formal/nigeria/nigeria-analysis.R
In jackolney/CascadeDashboard: A Shiny App for Investigating The Current Trajectory of HIV Care
####################################################################################################
# PEPFAR PHIA FILE
# Nigeria Cascade Tool Formal Analysis Script
# Model version include CD4 dependency on theta for only those with CD4 <200
####################################################################################################
rm(list=ls())
# AIM = Boil the calibration down to a set of REALLY NEAT FUNCTIONS.
setwd("~/git/CascadeDashboard/inst/app")
graphics.off()
quartz.options(w = 10, h = 8)
figFont <- "Avenir Next"
# Source initial files
source("../../formal/initial.R")
# GLOBAL
MasterName <- "Nigeria"
MasterData <- GetMasterDataSet(MasterName)
# Making the assumption of treat all from 2016
MasterData$treatment_guidelines[[6]] <- 2016
# I need to do an optim first to understand the parameter bounds
# ---- #
set.seed(100)
# ---- #
# These will be adjusted in due course:
MaxError <- 0.08
MinNumber <- 1000
# After first simulation, run this function (default = 5%)
# MaxError <- find_error_bound(runError, prop = 0.05)
# Define Parameter Range
parRange <- DefineParmRange(
rho = c(0.03, 0.07),
q = c(0.4, 0.6),
epsilon = c(100, 100),
kappa = c(3, 7),
gamma = c(2, 4),
theta = c(0, 0.1),
p = c(0.4, 0.6),
omega = c(0, 0.01)
)
# Run Calibration
start.time <- proc.time()
RunNSCalibration(
country = MasterName,
data = MasterData,
maxIterations = 1e4,
maxError = MaxError,
limit = MinNumber,
parRange = parRange,
targetIterations = 1e5)
finish.time <- proc.time() - start.time
finish.time[3] / 60
# 70 min runtime
graphics.off(); quartz.options(w = 8, h = 6)
BuildCD4CalibData_Thesis(year = 1, modelOut = modelOut)
quartz.save(file = "../../formal/nigeria/fig/cal/CD4-2010.pdf", type = "pdf")
graphics.off(); quartz.options(w = 8, h = 6)
BuildCD4CalibData_Thesis(year = 6, modelOut = modelOut)
quartz.save(file = "../../formal/nigeria/fig/cal/CD4-2015.pdf", type = "pdf")
# No PHIA for Nigeria
# graphics.off(); quartz.options(w = 9, h = 4)
# BuildPHIAPlot(data = CalibOut)
# quartz.save(file = "../../formal/nigeria/fig/cal/PHIA.pdf", type = "pdf")
####################################################################################################
#### PLOT ####
# Cascade in 2015
graphics.off(); quartz.options(w = 10, h = 4)
BuildCalibPlot_Thesis(data = CalibOut,
originalData = MasterData,
limit = MinNumber)
quartz.save(file = "../../formal/nigeria/fig/cal/cascade-2015.pdf", type = "pdf")
# Error Histogram
graphics.off(); quartz.options(w = 6, h = 3)
BuildCalibrationHistogram_Thesis(
runError = runError,
maxError = MaxError)
quartz.save(file = "../../formal/nigeria/fig/cal/calib-hist.pdf", type = "pdf")
# Calibration Detail
graphics.off(); quartz.options(w = 10, h = 8)
BuildCalibDetailPlot_Thesis(
data = CalibOut,
originalData = MasterData,
limit = MinNumber)
quartz.save(file = "../../formal/nigeria/fig/cal/calib-detail.pdf", type = "pdf")
# Parameter Histograms
graphics.off(); quartz.options(w = 10, h = 4)
BuildCalibrationParameterHistGroup_Thesis()
quartz.save(file = "../../formal/nigeria/fig/cal/par-hist.pdf", type = "pdf")
################################################################################
# DataReviewPlot
graphics.off(); quartz.options(w = 10, h = 4)
BuildDataReviewPlot_Thesis(data = MasterData$calib)
quartz.save(file = "../../formal/nigeria/fig/cal/calib-data.pdf", type = "pdf")
# save.image("../../formal/nigeria/data.RData")
# Parameter means
round(colMeans(CalibParamOut), 4)
# Parameter values
a <- paste0(round(Quantile_95(CalibParamOut[["rho"]])[["mean"]], 4), " [", round(Quantile_95(CalibParamOut[["rho"]])[["lower"]], 4), " to ", round(Quantile_95(CalibParamOut[["rho"]])[["upper"]], 4), "]")
b <- paste0(round(Quantile_95(CalibParamOut[["q"]])[["mean"]], 4), " [", round(Quantile_95(CalibParamOut[["q"]])[["lower"]], 4), " to ", round(Quantile_95(CalibParamOut[["q"]])[["upper"]], 4), "]")
c <- paste0(round(Quantile_95(CalibParamOut[["epsilon"]])[["mean"]], 4), " [", round(Quantile_95(CalibParamOut[["epsilon"]])[["lower"]], 4), " to ", round(Quantile_95(CalibParamOut[["epsilon"]])[["upper"]], 4), "]")
d <- paste0(round(Quantile_95(CalibParamOut[["kappa"]])[["mean"]], 4), " [", round(Quantile_95(CalibParamOut[["kappa"]])[["lower"]], 4), " to ", round(Quantile_95(CalibParamOut[["kappa"]])[["upper"]], 4), "]")
e <- paste0(round(Quantile_95(CalibParamOut[["gamma"]])[["mean"]], 4), " [", round(Quantile_95(CalibParamOut[["gamma"]])[["lower"]], 4), " to ", round(Quantile_95(CalibParamOut[["gamma"]])[["upper"]], 4), "]")
f <- paste0(round(Quantile_95(CalibParamOut[["theta"]])[["mean"]], 4), " [", round(Quantile_95(CalibParamOut[["theta"]])[["lower"]], 4), " to ", round(Quantile_95(CalibParamOut[["theta"]])[["upper"]], 4), "]")
g <- paste0(round(Quantile_95(CalibParamOut[["p"]])[["mean"]], 4), " [", round(Quantile_95(CalibParamOut[["p"]])[["lower"]], 4), " to ", round(Quantile_95(CalibParamOut[["p"]])[["upper"]], 4), "]")
h <- paste0(round(Quantile_95(CalibParamOut[["omega"]])[["mean"]], 4), " [", round(Quantile_95(CalibParamOut[["omega"]])[["lower"]], 4), " to ", round(Quantile_95(CalibParamOut[["omega"]])[["upper"]], 4), "]")
list(a,b,c,d,e,f,g,h)
Quantile_95(CalibParamOut[["rho"]])
Quantile_95(CalibParamOut[["q"]])
Quantile_95(CalibParamOut[["epsilon"]])
Quantile_95(CalibParamOut[["kappa"]])
Quantile_95(CalibParamOut[["gamma"]])
Quantile_95(CalibParamOut[["theta"]])
Quantile_95(CalibParamOut[["p"]])
Quantile_95(CalibParamOut[["omega"]])
# Mean of over-riding parameter bounds from non-shiny interface
################################################################################
# Projection
AdvCalib <- data.frame(NatMort = 0.005, HIVMort = 1)
# Single Powers Plot
graphics.off(); quartz.options(w = 8, h = 4)
GenSinglePowersPlot_Thesis()
quartz.save(file = "~/Desktop/fig/powers.pdf", type = "pdf")
# quartz.save(file = "~/Desktop/fig/powers.pdf", type = "pdf")
# CareCascade Plot
graphics.off(); quartz.options(w = 10, h = 4)
GenCascadePlot_Thesis()
# quartz.save(file = "~/Desktop/fig/cascade-projection.pdf", type = "pdf")
quartz.save(file = "../../formal/nigeria/fig/pro/cascade-projection.pdf", type = "pdf")
# What is the average value of beta?
# OutputBeta()
# 90-90-90 Plot
graphics.off(); quartz.options(w = 9, h = 4)
Gen909090Plot_Thesis()
# quartz.save(file = "~/Desktop/fig/90-90-90.pdf", type = "pdf")
quartz.save(file = "../../formal/nigeria/fig/pro/90-90-90.pdf", type = "pdf")
# Powers Plot
graphics.off(); quartz.options(w = 15, h = 4)
GenPowersCascadePlot_Thesis()
# quartz.save(file = "~/Desktop/fig/cascade-powers.pdf", type = "pdf")
quartz.save(file = "../../formal/nigeria/fig/pro/cascade-powers.pdf", type = "pdf")
# New Infections
graphics.off(); quartz.options(w = 6, h = 4)
GenNewInfPlot_Thesis()
# quartz.save(file = "~/Desktop/fig/new-infections.pdf", type = "pdf")
quartz.save(file = "../../formal/nigeria/fig/pro/new-infections.pdf", type = "pdf")
# AIDS Deaths
graphics.off(); quartz.options(w = 6, h = 4)
GenAidsDeathsPlot_Thesis()
# quartz.save(file = "~/Desktop/fig/AIDS-deaths.pdf", type = "pdf")
quartz.save(file = "../../formal/nigeria/fig/pro/AIDS-deaths.pdf", type = "pdf")
# Discrete Cascade
graphics.off(); quartz.options(w = 10, h = 4)
GenDiscreteCascade_Thesis()
# quartz.save(file = "~/Desktop/fig/cascade-discrete.pdf", type = "pdf")
quartz.save(file = "../../formal/nigeria/fig/pro/cascade-discrete.pdf", type = "pdf")
# CD4 distribution at ART initiation
graphics.off(); quartz.options(w = 8, h = 6)
BuildCD4Data_Thesis(year = 251)
# quartz.save(file = "~/Desktop/fig/CD4-2020.pdf", type = "pdf")
quartz.save(file = "../../formal/nigeria/fig/pro/CD4-2020.pdf", type = "pdf")
# NUMBERS
t0 <- GetCascadeData(1) # t0 = 1
t5 <- GetCascadeData(251) # t5 = (5 / 0.02) + 1 [t0]
# PLHIV Estimate in 2015
scales::comma(round(t0$res[1], -3))
1.394e+6
scales::comma(round(t5$res[1], -3))
1.516e+6
1.516e+6 / 1.394e+6
# DIAGNOSED
scales::comma(round(t0$res[2], -3))
1.044e+6
scales::comma(round(t5$res[2], -3))
1.296e+6
1.296e+6 / 1.044e+6
# On ART
scales::comma(round(t0$res[4], -3))
scales::comma(round(t5$res[4], -3))
round(t5$res[4], -3) / round(t0$res[4], -3)
37\% (0.899M to 1.233M)
# Viral suppression
scales::comma(round(t0$res[5], -3))
scales::comma(round(t5$res[5], -3))
round(t5$res[5], -3) / round(t0$res[5], -3)
40\% (0.791M to 1.104M)
23 - 14
t0
t0$res[5]/t0$res[1]
t5$res[5]/t5$res[1]
# edit on the 24/01/17 for new model that only has a CD4 dependency on theta for persons with CD4
# <200
save.image("../../formal/nigeria/data-28-03-17.RData")
# load("../../formal/nigeria/data-24-01-17.RData")
####################################################################################################
# if we were to adjust 'beta' such that it is reduced by 50%, then what functions would need to be
# adjusted? Remember, that we only wanted to adjust transmission between 2015 to 2020, not during
# calibration.
# Projection:
# GetModel()
# Optimisation:
# RunNSOptimisation()
# What about the baselineModel function that RunNSOptimisation() calls?
####################################################################################################
# Optimisation
intSwitch <- data.frame(
testing = TRUE,
linkage = TRUE,
preRetention = TRUE,
initiation = TRUE,
adherence = TRUE,
retention = TRUE
)
# These need updating
# and re-write this definition, it looks vile
# OptInput <- c()
# OptInput$intValue_rho <- parRange["rho", "max"]
# OptInput$intValue_q <- parRange["q", "max"]
# OptInput$intValue_kappa <- parRange["kappa", "min"]
# OptInput$intValue_gamma <- parRange["gamma", "max"]
# OptInput$intValue_sigma <- 0.5
# OptInput$intValue_omega <- parRange["omega", "min"]
OptInput <- c()
OptInput$intValue_rho <- 0.1
OptInput$intValue_q <- 1
OptInput$intValue_kappa <- 0
OptInput$intValue_gamma <- 10
OptInput$intValue_sigma <- 0.1
OptInput$intValue_omega <- 0
reactiveCost <- data.frame(
test = 10,
link = 40,
care = 40,
art = 367
)
# This is used by the function 'AdjustHIVTetsCost'
SafeReactiveCost <- data.frame(
test = 10,
link = 40,
care = 40,
art = 367
)
custom <- data.frame(target = 0.9^3)
AdvCalib <- data.frame(NatMort = 0.005, HIVMort = 1)
reactiveAdjustCost <- data.frame(switch = TRUE)
intLength = 2
AdjustHIVTestCost()
theOut <- RunNSOptimisation(propRuns = 0.1, intLength = intLength)
# Frontier Plot (optResults comes from RunNSOptimisation
graphics.off(); quartz.options(w = 8, h = 4)
BuildFrontierPlot_Thesis(CalibParamOut = CalibParamOut, optResults = optResults, target = 0.9^3)
quartz.save(file = "../../formal/nigeria/fig/opt/frontier.pdf", type = "pdf")
# FIGURE GENERATION
graphics.off(); quartz.options(w = 8, h = 4)
BuildChangesPlot_Thesis(CalibParamOut = CalibParamOut, optResults = optResults, target = 0.9^3)
quartz.save(file = "~/Desktop/fig/changes.pdf", type = "pdf")
quartz.save(file = "../../formal/nigeria/fig/opt/changes.pdf", type = "pdf")
################################################################################
# TABULATE RESULTS #
simLength <- dim(GetParaMatrixRun(cParamOut = CalibParamOut, runNumber = 1, length = intLength))[1]
optRuns <- WhichAchieved73(simData = theOut, simLength = simLength, target = custom$target)
optRuns
frontierList <- GetFrontiers(simData = theOut, optRuns = optRuns, simLength = simLength)
frontierList
intRes <- RunInterpolation(simData = theOut, optRuns = optRuns, simLength = simLength, frontierList = frontierList, target = custom$target)
colMeans(intRes)
results <- intRes[,c("iTest","iLink","iPreR","iInit","iAdhr","iRetn")]
results$iPreR <- abs(results$iPreR)
results$iRetn <- abs(results$iRetn)
results[results$iTest < 0, "iTest"] <- 0
results[results$iLink < 0, "iLink"] <- 0
results[results$iInit < 0, "iInit"] <- 0
results[results$iAdhr < 0, "iAdhr"] <- 0
results$run <- 1:dim(results)[1]
resTable <- results
resTable[resTable$iTest < 0, "iTest"] <- 0
resTable[resTable$iLink < 0, "iLink"] <- 0
resTable[resTable$iInit < 0, "iInit"] <- 0
resTable[resTable$iAdhr < 0, "iAdhr"] <- 0
colMeans(resTable)
# BASELINE
b1 <- paste0("iCost = ", scales::dollar(Quantile_95(BaselineCost)["mean"] / 5), " [", scales::dollar(Quantile_95(BaselineCost)["lower"] / 5), " to ", scales::dollar(Quantile_95(BaselineCost)["upper"] / 5), "]")
b2 <- paste0("iTest = ", scales::comma(round(Quantile_95(BaselineTest)["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(BaselineTest)["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(BaselineTest)["upper"] / 5, 0)), "]")
b3 <- paste0("iLink = ", scales::comma(round(Quantile_95(BaselineLink)["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(BaselineLink)["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(BaselineLink)["upper"] / 5, 0)), "]")
b4 <- paste0("iPreR = ", scales::comma(round(Quantile_95(BaselinePreR)["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(BaselinePreR)["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(BaselinePreR)["upper"] / 5, 0)), "]")
b5 <- paste0("iInit = ", scales::comma(round(Quantile_95(BaselineInit)["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(BaselineInit)["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(BaselineInit)["upper"] / 5, 0)), "]")
b6 <- paste0("iAdhr = ", scales::comma(round(Quantile_95(BaselineAdhr)["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(BaselineAdhr)["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(BaselineAdhr)["upper"] / 5, 0)), "]")
b7 <- paste0("iRetn = ", scales::comma(round(Quantile_95(BaselineRetn)["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(BaselineRetn)["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(BaselineRetn)["upper"] / 5, 0)), "]")
b1
b2
b3
b4
b5
b6
b7
# INTERVENTIONS
round(Quantile_95(intRes[,"iCost"])["mean"] / 1e6, 2)
i1 <- paste0("iCost = ", scales::dollar(Quantile_95(intRes[,"iCost"])["mean"] / 5), " [", scales::dollar(Quantile_95(intRes[,"iCost"])["lower"] / 5), " to ", scales::dollar(Quantile_95(intRes[,"iCost"])["upper"] / 5), "]")
i2 <- paste0("iTest = ", scales::comma(round(Quantile_95(resTable[,"iTest"])["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(resTable[,"iTest"])["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(resTable[,"iTest"])["upper"] / 5, 0)), "]")
i3 <- paste0("iLink = ", scales::comma(round(Quantile_95(resTable[,"iLink"])["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(resTable[,"iLink"])["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(resTable[,"iLink"])["upper"] / 5, 0)), "]")
i4 <- paste0("iPreR = ", scales::comma(round(Quantile_95(resTable[,"iPreR"])["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(resTable[,"iPreR"])["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(resTable[,"iPreR"])["upper"] / 5, 0)), "]")
i5 <- paste0("iInit = ", scales::comma(round(Quantile_95(resTable[,"iInit"])["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(resTable[,"iInit"])["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(resTable[,"iInit"])["upper"] / 5, 0)), "]")
i6 <- paste0("iAdhr = ", scales::comma(round(Quantile_95(resTable[,"iAdhr"])["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(resTable[,"iAdhr"])["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(resTable[,"iAdhr"])["upper"] / 5, 0)), "]")
i7 <- paste0("iRetn = ", scales::comma(round(Quantile_95(resTable[,"iRetn"])["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(resTable[,"iRetn"])["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(resTable[,"iRetn"])["upper"] / 5, 0)), "]")
i1
i2
i3
i4
i5
i6
i7
Quantile_95(resTable[,"iTest"]) / 5
Quantile_95(resTable[,"iLink"]) / 5
Quantile_95(resTable[,"iPreR"]) / 5
Quantile_95(resTable[,"iInit"]) / 5
Quantile_95(resTable[,"iAdhr"]) / 5
Quantile_95(resTable[,"iRetn"]) / 5
Quantile_95(intRes[,"iTCst"]) / 5
################################################################################
# SAVE IMAGE #
# save.image("../../formal/nigeria/data.RData")
# save.image("../../formal/nigeria/big-data.RData")
################################################################################
# PEPFAR PHIA 2016 Analysis
Get909090Data_2016 <- function(yr) {
result <- GetModel()
# Always aiming for 2020 here (5.02 / 0.02)
# year <- 251
year <- ((yr - 2015) / 0.02)
NX_data <- unlist(lapply(result, function(x) sum(x$N[year])))
DX_data <- unlist(lapply(result, function(x) sum(x$Dx[year], x$Care[year], x$PreLtfu[year], x$ART[year], x$Ltfu[year])))
TX_data <- unlist(lapply(result, function(x) sum(x$ART[year])))
VS_data <- unlist(lapply(result, function(x) sum(x$Vs[year])))
UN_90 <- Quantile_95(DX_data / NX_data)
UN_9090 <- Quantile_95(TX_data / DX_data)
UN_909090 <- Quantile_95(VS_data / TX_data)
res <- c(UN_90[["mean"]], UN_9090[["mean"]], UN_909090[["mean"]])
min <- c(UN_90[["lower"]], UN_9090[["lower"]], UN_909090[["lower"]])
max <- c(UN_90[["upper"]], UN_9090[["upper"]], UN_909090[["upper"]])
def <- c("Diagnosed / PLHIV", "On Treatment / Diagnosed", "Virally Suppressed / On Treatment")
out <- data.frame(def, res, min, max)
out$def <- factor(out$def, levels = c("Diagnosed / PLHIV", "On Treatment / Diagnosed", "Virally Suppressed / On Treatment"))
out
}
test <- Get909090Data_2016(yr = 2016)
Gen909090Plot_2016 <- function(yr) {
out <- Get909090Data_2016(yr = yr)
cfill <- rev(brewer.pal(9,"Blues")[6:8])
vbOut1 <- round(out[out$def == "Diagnosed / PLHIV", "res"] * 100, digits = 0)
vbOut2 <- round(out[out$def == "On Treatment / Diagnosed", "res"] * 100, digits = 0)
vbOut3 <- round(out[out$def == "Virally Suppressed / On Treatment", "res"] * 100, digits = 0)
ggOut <- ggplot(out, aes(x = def, y = res))
ggOut <- ggOut + geom_bar(aes(fill = def), position = 'dodge', stat = 'identity')
ggOut <- ggOut + geom_errorbar(mapping = aes(x = def, ymin = min, ymax = max), width = 0.2, size = 0.5)
ggOut <- ggOut + scale_y_continuous(limits = c(0, 1), breaks = seq(0, 1, 0.1), labels = scales::percent, expand = c(0, 0))
ggOut <- ggOut + scale_fill_manual(values = cfill)
ggOut <- ggOut + geom_abline(intercept = 0.9, slope = 0)
ggOut <- ggOut + theme_classic()
ggOut <- ggOut + theme(plot.title = element_text(hjust = 0.5))
ggOut <- ggOut + theme(title = element_text(size = 20))
ggOut <- ggOut + theme(axis.title = element_blank())
ggOut <- ggOut + theme(axis.ticks.x = element_blank())
ggOut <- ggOut + theme(axis.text.x = element_text(size = 12))
ggOut <- ggOut + theme(axis.text.y = element_text(size = 12))
ggOut <- ggOut + theme(legend.position = "none")
ggOut <- ggOut + theme(plot.background = element_blank())
ggOut <- ggOut + theme(panel.background = element_blank())
ggOut <- ggOut + theme(axis.line.y = element_line())
ggOut <- ggOut + theme(text = element_text(family = figFont))
ggOut <- ggOut + geom_label(aes(x = def, label = scales::percent(round(out$res, digits = 2))), size = 4)
ggOut
}
Gen909090Plot_2016(yr = 2016)
###
head(CalibOut)
test <- CalibOut
plhiv_2010 <- mean(test[test$source == "model" & test$indicator == "PLHIV" & test$year == 2010, "value"])
plhiv_2011 <- mean(test[test$source == "model" & test$indicator == "PLHIV" & test$year == 2011, "value"])
plhiv_2012 <- mean(test[test$source == "model" & test$indicator == "PLHIV" & test$year == 2012, "value"])
plhiv_2013 <- mean(test[test$source == "model" & test$indicator == "PLHIV" & test$year == 2013, "value"])
plhiv_2014 <- mean(test[test$source == "model" & test$indicator == "PLHIV" & test$year == 2014, "value"])
plhiv_2015 <- mean(test[test$source == "model" & test$indicator == "PLHIV" & test$year == 2015, "value"])
plhiv <- c(plhiv_2010, plhiv_2011, plhiv_2012, plhiv_2013, plhiv_2014, plhiv_2015)
inc <- as.double(MasterData$incidence[2,3:8])
inc
rate <- inc / plhiv
year <- seq(2010, 2015, 1)
df <- data.frame(year, rate)
graphics.off(); quartz.options(w = 5, h = 3)
ggplot(df, aes(x = year, y = rate)) +
geom_line() +
ggtitle("Transmission Rate", subtitle = "New Infections / Total PLHIV")
quartz.save(file = "~/Desktop/fig/transmission-rate.pdf", type = "pdf")
####################################################################################################
####################################################################################################
# CROI 2017 FIGURE GENERATION
# Baseline Changes Figure
build_changes_baseline_CROI <- function() {
theBase <- rbind(
data.frame(variable = "Testing", mean = mean(BaselineTest) / 5, strategy = "Baseline"),
data.frame(variable = "Linkage", mean = mean(BaselineLink) / 5, strategy = "Baseline"),
data.frame(variable = "Pre-ART\nRetention", mean = mean(BaselinePreR) / 5, strategy = "Baseline"),
data.frame(variable = "ART\nInitiation", mean = mean(BaselineInit) / 5, strategy = "Baseline"),
data.frame(variable = "ART\nRetention", mean = mean(BaselineRetn) / 5, strategy = "Baseline"),
data.frame(variable = "Viral\nSuppression", mean = mean(BaselineAdhr) / 5, strategy = "Baseline")
)
theBase$upper <- NA
theBase$lower <- NA
theBase$variable <- factor(theBase$variable, levels = c("Testing", "Linkage",
"Pre-ART\nRetention", "ART\nInitiation", "ART\nRetention", "Viral\nSuppression"))
# make retention values NEGATIVE
theBase[theBase$variable == "Pre-ART\nRetention", "mean"] <- - theBase[theBase$variable ==
"Pre-ART\nRetention", "mean"]
theBase[theBase$variable == "ART\nRetention", "mean"] <- - theBase[theBase$variable ==
"ART\nRetention", "mean"]
ggOut <- ggplot(theBase, aes(x = variable, y = mean, fill = strategy))
ggOut <- ggOut + geom_bar(stat = "identity", alpha = 1)
ggOut <- ggOut + scale_fill_manual(values = "#E41A1C")
ggOut <- ggOut + theme_classic()
ggOut <- ggOut + ylab("Annual Movement Through Care (2015 to 2020)")
ggOut <- ggOut + theme(axis.text.x = element_text(size = 10))
ggOut <- ggOut + theme(axis.title.x = element_blank())
ggOut <- ggOut + theme(axis.title.y = element_text(size = 10))
ggOut <- ggOut + theme(axis.text.y = element_text(size = 10))
ggOut <- ggOut + theme(axis.line.y = element_line())
ggOut <- ggOut + theme(axis.line.x = element_blank())
ggOut <- ggOut + scale_y_continuous(limits = c(-1e4, 8e4), labels = scales::comma, breaks =
scales::pretty_breaks(n = 8), expand = c(0, 0))
ggOut <- ggOut + theme(text = element_text(family = "Avenir Next"))
ggOut <- ggOut + theme(legend.position = 'right')
ggOut <- ggOut + theme(legend.title = element_blank())
ggOut <- ggOut + theme(legend.key.size = unit(0.5, "cm"))
ggOut <- ggOut + geom_hline(yintercept = 0)
ggOut <- ggOut + guides(fill = guide_legend(override.aes = list(alpha = 1)))
ggOut <- ggOut + theme(plot.background = element_blank())
ggOut <- ggOut + theme(legend.background = element_blank())
ggOut <- ggOut + theme(panel.background = element_blank())
ggOut <- ggOut + theme(axis.ticks.x = element_blank())
ggOut
}
graphics.off(); quartz.options(w = 8, h = 4)
build_changes_baseline_CROI()
quartz.save(file = "../../formal/nigeria/fig/opt/changes-baseline.pdf", type = "pdf")
# handy invert function
invert <- function(x) {
if (x <= 0) {
x <- abs(x)
} else {
x <- - x
}
x
}
# Complete Changes Figures
build_changes_CROI <- function(CalibParamOut, optResults, target) {
simLength <- dim(GetParaMatrixRun(cParamOut = CalibParamOut, runNumber = 1, length = 2))[1]
optRuns <- WhichAchieved73(simData = optResults, simLength = simLength, target = target)
frontierList <- GetFrontiers(simData = optResults, optRuns = optRuns, simLength = simLength)
intResult <- RunInterpolation(simData = optResults, optRuns = optRuns, simLength = simLength, frontierList = frontierList, target = target)
# Result Formatting
intResult <- intResult[,c("iTest","iLink","iPreR","iInit","iAdhr","iRetn")]
intResult['iPreR'] <- invert(intResult['iPreR'])
intResult['iRetn'] <- invert(intResult['iRetn'])
intResult[intResult$iTest < 0, 'iTest'] <- 0
intResult[intResult$iLink < 0, 'iLink'] <- 0
intResult[intResult$iInit < 0, 'iInit'] <- 0
intResult[intResult$iAhdr < 0, 'iAdhr'] <- 0
# Assign a 'run' number to simulations
intResult$run <- 1:dim(intResult)[1]
# Melt them
mRes <- reshape2::melt(intResult, id = "run")
## DIVIDE ALL VALUES BY FIVE
# Conversion from 5 year values to single years
mRes$value <- mRes$value / 5
# RENAME VARIABLES
mRes$variable <- as.character(mRes$variable)
mRes[mRes$variable == "iTest", "variable"] <- "Number of\nPLHIV to\nDiagnose"
mRes[mRes$variable == "iLink", "variable"] <- "Number of\nPLHIV to\nLink"
mRes[mRes$variable == "iPreR", "variable"] <- "Number of\nPLHIV to\nRetain in\nPre-ART Care"
mRes[mRes$variable == "iInit", "variable"] <- "Number of\nPLHIV to\nInitiate ART"
mRes[mRes$variable == "iAdhr", "variable"] <- "Number of\nPLHIV to\nMaintain Viral\nSuppression"
mRes[mRes$variable == "iRetn", "variable"] <- "Number of\nPLHIV to\nRetain on\nART"
mRes$variable <- factor(mRes$variable, levels = c("Number of\nPLHIV to\nDiagnose", "Number of\nPLHIV to\nLink", "Number of\nPLHIV to\nRetain in\nPre-ART Care", "Number of\nPLHIV to\nInitiate ART",
"Number of\nPLHIV to\nRetain on\nART", "Number of\nPLHIV to\nMaintain Viral\nSuppression"))
# EDITS FROM HERE
variable <- c("Number of\nPLHIV to\nDiagnose", "Number of\nPLHIV to\nLink",
"Number of\nPLHIV to\nRetain in\nPre-ART Care", "Number of\nPLHIV to\nInitiate ART", "Number of\nPLHIV to\nRetain on\nART", "Number of\nPLHIV to\nMaintain Viral\nSuppression")
mean <- c(
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nDiagnose", "value"])[["mean"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nLink", "value"])[["mean"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nRetain in\nPre-ART Care", "value"])[["mean"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nInitiate ART", "value"])[["mean"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nRetain on\nART", "value"])[["mean"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nMaintain Viral\nSuppression", "value"])[["mean"]]
)
upper <- c(
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nDiagnose", "value"])[["upper"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nLink", "value"])[["upper"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nRetain in\nPre-ART Care", "value"])[["upper"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nInitiate ART", "value"])[["upper"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nRetain on\nART", "value"])[["upper"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nMaintain Viral\nSuppression", "value"])[["upper"]]
)
lower <- c(
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nDiagnose", "value"])[["lower"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nLink", "value"])[["lower"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nRetain in\nPre-ART Care", "value"])[["lower"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nInitiate ART", "value"])[["lower"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nRetain on\nART", "value"])[["lower"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nMaintain Viral\nSuppression", "value"])[["lower"]]
)
strategy <- "Intervention"
outData <- data.frame(variable, mean, lower, upper, strategy)
# baseline data.frame
theBase <- rbind(
data.frame(variable = "Number of\nPLHIV to\nDiagnose",
mean = mean(BaselineTest) / 5,
strategy = "Baseline"),
data.frame(variable = "Number of\nPLHIV to\nLink",
mean = mean(BaselineLink) / 5,
strategy = "Baseline"),
data.frame(variable = "Number of\nPLHIV to\nRetain in\nPre-ART Care",
mean = mean(BaselinePreR) / 5,
strategy = "Baseline"),
data.frame(variable = "Number of\nPLHIV to\nInitiate ART",
mean = mean(BaselineInit) / 5,
strategy = "Baseline"),
data.frame(variable = "Number of\nPLHIV to\nRetain on\nART",
mean = mean(BaselineRetn) / 5,
strategy = "Baseline"),
data.frame(variable = "Number of\nPLHIV to\nMaintain Viral\nSuppression",
mean = mean(BaselineAdhr) / 5,
strategy = "Baseline")
)
theBase$upper <- NA
theBase$lower <- NA
final <- rbind(theBase, outData)
final$strategy <- factor(final$strategy, levels = c("Intervention", "Baseline"))
# Now we need the error_bar data.frame
value <- mean
mean <- mean + theBase$mean
upper <- upper + theBase$mean
lower <- lower + theBase$mean
theLabel <- data.frame(variable, value, mean, upper, lower)
ggOut <- ggplot(final, aes(x = variable, y = mean, fill = strategy))
ggOut <- ggOut + geom_bar(stat = "identity", alpha = 1)
ggOut <- ggOut + geom_hline(yintercept = 0)
ggOut <- ggOut + geom_errorbar(data = theLabel, aes(x = variable, y = mean, ymax = upper, ymin = lower), alpha = 1, width = 0.25, size = 0.5)
ggOut <- ggOut + geom_label(data = theLabel, aes(x = variable, y = mean, label = paste0("+",
scales::comma(round(value, 0)))), vjust = c(0.5, 0.5, 0, 0.5, 0.5, 0.5), family = "Avenir Next", colour = "black", size = 3, alpha = 1, show.legend = FALSE)
ggOut <- ggOut + scale_fill_manual(values = c("#4F8ABA","#E41A1C"))
ggOut <- ggOut + theme_classic()
ggOut <- ggOut + ylab("Annual Targets")
ggOut <- ggOut + theme(axis.text.x = element_text(size = 8))
ggOut <- ggOut + theme(axis.title.x = element_blank())
ggOut <- ggOut + theme(axis.title.y = element_text(size = 10))
ggOut <- ggOut + theme(axis.text.y = element_text(size = 10))
ggOut <- ggOut + theme(axis.line.y = element_line())
ggOut <- ggOut + theme(axis.line.x = element_blank())
ggOut <- ggOut + scale_y_continuous(limits = c(0, 11e4), labels = scales::comma, breaks =
scales::pretty_breaks(n = 11), expand = c(0, 0))
ggOut <- ggOut + theme(text = element_text(family = "Avenir Next"))
ggOut <- ggOut + theme(legend.position = 'right')
ggOut <- ggOut + theme(legend.title = element_blank())
ggOut <- ggOut + theme(legend.key.size = unit(0.5, "cm"))
ggOut <- ggOut + guides(fill = guide_legend(override.aes = list(alpha = 1)))
ggOut <- ggOut + theme(plot.background = element_blank())
ggOut <- ggOut + theme(legend.background = element_blank())
ggOut <- ggOut + theme(panel.background = element_blank())
ggOut <- ggOut + theme(axis.ticks.x = element_blank())
ggOut
}
graphics.off(); quartz.options(w = 8, h = 4)
build_changes_CROI(CalibParamOut = CalibParamOut, optResults = optResults, target = 0.9^3)
quartz.save(file = "../../formal/nigeria/fig/opt/changes.pdf", type = "pdf")
build_custom_frontier_plot <- function(CalibParamOut, optResults, target = target, ylim) {
simLength <- dim(GetParaMatrixRun(cParamOut = CalibParamOut, runNumber = 1, length = 2))[1]
optRuns <- WhichAchieved73(simData = optResults, simLength = simLength, target = target)
optResults$sim <- rep(x = 1:(dim(optResults)[1] / simLength), each = simLength)
allRuns <- GetFrontiers(simData = optResults, optRuns = 1:(dim(optResults)[1] / simLength), simLength = simLength)
interpol <- list()
for(n in 1:(dim(optResults)[1] / simLength)) {
lower <- (1 + simLength * (n - 1))
upper <- (simLength + simLength * (n - 1))
vals <- optResults[lower:upper,]
interpolation <- approx(x = vals[,"VS"][allRuns[[n]]], y = vals[,"Cost"][allRuns[[n]]])
interpol[[n]] <- interpolation
}
ggPlot <- ggplot(optResults, aes(x = VS, y = Cost))
ggPlot <- ggPlot + geom_point(col = '#4F8ABA', alpha = 0.2)
for(n in 1:(dim(optResults)[1] / simLength)) {
ggPlot <- ggPlot + geom_line(data = as.data.frame(interpol[[n]]), mapping = aes(x = x, y = y), col = 'black', alpha = 0.2, size = 0.5)
}
for(n in 1:length(optRuns)) {
ggPlot <- ggPlot + geom_line(data = as.data.frame(interpol[[optRuns[n]]]), mapping = aes(x = x, y = y), col = "red", alpha = 0.5, size = 0.75)
}
ggPlot <- ggPlot + geom_vline(xintercept = 0.9^3, alpha = 1)
ggPlot <- ggPlot + theme_classic()
ggPlot <- ggPlot + expand_limits(y = ylim)
ggPlot <- ggPlot + scale_y_continuous(labels = scales::scientific, breaks = scales::pretty_breaks(n = 5))
ggPlot <- ggPlot + scale_x_continuous(labels = scales::percent, breaks = scales::pretty_breaks(n = 5))
ggPlot <- ggPlot + theme(axis.text.x = element_text(size = 10))
ggPlot <- ggPlot + theme(axis.text.y = element_text(size = 10))
ggPlot <- ggPlot + theme(axis.title = element_text(size = 11))
ggPlot <- ggPlot + theme(axis.line.x = element_line())
ggPlot <- ggPlot + theme(axis.line.y = element_line())
ggPlot <- ggPlot + xlab("Viral Suppression")
ggPlot <- ggPlot + ylab("Additional Cost of Care")
ggPlot <- ggPlot + theme(text = element_text(family = figFont))
ggPlot
}
graphics.off(); quartz.options(w = 8, h = 4)
build_custom_frontier_plot(CalibParamOut = CalibParamOut, optResults = optResults, target = 0.9^3,
ylim = 2.5e8)
quartz.save(file = "../../formal/nigeria/fig/opt/frontier.pdf", type = "pdf")
####################################################################################################
### PAPER CHANGE FIGURE (Adapted from version presented at CROI 2017)
# new variable: absResults
# this maps the ABSOLUTE changes in care (not those relative to baseline) in the optResults df
build_changes_paper_figure <- function(target = 0.9^3) {
simLength <- dim(GetParaMatrixRun(cParamOut = CalibParamOut, runNumber = 1, length = 2))[1]
optRuns <- WhichAchieved73(simData = absResults, simLength = simLength, target = target)
frontierList <- GetFrontiers(simData = absResults, optRuns = optRuns, simLength = simLength)
intResult <- RunInterpolation(simData = absResults, optRuns = optRuns, simLength = simLength, frontierList = frontierList, target = target)
# Result Formatting
intResult <- intResult[,c("iTest","iLink","iPreR","iInit","iAdhr","iRetn")]
# Assign a 'run' number to simulations
intResult$run <- 1:dim(intResult)[1]
# Melt them
mRes <- reshape2::melt(intResult, id = "run")
## DIVIDE ALL VALUES BY FIVE
# Conversion from 5 year values to single years
mRes$value <- mRes$value / 5
# RENAME VARIABLES
mRes$variable <- as.character(mRes$variable)
mRes[mRes$variable == "iTest", "variable"] <- "Number of\nPLHIV to\nDiagnose"
mRes[mRes$variable == "iLink", "variable"] <- "Number of\nPLHIV to\nLink"
mRes[mRes$variable == "iPreR", "variable"] <- "Number of\nPLHIV\nLost From\nPre-ART Care"
mRes[mRes$variable == "iInit", "variable"] <- "Number of\nPLHIV to\nInitiate ART"
mRes[mRes$variable == "iAdhr", "variable"] <- "Number of\nPLHIV to\nMaintain Viral\nSuppression"
mRes[mRes$variable == "iRetn", "variable"] <- "Number of\nPLHIV\nLost From\nART Care"
mRes$variable <- factor(mRes$variable, levels = c("Number of\nPLHIV to\nDiagnose", "Number of\nPLHIV to\nLink", "Number of\nPLHIV\nLost From\nPre-ART Care", "Number of\nPLHIV to\nInitiate ART",
"Number of\nPLHIV\nLost From\nART Care", "Number of\nPLHIV to\nMaintain Viral\nSuppression"))
# EDITS FROM HERE
variable <- c("Number of\nPLHIV to\nDiagnose", "Number of\nPLHIV to\nLink",
"Number of\nPLHIV\nLost From\nPre-ART Care", "Number of\nPLHIV to\nInitiate ART", "Number of\nPLHIV\nLost From\nART Care", "Number of\nPLHIV to\nMaintain Viral\nSuppression")
mean <- c(
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nDiagnose", "value"])[["mean"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nLink", "value"])[["mean"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV\nLost From\nPre-ART Care", "value"])[["mean"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nInitiate ART", "value"])[["mean"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV\nLost From\nART Care", "value"])[["mean"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nMaintain Viral\nSuppression", "value"])[["mean"]]
)
upper <- c(
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nDiagnose", "value"])[["upper"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nLink", "value"])[["upper"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV\nLost From\nPre-ART Care", "value"])[["upper"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nInitiate ART", "value"])[["upper"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV\nLost From\nART Care", "value"])[["upper"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nMaintain Viral\nSuppression", "value"])[["upper"]]
)
lower <- c(
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nDiagnose", "value"])[["lower"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nLink", "value"])[["lower"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV\nLost From\nPre-ART Care", "value"])[["lower"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nInitiate ART", "value"])[["lower"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV\nLost From\nART Care", "value"])[["lower"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nMaintain Viral\nSuppression", "value"])[["lower"]]
)
strategy <- "Intervention"
outData <- data.frame(variable, mean, lower, upper, strategy)
# baseline data.frame
theBase <- rbind(
data.frame(variable = "Number of\nPLHIV to\nDiagnose",
mean = Quantile_95(BaselineTest)[["mean"]] / 5,
lower = Quantile_95(BaselineTest)[["lower"]] / 5,
upper = Quantile_95(BaselineTest)[["upper"]] / 5,
strategy = "Baseline"),
data.frame(variable = "Number of\nPLHIV to\nLink",
mean = Quantile_95(BaselineLink)[["mean"]] / 5,
lower = Quantile_95(BaselineLink)[["lower"]] / 5,
upper = Quantile_95(BaselineLink)[["upper"]] / 5,
strategy = "Baseline"),
data.frame(variable = "Number of\nPLHIV\nLost From\nPre-ART Care",
mean = Quantile_95(BaselinePreR)[["mean"]] / 5,
lower = Quantile_95(BaselinePreR)[["lower"]] / 5,
upper = Quantile_95(BaselinePreR)[["upper"]] / 5,
strategy = "Baseline"),
data.frame(variable = "Number of\nPLHIV to\nInitiate ART",
mean = Quantile_95(BaselineInit)[["mean"]] / 5,
lower = Quantile_95(BaselineInit)[["lower"]] / 5,
upper = Quantile_95(BaselineInit)[["upper"]] / 5,
strategy = "Baseline"),
data.frame(variable = "Number of\nPLHIV\nLost From\nART Care",
mean = Quantile_95(BaselineRetn)[["mean"]] / 5,
lower = Quantile_95(BaselineRetn)[["lower"]] / 5,
upper = Quantile_95(BaselineRetn)[["upper"]] / 5,
strategy = "Baseline"),
data.frame(variable = "Number of\nPLHIV to\nMaintain Viral\nSuppression",
mean = Quantile_95(BaselineAdhr)[["mean"]] / 5,
lower = Quantile_95(BaselineAdhr)[["lower"]] / 5,
upper = Quantile_95(BaselineAdhr)[["upper"]] / 5,
strategy = "Baseline")
)
final <- rbind(theBase, outData)
final$strategy <- factor(final$strategy, levels = c("Baseline", "Intervention"))
# WHAT I NEED
# -> Single data.frame containing 'baseline' 'intervention'
# -> cols = Intervention, mean, upper, lower
# -> IGNORE geom_label for now (I think it is too complicated with a geom_label call)
# need to re-run the simulations and then spit out ANOTHER data.frame that just shows things like
# the baseline changes but for interventions
# Leave option for labels
# ggOut <- ggOut + geom_label(data = theLabel, aes(x = variable, y = mean, label = paste0("+",
# scales::comma(round(value, 0)))), vjust = c(0.5, 0.5, 0, 0.5, 0.5, 0.5), family = "Avenir
# Next", colour = "black", size = 3, alpha = 1, show.legend = FALSE)
ggOut <- ggplot(final, aes(x = variable, y = mean, fill = strategy))
ggOut <- ggOut + geom_bar(position = "dodge", stat = "identity", alpha = 1)
ggOut <- ggOut + geom_errorbar(aes(x = variable, ymax = upper, ymin = lower), position =
position_dodge(0.9), alpha = 1, width = 0.25, size = 0.5)
ggOut <- ggOut + scale_fill_manual(values = c("#E41A1C","#4F8ABA"))
ggOut <- ggOut + theme_classic()
ggOut <- ggOut + ylab("Annual Targets")
ggOut <- ggOut + theme(axis.text.x = element_text(size = 8))
ggOut <- ggOut + theme(axis.title.x = element_blank())
ggOut <- ggOut + theme(axis.title.y = element_text(size = 10))
ggOut <- ggOut + theme(axis.text.y = element_text(size = 10))
ggOut <- ggOut + theme(axis.line.y = element_line())
ggOut <- ggOut + theme(axis.line.x = element_blank())
ggOut <- ggOut + scale_y_continuous(limits = c(0, 12e4), labels = scales::comma, breaks =
scales::pretty_breaks(n = 12), expand = c(0, 0))
ggOut <- ggOut + theme(text = element_text(family = "Avenir Next"))
ggOut <- ggOut + theme(legend.position = 'right')
ggOut <- ggOut + theme(legend.title = element_blank())
ggOut <- ggOut + theme(legend.key.size = unit(0.5, "cm"))
ggOut <- ggOut + guides(fill = guide_legend(override.aes = list(alpha = 1)))
ggOut <- ggOut + theme(plot.background = element_blank())
ggOut <- ggOut + theme(legend.background = element_blank())
ggOut <- ggOut + theme(panel.background = element_blank())
ggOut <- ggOut + theme(axis.ticks.x = element_blank())
ggOut
}
graphics.off(); quartz.options(w = 8, h = 4)
build_changes_paper_figure()
quartz.save(file = "../../formal/nigeria/fig/opt/changes-dodge.pdf", type = "pdf")
jackolney/CascadeDashboard documentation built on May 18, 2019, 7:56 a.m.
R Package Documentation
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####################################################################################################
# PEPFAR PHIA FILE
# Nigeria Cascade Tool Formal Analysis Script
# Model version include CD4 dependency on theta for only those with CD4 <200
####################################################################################################
rm(list=ls())
# AIM = Boil the calibration down to a set of REALLY NEAT FUNCTIONS.
setwd("~/git/CascadeDashboard/inst/app")
graphics.off()
quartz.options(w = 10, h = 8)
figFont <- "Avenir Next"
# Source initial files
source("../../formal/initial.R")
# GLOBAL
MasterName <- "Nigeria"
MasterData <- GetMasterDataSet(MasterName)
# Making the assumption of treat all from 2016
MasterData$treatment_guidelines[[6]] <- 2016
# I need to do an optim first to understand the parameter bounds
# ---- #
set.seed(100)
# ---- #
# These will be adjusted in due course:
MaxError <- 0.08
MinNumber <- 1000
# After first simulation, run this function (default = 5%)
# MaxError <- find_error_bound(runError, prop = 0.05)
# Define Parameter Range
parRange <- DefineParmRange(
rho = c(0.03, 0.07),
q = c(0.4, 0.6),
epsilon = c(100, 100),
kappa = c(3, 7),
gamma = c(2, 4),
theta = c(0, 0.1),
p = c(0.4, 0.6),
omega = c(0, 0.01)
)
# Run Calibration
start.time <- proc.time()
RunNSCalibration(
country = MasterName,
data = MasterData,
maxIterations = 1e4,
maxError = MaxError,
limit = MinNumber,
parRange = parRange,
targetIterations = 1e5)
finish.time <- proc.time() - start.time
finish.time[3] / 60
# 70 min runtime
graphics.off(); quartz.options(w = 8, h = 6)
BuildCD4CalibData_Thesis(year = 1, modelOut = modelOut)
quartz.save(file = "../../formal/nigeria/fig/cal/CD4-2010.pdf", type = "pdf")
graphics.off(); quartz.options(w = 8, h = 6)
BuildCD4CalibData_Thesis(year = 6, modelOut = modelOut)
quartz.save(file = "../../formal/nigeria/fig/cal/CD4-2015.pdf", type = "pdf")
# No PHIA for Nigeria
# graphics.off(); quartz.options(w = 9, h = 4)
# BuildPHIAPlot(data = CalibOut)
# quartz.save(file = "../../formal/nigeria/fig/cal/PHIA.pdf", type = "pdf")
####################################################################################################
#### PLOT ####
# Cascade in 2015
graphics.off(); quartz.options(w = 10, h = 4)
BuildCalibPlot_Thesis(data = CalibOut,
originalData = MasterData,
limit = MinNumber)
quartz.save(file = "../../formal/nigeria/fig/cal/cascade-2015.pdf", type = "pdf")
# Error Histogram
graphics.off(); quartz.options(w = 6, h = 3)
BuildCalibrationHistogram_Thesis(
runError = runError,
maxError = MaxError)
quartz.save(file = "../../formal/nigeria/fig/cal/calib-hist.pdf", type = "pdf")
# Calibration Detail
graphics.off(); quartz.options(w = 10, h = 8)
BuildCalibDetailPlot_Thesis(
data = CalibOut,
originalData = MasterData,
limit = MinNumber)
quartz.save(file = "../../formal/nigeria/fig/cal/calib-detail.pdf", type = "pdf")
# Parameter Histograms
graphics.off(); quartz.options(w = 10, h = 4)
BuildCalibrationParameterHistGroup_Thesis()
quartz.save(file = "../../formal/nigeria/fig/cal/par-hist.pdf", type = "pdf")
################################################################################
# DataReviewPlot
graphics.off(); quartz.options(w = 10, h = 4)
BuildDataReviewPlot_Thesis(data = MasterData$calib)
quartz.save(file = "../../formal/nigeria/fig/cal/calib-data.pdf", type = "pdf")
# save.image("../../formal/nigeria/data.RData")
# Parameter means
round(colMeans(CalibParamOut), 4)
# Parameter values
a <- paste0(round(Quantile_95(CalibParamOut[["rho"]])[["mean"]], 4), " [", round(Quantile_95(CalibParamOut[["rho"]])[["lower"]], 4), " to ", round(Quantile_95(CalibParamOut[["rho"]])[["upper"]], 4), "]")
b <- paste0(round(Quantile_95(CalibParamOut[["q"]])[["mean"]], 4), " [", round(Quantile_95(CalibParamOut[["q"]])[["lower"]], 4), " to ", round(Quantile_95(CalibParamOut[["q"]])[["upper"]], 4), "]")
c <- paste0(round(Quantile_95(CalibParamOut[["epsilon"]])[["mean"]], 4), " [", round(Quantile_95(CalibParamOut[["epsilon"]])[["lower"]], 4), " to ", round(Quantile_95(CalibParamOut[["epsilon"]])[["upper"]], 4), "]")
d <- paste0(round(Quantile_95(CalibParamOut[["kappa"]])[["mean"]], 4), " [", round(Quantile_95(CalibParamOut[["kappa"]])[["lower"]], 4), " to ", round(Quantile_95(CalibParamOut[["kappa"]])[["upper"]], 4), "]")
e <- paste0(round(Quantile_95(CalibParamOut[["gamma"]])[["mean"]], 4), " [", round(Quantile_95(CalibParamOut[["gamma"]])[["lower"]], 4), " to ", round(Quantile_95(CalibParamOut[["gamma"]])[["upper"]], 4), "]")
f <- paste0(round(Quantile_95(CalibParamOut[["theta"]])[["mean"]], 4), " [", round(Quantile_95(CalibParamOut[["theta"]])[["lower"]], 4), " to ", round(Quantile_95(CalibParamOut[["theta"]])[["upper"]], 4), "]")
g <- paste0(round(Quantile_95(CalibParamOut[["p"]])[["mean"]], 4), " [", round(Quantile_95(CalibParamOut[["p"]])[["lower"]], 4), " to ", round(Quantile_95(CalibParamOut[["p"]])[["upper"]], 4), "]")
h <- paste0(round(Quantile_95(CalibParamOut[["omega"]])[["mean"]], 4), " [", round(Quantile_95(CalibParamOut[["omega"]])[["lower"]], 4), " to ", round(Quantile_95(CalibParamOut[["omega"]])[["upper"]], 4), "]")
list(a,b,c,d,e,f,g,h)
Quantile_95(CalibParamOut[["rho"]])
Quantile_95(CalibParamOut[["q"]])
Quantile_95(CalibParamOut[["epsilon"]])
Quantile_95(CalibParamOut[["kappa"]])
Quantile_95(CalibParamOut[["gamma"]])
Quantile_95(CalibParamOut[["theta"]])
Quantile_95(CalibParamOut[["p"]])
Quantile_95(CalibParamOut[["omega"]])
# Mean of over-riding parameter bounds from non-shiny interface
################################################################################
# Projection
AdvCalib <- data.frame(NatMort = 0.005, HIVMort = 1)
# Single Powers Plot
graphics.off(); quartz.options(w = 8, h = 4)
GenSinglePowersPlot_Thesis()
quartz.save(file = "~/Desktop/fig/powers.pdf", type = "pdf")
# quartz.save(file = "~/Desktop/fig/powers.pdf", type = "pdf")
# CareCascade Plot
graphics.off(); quartz.options(w = 10, h = 4)
GenCascadePlot_Thesis()
# quartz.save(file = "~/Desktop/fig/cascade-projection.pdf", type = "pdf")
quartz.save(file = "../../formal/nigeria/fig/pro/cascade-projection.pdf", type = "pdf")
# What is the average value of beta?
# OutputBeta()
# 90-90-90 Plot
graphics.off(); quartz.options(w = 9, h = 4)
Gen909090Plot_Thesis()
# quartz.save(file = "~/Desktop/fig/90-90-90.pdf", type = "pdf")
quartz.save(file = "../../formal/nigeria/fig/pro/90-90-90.pdf", type = "pdf")
# Powers Plot
graphics.off(); quartz.options(w = 15, h = 4)
GenPowersCascadePlot_Thesis()
# quartz.save(file = "~/Desktop/fig/cascade-powers.pdf", type = "pdf")
quartz.save(file = "../../formal/nigeria/fig/pro/cascade-powers.pdf", type = "pdf")
# New Infections
graphics.off(); quartz.options(w = 6, h = 4)
GenNewInfPlot_Thesis()
# quartz.save(file = "~/Desktop/fig/new-infections.pdf", type = "pdf")
quartz.save(file = "../../formal/nigeria/fig/pro/new-infections.pdf", type = "pdf")
# AIDS Deaths
graphics.off(); quartz.options(w = 6, h = 4)
GenAidsDeathsPlot_Thesis()
# quartz.save(file = "~/Desktop/fig/AIDS-deaths.pdf", type = "pdf")
quartz.save(file = "../../formal/nigeria/fig/pro/AIDS-deaths.pdf", type = "pdf")
# Discrete Cascade
graphics.off(); quartz.options(w = 10, h = 4)
GenDiscreteCascade_Thesis()
# quartz.save(file = "~/Desktop/fig/cascade-discrete.pdf", type = "pdf")
quartz.save(file = "../../formal/nigeria/fig/pro/cascade-discrete.pdf", type = "pdf")
# CD4 distribution at ART initiation
graphics.off(); quartz.options(w = 8, h = 6)
BuildCD4Data_Thesis(year = 251)
# quartz.save(file = "~/Desktop/fig/CD4-2020.pdf", type = "pdf")
quartz.save(file = "../../formal/nigeria/fig/pro/CD4-2020.pdf", type = "pdf")
# NUMBERS
t0 <- GetCascadeData(1) # t0 = 1
t5 <- GetCascadeData(251) # t5 = (5 / 0.02) + 1 [t0]
# PLHIV Estimate in 2015
scales::comma(round(t0$res[1], -3))
1.394e+6
scales::comma(round(t5$res[1], -3))
1.516e+6
1.516e+6 / 1.394e+6
# DIAGNOSED
scales::comma(round(t0$res[2], -3))
1.044e+6
scales::comma(round(t5$res[2], -3))
1.296e+6
1.296e+6 / 1.044e+6
# On ART
scales::comma(round(t0$res[4], -3))
scales::comma(round(t5$res[4], -3))
round(t5$res[4], -3) / round(t0$res[4], -3)
37\% (0.899M to 1.233M)
# Viral suppression
scales::comma(round(t0$res[5], -3))
scales::comma(round(t5$res[5], -3))
round(t5$res[5], -3) / round(t0$res[5], -3)
40\% (0.791M to 1.104M)
23 - 14
t0
t0$res[5]/t0$res[1]
t5$res[5]/t5$res[1]
# edit on the 24/01/17 for new model that only has a CD4 dependency on theta for persons with CD4
# <200
save.image("../../formal/nigeria/data-28-03-17.RData")
# load("../../formal/nigeria/data-24-01-17.RData")
####################################################################################################
# if we were to adjust 'beta' such that it is reduced by 50%, then what functions would need to be
# adjusted? Remember, that we only wanted to adjust transmission between 2015 to 2020, not during
# calibration.
# Projection:
# GetModel()
# Optimisation:
# RunNSOptimisation()
# What about the baselineModel function that RunNSOptimisation() calls?
####################################################################################################
# Optimisation
intSwitch <- data.frame(
testing = TRUE,
linkage = TRUE,
preRetention = TRUE,
initiation = TRUE,
adherence = TRUE,
retention = TRUE
)
# These need updating
# and re-write this definition, it looks vile
# OptInput <- c()
# OptInput$intValue_rho <- parRange["rho", "max"]
# OptInput$intValue_q <- parRange["q", "max"]
# OptInput$intValue_kappa <- parRange["kappa", "min"]
# OptInput$intValue_gamma <- parRange["gamma", "max"]
# OptInput$intValue_sigma <- 0.5
# OptInput$intValue_omega <- parRange["omega", "min"]
OptInput <- c()
OptInput$intValue_rho <- 0.1
OptInput$intValue_q <- 1
OptInput$intValue_kappa <- 0
OptInput$intValue_gamma <- 10
OptInput$intValue_sigma <- 0.1
OptInput$intValue_omega <- 0
reactiveCost <- data.frame(
test = 10,
link = 40,
care = 40,
art = 367
)
# This is used by the function 'AdjustHIVTetsCost'
SafeReactiveCost <- data.frame(
test = 10,
link = 40,
care = 40,
art = 367
)
custom <- data.frame(target = 0.9^3)
AdvCalib <- data.frame(NatMort = 0.005, HIVMort = 1)
reactiveAdjustCost <- data.frame(switch = TRUE)
intLength = 2
AdjustHIVTestCost()
theOut <- RunNSOptimisation(propRuns = 0.1, intLength = intLength)
# Frontier Plot (optResults comes from RunNSOptimisation
graphics.off(); quartz.options(w = 8, h = 4)
BuildFrontierPlot_Thesis(CalibParamOut = CalibParamOut, optResults = optResults, target = 0.9^3)
quartz.save(file = "../../formal/nigeria/fig/opt/frontier.pdf", type = "pdf")
# FIGURE GENERATION
graphics.off(); quartz.options(w = 8, h = 4)
BuildChangesPlot_Thesis(CalibParamOut = CalibParamOut, optResults = optResults, target = 0.9^3)
quartz.save(file = "~/Desktop/fig/changes.pdf", type = "pdf")
quartz.save(file = "../../formal/nigeria/fig/opt/changes.pdf", type = "pdf")
################################################################################
# TABULATE RESULTS #
simLength <- dim(GetParaMatrixRun(cParamOut = CalibParamOut, runNumber = 1, length = intLength))[1]
optRuns <- WhichAchieved73(simData = theOut, simLength = simLength, target = custom$target)
optRuns
frontierList <- GetFrontiers(simData = theOut, optRuns = optRuns, simLength = simLength)
frontierList
intRes <- RunInterpolation(simData = theOut, optRuns = optRuns, simLength = simLength, frontierList = frontierList, target = custom$target)
colMeans(intRes)
results <- intRes[,c("iTest","iLink","iPreR","iInit","iAdhr","iRetn")]
results$iPreR <- abs(results$iPreR)
results$iRetn <- abs(results$iRetn)
results[results$iTest < 0, "iTest"] <- 0
results[results$iLink < 0, "iLink"] <- 0
results[results$iInit < 0, "iInit"] <- 0
results[results$iAdhr < 0, "iAdhr"] <- 0
results$run <- 1:dim(results)[1]
resTable <- results
resTable[resTable$iTest < 0, "iTest"] <- 0
resTable[resTable$iLink < 0, "iLink"] <- 0
resTable[resTable$iInit < 0, "iInit"] <- 0
resTable[resTable$iAdhr < 0, "iAdhr"] <- 0
colMeans(resTable)
# BASELINE
b1 <- paste0("iCost = ", scales::dollar(Quantile_95(BaselineCost)["mean"] / 5), " [", scales::dollar(Quantile_95(BaselineCost)["lower"] / 5), " to ", scales::dollar(Quantile_95(BaselineCost)["upper"] / 5), "]")
b2 <- paste0("iTest = ", scales::comma(round(Quantile_95(BaselineTest)["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(BaselineTest)["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(BaselineTest)["upper"] / 5, 0)), "]")
b3 <- paste0("iLink = ", scales::comma(round(Quantile_95(BaselineLink)["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(BaselineLink)["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(BaselineLink)["upper"] / 5, 0)), "]")
b4 <- paste0("iPreR = ", scales::comma(round(Quantile_95(BaselinePreR)["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(BaselinePreR)["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(BaselinePreR)["upper"] / 5, 0)), "]")
b5 <- paste0("iInit = ", scales::comma(round(Quantile_95(BaselineInit)["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(BaselineInit)["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(BaselineInit)["upper"] / 5, 0)), "]")
b6 <- paste0("iAdhr = ", scales::comma(round(Quantile_95(BaselineAdhr)["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(BaselineAdhr)["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(BaselineAdhr)["upper"] / 5, 0)), "]")
b7 <- paste0("iRetn = ", scales::comma(round(Quantile_95(BaselineRetn)["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(BaselineRetn)["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(BaselineRetn)["upper"] / 5, 0)), "]")
b1
b2
b3
b4
b5
b6
b7
# INTERVENTIONS
round(Quantile_95(intRes[,"iCost"])["mean"] / 1e6, 2)
i1 <- paste0("iCost = ", scales::dollar(Quantile_95(intRes[,"iCost"])["mean"] / 5), " [", scales::dollar(Quantile_95(intRes[,"iCost"])["lower"] / 5), " to ", scales::dollar(Quantile_95(intRes[,"iCost"])["upper"] / 5), "]")
i2 <- paste0("iTest = ", scales::comma(round(Quantile_95(resTable[,"iTest"])["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(resTable[,"iTest"])["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(resTable[,"iTest"])["upper"] / 5, 0)), "]")
i3 <- paste0("iLink = ", scales::comma(round(Quantile_95(resTable[,"iLink"])["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(resTable[,"iLink"])["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(resTable[,"iLink"])["upper"] / 5, 0)), "]")
i4 <- paste0("iPreR = ", scales::comma(round(Quantile_95(resTable[,"iPreR"])["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(resTable[,"iPreR"])["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(resTable[,"iPreR"])["upper"] / 5, 0)), "]")
i5 <- paste0("iInit = ", scales::comma(round(Quantile_95(resTable[,"iInit"])["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(resTable[,"iInit"])["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(resTable[,"iInit"])["upper"] / 5, 0)), "]")
i6 <- paste0("iAdhr = ", scales::comma(round(Quantile_95(resTable[,"iAdhr"])["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(resTable[,"iAdhr"])["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(resTable[,"iAdhr"])["upper"] / 5, 0)), "]")
i7 <- paste0("iRetn = ", scales::comma(round(Quantile_95(resTable[,"iRetn"])["mean"] / 5, 0)), " [", scales::comma(round(Quantile_95(resTable[,"iRetn"])["lower"] / 5, 0)), " to ", scales::comma(round(Quantile_95(resTable[,"iRetn"])["upper"] / 5, 0)), "]")
i1
i2
i3
i4
i5
i6
i7
Quantile_95(resTable[,"iTest"]) / 5
Quantile_95(resTable[,"iLink"]) / 5
Quantile_95(resTable[,"iPreR"]) / 5
Quantile_95(resTable[,"iInit"]) / 5
Quantile_95(resTable[,"iAdhr"]) / 5
Quantile_95(resTable[,"iRetn"]) / 5
Quantile_95(intRes[,"iTCst"]) / 5
################################################################################
# SAVE IMAGE #
# save.image("../../formal/nigeria/data.RData")
# save.image("../../formal/nigeria/big-data.RData")
################################################################################
# PEPFAR PHIA 2016 Analysis
Get909090Data_2016 <- function(yr) {
result <- GetModel()
# Always aiming for 2020 here (5.02 / 0.02)
# year <- 251
year <- ((yr - 2015) / 0.02)
NX_data <- unlist(lapply(result, function(x) sum(x$N[year])))
DX_data <- unlist(lapply(result, function(x) sum(x$Dx[year], x$Care[year], x$PreLtfu[year], x$ART[year], x$Ltfu[year])))
TX_data <- unlist(lapply(result, function(x) sum(x$ART[year])))
VS_data <- unlist(lapply(result, function(x) sum(x$Vs[year])))
UN_90 <- Quantile_95(DX_data / NX_data)
UN_9090 <- Quantile_95(TX_data / DX_data)
UN_909090 <- Quantile_95(VS_data / TX_data)
res <- c(UN_90[["mean"]], UN_9090[["mean"]], UN_909090[["mean"]])
min <- c(UN_90[["lower"]], UN_9090[["lower"]], UN_909090[["lower"]])
max <- c(UN_90[["upper"]], UN_9090[["upper"]], UN_909090[["upper"]])
def <- c("Diagnosed / PLHIV", "On Treatment / Diagnosed", "Virally Suppressed / On Treatment")
out <- data.frame(def, res, min, max)
out$def <- factor(out$def, levels = c("Diagnosed / PLHIV", "On Treatment / Diagnosed", "Virally Suppressed / On Treatment"))
out
}
test <- Get909090Data_2016(yr = 2016)
Gen909090Plot_2016 <- function(yr) {
out <- Get909090Data_2016(yr = yr)
cfill <- rev(brewer.pal(9,"Blues")[6:8])
vbOut1 <- round(out[out$def == "Diagnosed / PLHIV", "res"] * 100, digits = 0)
vbOut2 <- round(out[out$def == "On Treatment / Diagnosed", "res"] * 100, digits = 0)
vbOut3 <- round(out[out$def == "Virally Suppressed / On Treatment", "res"] * 100, digits = 0)
ggOut <- ggplot(out, aes(x = def, y = res))
ggOut <- ggOut + geom_bar(aes(fill = def), position = 'dodge', stat = 'identity')
ggOut <- ggOut + geom_errorbar(mapping = aes(x = def, ymin = min, ymax = max), width = 0.2, size = 0.5)
ggOut <- ggOut + scale_y_continuous(limits = c(0, 1), breaks = seq(0, 1, 0.1), labels = scales::percent, expand = c(0, 0))
ggOut <- ggOut + scale_fill_manual(values = cfill)
ggOut <- ggOut + geom_abline(intercept = 0.9, slope = 0)
ggOut <- ggOut + theme_classic()
ggOut <- ggOut + theme(plot.title = element_text(hjust = 0.5))
ggOut <- ggOut + theme(title = element_text(size = 20))
ggOut <- ggOut + theme(axis.title = element_blank())
ggOut <- ggOut + theme(axis.ticks.x = element_blank())
ggOut <- ggOut + theme(axis.text.x = element_text(size = 12))
ggOut <- ggOut + theme(axis.text.y = element_text(size = 12))
ggOut <- ggOut + theme(legend.position = "none")
ggOut <- ggOut + theme(plot.background = element_blank())
ggOut <- ggOut + theme(panel.background = element_blank())
ggOut <- ggOut + theme(axis.line.y = element_line())
ggOut <- ggOut + theme(text = element_text(family = figFont))
ggOut <- ggOut + geom_label(aes(x = def, label = scales::percent(round(out$res, digits = 2))), size = 4)
ggOut
}
Gen909090Plot_2016(yr = 2016)
###
head(CalibOut)
test <- CalibOut
plhiv_2010 <- mean(test[test$source == "model" & test$indicator == "PLHIV" & test$year == 2010, "value"])
plhiv_2011 <- mean(test[test$source == "model" & test$indicator == "PLHIV" & test$year == 2011, "value"])
plhiv_2012 <- mean(test[test$source == "model" & test$indicator == "PLHIV" & test$year == 2012, "value"])
plhiv_2013 <- mean(test[test$source == "model" & test$indicator == "PLHIV" & test$year == 2013, "value"])
plhiv_2014 <- mean(test[test$source == "model" & test$indicator == "PLHIV" & test$year == 2014, "value"])
plhiv_2015 <- mean(test[test$source == "model" & test$indicator == "PLHIV" & test$year == 2015, "value"])
plhiv <- c(plhiv_2010, plhiv_2011, plhiv_2012, plhiv_2013, plhiv_2014, plhiv_2015)
inc <- as.double(MasterData$incidence[2,3:8])
inc
rate <- inc / plhiv
year <- seq(2010, 2015, 1)
df <- data.frame(year, rate)
graphics.off(); quartz.options(w = 5, h = 3)
ggplot(df, aes(x = year, y = rate)) +
geom_line() +
ggtitle("Transmission Rate", subtitle = "New Infections / Total PLHIV")
quartz.save(file = "~/Desktop/fig/transmission-rate.pdf", type = "pdf")
####################################################################################################
####################################################################################################
# CROI 2017 FIGURE GENERATION
# Baseline Changes Figure
build_changes_baseline_CROI <- function() {
theBase <- rbind(
data.frame(variable = "Testing", mean = mean(BaselineTest) / 5, strategy = "Baseline"),
data.frame(variable = "Linkage", mean = mean(BaselineLink) / 5, strategy = "Baseline"),
data.frame(variable = "Pre-ART\nRetention", mean = mean(BaselinePreR) / 5, strategy = "Baseline"),
data.frame(variable = "ART\nInitiation", mean = mean(BaselineInit) / 5, strategy = "Baseline"),
data.frame(variable = "ART\nRetention", mean = mean(BaselineRetn) / 5, strategy = "Baseline"),
data.frame(variable = "Viral\nSuppression", mean = mean(BaselineAdhr) / 5, strategy = "Baseline")
)
theBase$upper <- NA
theBase$lower <- NA
theBase$variable <- factor(theBase$variable, levels = c("Testing", "Linkage",
"Pre-ART\nRetention", "ART\nInitiation", "ART\nRetention", "Viral\nSuppression"))
# make retention values NEGATIVE
theBase[theBase$variable == "Pre-ART\nRetention", "mean"] <- - theBase[theBase$variable ==
"Pre-ART\nRetention", "mean"]
theBase[theBase$variable == "ART\nRetention", "mean"] <- - theBase[theBase$variable ==
"ART\nRetention", "mean"]
ggOut <- ggplot(theBase, aes(x = variable, y = mean, fill = strategy))
ggOut <- ggOut + geom_bar(stat = "identity", alpha = 1)
ggOut <- ggOut + scale_fill_manual(values = "#E41A1C")
ggOut <- ggOut + theme_classic()
ggOut <- ggOut + ylab("Annual Movement Through Care (2015 to 2020)")
ggOut <- ggOut + theme(axis.text.x = element_text(size = 10))
ggOut <- ggOut + theme(axis.title.x = element_blank())
ggOut <- ggOut + theme(axis.title.y = element_text(size = 10))
ggOut <- ggOut + theme(axis.text.y = element_text(size = 10))
ggOut <- ggOut + theme(axis.line.y = element_line())
ggOut <- ggOut + theme(axis.line.x = element_blank())
ggOut <- ggOut + scale_y_continuous(limits = c(-1e4, 8e4), labels = scales::comma, breaks =
scales::pretty_breaks(n = 8), expand = c(0, 0))
ggOut <- ggOut + theme(text = element_text(family = "Avenir Next"))
ggOut <- ggOut + theme(legend.position = 'right')
ggOut <- ggOut + theme(legend.title = element_blank())
ggOut <- ggOut + theme(legend.key.size = unit(0.5, "cm"))
ggOut <- ggOut + geom_hline(yintercept = 0)
ggOut <- ggOut + guides(fill = guide_legend(override.aes = list(alpha = 1)))
ggOut <- ggOut + theme(plot.background = element_blank())
ggOut <- ggOut + theme(legend.background = element_blank())
ggOut <- ggOut + theme(panel.background = element_blank())
ggOut <- ggOut + theme(axis.ticks.x = element_blank())
ggOut
}
graphics.off(); quartz.options(w = 8, h = 4)
build_changes_baseline_CROI()
quartz.save(file = "../../formal/nigeria/fig/opt/changes-baseline.pdf", type = "pdf")
# handy invert function
invert <- function(x) {
if (x <= 0) {
x <- abs(x)
} else {
x <- - x
}
x
}
# Complete Changes Figures
build_changes_CROI <- function(CalibParamOut, optResults, target) {
simLength <- dim(GetParaMatrixRun(cParamOut = CalibParamOut, runNumber = 1, length = 2))[1]
optRuns <- WhichAchieved73(simData = optResults, simLength = simLength, target = target)
frontierList <- GetFrontiers(simData = optResults, optRuns = optRuns, simLength = simLength)
intResult <- RunInterpolation(simData = optResults, optRuns = optRuns, simLength = simLength, frontierList = frontierList, target = target)
# Result Formatting
intResult <- intResult[,c("iTest","iLink","iPreR","iInit","iAdhr","iRetn")]
intResult['iPreR'] <- invert(intResult['iPreR'])
intResult['iRetn'] <- invert(intResult['iRetn'])
intResult[intResult$iTest < 0, 'iTest'] <- 0
intResult[intResult$iLink < 0, 'iLink'] <- 0
intResult[intResult$iInit < 0, 'iInit'] <- 0
intResult[intResult$iAhdr < 0, 'iAdhr'] <- 0
# Assign a 'run' number to simulations
intResult$run <- 1:dim(intResult)[1]
# Melt them
mRes <- reshape2::melt(intResult, id = "run")
## DIVIDE ALL VALUES BY FIVE
# Conversion from 5 year values to single years
mRes$value <- mRes$value / 5
# RENAME VARIABLES
mRes$variable <- as.character(mRes$variable)
mRes[mRes$variable == "iTest", "variable"] <- "Number of\nPLHIV to\nDiagnose"
mRes[mRes$variable == "iLink", "variable"] <- "Number of\nPLHIV to\nLink"
mRes[mRes$variable == "iPreR", "variable"] <- "Number of\nPLHIV to\nRetain in\nPre-ART Care"
mRes[mRes$variable == "iInit", "variable"] <- "Number of\nPLHIV to\nInitiate ART"
mRes[mRes$variable == "iAdhr", "variable"] <- "Number of\nPLHIV to\nMaintain Viral\nSuppression"
mRes[mRes$variable == "iRetn", "variable"] <- "Number of\nPLHIV to\nRetain on\nART"
mRes$variable <- factor(mRes$variable, levels = c("Number of\nPLHIV to\nDiagnose", "Number of\nPLHIV to\nLink", "Number of\nPLHIV to\nRetain in\nPre-ART Care", "Number of\nPLHIV to\nInitiate ART",
"Number of\nPLHIV to\nRetain on\nART", "Number of\nPLHIV to\nMaintain Viral\nSuppression"))
# EDITS FROM HERE
variable <- c("Number of\nPLHIV to\nDiagnose", "Number of\nPLHIV to\nLink",
"Number of\nPLHIV to\nRetain in\nPre-ART Care", "Number of\nPLHIV to\nInitiate ART", "Number of\nPLHIV to\nRetain on\nART", "Number of\nPLHIV to\nMaintain Viral\nSuppression")
mean <- c(
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nDiagnose", "value"])[["mean"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nLink", "value"])[["mean"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nRetain in\nPre-ART Care", "value"])[["mean"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nInitiate ART", "value"])[["mean"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nRetain on\nART", "value"])[["mean"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nMaintain Viral\nSuppression", "value"])[["mean"]]
)
upper <- c(
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nDiagnose", "value"])[["upper"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nLink", "value"])[["upper"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nRetain in\nPre-ART Care", "value"])[["upper"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nInitiate ART", "value"])[["upper"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nRetain on\nART", "value"])[["upper"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nMaintain Viral\nSuppression", "value"])[["upper"]]
)
lower <- c(
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nDiagnose", "value"])[["lower"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nLink", "value"])[["lower"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nRetain in\nPre-ART Care", "value"])[["lower"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nInitiate ART", "value"])[["lower"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nRetain on\nART", "value"])[["lower"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nMaintain Viral\nSuppression", "value"])[["lower"]]
)
strategy <- "Intervention"
outData <- data.frame(variable, mean, lower, upper, strategy)
# baseline data.frame
theBase <- rbind(
data.frame(variable = "Number of\nPLHIV to\nDiagnose",
mean = mean(BaselineTest) / 5,
strategy = "Baseline"),
data.frame(variable = "Number of\nPLHIV to\nLink",
mean = mean(BaselineLink) / 5,
strategy = "Baseline"),
data.frame(variable = "Number of\nPLHIV to\nRetain in\nPre-ART Care",
mean = mean(BaselinePreR) / 5,
strategy = "Baseline"),
data.frame(variable = "Number of\nPLHIV to\nInitiate ART",
mean = mean(BaselineInit) / 5,
strategy = "Baseline"),
data.frame(variable = "Number of\nPLHIV to\nRetain on\nART",
mean = mean(BaselineRetn) / 5,
strategy = "Baseline"),
data.frame(variable = "Number of\nPLHIV to\nMaintain Viral\nSuppression",
mean = mean(BaselineAdhr) / 5,
strategy = "Baseline")
)
theBase$upper <- NA
theBase$lower <- NA
final <- rbind(theBase, outData)
final$strategy <- factor(final$strategy, levels = c("Intervention", "Baseline"))
# Now we need the error_bar data.frame
value <- mean
mean <- mean + theBase$mean
upper <- upper + theBase$mean
lower <- lower + theBase$mean
theLabel <- data.frame(variable, value, mean, upper, lower)
ggOut <- ggplot(final, aes(x = variable, y = mean, fill = strategy))
ggOut <- ggOut + geom_bar(stat = "identity", alpha = 1)
ggOut <- ggOut + geom_hline(yintercept = 0)
ggOut <- ggOut + geom_errorbar(data = theLabel, aes(x = variable, y = mean, ymax = upper, ymin = lower), alpha = 1, width = 0.25, size = 0.5)
ggOut <- ggOut + geom_label(data = theLabel, aes(x = variable, y = mean, label = paste0("+",
scales::comma(round(value, 0)))), vjust = c(0.5, 0.5, 0, 0.5, 0.5, 0.5), family = "Avenir Next", colour = "black", size = 3, alpha = 1, show.legend = FALSE)
ggOut <- ggOut + scale_fill_manual(values = c("#4F8ABA","#E41A1C"))
ggOut <- ggOut + theme_classic()
ggOut <- ggOut + ylab("Annual Targets")
ggOut <- ggOut + theme(axis.text.x = element_text(size = 8))
ggOut <- ggOut + theme(axis.title.x = element_blank())
ggOut <- ggOut + theme(axis.title.y = element_text(size = 10))
ggOut <- ggOut + theme(axis.text.y = element_text(size = 10))
ggOut <- ggOut + theme(axis.line.y = element_line())
ggOut <- ggOut + theme(axis.line.x = element_blank())
ggOut <- ggOut + scale_y_continuous(limits = c(0, 11e4), labels = scales::comma, breaks =
scales::pretty_breaks(n = 11), expand = c(0, 0))
ggOut <- ggOut + theme(text = element_text(family = "Avenir Next"))
ggOut <- ggOut + theme(legend.position = 'right')
ggOut <- ggOut + theme(legend.title = element_blank())
ggOut <- ggOut + theme(legend.key.size = unit(0.5, "cm"))
ggOut <- ggOut + guides(fill = guide_legend(override.aes = list(alpha = 1)))
ggOut <- ggOut + theme(plot.background = element_blank())
ggOut <- ggOut + theme(legend.background = element_blank())
ggOut <- ggOut + theme(panel.background = element_blank())
ggOut <- ggOut + theme(axis.ticks.x = element_blank())
ggOut
}
graphics.off(); quartz.options(w = 8, h = 4)
build_changes_CROI(CalibParamOut = CalibParamOut, optResults = optResults, target = 0.9^3)
quartz.save(file = "../../formal/nigeria/fig/opt/changes.pdf", type = "pdf")
build_custom_frontier_plot <- function(CalibParamOut, optResults, target = target, ylim) {
simLength <- dim(GetParaMatrixRun(cParamOut = CalibParamOut, runNumber = 1, length = 2))[1]
optRuns <- WhichAchieved73(simData = optResults, simLength = simLength, target = target)
optResults$sim <- rep(x = 1:(dim(optResults)[1] / simLength), each = simLength)
allRuns <- GetFrontiers(simData = optResults, optRuns = 1:(dim(optResults)[1] / simLength), simLength = simLength)
interpol <- list()
for(n in 1:(dim(optResults)[1] / simLength)) {
lower <- (1 + simLength * (n - 1))
upper <- (simLength + simLength * (n - 1))
vals <- optResults[lower:upper,]
interpolation <- approx(x = vals[,"VS"][allRuns[[n]]], y = vals[,"Cost"][allRuns[[n]]])
interpol[[n]] <- interpolation
}
ggPlot <- ggplot(optResults, aes(x = VS, y = Cost))
ggPlot <- ggPlot + geom_point(col = '#4F8ABA', alpha = 0.2)
for(n in 1:(dim(optResults)[1] / simLength)) {
ggPlot <- ggPlot + geom_line(data = as.data.frame(interpol[[n]]), mapping = aes(x = x, y = y), col = 'black', alpha = 0.2, size = 0.5)
}
for(n in 1:length(optRuns)) {
ggPlot <- ggPlot + geom_line(data = as.data.frame(interpol[[optRuns[n]]]), mapping = aes(x = x, y = y), col = "red", alpha = 0.5, size = 0.75)
}
ggPlot <- ggPlot + geom_vline(xintercept = 0.9^3, alpha = 1)
ggPlot <- ggPlot + theme_classic()
ggPlot <- ggPlot + expand_limits(y = ylim)
ggPlot <- ggPlot + scale_y_continuous(labels = scales::scientific, breaks = scales::pretty_breaks(n = 5))
ggPlot <- ggPlot + scale_x_continuous(labels = scales::percent, breaks = scales::pretty_breaks(n = 5))
ggPlot <- ggPlot + theme(axis.text.x = element_text(size = 10))
ggPlot <- ggPlot + theme(axis.text.y = element_text(size = 10))
ggPlot <- ggPlot + theme(axis.title = element_text(size = 11))
ggPlot <- ggPlot + theme(axis.line.x = element_line())
ggPlot <- ggPlot + theme(axis.line.y = element_line())
ggPlot <- ggPlot + xlab("Viral Suppression")
ggPlot <- ggPlot + ylab("Additional Cost of Care")
ggPlot <- ggPlot + theme(text = element_text(family = figFont))
ggPlot
}
graphics.off(); quartz.options(w = 8, h = 4)
build_custom_frontier_plot(CalibParamOut = CalibParamOut, optResults = optResults, target = 0.9^3,
ylim = 2.5e8)
quartz.save(file = "../../formal/nigeria/fig/opt/frontier.pdf", type = "pdf")
####################################################################################################
### PAPER CHANGE FIGURE (Adapted from version presented at CROI 2017)
# new variable: absResults
# this maps the ABSOLUTE changes in care (not those relative to baseline) in the optResults df
build_changes_paper_figure <- function(target = 0.9^3) {
simLength <- dim(GetParaMatrixRun(cParamOut = CalibParamOut, runNumber = 1, length = 2))[1]
optRuns <- WhichAchieved73(simData = absResults, simLength = simLength, target = target)
frontierList <- GetFrontiers(simData = absResults, optRuns = optRuns, simLength = simLength)
intResult <- RunInterpolation(simData = absResults, optRuns = optRuns, simLength = simLength, frontierList = frontierList, target = target)
# Result Formatting
intResult <- intResult[,c("iTest","iLink","iPreR","iInit","iAdhr","iRetn")]
# Assign a 'run' number to simulations
intResult$run <- 1:dim(intResult)[1]
# Melt them
mRes <- reshape2::melt(intResult, id = "run")
## DIVIDE ALL VALUES BY FIVE
# Conversion from 5 year values to single years
mRes$value <- mRes$value / 5
# RENAME VARIABLES
mRes$variable <- as.character(mRes$variable)
mRes[mRes$variable == "iTest", "variable"] <- "Number of\nPLHIV to\nDiagnose"
mRes[mRes$variable == "iLink", "variable"] <- "Number of\nPLHIV to\nLink"
mRes[mRes$variable == "iPreR", "variable"] <- "Number of\nPLHIV\nLost From\nPre-ART Care"
mRes[mRes$variable == "iInit", "variable"] <- "Number of\nPLHIV to\nInitiate ART"
mRes[mRes$variable == "iAdhr", "variable"] <- "Number of\nPLHIV to\nMaintain Viral\nSuppression"
mRes[mRes$variable == "iRetn", "variable"] <- "Number of\nPLHIV\nLost From\nART Care"
mRes$variable <- factor(mRes$variable, levels = c("Number of\nPLHIV to\nDiagnose", "Number of\nPLHIV to\nLink", "Number of\nPLHIV\nLost From\nPre-ART Care", "Number of\nPLHIV to\nInitiate ART",
"Number of\nPLHIV\nLost From\nART Care", "Number of\nPLHIV to\nMaintain Viral\nSuppression"))
# EDITS FROM HERE
variable <- c("Number of\nPLHIV to\nDiagnose", "Number of\nPLHIV to\nLink",
"Number of\nPLHIV\nLost From\nPre-ART Care", "Number of\nPLHIV to\nInitiate ART", "Number of\nPLHIV\nLost From\nART Care", "Number of\nPLHIV to\nMaintain Viral\nSuppression")
mean <- c(
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nDiagnose", "value"])[["mean"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nLink", "value"])[["mean"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV\nLost From\nPre-ART Care", "value"])[["mean"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nInitiate ART", "value"])[["mean"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV\nLost From\nART Care", "value"])[["mean"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nMaintain Viral\nSuppression", "value"])[["mean"]]
)
upper <- c(
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nDiagnose", "value"])[["upper"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nLink", "value"])[["upper"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV\nLost From\nPre-ART Care", "value"])[["upper"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nInitiate ART", "value"])[["upper"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV\nLost From\nART Care", "value"])[["upper"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nMaintain Viral\nSuppression", "value"])[["upper"]]
)
lower <- c(
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nDiagnose", "value"])[["lower"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nLink", "value"])[["lower"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV\nLost From\nPre-ART Care", "value"])[["lower"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nInitiate ART", "value"])[["lower"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV\nLost From\nART Care", "value"])[["lower"]],
Quantile_95(mRes[mRes$variable == "Number of\nPLHIV to\nMaintain Viral\nSuppression", "value"])[["lower"]]
)
strategy <- "Intervention"
outData <- data.frame(variable, mean, lower, upper, strategy)
# baseline data.frame
theBase <- rbind(
data.frame(variable = "Number of\nPLHIV to\nDiagnose",
mean = Quantile_95(BaselineTest)[["mean"]] / 5,
lower = Quantile_95(BaselineTest)[["lower"]] / 5,
upper = Quantile_95(BaselineTest)[["upper"]] / 5,
strategy = "Baseline"),
data.frame(variable = "Number of\nPLHIV to\nLink",
mean = Quantile_95(BaselineLink)[["mean"]] / 5,
lower = Quantile_95(BaselineLink)[["lower"]] / 5,
upper = Quantile_95(BaselineLink)[["upper"]] / 5,
strategy = "Baseline"),
data.frame(variable = "Number of\nPLHIV\nLost From\nPre-ART Care",
mean = Quantile_95(BaselinePreR)[["mean"]] / 5,
lower = Quantile_95(BaselinePreR)[["lower"]] / 5,
upper = Quantile_95(BaselinePreR)[["upper"]] / 5,
strategy = "Baseline"),
data.frame(variable = "Number of\nPLHIV to\nInitiate ART",
mean = Quantile_95(BaselineInit)[["mean"]] / 5,
lower = Quantile_95(BaselineInit)[["lower"]] / 5,
upper = Quantile_95(BaselineInit)[["upper"]] / 5,
strategy = "Baseline"),
data.frame(variable = "Number of\nPLHIV\nLost From\nART Care",
mean = Quantile_95(BaselineRetn)[["mean"]] / 5,
lower = Quantile_95(BaselineRetn)[["lower"]] / 5,
upper = Quantile_95(BaselineRetn)[["upper"]] / 5,
strategy = "Baseline"),
data.frame(variable = "Number of\nPLHIV to\nMaintain Viral\nSuppression",
mean = Quantile_95(BaselineAdhr)[["mean"]] / 5,
lower = Quantile_95(BaselineAdhr)[["lower"]] / 5,
upper = Quantile_95(BaselineAdhr)[["upper"]] / 5,
strategy = "Baseline")
)
final <- rbind(theBase, outData)
final$strategy <- factor(final$strategy, levels = c("Baseline", "Intervention"))
# WHAT I NEED
# -> Single data.frame containing 'baseline' 'intervention'
# -> cols = Intervention, mean, upper, lower
# -> IGNORE geom_label for now (I think it is too complicated with a geom_label call)
# need to re-run the simulations and then spit out ANOTHER data.frame that just shows things like
# the baseline changes but for interventions
# Leave option for labels
# ggOut <- ggOut + geom_label(data = theLabel, aes(x = variable, y = mean, label = paste0("+",
# scales::comma(round(value, 0)))), vjust = c(0.5, 0.5, 0, 0.5, 0.5, 0.5), family = "Avenir
# Next", colour = "black", size = 3, alpha = 1, show.legend = FALSE)
ggOut <- ggplot(final, aes(x = variable, y = mean, fill = strategy))
ggOut <- ggOut + geom_bar(position = "dodge", stat = "identity", alpha = 1)
ggOut <- ggOut + geom_errorbar(aes(x = variable, ymax = upper, ymin = lower), position =
position_dodge(0.9), alpha = 1, width = 0.25, size = 0.5)
ggOut <- ggOut + scale_fill_manual(values = c("#E41A1C","#4F8ABA"))
ggOut <- ggOut + theme_classic()
ggOut <- ggOut + ylab("Annual Targets")
ggOut <- ggOut + theme(axis.text.x = element_text(size = 8))
ggOut <- ggOut + theme(axis.title.x = element_blank())
ggOut <- ggOut + theme(axis.title.y = element_text(size = 10))
ggOut <- ggOut + theme(axis.text.y = element_text(size = 10))
ggOut <- ggOut + theme(axis.line.y = element_line())
ggOut <- ggOut + theme(axis.line.x = element_blank())
ggOut <- ggOut + scale_y_continuous(limits = c(0, 12e4), labels = scales::comma, breaks =
scales::pretty_breaks(n = 12), expand = c(0, 0))
ggOut <- ggOut + theme(text = element_text(family = "Avenir Next"))
ggOut <- ggOut + theme(legend.position = 'right')
ggOut <- ggOut + theme(legend.title = element_blank())
ggOut <- ggOut + theme(legend.key.size = unit(0.5, "cm"))
ggOut <- ggOut + guides(fill = guide_legend(override.aes = list(alpha = 1)))
ggOut <- ggOut + theme(plot.background = element_blank())
ggOut <- ggOut + theme(legend.background = element_blank())
ggOut <- ggOut + theme(panel.background = element_blank())
ggOut <- ggOut + theme(axis.ticks.x = element_blank())
ggOut
}
graphics.off(); quartz.options(w = 8, h = 4)
build_changes_paper_figure()
quartz.save(file = "../../formal/nigeria/fig/opt/changes-dodge.pdf", type = "pdf")
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