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indiana-hiv-util.R
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library(splines)
library(RColorBrewer)
source("indiana-hiv-load.R")
source("indiana-hiv-settings.R")
#############################################
plot_dx_rate = function(obj) {
dxrate_mid_smooth2 = obj$dxrate_mid_smooth2
dxrate_hi_smooth = obj$dxrate_hi_smooth
dxrate_lo_smooth = obj$dxrate_lo_smooth
ymax = max(dxrate_hi_smooth)
plot(dayseq, dxrate_mid_smooth2,
type="n",
xlim=range(dayseq),
ylim=c(0,ymax),
axes=FALSE, ylab="Case-finding rate")
axis(1,at=monthdayseq, lab=monthlabseq)
axis(2)
# actual
polygon(c(dayseq,rev(dayseq)), c(dxrate_lo_smooth, rev(dxrate_hi_smooth)), col=mydarkorange, border=mydarkorange)
# projected
lines(dayseq, dxrate_mid_smooth2, col=myorange, lwd=2)
legend(0, 0.9*ymax,
c("Case-finding rate (actual)", "Case-finding rate (projected)"),
lty=c(0,1),
lwd=c(NA,2),
pch=c(22,NA),
pt.cex=c(3,NA),
col=c(mydarkorange, myorange),
border=c(mydarkorange, myorange),
pt.bg=c(mydarkorange, myorange),
bg="white", bty="n", cex=text_cex)
mtext("A", side=3, adj=0, line=-1.0, cex=2)
}
################################
################################
plot_methods_illustration1 = function() {
smooth_dx = smoothers[[1]]$dxrange[2]
smooth_Iudx = smoothers[[1]]$Iudxrange[2]
smooth_I = smoothers[[1]]$Irange[2]
smooth_S = smoothers[[1]]$Srange[2]
smoother = smoothernames[1]
# Get data under actual intvx
obj_actual = get_indiana_bounds(N_init, intvx_actual_date, end_date,
smooth_dx, smooth_Iudx, smooth_I, smooth_S, smoother,
removal_rate_mid, calibration_scale_init)
I_lo_actual = obj_actual$I_lo
I_hi_actual = obj_actual$I_hi
Iudx_lo_actual = obj_actual$Iudx_lo
Iudx_hi_actual = obj_actual$Iudx_hi
Iudx_lo2_actual = obj_actual$Iudx_lo2
Iudx_hi2_actual = obj_actual$Iudx_hi2
dxrate_hi_smooth = obj_actual$dxrate_hi_smooth
dxrate_lo_smooth = obj_actual$dxrate_lo_smooth
par(mfrow=c(2,1), mar=c(2.7,4.5,1,1), bty="n", cex.lab=1.2, cex.axis=1.2)
#layout(matrix(c(1,2), byrow=TRUE, nrow=2), heights=c(1,2))
# Fig 1A
plot(dayseq, dx,
type="n",
xlim=c(0,max(dayseq)),
ylim=c(0,max(I_hi_actual)),
axes=FALSE, ylab="People")
axis(1,at=monthdayseq, lab=monthlabseq)
axis(2)
polygon(c(dayseq,rev(dayseq)), c(I_lo_actual,rev(I_hi_actual)), col=mydarkgray, border=mydarkgray)
lines(dayseq, dx, lwd=2, col=mydarkblue)
#newcases = c(0,diff(dx))
#sapply(which(newcases>0), function(i) lines(c(i,i),c(0,newcases[i]), lwd=2, col=mydarkblue))
legend(0, 150,
c("Cumulative HIV incidence (Campbell et al, 2017)",
"Cumulative HIV Diagnoses (Peters et al, 2016)"),
lty=c(0, 1),
pch=c(22,NA),
pt.cex=c(3,NA),
lwd=c(1,2),
col=c(mydarkgray, mydarkblue),
border=c(mydarkgray,NA),
pt.bg=c(mydarkgray, NA),
bg="white", bty="n", cex=text_cex)
mtext("A", side=3, adj=0, line=-1.2, cex=2)
# Fig 1B
plot(dayseq, dx,
type="n",
xlim=range(dayseq),
ylim=c(0,max(dx)),
axes=FALSE, ylab="People")
axis(1,at=monthdayseq, lab=monthlabseq)
axis(2)
polygon(c(dayseq,rev(dayseq)), c(Iudx_lo_actual,rev(Iudx_hi_actual)), col=mydarkred, border=mydarkred)
#polygon(c(dayseq,rev(dayseq)), c(Iudx_lo2_actual,rev(Iudx_hi2_actual)), col=myred, border=myred)
#lines(dayseq, dx_smooth, lwd=2, col=mydarkblue)
ymax = 170
arrows(first_dx_day, ymax*0.8,
first_dx_day, Iudx_hi_actual[dayseq==first_dx_day], length=0.05)
text(first_dx_day, ymax*0.8,
"First diagnosis", pos=2, cex=text_cex, offset=0.3)
arrows(investigation_begin_day, ymax*0.9,
investigation_begin_day, Iudx_hi_actual[dayseq==investigation_begin_day], length=0.05)
text(investigation_begin_day, ymax*0.9,
"Investigation begins", pos=2, cex=text_cex, offset=0.3)
arrows(emergency_declared_day, ymax*1.0,
emergency_declared_day, Iudx_hi_actual[dayseq==emergency_declared_day], length=0.05)
text(emergency_declared_day, ymax*1.0,
"Emergency declared", pos=2, cex=text_cex, offset=0.3)
arrows(clinic_opened_day, ymax*0.9,
clinic_opened_day, Iudx_hi_actual[dayseq==clinic_opened_day], length=0.05)
text(clinic_opened_day, ymax*0.9,
"HIV clinic opens", pos=4, cex=text_cex, offset=0.3)
arrows(sep_started_day, ymax*0.8,
sep_started_day, Iudx_hi_actual[dayseq==sep_started_day], length=0.05)
text(sep_started_day, ymax*0.8,
"SEP begins", pos=4, cex=text_cex, offset=0.3)
legend(0, 150,
"Undiagnosed HIV+",
border=mydarkred,
lty=0,
pch=22,
pt.cex=3,
col=mydarkred,
pt.bg=mydarkred,
bg="white", bty="n", cex=text_cex)
mtext("B", side=3, adj=0, line=-1.0, cex=2)
}
#####################################
plot_methods_illustration2 = function() {
smooth_dx = smoothers[[1]]$dxrange[2]
smooth_Iudx = smoothers[[1]]$Iudxrange[2]
smooth_I = smoothers[[1]]$Irange[2]
smooth_S = smoothers[[1]]$Srange[2]
smoother = smoothernames[1]
# Get data under actual intvx
obj_actual = get_indiana_bounds(N_init, intvx_actual_date, end_date,
smooth_dx, smooth_Iudx, smooth_I, smooth_S, smoother,
removal_rate_mid, calibration_scale_init)
I_lo_actual = obj_actual$I_lo
I_hi_actual = obj_actual$I_hi
Iudx_lo_actual = obj_actual$Iudx_lo
Iudx_hi_actual = obj_actual$Iudx_hi
Iudx_lo2_actual = obj_actual$Iudx_lo2
Iudx_hi2_actual = obj_actual$Iudx_hi2
dxrate_hi_smooth = obj_actual$dxrate_hi_smooth
dxrate_lo_smooth = obj_actual$dxrate_lo_smooth
#dday = intvxday + scaleup_peak_offset
obj = get_indiana_bounds(N_init, intvx_mid_date, intvx_mid_date+scaleup_peak_offset,
smooth_dx, smooth_Iudx, smooth_I, smooth_S, smoother,
removal_rate_mid, calibration_scale_init)
#I_lo = obj$I_lo
#I_hi = obj$I_hi
I_lo2 = obj$I_lo2
I_hi2 = obj$I_hi2
S_lo = obj$S_lo
S_hi = obj$S_hi
S_lo2 = obj$S_lo2
S_hi2 = obj$S_hi2
Iudx_lo2 = obj$Iudx_lo2
Iudx_hi2 = obj$Iudx_hi2
Idx_lo2 = obj$Idx_lo2
Idx_hi2 = obj$Idx_hi2
dx_smooth = obj$dx_smooth
dxrate_hi_smooth2 = obj$dxrate_hi_smooth2
dxrate_lo_smooth2 = obj$dxrate_lo_smooth2
par(mfrow=c(2,1), mar=c(2.7,4.5,1,1), bty="n", cex.lab=1.2, cex.axis=1.2)
# Fig 2A
plot(dayseq, dx,
type="n",
xlim=range(dayseq),
ylim=c(0,max(dxrate_hi_smooth)),
axes=FALSE, ylab="Case-finding rate")
axis(1,at=monthdayseq, lab=monthlabseq)
axis(2)
polygon(c(dayseq,rev(dayseq)), c(dxrate_lo_smooth, rev(dxrate_hi_smooth)), col=mydarkorange, border=mydarkorange)
lines(dayseq, obj_actual$dxrate_mid_smooth2, col=myorange, lwd=2)
ymax = max(dxrate_hi_smooth)
arrows(first_dx_day, 0.7*ymax,
first_dx_day, obj_actual$dxrate_mid_smooth[dayseq==first_dx_day], length=0.05)
text(first_dx_day, 0.7*ymax,
"First Diagnosis", pos=2, cex=text_cex, offset=0.3)
arrows(first_dx_day+scaleup_peak_offset, 0.9*ymax,
first_dx_day+scaleup_peak_offset, obj_actual$dxrate_mid_smooth[dayseq==(first_dx_day+scaleup_peak_offset)], length=0.05)
text(first_dx_day+scaleup_peak_offset, 0.9*ymax,
"Target case-finding rate", pos=2, cex=text_cex, offset=0.3)
legend(0, 0.5*max(obj_actual$dxrate_hi_smooth),
c("Case-finding rate bounds (reconstructed from raw data)",
"Case-finding rate midpoint"),
border=c(myorange,NA),
lty=c(0,1),
lwd=c(NA,2),
pch=c(22,NA),
pt.cex=c(3,NA),
col=c(mydarkorange,myorange),
pt.bg=c(mydarkorange,NA),
bg="white", bty="n", cex=text_cex)
mtext("A", side=3, adj=0, line=-1.2, cex=2)
# Fig 2B
plot(dayseq, dx,
type="n",
xlim=range(dayseq),
ylim=c(0,max(dxrate_hi_smooth)),
axes=FALSE, ylab="Case-finding rate")
axis(1,at=monthdayseq, lab=monthlabseq)
axis(2)
polygon(c(dayseq,rev(dayseq)), c(dxrate_lo_smooth, rev(dxrate_hi_smooth)), col=mydarkorange, border=mydarkorange)
lines(dayseq, obj$dxrate_mid_smooth2, col=myorange, lwd=2)
#ymax = max(dxrate_hi_smooth)
arrows(intvx_mid_day, 0.7*ymax,
intvx_mid_day, dxrate_hi_smooth[dayseq==intvx_mid_day], length=0.05)
text(intvx_mid_day, 0.7*ymax,
"First Diagnosis (counterfactual)", pos=2, cex=text_cex, offset=0.3)
arrows(intvx_mid_day+scaleup_peak_offset, 0.9*ymax,
intvx_mid_day+scaleup_peak_offset, obj$dxrate_mid_smooth[dayseq==(intvx_mid_day+scaleup_peak_offset)], length=0.05)
text(intvx_mid_day+scaleup_peak_offset, 0.9*ymax,
"Target case-finding rate (counterfactual)", pos=2, cex=text_cex, offset=0.3)
legend(0, 0.5*max(dxrate_hi_smooth),
"Case-finding rate (counterfactual)",
lty=c(1),
lwd=2,
col=c(myorange),
bg="white", bty="n", cex=text_cex)
#legend(0, 0.5*max(dxrate_hi_smooth),
#c("Case-finding rate (reconstructed from raw data)",
#"Case-finding rate (counterfactual)"),
#border=c(myorange,NA),
#lty=c(0,1),
#pch=c(22,NA),
#pt.cex=c(3,NA),
#col=c(mydarkorange,myorange),
#pt.bg=c(mydarkorange,NA),
#bg="white", bty="n", cex=text_cex)
mtext("B", side=3, adj=0, line=-1.2, cex=2)
# Detail plot
}
############################################
############################################
############################################
############################################
# NOT USED!
plot_transmission_rate = function(obj) {
beta_lo = obj$beta_lo
beta_hi = obj$beta_hi
plot(daily_timescale, beta_hi, type="n", ylim=c(0,max(beta_hi)), xlim=c(0,max(ndays)), axes=FALSE, ylab="Infection rate")
polygon(c(daily_timescale,rev(daily_timescale)), c(beta_lo, rev(beta_hi)), col=mygray)
axis(1,at=monthseq[indices], lab=monthlabs[indices])
axis(2)
}
############################################
############################################
############################################
############################################
get_indiana_bounds = function(N, intvx_date, intvx_end_date, smooth_dx,
smooth_Iudx, smooth_I, smooth_S, smoother,
removal_rate, calibration_scale, beta_scale=1) {
intvx_day = as.numeric(intvx_date - zero_date)
intvx_end_day = as.numeric(intvx_end_date - zero_date)
smooth_method = smoothers[[which(smoothernames==smoother)]]$f
infections_mean = (infections_lo + infections_hi) / 2
infections_lo_tmp = pmax(0,infections_mean - calibration_scale*(infections_mean-infections_lo))
infections_hi_tmp = infections_mean + calibration_scale*(infections_hi-infections_mean)
ylo = rep(NA, length(dayseq))
yhi = rep(NA, length(dayseq))
ylo[1] = infections_lo_tmp[1]
yhi[1] = infections_hi_tmp[1]
for(i in 2:ndays) {
yhi[i] = max(c(yhi[1:(i-1)], infections_hi_tmp[i]))
ylo[i] = min(infections_lo_tmp[i:ndays])
}
infections_lo = ylo
infections_hi = yhi
I_hi = infections_hi
I_lo = pmax(infections_lo,dx)
Iudx_lo = pmax(0,I_lo - dx)
Iudx_hi = pmin(N,I_hi - dx)
S_hi = pmax(0,N - I_lo)
S_lo = pmin(N,N - I_hi)
S_hi_smooth = smooth_method(dayseq, S_hi, v=smooth_S)
S_lo_smooth = smooth_method(dayseq, S_lo, v=smooth_S)
I_hi_smooth = pmax(1,smooth_method(dayseq, I_hi, v=smooth_I))
I_lo_smooth = pmax(1,smooth_method(dayseq, I_lo, v=smooth_I))
Iudx_lo_smooth = pmax(1,smooth_method(dayseq, Iudx_lo, v=smooth_Iudx))
Iudx_hi_smooth = pmax(1,smooth_method(dayseq, Iudx_hi, v=smooth_Iudx))
dx_smooth = dx
backlag = 200
dx_smooth[(first_dx_day-backlag):ndays] = smooth_method(dayseq[(first_dx_day-backlag):ndays], dx[(first_dx_day-backlag):ndays], v=smooth_dx)
dx_smooth[dx_smooth<0] = 0
dx_smooth_diff = c(0,pmax(0,diff(dx_smooth)))
dxrate_hi_smooth = dx_smooth_diff/Iudx_lo_smooth
dxrate_lo_smooth = dx_smooth_diff/Iudx_hi_smooth
#print(I_hi_smooth)
#print(I_lo_smooth)
# estimate bounds for beta
daymax = first_dx_day
beta_lo = (I_lo_smooth[daymax] - I_hi[1])/(I_hi_smooth[1:daymax] %*% (N-I_hi_smooth[1:daymax]))
beta_hi = (I_hi_smooth[daymax] - I_lo[1])/(Iudx_lo_smooth[1:daymax] %*% (N-Iudx_lo_smooth[1:daymax]))
beta_mid = rep((beta_lo+beta_hi)/2, ndays)
# scale reduction in beta
beta_mid[intvx_day:ndays] = beta_scale*beta_mid[intvx_day:ndays]
peak_dx_day = min(end_day,first_dx_day+intvx_end_day-intvx_day)
dxrate_lo_smooth2 = rep(0,ndays)
dxrate_lo_smooth2[intvx_day:(intvx_day+peak_dx_day-first_dx_day)] = dxrate_lo_smooth[first_dx_day:peak_dx_day]
dxrate_lo_smooth2[(intvx_day+peak_dx_day-first_dx_day+1):ndays] = dxrate_lo_smooth[peak_dx_day]
dxrate_hi_smooth2 = rep(0,ndays)
dxrate_hi_smooth2[intvx_day:(intvx_day+peak_dx_day-first_dx_day)] = dxrate_hi_smooth[first_dx_day:peak_dx_day]
dxrate_hi_smooth2[(intvx_day+peak_dx_day-first_dx_day+1):ndays] = dxrate_hi_smooth[peak_dx_day]
dxrate_mid_smooth2 = (dxrate_lo_smooth2 + dxrate_hi_smooth2)/2
S_lo2 = S_lo
S_hi2 = S_hi
I_lo2 = I_lo
I_hi2 = I_hi
Iudx_lo2 = Iudx_lo
Iudx_hi2 = Iudx_hi
Idx_lo2 = rep(0,length(dayseq))
Idx_hi2 = rep(0,length(dayseq))
R_lo = rep(0, ndays)
R_hi = rep(0, ndays)
cumdx_lo = rep(0, ndays)
cumdx_hi = rep(0, ndays)
for(i in intvx_day:ndays) {
new_dx_hi = dxrate_mid_smooth2[i-1]*Iudx_hi2[i-1]
new_dx_lo = dxrate_mid_smooth2[i-1]*Iudx_lo2[i-1]
new_removal_lo = removal_rate*Idx_lo2[i-1]
new_removal_hi = removal_rate*Idx_hi2[i-1]
new_infect_hi = beta_mid[i]*(Iudx_hi2[i-1] + Idx_hi2[i-1])*S_hi2[i-1]
new_infect_lo = beta_mid[i]*(Iudx_lo2[i-1] + Idx_lo2[i-1])*S_lo2[i-1]
Iudx_lo2[i] = pmin(N,pmax(0,Iudx_lo2[i-1] + new_infect_lo - new_dx_lo))
Iudx_hi2[i] = pmin(N,pmax(0,Iudx_hi2[i-1] + new_infect_hi - new_dx_hi))
Idx_lo2[i] = pmin(N,Idx_lo2[i-1] + new_dx_lo - new_removal_lo)
Idx_hi2[i] = pmin(N,Idx_hi2[i-1] + new_dx_hi - new_removal_hi)
cumdx_lo[i] = pmin(N,cumdx_lo[i-1] + new_dx_lo)
cumdx_hi[i] = pmin(N,cumdx_hi[i-1] + new_dx_hi)
R_lo[i] = R_lo[i-1] + new_removal_lo
R_hi[i] = R_hi[i-1] + new_removal_hi
I_lo2[i] = pmin(N, I_lo2[i-1] + new_infect_lo) #pmin(N,Iudx_lo2[i] + Idx_lo2[i] + R_lo[i])
I_hi2[i] = pmin(N, I_hi2[i-1] + new_infect_hi) #pmin(N,Iudx_hi2[i] + Idx_hi2[i] + R_hi[i])
S_lo2[i] = pmax(0,N - I_hi2[i])
S_hi2[i] = pmax(0,N - I_lo2[i])
}
return(list(I_lo=I_lo,
I_hi=I_hi,
I_lo2=I_lo2,
I_hi2=I_hi2,
I_lo_smooth=I_lo_smooth,
I_hi_smooth=I_hi_smooth,
S_lo=S_lo,
S_hi=S_hi,
S_lo2=S_lo2,
S_hi2=S_hi2,
Iudx_lo_smooth=Iudx_lo_smooth,
Iudx_hi_smooth=Iudx_hi_smooth,
Iudx_lo2=Iudx_lo2,
Iudx_hi2=Iudx_hi2,
Iudx_lo=Iudx_lo,
Iudx_hi=Iudx_hi,
Idx_lo2=Idx_lo2,
Idx_hi2=Idx_hi2,
cumdx_lo=cumdx_lo,
cumdx_hi=cumdx_hi,
R_lo=R_lo,
R_hi=R_hi,
dx_smooth=dx_smooth,
dxrate_lo_smooth=dxrate_lo_smooth,
dxrate_hi_smooth=dxrate_hi_smooth,
dxrate_lo_smooth2=dxrate_lo_smooth2,
dxrate_hi_smooth2=dxrate_hi_smooth2,
dxrate_mid_smooth2=dxrate_mid_smooth2,
beta_lo=beta_lo,
beta_hi=beta_hi,
N=N))
}
###############################################
#############################################
plot_infections_by_N = function() {
smooth_dx = smoothers[[1]]$dxrange[2]
smooth_Iudx = smoothers[[1]]$Iudxrange[2]
smooth_I = smoothers[[1]]$Irange[2]
smooth_S = smoothers[[1]]$Srange[2]
smoother = smoothernames[1]
intvx_dates = c(intvx_early_date+2, intvx_mid_date, intvx_actual_date)
a = 0.3
mycols = rev(c(rgb(1,0,0,alpha=a), rgb(0,1,0,alpha=a), rgb(0,0,1,alpha=a)))
Ns = seq(215,4000,length.out=50)
I_hi_end = array(NA,dim=c(length(Ns),length(intvx_dates)))
I_lo_end = array(NA,dim=c(length(Ns),length(intvx_dates)))
par(mfrow=c(3,1), mar=c(4.0,4.5,1,1.0), bty="n", cex.lab=1.2, cex.axis=1.2)
ymax = 450
for(j in 1:length(intvx_dates)) {
for(i in 1:length(Ns)) {
idate = intvx_dates[j]
obj = get_indiana_bounds(Ns[i], idate, idate+scaleup_peak_offset, smooth_dx, smooth_Iudx, smooth_I, smooth_S, smoother, removal_rate_mid, calibration_scale_init)
I_lo_end[i,j] = obj$I_lo2[ndays]
I_hi_end[i,j] = obj$I_hi2[ndays]
}
plot(0, type="n", ylim=c(0,ymax), xlim=c(215,max(Ns)),
ylab=paste("HIV infections by", format(end_date, "%B %d, %Y")),
xlab="Population size N", lwd=2, axes=FALSE)
axis(1,at=c(215,1000,2000,3000,4000))
axis(2)
polygon(c(Ns,rev(Ns)), c(I_hi_end[,j], rev(I_lo_end[,j])), col=mycols[j], border=mycols[j])
polygon(c(215,4000,4000,215), c(rep(obj$I_lo[ndays],2), rep(obj$I_hi[ndays],2)), col=mygray, border=mygray)
text(1000, obj$I_lo[ndays],
paste("Actual infections by", format(end_date, "%B %d, %Y"), ":",
round(obj$I_lo[ndays]), "-", round(obj$I_hi[ndays])), pos=3, cex=text_cex)
legend(215,ymax, c(paste("Intervention on", format(intvx_dates[j], "%B %d, %Y")),
paste("Infections on", format(end_date, "%B %d, %Y"),
"under actual circumstances")),
pch=22, pt.cex=2, cex=text_cex, col=c(mycols[j],mygray), pt.bg=c(mycols[j],mygray), bty="n")
}
}
#############################################
#############################################
plot_infections_by_intvx_date = function() {
smooth_dx = smoothers[[1]]$dxrange[2]
smooth_Iudx = smoothers[[1]]$Iudxrange[2]
smooth_I = smoothers[[1]]$Irange[2]
smooth_S = smoothers[[1]]$Srange[2]
smoother = smoothernames[1]
idates = seq(zero_date+2, first_dx_date, by=1)
idays = difftime(idates, zero_date)
I_hi_end = rep(NA,length(idates))
I_lo_end = rep(NA,length(idates))
for(i in 1:length(idates)) {
idate = idates[i]
obj = get_indiana_bounds(N_init, idate, idate+scaleup_peak_offset, smooth_dx,
smooth_Iudx, smooth_I, smooth_S, smoother, removal_rate_init, calibration_scale_init)
I_lo_end[i] = obj$I_lo2[ndays]
I_hi_end[i] = obj$I_hi2[ndays]
}
#par(mar=c(4.0,4.5,1,1.0), bty="n", cex.lab=1.2, cex.axis=1.2)
ymax = max(I_hi_end)
par(mar=c(4.0,4.5,1,1.0), bty="n", cex.lab=1.2, cex.axis=1.2)
plot(0, type="n", ylim=range(c(I_hi_end,I_lo_end)), xlim=c(0,first_dx_day+70),
ylab=paste("HIV infections by", format(end_date, "%B %d, %Y")),
xlab="Counterfactual intervention date", lwd=2, axes=FALSE)
axis(1,at=monthdayseq[1:5], lab=monthlabseq[1:5])
axis(2)
polygon(c(idays,rev(idays)), c(I_hi_end, rev(I_lo_end)), col=mygray, border="gray")
points(first_dx_day, (obj$I_lo[ndays]+obj$I_lo[ndays])/2,
pch=3, cex=2, col="black", bg="black")
text(first_dx_day, (obj$I_lo[ndays]+obj$I_lo[ndays])/2,
paste("Actual infections by", format(end_date, "%B %d, %Y"), ":",
round(obj$I_lo[ndays]), "-", round(obj$I_hi[ndays])),
cex=text_cex,
pos=2,offset=1)
}
###############################################
###############################################
plot_infections_by_incidence_factor = function() {
smooth_dx = smoothers[[1]]$dxrange[2]
smooth_Iudx = smoothers[[1]]$Iudxrange[2]
smooth_I = smoothers[[1]]$Irange[2]
smooth_S = smoothers[[1]]$Srange[2]
smoother = smoothernames[1]
intvx_dates = c(intvx_early_date+2, intvx_mid_date, intvx_actual_date)
a = 0.3
mycols = rev(c(rgb(1,0,0,alpha=a), rgb(0,1,0,alpha=a), rgb(0,0,1,alpha=a)))
incidence_factors = seq(1,2,length.out=50)
I_hi_end = array(NA,dim=c(length(incidence_factors),length(intvx_dates)))
I_lo_end = array(NA,dim=c(length(incidence_factors),length(intvx_dates)))
I_hi_actual_end = rep(NA,length(incidence_factors))
I_lo_actual_end = rep(NA,length(incidence_factors))
par(mar=c(4.0,4.5,1,1.0), mfrow=c(3,1), bty="n", cex.lab=1.2, cex.axis=1.2)
ymax = N_init
for(j in 1:length(intvx_dates)) {
for(i in 1:length(incidence_factors)) {
idate = intvx_dates[j]
obj = get_indiana_bounds(N_init, idate, idate+scaleup_peak_offset, smooth_dx,
smooth_Iudx, smooth_I, smooth_S, smoother, removal_rate_init, incidence_factors[i])
I_lo_end[i,j] = obj$I_lo2[ndays]
I_hi_end[i,j] = obj$I_hi2[ndays]
I_lo_actual_end[i] = obj$I_lo[ndays] # non-projected incidence
I_hi_actual_end[i] = obj$I_hi[ndays]
}
plot(0, type="n", ylim=c(0,ymax), xlim=c(1,max(incidence_factors)),
ylab=paste("HIV infections by", format(end_date, "%B %d, %Y")),
xlab="Incidence factor", lwd=2)
polygon(c(incidence_factors,rev(incidence_factors)),
c(I_hi_end[,j], rev(I_lo_end[,j])), col=mycols[j], border=mycols[j])
polygon(c(incidence_factors,rev(incidence_factors)),
c(I_hi_actual_end, rev(I_lo_actual_end)), col=mygray, border=mygray)
legend(1.04,ymax,
c(paste("Infections on", format(end_date, "%B %d, %Y"),
"under intervention on", format(intvx_dates[j], "%B %d, %Y")),
paste("Infections on", format(end_date, "%B %d, %Y"),
"under actual circumstances")),
pch=22,
cex=text_cex,
pt.cex=2,
col=c(mycols[j], mygray),
pt.bg=c(mycols[j],mygray),
bty="n")
}
#text(1.05, obj$I_hi[ndays],
#paste("Actual infections by", format(end_date, "%B %d, %Y"), ":",
#round(obj$I_lo[ndays]), "-", round(obj$I_hi[ndays])),
#pos=3)
}
###############################################
###############################################
plot_infections_by_rho = function() {
smooth_dx = smoothers[[1]]$dxrange[2]
smooth_Iudx = smoothers[[1]]$Iudxrange[2]
smooth_I = smoothers[[1]]$Irange[2]
smooth_S = smoothers[[1]]$Srange[2]
smoother = smoothernames[1]
intvx_dates = c(intvx_early_date+2, intvx_mid_date, intvx_actual_date)
a = 0.3
mycols = rev(c(rgb(1,0,0,alpha=a), rgb(0,1,0,alpha=a), rgb(0,0,1,alpha=a)))
rhos = seq(0,0.1,length.out=50)
I_hi_end = array(NA,dim=c(length(rhos),length(intvx_dates)))
I_lo_end = array(NA,dim=c(length(rhos),length(intvx_dates)))
par(mfrow=c(3,1), mar=c(4.0,4.5,1,1.0), bty="n", cex.lab=1.2, cex.axis=1.2)
ymax = N_init
for(j in 1:length(intvx_dates)) {
for(i in 1:length(rhos)) {
idate = intvx_dates[j]
obj = get_indiana_bounds(N_init, idate, idate+scaleup_peak_offset, smooth_dx,
smooth_Iudx, smooth_I, smooth_S, smoother, rhos[i], calibration_scale_init)
I_lo_end[i,j] = obj$I_lo2[ndays]
I_hi_end[i,j] = obj$I_hi2[ndays]
}
plot(0, type="n", ylim=c(0,ymax), xlim=c(0,max(rhos)),
ylab=paste("Projected HIV infections by", format(end_date, "%B %d, %Y")),
xlab="Removal rate", lwd=2)
polygon(c(rhos,rev(rhos)), c(I_hi_end[,j], rev(I_lo_end[,j])), col=mycols[j], border=mycols[j])
polygon(c(0,0.1,0.1,0), c(rep(obj$I_lo[ndays],2), rep(obj$I_hi[ndays],2)), col=mygray, border=mygray)
text(0.05, obj$I_hi[ndays],
paste("Actual infections by", format(end_date, "%B %d, %Y"), ":", round(obj$I_lo[ndays]), "-",
round(obj$I_hi[ndays]), cex=text_cex),
pos=3)
legend(0.04,ymax, c(paste("Intervention on", format(intvx_dates[j],"%B %d, %Y")),
paste("Infections on", format(end_date, "%B %d, %Y"), "under actual circumstances")
),
pch=22, pt.cex=2, cex=text_cex, col=c(mycols[j],mygray), pt.bg=c(mycols[j],mygray), bty="n")
}
}
###############################################
###############################################
plot_infections_by_beta_scale = function() {
smooth_dx = smoothers[[1]]$dxrange[2]
smooth_Iudx = smoothers[[1]]$Iudxrange[2]
smooth_I = smoothers[[1]]$Irange[2]
smooth_S = smoothers[[1]]$Srange[2]
smoother = smoothernames[1]
intvx_dates = c(intvx_early_date+2, intvx_mid_date, intvx_actual_date)
a = 0.3
mycols = rev(c(rgb(1,0,0,alpha=a), rgb(0,1,0,alpha=a), rgb(0,0,1,alpha=a)))
beta_scales = seq(0,1,length.out=50)
I_hi_end = array(NA,dim=c(length(beta_scales),length(intvx_dates)))
I_lo_end = array(NA,dim=c(length(beta_scales),length(intvx_dates)))
par(mfrow=c(3,1), mar=c(4.0,4.5,1,1.0), bty="n", cex.lab=1.2, cex.axis=1.2)
ymax = N_init
for(j in 1:length(intvx_dates)) {
for(i in 1:length(beta_scales)) {
idate = intvx_dates[j]
obj = get_indiana_bounds(N_init, idate, idate+scaleup_peak_offset, smooth_dx,
smooth_Iudx, smooth_I, smooth_S, smoother,
removal_rate=removal_rate_init,
calibration_scale=calibration_scale_init,
beta_scale=beta_scales[i])
I_lo_end[i,j] = obj$I_lo2[ndays]
I_hi_end[i,j] = obj$I_hi2[ndays]
}
plot(0, type="n", ylim=c(0,ymax), xlim=c(0,max(beta_scales)),
ylab=paste("HIV infections by", format(end_date, "%B %d, %Y")),
xlab="Transmission rate reduction proportion", lwd=2)
polygon(c(beta_scales,rev(beta_scales)), c(I_hi_end[,j], rev(I_lo_end[,j])), col=mycols[j], border=mycols[j])
polygon(c(0,1,1,0), c(rep(obj$I_lo[ndays],2), rep(obj$I_hi[ndays],2)), col=mygray, border=mygray)
text(0.5, obj$I_hi[ndays],
paste("Actual infections by", format(end_date, "%B %d, %Y"), ":", round(obj$I_lo[ndays]), "-",
round(obj$I_hi[ndays])),
pos=3)
legend(0.00,ymax, c(paste("Intervention on", format(intvx_dates[j],"%B %d, %Y")),
paste("Infections on", format(end_date, "%B %d, %Y"), "under actual circumstances")
),
pch=22, pt.cex=2, cex=text_cex, col=c(mycols[j],mygray), pt.bg=c(mycols[j],mygray), bty="n")
}
}
###############################################
###############################################
plot_indiana_bounds = function(N, intvxday, dday, showDates, smooth_dx,
smooth_Iudx, smooth_I, smooth_S, showSusc, smoother,
removal_rate, plotType, calibration_scale, beta_scale=1,
print_results=FALSE) {
obj = get_indiana_bounds(N, intvxday, dday, smooth_dx, smooth_Iudx, smooth_I,
smooth_S, smoother, removal_rate, calibration_scale, beta_scale)
if(print_results) {
cat("Intervention on", format(intvxday, "%B %d, %Y"), "\n")
cat(" Infections: [", round(obj$I_lo2[ndays]), ",", round(obj$I_hi2[ndays]), "] by ", format(end_date, "%B %d, %Y"), "\n", sep="")
cat(" actual diagnoses:", dx[ndays], "\n")
cat(" actual infections: [", obj$I_lo[ndays], ",", obj$I_hi[ndays], "]\n")
cat(" reduction of at least", 1-round(obj$I_hi2[ndays])/dx[ndays], "in diagnoses\n")
cat(" reduction of at least", 1-round(obj$I_hi2[ndays])/obj$I_lo[ndays], "in infections\n")
cat(" infections averted: at least", obj$I_lo[ndays] - obj$I_hi2[ndays], "\n")
idx = which.max(obj$Iudx_hi)
cat(" Peak Iudx: [", obj$Iudx_lo[idx], ",", obj$Iudx_hi[idx], "] on", format(dateseq[idx], "%B %d, %Y"), "\n")
cat(" [", obj$Iudx_lo[emergency_declared_day], ",", obj$Iudx_hi[emergency_declared_day], "] on ", format(emergency_declared_date,"%B %d, %Y"), "\n")
cat(" beta in [", obj$beta_lo, ",", obj$beta_hi, "]\n")
cat(" gamma(t) in [", 0, ",", max(obj$dxrate_lo_smooth), "]\n")
}
par(bty="n", cex=text_cex, cex.lab=text_cex, cex.axis=text_cex,
mar=c(2.7,4.5,1,0.0))
#layout(matrix(c(1,2,3), nrow=3), heights=c(1,1,3))
if(plotType!="calibration") {
layout(matrix(c(1,2), nrow=2), heights=c(1,3))
plot_dx_rate(obj)
#plot_transmission_rate(obj)
}
plot_epidemic_curves(obj, showDates, showSusc, plotType, calibration_scale)
}
##################################################
##################################################
plot_epidemic_curves = function(obj, showDates, showSusc, plotType, calibration_scale) {
I_lo = obj$I_lo
I_hi = obj$I_hi
I_lo_smooth = obj$I_lo_smooth
I_hi_smooth = obj$I_hi_smooth
I_lo2 = obj$I_lo2
I_hi2 = obj$I_hi2
S_lo = obj$S_lo
S_hi = obj$S_hi
S_lo2 = obj$S_lo2
S_hi2 = obj$S_hi2
Iudx_lo = obj$Iudx_lo
Iudx_hi = obj$Iudx_hi
Iudx_lo2 = obj$Iudx_lo2
Iudx_hi2 = obj$Iudx_hi2
Idx_lo2 = obj$Idx_lo2
Idx_hi2 = obj$Idx_hi2
cumdx_lo = obj$cumdx_lo
cumdx_hi = obj$cumdx_hi
Iudx_lo_smooth = obj$Iudx_lo_smooth
Iudx_hi_smooth = obj$Iudx_hi_smooth
R_lo = obj$R_lo
R_hi = obj$R_hi
dx_smooth = obj$dx_smooth
N = obj$N
if(plotType=="model") {
if(showSusc) {
ymax = N
} else {
ymax = max(c(I_hi, I_hi2, Iudx_hi, Iudx_hi2, Idx_hi2))
}
plot(0, type="n", ylim=c(0,ymax), xlim=c(0,max(ndays)), #xlim=c(dayseq[sim_start_idx],max(ndays)),
ylab="People", xlab="", lwd=2, axes=FALSE)
axis(1,at=monthdayseq, lab=monthlabseq)
axis(2)
if(showSusc) {
legend(0, 0.9*ymax,
c("Susceptible HIV- (actual)",
"Undiagnosed HIV+ (actual)",
paste("Total HIV+ (actual ", calibration_scale*100,"%)", sep=""),
"Cumulative HIV Diagnoses (actual)"),
border=c(mydarkgreen,mydarkred,mydarkgray,NA),
lty=c(0, 0, 0,1),
pch=c(22,22,22,NA),
pt.cex=c(3,3,3,NA),
lwd=c(1,1,1,2),
col=c(mydarkgreen, mydarkred,mydarkgray,"black"),
pt.bg=c(mydarkgreen, mydarkred,mydarkgray,NA),
bg="white", bty="n", cex=text_cex)
legend(0, 0.7*ymax,
c("Susceptible HIV- (projected)",
"Undiagnosed HIV+ (projected)",
"Diagnosed HIV+ infectious (projected)",
"Diagnosed HIV+ removed (projected)"),
col=c(mygreen, myred, mypurple, myblue),
border=c(mygreen, myred, mypurple, myblue),
pt.bg=c(mygreen, myred, mypurple, myblue),
lty=0,
pch=22,
pt.cex=c(3,3,3,3),
bg="white", bty="n", cex=text_cex)
} else {
legend(0, 0.9*ymax,
c("Undiagnosed HIV+ (actual)",
paste("Total HIV+ (actual ", calibration_scale*100,"%)", sep=""),
"Cumulative HIV Diagnoses (actual)"),
border=c(mydarkred,mydarkgray,NA),
lty=c(0,0,1),
pch=c(22,22,NA),
pt.cex=c(3),
lwd=c(1,1,2),
col=c(mydarkred,mydarkgray,"black"),
pt.bg=c(mydarkred,mydarkgray,NA),
bg="white", bty="n", cex=text_cex)
legend(0, 0.7*ymax,
c("Undiagnosed HIV+ (projected)",
"Diagnosed HIV+ infectious (projected)",
"Diagnosed HIV+ removed (projected)"),
col=c(myred, mypurple, myblue),
border=c(myred, mypurple, myblue),
pt.bg=c(myred, mypurple, myblue),
lty=0,
pch=22,
pt.cex=c(3,3),
bg="white", bty="n", cex=text_cex)
}
abline(h=N, lty="dashed")
# actual data:
polygon(c(dayseq,rev(dayseq)), c(Iudx_lo,rev(Iudx_hi)), col=mydarkred, border=mydarkred)
if(showSusc) polygon(c(dayseq,rev(dayseq)), c(S_lo,rev(S_hi)), col=mydarkgreen, border=mydarkgreen)
polygon(c(dayseq,rev(dayseq)), c(I_lo,rev(I_hi)), col=mydarkgray, border=mydarkgray)
lines(dayseq, dx, lwd=2, col="black")
# projected
if(showSusc) polygon(c(dayseq,rev(dayseq)), c(S_lo2,rev(S_hi2)), col=mygreen, border=mygreen)
#polygon(c(dayseq,rev(dayseq)), c(I_lo2,rev(I_hi2)), col=mygray, border=mygray)
polygon(c(dayseq,rev(dayseq)), c(Iudx_lo2,rev(Iudx_hi2)), col=myred, border=myred)
polygon(c(dayseq,rev(dayseq)), c(Idx_lo2,rev(Idx_hi2)), col=mypurple, border=mypurple)
polygon(c(dayseq, rev(dayseq)), c(R_lo, rev(R_hi)), col=myblue, border=myblue)
} else if(plotType=="raw") {
ymax = max(I_hi, I_hi2, Iudx_hi, Iudx_hi2, Idx_hi2)
plot(0, type="n", ylim=c(0,ymax), xlim=c(0,max(ndays)), #xlim=c(dayseq[sim_start_idx],max(ndays)),
ylab="People", xlab="", lwd=2, axes=FALSE)
axis(1,at=monthdayseq, lab=monthlabseq)
axis(2)
legend(0, 0.9*ymax,
c("Undiagnosed HIV+ (raw data)",
"Undiagnosed HIV+ (model projection)",
"Cumulative HIV incidence (raw data)",