formal/UNAIDS/functions.R
In jackolney/CascadeDashboard: A Shiny App for Investigating The Current Trajectory of HIV Care
# Write data to spreadsheet
write_spreadsheet <- function(country_name, global_out, path) {
# Create WorkBook
wb <- createWorkbook()
#####
## Sheet 1 (90-90-90)
sheet1 <- createSheet(wb, sheetName = "90-90-90")
cb <- CellBlock(sheet = sheet1, startRow = 1, startColumn = 1, noRows = 28, noColumns = 11)
cs <- CellStyle(wb) + Font(wb, isBold = TRUE, heightInPoints = 12) + Alignment(h = "ALIGN_LEFT")
# Set headers
CB.setRowData(cellBlock = cb,
x = c("country",
"1st 90 in 2020",
"2nd 90 in 2020",
"3rd 90 in 2020",
"1st 90 lower 95% CI",
"2nd 90 lower 95% CI",
"3rd 90 lower 95% CI",
"1st 90 upper 95% CI",
"2nd 90 upper 95% CI",
"3rd 90 upper 95% CI",
"Notes"),
rowIndex = 1, colOffset = 0, rowStyle = cs)
# Set colWidths
setColumnWidth(sheet = sheet1, colIndex = 1, colWidth = 12)
setColumnWidth(sheet = sheet1, colIndex = 2:10, colWidth = 20)
setColumnWidth(sheet = sheet1, colIndex = 11, colWidth = 30)
# ADD DATA
CB.setRowData(cellBlock = cb, x = global_out[[1]], rowIndex = 2, colOffset = 0)
# Borders
TitleBorder <- Border(color = "black", position = c("TOP","BOTTOM","LEFT","RIGHT"),
pen = c("BORDER_THIN","BORDER_THIN","BORDER_THIN","BORDER_THIN"))
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 1)
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 2)
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 3)
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 4)
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 5)
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 6)
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 7)
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 8)
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 9)
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 10)
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 11)
#####
## Sheet 2 (Cascade in 2015)
sheet2 <- createSheet(wb , sheetName = "2015")
cb2 <- CellBlock(sheet = sheet2, startRow = 1, startColumn = 1, noRows = 28, noColumns = 16)
# Set headers
CB.setRowData(cellBlock = cb2, x = c(
"country",
"PLHIV",
"PLHIV Diagnosed",
"PLHIV In Care",
"PLHIV On ART",
"PLHIV Virally Suppressed",
"PLHIV lower 95% CI",
"PLHIV Diagnosed lower 95% CI",
"PLHIV In Care lower 95% CI",
"PLHIV On ART lower 95% CI",
"PLHIV Virally Suppressed lower 95% CI",
"PLHIV upper 95% CI",
"PLHIV Diagnosed upper 95% CI",
"PLHIV In Care upper 95% CI",
"PLHIV On ART upper 95% CI",
"PLHIV Virally Suppressed upper 95% CI"),
rowIndex = 1, colOffset = 0, rowStyle = cs)
setColumnWidth(sheet = sheet2, colIndex = 1, colWidth = 12)
setColumnWidth(sheet = sheet2, colIndex = 2:16, colWidth = 20)
# ADD DATA
CB.setRowData(cellBlock = cb2, x = global_out[[2]], rowIndex = 2, colOffset = 0)
# Borders
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 1)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 2)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 3)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 4)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 5)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 6)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 7)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 8)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 9)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 10)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 11)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 12)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 13)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 14)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 15)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 16)
#####
## Sheet 3 (Cascade in 2020)
sheet3 <- createSheet(wb , sheetName = "2020")
cb3 <- CellBlock(sheet = sheet3, startRow = 1, startColumn = 1, noRows = 28, noColumns = 16)
# Set headers
CB.setRowData(cellBlock = cb3, x = c(
"country",
"PLHIV",
"PLHIV Diagnosed",
"PLHIV In Care",
"PLHIV On ART",
"PLHIV Virally Suppressed",
"PLHIV lower 95% CI",
"PLHIV Diagnosed lower 95% CI",
"PLHIV In Care lower 95% CI",
"PLHIV On ART lower 95% CI",
"PLHIV Virally Suppressed lower 95% CI",
"PLHIV upper 95% CI",
"PLHIV Diagnosed upper 95% CI",
"PLHIV In Care upper 95% CI",
"PLHIV On ART upper 95% CI",
"PLHIV Virally Suppressed upper 95% CI"),
rowIndex = 1, colOffset = 0, rowStyle = cs)
setColumnWidth(sheet = sheet3, colIndex = 1, colWidth = 12)
setColumnWidth(sheet = sheet3, colIndex = 2:16, colWidth = 20)
# ADD DATA
CB.setRowData(cellBlock = cb3, x = global_out[[3]], rowIndex = 2, colOffset = 0)
# Borders
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 1)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 2)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 3)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 4)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 5)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 6)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 7)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 8)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 9)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 10)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 11)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 12)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 13)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 14)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 15)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 16)
#####
## Sheet 4 (AIDS Deaths)
sheet4 <- createSheet(wb , sheetName = "AIDS Deaths")
cb4 <- CellBlock(sheet = sheet4, startRow = 1, startColumn = 1, noRows = 28, noColumns = 16)
# Set headers
CB.setRowData(cellBlock = cb4, x = c(
"country",
"2015",
"2016",
"2017",
"2018",
"2019",
"2015 lower 95% CI",
"2016 lower 95% CI",
"2017 lower 95% CI",
"2018 lower 95% CI",
"2019 lower 95% CI",
"2015 upper 95% CI",
"2016 upper 95% CI",
"2017 upper 95% CI",
"2018 upper 95% CI",
"2019 upper 95% CI"),
rowIndex = 1, colOffset = 0, rowStyle = cs)
setColumnWidth(sheet = sheet4, colIndex = 1, colWidth = 12)
setColumnWidth(sheet = sheet4, colIndex = 2:16, colWidth = 20)
# ADD DATA
CB.setRowData(cellBlock = cb4, x = global_out[[4]], rowIndex = 2, colOffset = 0)
# Borders
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 1)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 2)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 3)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 4)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 5)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 6)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 7)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 8)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 9)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 10)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 11)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 12)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 13)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 14)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 15)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 16)
#####
## Sheet 5 (New Infections)
sheet5 <- createSheet(wb , sheetName = "New Infections")
cb5 <- CellBlock(sheet = sheet5, startRow = 1, startColumn = 1, noRows = 28, noColumns = 16)
# Set headers
CB.setRowData(cellBlock = cb5, x = c(
"country",
"2015",
"2016",
"2017",
"2018",
"2019",
"2015 lower 95% CI",
"2016 lower 95% CI",
"2017 lower 95% CI",
"2018 lower 95% CI",
"2019 lower 95% CI",
"2015 upper 95% CI",
"2016 upper 95% CI",
"2017 upper 95% CI",
"2018 upper 95% CI",
"2019 upper 95% CI"),
rowIndex = 1, colOffset = 0, rowStyle = cs)
setColumnWidth(sheet = sheet5, colIndex = 1, colWidth = 12)
setColumnWidth(sheet = sheet5, colIndex = 2:16, colWidth = 20)
# ADD DATA
CB.setRowData(cellBlock = cb5, x = global_out[[5]], rowIndex = 2, colOffset = 0)
# Borders
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 1)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 2)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 3)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 4)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 5)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 6)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 7)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 8)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 9)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 10)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 11)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 12)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 13)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 14)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 15)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 16)
# Save that shit.
# SAVE BY COUNTRY_NAME
saveWorkbook(wb, file = paste0(path, country_name, ".xlsx"))
}
# Build spreadsheet data structure
get_spreadsheet_data <- function(country_name, notes) {
# Global Output that will constitute one line of each workbook
global_out <- list()
####################################################################################################
# Sheet one (90-90-90)
# "country", "1st 90 in 2020", "lower 95% CI", "upper 95% CI", "2nd 90 in 2020", "lower 95% CI", "upper 95% CI", "3rd 90 in 2020", "lower 95% CI", "upper 95% CI",
# "Notes"
# just declare it
AdvCalib <- data.frame(NatMort = 0.005, HIVMort = 1)
# Can we extract the confidence intervals too? - YES.
out <- Get909090Data()
# First 90
x_1 = round(out[out$def == "Diagnosed / PLHIV", "res"], digits = 2)
min_1 = round(out[out$def == "Diagnosed / PLHIV", "min"], digits = 2)
max_1 = round(out[out$def == "Diagnosed / PLHIV", "max"], digits = 2)
# u1st_90 <- paste0(x_1, " (", min_1, " to ", max_1, ")")
# Second 90
x_2 = round(out[out$def == "On Treatment / Diagnosed", "res"], digits = 2)
min_2 = round(out[out$def == "On Treatment / Diagnosed", "min"], digits = 2)
max_2 = round(out[out$def == "On Treatment / Diagnosed", "max"], digits = 2)
# u2nd_90 <- paste0(x_2, " (", min_2, " to ", max_2, ")")
# Third 90
x_3 = round(out[out$def == "Virally Suppressed / On Treatment", "res"], digits = 2)
min_3 = round(out[out$def == "Virally Suppressed / On Treatment", "min"], digits = 2)
max_3 = round(out[out$def == "Virally Suppressed / On Treatment", "max"], digits = 2)
# u3rd_90 <- paste0(x_3, " (", min_3, " to ", max_3, ")")
# NOTES
# comes in as arg now
# notes <- "Good fit."
global_out[[1]] <- c(country_name, x_1, x_2, x_3, min_1, min_2, min_3, max_1, max_2, max_3, notes)
####################################################################################################
# Sheet two (Cascade in 2015)
# "country", "PLHIV", "Diagnosed", "In Care", "On ART", "Virally Suppressed"
out_t0 <- GetCascadeData(1) # t0 = 1
# PLHIV
plhiv_x <- round(out_t0[out_t0$def == "PLHIV", "res"], digits = 0)
plhiv_min <- round(out_t0[out_t0$def == "PLHIV", "min"], digits = 0)
plhiv_max <- round(out_t0[out_t0$def == "PLHIV", "max"], digits = 0)
# plhiv <- paste0(plhiv_x, " (", plhiv_min, " to ", plhiv_max, ")")
# Diagnosed
diag_x <- round(out_t0[out_t0$def == "Diagnosed", "res"], digits = 0)
diag_min <- round(out_t0[out_t0$def == "Diagnosed", "min"], digits = 0)
diag_max <- round(out_t0[out_t0$def == "Diagnosed", "max"], digits = 0)
# diagnosed <- paste0(diag_x, " (", diag_min, " to ", diag_max, ")")
# In Care
care_x <- round(out_t0[out_t0$def == "In Care", "res"], digits = 0)
care_min <- round(out_t0[out_t0$def == "In Care", "min"], digits = 0)
care_max <- round(out_t0[out_t0$def == "In Care", "max"], digits = 0)
# care <- paste0(care_x, " (", care_min, " to ", care_max, ")")
# On ART
art_x <- round(out_t0[out_t0$def == "Treatment", "res"], digits = 0)
art_min <- round(out_t0[out_t0$def == "Treatment", "min"], digits = 0)
art_max <- round(out_t0[out_t0$def == "Treatment", "max"], digits = 0)
# art <- paste0(art_x, " (", art_min, " to ", art_max, ")")
# Virally Suppressed
supp_x <- round(out_t0[out_t0$def == "Suppressed", "res"], digits = 0)
supp_min <- round(out_t0[out_t0$def == "Suppressed", "min"], digits = 0)
supp_max <- round(out_t0[out_t0$def == "Suppressed", "max"], digits = 0)
# supp <- paste0(supp_x, " (", supp_min, " to ", supp_max, ")")
global_out[[2]] <- c(country_name, plhiv_x, diag_x, care_x, art_x, supp_x, plhiv_min, diag_min,
care_min, art_min, supp_min, plhiv_max, diag_max, care_max, art_max, supp_max)
####################################################################################################
# Sheet three (Cascade in 2020)
# "country", "PLHIV", "Diagnosed", "In Care", "On ART", "Virally Suppressed"
out_t5 <- GetCascadeData(251) # t5 = (5 / 0.02) + 1 [t0]
# PLHIV
plhiv_x <- round(out_t5[out_t5$def == "PLHIV", "res"], digits = 0)
plhiv_min <- round(out_t5[out_t5$def == "PLHIV", "min"], digits = 0)
plhiv_max <- round(out_t5[out_t5$def == "PLHIV", "max"], digits = 0)
# plhiv <- paste0(plhiv_x, " (", plhiv_min, " to ", plhiv_max, ")")
# Diagnosed
diag_x <- round(out_t5[out_t5$def == "Diagnosed", "res"], digits = 0)
diag_min <- round(out_t5[out_t5$def == "Diagnosed", "min"], digits = 0)
diag_max <- round(out_t5[out_t5$def == "Diagnosed", "max"], digits = 0)
# diagnosed <- paste0(diag_x, " (", diag_min, " to ", diag_max, ")")
# In Care
care_x <- round(out_t5[out_t5$def == "In Care", "res"], digits = 0)
care_min <- round(out_t5[out_t5$def == "In Care", "min"], digits = 0)
care_max <- round(out_t5[out_t5$def == "In Care", "max"], digits = 0)
# care <- paste0(care_x, " (", care_min, " to ", care_max, ")")
# On ART
art_x <- round(out_t5[out_t5$def == "Treatment", "res"], digits = 0)
art_min <- round(out_t5[out_t5$def == "Treatment", "min"], digits = 0)
art_max <- round(out_t5[out_t5$def == "Treatment", "max"], digits = 0)
# art <- paste0(art_x, " (", art_min, " to ", art_max, ")")
# Virally Suppressed
supp_x <- round(out_t5[out_t5$def == "Suppressed", "res"], digits = 0)
supp_min <- round(out_t5[out_t5$def == "Suppressed", "min"], digits = 0)
supp_max <- round(out_t5[out_t5$def == "Suppressed", "max"], digits = 0)
# supp <- paste0(supp_x, " (", supp_min, " to ", supp_max, ")")
global_out[[3]] <- c(country_name, plhiv_x, diag_x, care_x, art_x, supp_x, plhiv_min, diag_min,
care_min, art_min, supp_min, plhiv_max, diag_max, care_max, art_max, supp_max)
####################################################################################################
# Sheet four (AIDS Deaths)
# "country", "2015", "2016", "2017", "2018", "2019"
ad <- round(get_aids_deaths_data(), digits = 0)
ad_2015_x <- ad[ad$timeOut == 2015, "HivMortality"]
ad_2015_min <- ad[ad$timeOut == 2015, "min"]
ad_2015_max <- ad[ad$timeOut == 2015, "max"]
ad_2016_x <- ad[ad$timeOut == 2016, "HivMortality"]
ad_2016_min <- ad[ad$timeOut == 2016, "min"]
ad_2016_max <- ad[ad$timeOut == 2016, "max"]
ad_2017_x <- ad[ad$timeOut == 2017, "HivMortality"]
ad_2017_min <- ad[ad$timeOut == 2017, "min"]
ad_2017_max <- ad[ad$timeOut == 2017, "max"]
ad_2018_x <- ad[ad$timeOut == 2018, "HivMortality"]
ad_2018_min <- ad[ad$timeOut == 2018, "min"]
ad_2018_max <- ad[ad$timeOut == 2018, "max"]
ad_2019_x <- ad[ad$timeOut == 2019, "HivMortality"]
ad_2019_min <- ad[ad$timeOut == 2019, "min"]
ad_2019_max <- ad[ad$timeOut == 2019, "max"]
global_out[[4]] <- c(country_name, ad_2015_x, ad_2016_x, ad_2017_x, ad_2018_x, ad_2019_x,
ad_2015_min, ad_2016_min, ad_2017_min, ad_2018_min, ad_2019_min, ad_2015_max, ad_2016_max,
ad_2017_max, ad_2018_max, ad_2019_max)
####################################################################################################
# Sheet five (New Infections)
# "country", "2015", "2016", "2017", "2018", "2019"
ni <- round(get_new_infections_data(), digits = 0)
ni_2015_x <- ni[ni$timeOut == 2015, "NewInf"]
ni_2015_min <- ni[ni$timeOut == 2015, "min"]
ni_2015_max <- ni[ni$timeOut == 2015, "max"]
ni_2016_x <- ni[ni$timeOut == 2016, "NewInf"]
ni_2016_min <- ni[ni$timeOut == 2016, "min"]
ni_2016_max <- ni[ni$timeOut == 2016, "max"]
ni_2017_x <- ni[ni$timeOut == 2017, "NewInf"]
ni_2017_min <- ni[ni$timeOut == 2017, "min"]
ni_2017_max <- ni[ni$timeOut == 2017, "max"]
ni_2018_x <- ni[ni$timeOut == 2018, "NewInf"]
ni_2018_min <- ni[ni$timeOut == 2018, "min"]
ni_2018_max <- ni[ni$timeOut == 2018, "max"]
ni_2019_x <- ni[ni$timeOut == 2019, "NewInf"]
ni_2019_min <- ni[ni$timeOut == 2019, "min"]
ni_2019_max <- ni[ni$timeOut == 2019, "max"]
global_out[[5]] <- c(country_name, ni_2015_x, ni_2016_x, ni_2017_x, ni_2018_x, ni_2019_x,
ni_2015_min, ni_2016_min, ni_2017_min, ni_2018_min, ni_2019_min, ni_2015_max, ni_2016_max,
ni_2017_max, ni_2018_max, ni_2019_max)
# return the global_out list
global_out
}
# Extract AIDS Deaths Data from model results
get_aids_deaths_data <- function() {
result <- GetModel()
out <- c()
min <- c()
max <- c()
for (j in 1:251) {
dat <- Quantile_95(unlist(lapply(result, function(x) sum(x$HivMortality[j]))))
out[j] <- dat[["mean"]]
min[j] <- dat[["lower"]]
max[j] <- dat[["upper"]]
}
HM_out <- c(0, diff(out))
HM_min <- c(0, diff(min))
HM_max <- c(0, diff(max))
times <- seq(0, 5, 0.02)
combo <- cbind(times, HM_out, HM_min, HM_max)
# Calculate time intervals
yr2015 <- times[times >= 0 & times <= 1]
yr2016 <- times[times > 1 & times <= 2]
yr2017 <- times[times > 2 & times <= 3]
yr2018 <- times[times > 3 & times <= 4]
yr2019 <- times[times > 4 & times <= 5]
# count between years to calculate bars
bar1 <- combo[times %in% yr2015,]
bar2 <- combo[times %in% yr2016,]
bar3 <- combo[times %in% yr2017,]
bar4 <- combo[times %in% yr2018,]
bar5 <- combo[times %in% yr2019,]
HivMortality <- c(
sum(bar1[,"HM_out"]),
sum(bar2[,"HM_out"]),
sum(bar3[,"HM_out"]),
sum(bar4[,"HM_out"]),
sum(bar5[,"HM_out"])
)
min <- c(
sum(bar1[,"HM_min"]),
sum(bar2[,"HM_min"]),
sum(bar3[,"HM_min"]),
sum(bar4[,"HM_min"]),
sum(bar5[,"HM_min"])
)
max <- c(
sum(bar1[,"HM_max"]),
sum(bar2[,"HM_max"]),
sum(bar3[,"HM_max"]),
sum(bar4[,"HM_max"]),
sum(bar5[,"HM_max"])
)
timeOut <- seq(2015, 2019, 1)
df <- data.frame(timeOut, HivMortality, min, max)
df
}
# Extract New Infections Data from model results
get_new_infections_data <- function() {
result <- GetModel()
out <- c()
min <- c()
max <- c()
for (j in 1:251) {
dat <- Quantile_95(unlist(lapply(result, function(x) sum(x$NewInf[j]))))
out[j] <- dat[["mean"]]
min[j] <- dat[["lower"]]
max[j] <- dat[["upper"]]
}
NI_out <- c(0, diff(out))
NI_min <- c(0, diff(min))
NI_max <- c(0, diff(max))
times <- seq(0, 5, 0.02)
combo <- cbind(times, NI_out, NI_min, NI_max)
# Calculate time intervals
yr2015 <- times[times >= 0 & times <= 1]
yr2016 <- times[times > 1 & times <= 2]
yr2017 <- times[times > 2 & times <= 3]
yr2018 <- times[times > 3 & times <= 4]
yr2019 <- times[times > 4 & times <= 5]
# count between years to calculate bars
bar1 <- combo[times %in% yr2015,]
bar2 <- combo[times %in% yr2016,]
bar3 <- combo[times %in% yr2017,]
bar4 <- combo[times %in% yr2018,]
bar5 <- combo[times %in% yr2019,]
NewInf <- c(
sum(bar1[,"NI_out"]),
sum(bar2[,"NI_out"]),
sum(bar3[,"NI_out"]),
sum(bar4[,"NI_out"]),
sum(bar5[,"NI_out"])
)
min <- c(
sum(bar1[,"NI_min"]),
sum(bar2[,"NI_min"]),
sum(bar3[,"NI_min"]),
sum(bar4[,"NI_min"]),
sum(bar5[,"NI_min"])
)
max <- c(
sum(bar1[,"NI_max"]),
sum(bar2[,"NI_max"]),
sum(bar3[,"NI_max"]),
sum(bar4[,"NI_max"]),
sum(bar5[,"NI_max"])
)
timeOut <- seq(2015, 2019, 1)
df <- data.frame(timeOut, NewInf, min, max)
df
}
jackolney/CascadeDashboard documentation built on May 18, 2019, 7:56 a.m.
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# Write data to spreadsheet
write_spreadsheet <- function(country_name, global_out, path) {
# Create WorkBook
wb <- createWorkbook()
#####
## Sheet 1 (90-90-90)
sheet1 <- createSheet(wb, sheetName = "90-90-90")
cb <- CellBlock(sheet = sheet1, startRow = 1, startColumn = 1, noRows = 28, noColumns = 11)
cs <- CellStyle(wb) + Font(wb, isBold = TRUE, heightInPoints = 12) + Alignment(h = "ALIGN_LEFT")
# Set headers
CB.setRowData(cellBlock = cb,
x = c("country",
"1st 90 in 2020",
"2nd 90 in 2020",
"3rd 90 in 2020",
"1st 90 lower 95% CI",
"2nd 90 lower 95% CI",
"3rd 90 lower 95% CI",
"1st 90 upper 95% CI",
"2nd 90 upper 95% CI",
"3rd 90 upper 95% CI",
"Notes"),
rowIndex = 1, colOffset = 0, rowStyle = cs)
# Set colWidths
setColumnWidth(sheet = sheet1, colIndex = 1, colWidth = 12)
setColumnWidth(sheet = sheet1, colIndex = 2:10, colWidth = 20)
setColumnWidth(sheet = sheet1, colIndex = 11, colWidth = 30)
# ADD DATA
CB.setRowData(cellBlock = cb, x = global_out[[1]], rowIndex = 2, colOffset = 0)
# Borders
TitleBorder <- Border(color = "black", position = c("TOP","BOTTOM","LEFT","RIGHT"),
pen = c("BORDER_THIN","BORDER_THIN","BORDER_THIN","BORDER_THIN"))
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 1)
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 2)
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 3)
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 4)
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 5)
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 6)
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 7)
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 8)
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 9)
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 10)
CB.setBorder(cb, border = TitleBorder, rowIndex = 1:28, colIndex = 11)
#####
## Sheet 2 (Cascade in 2015)
sheet2 <- createSheet(wb , sheetName = "2015")
cb2 <- CellBlock(sheet = sheet2, startRow = 1, startColumn = 1, noRows = 28, noColumns = 16)
# Set headers
CB.setRowData(cellBlock = cb2, x = c(
"country",
"PLHIV",
"PLHIV Diagnosed",
"PLHIV In Care",
"PLHIV On ART",
"PLHIV Virally Suppressed",
"PLHIV lower 95% CI",
"PLHIV Diagnosed lower 95% CI",
"PLHIV In Care lower 95% CI",
"PLHIV On ART lower 95% CI",
"PLHIV Virally Suppressed lower 95% CI",
"PLHIV upper 95% CI",
"PLHIV Diagnosed upper 95% CI",
"PLHIV In Care upper 95% CI",
"PLHIV On ART upper 95% CI",
"PLHIV Virally Suppressed upper 95% CI"),
rowIndex = 1, colOffset = 0, rowStyle = cs)
setColumnWidth(sheet = sheet2, colIndex = 1, colWidth = 12)
setColumnWidth(sheet = sheet2, colIndex = 2:16, colWidth = 20)
# ADD DATA
CB.setRowData(cellBlock = cb2, x = global_out[[2]], rowIndex = 2, colOffset = 0)
# Borders
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 1)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 2)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 3)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 4)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 5)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 6)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 7)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 8)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 9)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 10)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 11)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 12)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 13)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 14)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 15)
CB.setBorder(cb2, border = TitleBorder, rowIndex = 1:28, colIndex = 16)
#####
## Sheet 3 (Cascade in 2020)
sheet3 <- createSheet(wb , sheetName = "2020")
cb3 <- CellBlock(sheet = sheet3, startRow = 1, startColumn = 1, noRows = 28, noColumns = 16)
# Set headers
CB.setRowData(cellBlock = cb3, x = c(
"country",
"PLHIV",
"PLHIV Diagnosed",
"PLHIV In Care",
"PLHIV On ART",
"PLHIV Virally Suppressed",
"PLHIV lower 95% CI",
"PLHIV Diagnosed lower 95% CI",
"PLHIV In Care lower 95% CI",
"PLHIV On ART lower 95% CI",
"PLHIV Virally Suppressed lower 95% CI",
"PLHIV upper 95% CI",
"PLHIV Diagnosed upper 95% CI",
"PLHIV In Care upper 95% CI",
"PLHIV On ART upper 95% CI",
"PLHIV Virally Suppressed upper 95% CI"),
rowIndex = 1, colOffset = 0, rowStyle = cs)
setColumnWidth(sheet = sheet3, colIndex = 1, colWidth = 12)
setColumnWidth(sheet = sheet3, colIndex = 2:16, colWidth = 20)
# ADD DATA
CB.setRowData(cellBlock = cb3, x = global_out[[3]], rowIndex = 2, colOffset = 0)
# Borders
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 1)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 2)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 3)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 4)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 5)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 6)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 7)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 8)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 9)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 10)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 11)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 12)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 13)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 14)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 15)
CB.setBorder(cb3, border = TitleBorder, rowIndex = 1:28, colIndex = 16)
#####
## Sheet 4 (AIDS Deaths)
sheet4 <- createSheet(wb , sheetName = "AIDS Deaths")
cb4 <- CellBlock(sheet = sheet4, startRow = 1, startColumn = 1, noRows = 28, noColumns = 16)
# Set headers
CB.setRowData(cellBlock = cb4, x = c(
"country",
"2015",
"2016",
"2017",
"2018",
"2019",
"2015 lower 95% CI",
"2016 lower 95% CI",
"2017 lower 95% CI",
"2018 lower 95% CI",
"2019 lower 95% CI",
"2015 upper 95% CI",
"2016 upper 95% CI",
"2017 upper 95% CI",
"2018 upper 95% CI",
"2019 upper 95% CI"),
rowIndex = 1, colOffset = 0, rowStyle = cs)
setColumnWidth(sheet = sheet4, colIndex = 1, colWidth = 12)
setColumnWidth(sheet = sheet4, colIndex = 2:16, colWidth = 20)
# ADD DATA
CB.setRowData(cellBlock = cb4, x = global_out[[4]], rowIndex = 2, colOffset = 0)
# Borders
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 1)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 2)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 3)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 4)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 5)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 6)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 7)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 8)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 9)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 10)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 11)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 12)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 13)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 14)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 15)
CB.setBorder(cb4, border = TitleBorder, rowIndex = 1:28, colIndex = 16)
#####
## Sheet 5 (New Infections)
sheet5 <- createSheet(wb , sheetName = "New Infections")
cb5 <- CellBlock(sheet = sheet5, startRow = 1, startColumn = 1, noRows = 28, noColumns = 16)
# Set headers
CB.setRowData(cellBlock = cb5, x = c(
"country",
"2015",
"2016",
"2017",
"2018",
"2019",
"2015 lower 95% CI",
"2016 lower 95% CI",
"2017 lower 95% CI",
"2018 lower 95% CI",
"2019 lower 95% CI",
"2015 upper 95% CI",
"2016 upper 95% CI",
"2017 upper 95% CI",
"2018 upper 95% CI",
"2019 upper 95% CI"),
rowIndex = 1, colOffset = 0, rowStyle = cs)
setColumnWidth(sheet = sheet5, colIndex = 1, colWidth = 12)
setColumnWidth(sheet = sheet5, colIndex = 2:16, colWidth = 20)
# ADD DATA
CB.setRowData(cellBlock = cb5, x = global_out[[5]], rowIndex = 2, colOffset = 0)
# Borders
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 1)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 2)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 3)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 4)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 5)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 6)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 7)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 8)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 9)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 10)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 11)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 12)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 13)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 14)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 15)
CB.setBorder(cb5, border = TitleBorder, rowIndex = 1:28, colIndex = 16)
# Save that shit.
# SAVE BY COUNTRY_NAME
saveWorkbook(wb, file = paste0(path, country_name, ".xlsx"))
}
# Build spreadsheet data structure
get_spreadsheet_data <- function(country_name, notes) {
# Global Output that will constitute one line of each workbook
global_out <- list()
####################################################################################################
# Sheet one (90-90-90)
# "country", "1st 90 in 2020", "lower 95% CI", "upper 95% CI", "2nd 90 in 2020", "lower 95% CI", "upper 95% CI", "3rd 90 in 2020", "lower 95% CI", "upper 95% CI",
# "Notes"
# just declare it
AdvCalib <- data.frame(NatMort = 0.005, HIVMort = 1)
# Can we extract the confidence intervals too? - YES.
out <- Get909090Data()
# First 90
x_1 = round(out[out$def == "Diagnosed / PLHIV", "res"], digits = 2)
min_1 = round(out[out$def == "Diagnosed / PLHIV", "min"], digits = 2)
max_1 = round(out[out$def == "Diagnosed / PLHIV", "max"], digits = 2)
# u1st_90 <- paste0(x_1, " (", min_1, " to ", max_1, ")")
# Second 90
x_2 = round(out[out$def == "On Treatment / Diagnosed", "res"], digits = 2)
min_2 = round(out[out$def == "On Treatment / Diagnosed", "min"], digits = 2)
max_2 = round(out[out$def == "On Treatment / Diagnosed", "max"], digits = 2)
# u2nd_90 <- paste0(x_2, " (", min_2, " to ", max_2, ")")
# Third 90
x_3 = round(out[out$def == "Virally Suppressed / On Treatment", "res"], digits = 2)
min_3 = round(out[out$def == "Virally Suppressed / On Treatment", "min"], digits = 2)
max_3 = round(out[out$def == "Virally Suppressed / On Treatment", "max"], digits = 2)
# u3rd_90 <- paste0(x_3, " (", min_3, " to ", max_3, ")")
# NOTES
# comes in as arg now
# notes <- "Good fit."
global_out[[1]] <- c(country_name, x_1, x_2, x_3, min_1, min_2, min_3, max_1, max_2, max_3, notes)
####################################################################################################
# Sheet two (Cascade in 2015)
# "country", "PLHIV", "Diagnosed", "In Care", "On ART", "Virally Suppressed"
out_t0 <- GetCascadeData(1) # t0 = 1
# PLHIV
plhiv_x <- round(out_t0[out_t0$def == "PLHIV", "res"], digits = 0)
plhiv_min <- round(out_t0[out_t0$def == "PLHIV", "min"], digits = 0)
plhiv_max <- round(out_t0[out_t0$def == "PLHIV", "max"], digits = 0)
# plhiv <- paste0(plhiv_x, " (", plhiv_min, " to ", plhiv_max, ")")
# Diagnosed
diag_x <- round(out_t0[out_t0$def == "Diagnosed", "res"], digits = 0)
diag_min <- round(out_t0[out_t0$def == "Diagnosed", "min"], digits = 0)
diag_max <- round(out_t0[out_t0$def == "Diagnosed", "max"], digits = 0)
# diagnosed <- paste0(diag_x, " (", diag_min, " to ", diag_max, ")")
# In Care
care_x <- round(out_t0[out_t0$def == "In Care", "res"], digits = 0)
care_min <- round(out_t0[out_t0$def == "In Care", "min"], digits = 0)
care_max <- round(out_t0[out_t0$def == "In Care", "max"], digits = 0)
# care <- paste0(care_x, " (", care_min, " to ", care_max, ")")
# On ART
art_x <- round(out_t0[out_t0$def == "Treatment", "res"], digits = 0)
art_min <- round(out_t0[out_t0$def == "Treatment", "min"], digits = 0)
art_max <- round(out_t0[out_t0$def == "Treatment", "max"], digits = 0)
# art <- paste0(art_x, " (", art_min, " to ", art_max, ")")
# Virally Suppressed
supp_x <- round(out_t0[out_t0$def == "Suppressed", "res"], digits = 0)
supp_min <- round(out_t0[out_t0$def == "Suppressed", "min"], digits = 0)
supp_max <- round(out_t0[out_t0$def == "Suppressed", "max"], digits = 0)
# supp <- paste0(supp_x, " (", supp_min, " to ", supp_max, ")")
global_out[[2]] <- c(country_name, plhiv_x, diag_x, care_x, art_x, supp_x, plhiv_min, diag_min,
care_min, art_min, supp_min, plhiv_max, diag_max, care_max, art_max, supp_max)
####################################################################################################
# Sheet three (Cascade in 2020)
# "country", "PLHIV", "Diagnosed", "In Care", "On ART", "Virally Suppressed"
out_t5 <- GetCascadeData(251) # t5 = (5 / 0.02) + 1 [t0]
# PLHIV
plhiv_x <- round(out_t5[out_t5$def == "PLHIV", "res"], digits = 0)
plhiv_min <- round(out_t5[out_t5$def == "PLHIV", "min"], digits = 0)
plhiv_max <- round(out_t5[out_t5$def == "PLHIV", "max"], digits = 0)
# plhiv <- paste0(plhiv_x, " (", plhiv_min, " to ", plhiv_max, ")")
# Diagnosed
diag_x <- round(out_t5[out_t5$def == "Diagnosed", "res"], digits = 0)
diag_min <- round(out_t5[out_t5$def == "Diagnosed", "min"], digits = 0)
diag_max <- round(out_t5[out_t5$def == "Diagnosed", "max"], digits = 0)
# diagnosed <- paste0(diag_x, " (", diag_min, " to ", diag_max, ")")
# In Care
care_x <- round(out_t5[out_t5$def == "In Care", "res"], digits = 0)
care_min <- round(out_t5[out_t5$def == "In Care", "min"], digits = 0)
care_max <- round(out_t5[out_t5$def == "In Care", "max"], digits = 0)
# care <- paste0(care_x, " (", care_min, " to ", care_max, ")")
# On ART
art_x <- round(out_t5[out_t5$def == "Treatment", "res"], digits = 0)
art_min <- round(out_t5[out_t5$def == "Treatment", "min"], digits = 0)
art_max <- round(out_t5[out_t5$def == "Treatment", "max"], digits = 0)
# art <- paste0(art_x, " (", art_min, " to ", art_max, ")")
# Virally Suppressed
supp_x <- round(out_t5[out_t5$def == "Suppressed", "res"], digits = 0)
supp_min <- round(out_t5[out_t5$def == "Suppressed", "min"], digits = 0)
supp_max <- round(out_t5[out_t5$def == "Suppressed", "max"], digits = 0)
# supp <- paste0(supp_x, " (", supp_min, " to ", supp_max, ")")
global_out[[3]] <- c(country_name, plhiv_x, diag_x, care_x, art_x, supp_x, plhiv_min, diag_min,
care_min, art_min, supp_min, plhiv_max, diag_max, care_max, art_max, supp_max)
####################################################################################################
# Sheet four (AIDS Deaths)
# "country", "2015", "2016", "2017", "2018", "2019"
ad <- round(get_aids_deaths_data(), digits = 0)
ad_2015_x <- ad[ad$timeOut == 2015, "HivMortality"]
ad_2015_min <- ad[ad$timeOut == 2015, "min"]
ad_2015_max <- ad[ad$timeOut == 2015, "max"]
ad_2016_x <- ad[ad$timeOut == 2016, "HivMortality"]
ad_2016_min <- ad[ad$timeOut == 2016, "min"]
ad_2016_max <- ad[ad$timeOut == 2016, "max"]
ad_2017_x <- ad[ad$timeOut == 2017, "HivMortality"]
ad_2017_min <- ad[ad$timeOut == 2017, "min"]
ad_2017_max <- ad[ad$timeOut == 2017, "max"]
ad_2018_x <- ad[ad$timeOut == 2018, "HivMortality"]
ad_2018_min <- ad[ad$timeOut == 2018, "min"]
ad_2018_max <- ad[ad$timeOut == 2018, "max"]
ad_2019_x <- ad[ad$timeOut == 2019, "HivMortality"]
ad_2019_min <- ad[ad$timeOut == 2019, "min"]
ad_2019_max <- ad[ad$timeOut == 2019, "max"]
global_out[[4]] <- c(country_name, ad_2015_x, ad_2016_x, ad_2017_x, ad_2018_x, ad_2019_x,
ad_2015_min, ad_2016_min, ad_2017_min, ad_2018_min, ad_2019_min, ad_2015_max, ad_2016_max,
ad_2017_max, ad_2018_max, ad_2019_max)
####################################################################################################
# Sheet five (New Infections)
# "country", "2015", "2016", "2017", "2018", "2019"
ni <- round(get_new_infections_data(), digits = 0)
ni_2015_x <- ni[ni$timeOut == 2015, "NewInf"]
ni_2015_min <- ni[ni$timeOut == 2015, "min"]
ni_2015_max <- ni[ni$timeOut == 2015, "max"]
ni_2016_x <- ni[ni$timeOut == 2016, "NewInf"]
ni_2016_min <- ni[ni$timeOut == 2016, "min"]
ni_2016_max <- ni[ni$timeOut == 2016, "max"]
ni_2017_x <- ni[ni$timeOut == 2017, "NewInf"]
ni_2017_min <- ni[ni$timeOut == 2017, "min"]
ni_2017_max <- ni[ni$timeOut == 2017, "max"]
ni_2018_x <- ni[ni$timeOut == 2018, "NewInf"]
ni_2018_min <- ni[ni$timeOut == 2018, "min"]
ni_2018_max <- ni[ni$timeOut == 2018, "max"]
ni_2019_x <- ni[ni$timeOut == 2019, "NewInf"]
ni_2019_min <- ni[ni$timeOut == 2019, "min"]
ni_2019_max <- ni[ni$timeOut == 2019, "max"]
global_out[[5]] <- c(country_name, ni_2015_x, ni_2016_x, ni_2017_x, ni_2018_x, ni_2019_x,
ni_2015_min, ni_2016_min, ni_2017_min, ni_2018_min, ni_2019_min, ni_2015_max, ni_2016_max,
ni_2017_max, ni_2018_max, ni_2019_max)
# return the global_out list
global_out
}
# Extract AIDS Deaths Data from model results
get_aids_deaths_data <- function() {
result <- GetModel()
out <- c()
min <- c()
max <- c()
for (j in 1:251) {
dat <- Quantile_95(unlist(lapply(result, function(x) sum(x$HivMortality[j]))))
out[j] <- dat[["mean"]]
min[j] <- dat[["lower"]]
max[j] <- dat[["upper"]]
}
HM_out <- c(0, diff(out))
HM_min <- c(0, diff(min))
HM_max <- c(0, diff(max))
times <- seq(0, 5, 0.02)
combo <- cbind(times, HM_out, HM_min, HM_max)
# Calculate time intervals
yr2015 <- times[times >= 0 & times <= 1]
yr2016 <- times[times > 1 & times <= 2]
yr2017 <- times[times > 2 & times <= 3]
yr2018 <- times[times > 3 & times <= 4]
yr2019 <- times[times > 4 & times <= 5]
# count between years to calculate bars
bar1 <- combo[times %in% yr2015,]
bar2 <- combo[times %in% yr2016,]
bar3 <- combo[times %in% yr2017,]
bar4 <- combo[times %in% yr2018,]
bar5 <- combo[times %in% yr2019,]
HivMortality <- c(
sum(bar1[,"HM_out"]),
sum(bar2[,"HM_out"]),
sum(bar3[,"HM_out"]),
sum(bar4[,"HM_out"]),
sum(bar5[,"HM_out"])
)
min <- c(
sum(bar1[,"HM_min"]),
sum(bar2[,"HM_min"]),
sum(bar3[,"HM_min"]),
sum(bar4[,"HM_min"]),
sum(bar5[,"HM_min"])
)
max <- c(
sum(bar1[,"HM_max"]),
sum(bar2[,"HM_max"]),
sum(bar3[,"HM_max"]),
sum(bar4[,"HM_max"]),
sum(bar5[,"HM_max"])
)
timeOut <- seq(2015, 2019, 1)
df <- data.frame(timeOut, HivMortality, min, max)
df
}
# Extract New Infections Data from model results
get_new_infections_data <- function() {
result <- GetModel()
out <- c()
min <- c()
max <- c()
for (j in 1:251) {
dat <- Quantile_95(unlist(lapply(result, function(x) sum(x$NewInf[j]))))
out[j] <- dat[["mean"]]
min[j] <- dat[["lower"]]
max[j] <- dat[["upper"]]
}
NI_out <- c(0, diff(out))
NI_min <- c(0, diff(min))
NI_max <- c(0, diff(max))
times <- seq(0, 5, 0.02)
combo <- cbind(times, NI_out, NI_min, NI_max)
# Calculate time intervals
yr2015 <- times[times >= 0 & times <= 1]
yr2016 <- times[times > 1 & times <= 2]
yr2017 <- times[times > 2 & times <= 3]
yr2018 <- times[times > 3 & times <= 4]
yr2019 <- times[times > 4 & times <= 5]
# count between years to calculate bars
bar1 <- combo[times %in% yr2015,]
bar2 <- combo[times %in% yr2016,]
bar3 <- combo[times %in% yr2017,]
bar4 <- combo[times %in% yr2018,]
bar5 <- combo[times %in% yr2019,]
NewInf <- c(
sum(bar1[,"NI_out"]),
sum(bar2[,"NI_out"]),
sum(bar3[,"NI_out"]),
sum(bar4[,"NI_out"]),
sum(bar5[,"NI_out"])
)
min <- c(
sum(bar1[,"NI_min"]),
sum(bar2[,"NI_min"]),
sum(bar3[,"NI_min"]),
sum(bar4[,"NI_min"]),
sum(bar5[,"NI_min"])
)
max <- c(
sum(bar1[,"NI_max"]),
sum(bar2[,"NI_max"]),
sum(bar3[,"NI_max"]),
sum(bar4[,"NI_max"]),
sum(bar5[,"NI_max"])
)
timeOut <- seq(2015, 2019, 1)
df <- data.frame(timeOut, NewInf, min, max)
df
}
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