp = rep(c(0.5,0.6,0.7,0.8, 0.9), each =128),
foi_sn = rep(c(1.5,1.4,1.3,1.2,1.0), each =128)
)
saveRDS(sweep,"0_sweep_imm4_varyfoi.RDS")
sweep0<- sweep%>%filter(kappa3 ==1/2500)%>%
filter(foi_sp==0.5)
sweep0.5 <-rbind(sweep0, sweep0,sweep0,sweep0,sweep0, sweep0,sweep0)
sweep0.5<- sweep0.5%>%
mutate(sero_thresh = rep(c(0.5,0.55,0.6,0.65,0.7,0.75,0.8), each=32))
sweep0.6 <-rbind(sweep0, sweep0,sweep0,sweep0,sweep0, sweep0,sweep0)
sweep0.6<- sweep0.6%>%
mutate(foi_sp = 0.6, foi_sn=1.4,
sero_thresh = rep(c(0.5,0.55,0.6,0.65,0.7,0.75,0.8), each=32))
sweep0.7 <-rbind(sweep0, sweep0,sweep0,sweep0,sweep0, sweep0,sweep0)
sweep0.7<- sweep0.7%>%
mutate(foi_sp = 0.7, foi_sn = 1.3,
sero_thresh = rep(c(0.5,0.55,0.6,0.65,0.7,0.75,0.8), each=32))
sweep0.8 <-rbind(sweep0, sweep0,sweep0,sweep0,sweep0, sweep0,sweep0)
sweep0.8<- sweep0.8%>%
mutate(foi_sp=0.8, foi_sn=1.2,
sero_thresh = rep(c(0.5,0.55,0.6,0.65,0.7,0.75,0.8), each=32))
sweep0.9 <-rbind(sweep0, sweep0,sweep0,sweep0,sweep0, sweep0,sweep0)
sweep0.9<- sweep0.9%>%
mutate(foi_sp=0.9, foi_sn=1.1,
sero_thresh = rep(c(0.5,0.55,0.6,0.65,0.7,0.75,0.8), each=32))
sweep_vax <- rbind(sweep0.5,sweep0.6,sweep0.7,sweep0.8,sweep0.9)
saveRDS(sweep_vax,"0_sweep_imm4_varyfoi_vax.RDS")
sweep_vax <- readRDS("1_main/0_sweep_imm4_varyfoi_vax.RDS")
sweep_vax0<- sweep_vax%>%
filter(foi_sp %in% c(0.5,0.6))%>%
filter(sero_thresh==0.5)%>%
mutate(sero_thresh=0)
sweep<- rbind(sweep_vax0,sweep_vax0, sweep_vax0, sweep_vax0)
sweep<- sweep%>%
mutate(vax_first = rep(c(435,800), each=128),
vax_int = rep(c(365, 730, 365, 730),each=64),
vax_start = rep(c((435/365)%%1,
(435/730)%%1,
(800/365)%%1,
(800/730)%%1),each=64),
vax_end = rep(c((465/365)%%1,
(465/730)%%1,
(830/365)%%1,
(830/730)%%1),each=64))
saveRDS(sweep, "1_sweep_imm4_varyfoi_vax_int_pt1.RDS")
sweep_vax <- readRDS("1_main/0_sweep_imm4_varyfoi_vax.RDS")
sweep_vax0<- sweep_vax%>%
filter(foi_sp %in% c(0.7,0.8,0.9))%>%
filter(sero_thresh==0.5)%>%
mutate(sero_thresh=0)
sweep<- rbind(sweep_vax0,sweep_vax0, sweep_vax0, sweep_vax0)
sweep<- sweep%>%
mutate(vax_first = rep(c(435,800), each=192),
vax_int = rep(c(365, 730, 365, 730),each=96),
vax_start = rep(c((435/365)%%1,
(435/730)%%1,
(800/365)%%1,
(800/730)%%1),each=96),
vax_end = rep(c((465/365)%%1,
(465/730)%%1,
(830/365)%%1,
(830/730)%%1),each=96))
saveRDS(sweep, "1_main/1_sweep_imm4_varyfoi_vax_int_pt2.RDS")
sweep_vax <- readRDS("1_main/0_sweep_imm4_varyfoi_vax.RDS")
sweep_vax0<- sweep_vax%>%
filter(foi_sp %in% c(0.5,0.6,0.7,0.8,0.9))%>%
filter(sero_thresh==0.5)%>%
mutate(sero_thresh=0)
sweep_int <- rbind(sweep_vax0,sweep_vax0)%>%
mutate(vax_first = 0,
vax_int = rep(c(365,730), each=160),
vax_start = rep(c(300/365, 300/730),each=160),
vax_end = rep(c(330/365, 330/730),each=160))
saveRDS(sweep_int, "1_main/1_sweep_imm4_varyfoi_vax_int_pt3.RDS")
sweep_int<- sweep_int%>%arrange(sweep_unique)
sweep_int_pt1<- readRDS("1_main/1_sweep_imm4_varyfoi_vax_int_pt1.RDS")
###200 runs of kappa 2500, foi_sp0.6
sweep0<-readRDS("1_main/0_sweep_sero.RDS")
sweep<- readRDS("1_main/0_sweep_imm4.RDS")
sweep_r0 <- sweep0%>%group_by(sweep_unique)%>%slice(1)
sweep_r0 <- sweep_r0%>%filter(sweep_unique>32&sweep_unique<=192)
sweep<- sweep%>%
filter(omega2_pc==1/180)%>%
filter(kappa3==1/2500)%>%
filter(sero_thresh==0)
sweep <- rbind(sweep,sweep,sweep,sweep,sweep)
sweep <- sweep%>%
mutate(r00=sweep_r0$r00,
r01=sweep_r0$r01,
r02=sweep_r0$r02,
r03=sweep_r0$r03,
r04=sweep_r0$r04,
r05=sweep_r0$r05,
r06=sweep_r0$r06,
r07=sweep_r0$r07,
r08=sweep_r0$r08,
r09=sweep_r0$r09,
sweep_unique = sweep_r0$sweep_unique)
sweep <- sweep%>%mutate(
foi_sp = 0.6,
foi_sn = 1.4)
##Now add the different serothresh
sweep_thresh <- rbind(sweep,sweep,sweep,sweep,sweep,sweep,sweep,sweep)
sweep_thresh <- sweep_thresh%>%
mutate(sero_thresh = rep(c(0,0.5,0.55,0.6,0.65,0.7,0.75,0.8), each=160))
saveRDS(sweep_thresh, "1_main/0_sweep_imm4_foisp0.6.RDS")
##Interval vax
sweep_int<- rbind(sweep,sweep,sweep,sweep)
sweep_int<- sweep_int%>%
mutate(vax_first = rep(c(435,800), each=320),
vax_int = rep(c(365, 730, 365, 730),each=160),
vax_start = rep(c((435/365)%%1,
(435/730)%%1,
(800/365)%%1,
(800/730)%%1),each=160),
vax_end = rep(c((465/365)%%1,
(465/730)%%1,
(830/365)%%1,
(830/730)%%1),each=160))
sweep_int2 <- rbind(sweep,sweep)%>%
mutate(vax_first = 0,
vax_int = rep(c(365,730), each=160),
vax_start = rep(c(300/365, 300/730),each=160),
vax_end = rep(c(330/365, 330/730),each=160))
sweep_int <- rbind(sweep_int, sweep_int2)
saveRDS(sweep_int, "1_main/0_sweep_imm4_foisp0.6_int.RDS")
##100 runs Sweep kappa for foi_sp=0.6
sweep0<-readRDS("1_main/0_sweep_sero.RDS")
sweep<- readRDS("1_main/0_sweep_imm4.RDS")
sweep_r0 <- sweep0%>%group_by(sweep_unique)%>%slice(1)
sweep_r0 <- sweep_r0%>%filter(sweep_unique<=96)
sweep<- sweep%>%
filter(omega2_pc==1/180)%>%
filter(kappa3==1/500)%>%
filter(sero_thresh==0)
sweep <- rbind(sweep,sweep,sweep)
sweep <- sweep%>%
mutate(r00=sweep_r0$r00,
r01=sweep_r0$r01,
r02=sweep_r0$r02,
r03=sweep_r0$r03,
r04=sweep_r0$r04,
r05=sweep_r0$r05,
r06=sweep_r0$r06,
r07=sweep_r0$r07,
r08=sweep_r0$r08,
r09=sweep_r0$r09,
sweep_unique = sweep_r0$sweep_unique)
sweep <- sweep%>%mutate(
foi_sp = 0.6,
foi_sn = 1.4)
##Now add the different serothresh
sweep_thresh <- rbind(sweep,sweep,sweep,sweep)
sweep_thresh <- sweep_thresh%>%
mutate(sero_thresh = rep(c(0.5,0.6,0.7,0.8), each=96))
sweep_kappa <- rbind(sweep_thresh,sweep_thresh,sweep_thresh,
sweep_thresh, sweep_thresh,sweep_thresh)
sweep_kappa <- sweep_kappa%>%
mutate(kappa2 = rep(c(1/500,1/1000,1/1500,1/2000,1/3000,1/3500), each=384),
kappa3 = rep(c(1/500,1/1000,1/1500,1/2000,1/3000,1/3500), each=384))
saveRDS(sweep_kappa, "0_sweep_imm4_foi0.6_sweepkappa_vax.RDS")
##Need vaxed scenarios for the sweepkappa....
###Redo foi_sp no vax 0.9....
sweep<- readRDS("3_foisweep/0_sweep_imm4_varyfoi_novax.RDS")
sweep<- sweep%>%filter(foi_sp==0.9)
sweep<- sweep%>%mutate(foi_sn=1.1)
saveRDS(sweep,"3_foisweep/0_sweep_imm4_varyfoi_foisp0.9_redo.RDS")