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app.r
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app.r
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# libraries
library(shiny)
library(shinydashboard)
library(leaflet)
library(htmlwidgets)
library(bslib)
library(tidycensus)
library(sf)
library(plotly)
library(forcats)
library(shinyWidgets)
library(listviewer)
library(jsonlite)
library(dlnm)
library(DT)
library(dplyr)
library(shinycssloaders)
#setwd('L:\\Lab\\CPHEA_TempUHI\\SCleland\\Dashboard')
#setwd('C:\\Users\\SCLELA01\\OneDrive - Environmental Protection Agency (EPA)\\Profile\\Documents\\Dashboard_Temp')
# Define color palettes
palettes <- data.frame("Variable" = c("uhi","uhiq","hosp","temp","range","temp.99"),
"Color" = c("RdYlBu","RdYlBu","PuRd","RdYlBu","Purple-Green","Heat"))
palettes_cbsa <- data.frame("CBSAVariable" = c("rr.99","an.heat","mht","ar.heat"),
"Color" = c("Geyser","Fall","Temps","TealRose"))
sub_palettes <- list("PrimaryAll" = "black",
"UHIIAll" = c("#66C0E4","#E34D34"),
"PrimaryCKD" = c("#CC99BB","#771155"),
"PrimaryDiabetes" = c("#77AADD","#114477"),
"UHIICKD" = c("#66C0E4","#E34D34","#66C0E4","#E34D34"),
"UHIIDiabetes" = c("#66C0E4","#E34D34","#66C0E4","#E34D34"),
"PrimaryRace" = c("#117744","#88CCAA"),
"PrimarySex" = c( "#777711","#DDDD77"),
"UHIIRace" = c("#66C0E4","#E34D34","#66C0E4","#E34D34"),
"UHIISex" = c("#66C0E4","#E34D34","#66C0E4","#E34D34"),
"PrimaryAge" = c("#771122", "#AA4455", "#DD7788"),
"UHIIAge" = c("#66C0E4","#E34D34","#66C0E4","#E34D34","#66C0E4","#E34D34")
)
sub_linetypes <- list("PrimaryAll" = 1,
"UHIIAll" = c(2,6),
"PrimaryCKD" = c(1,1),
"PrimaryDiabetes" = c(1,1),
"UHIICKD" = c(2,6,2,6),
"UHIIDiabetes" = c(2,6,2,6),
"PrimaryRace" = c(1,1),
"PrimarySex" = c(1,1),
"UHIIRace" = c(2,6,2,6),
"UHIISex" = c(2,6,2,6),
"PrimaryAge" = c(1,1,1),
"UHIIAge" = c(2,6,2,6,2,6)
)
# Read in datasets
zips_shape <- readRDS('./data/simp_05_zip_shapes_with_data.RDS')
cbsa_all <- readRDS('./data/cbsa_rr_an_results.RDS')
cbsa_all$Koppen.Simple <- gsub(",.*$","",cbsa_all$Koppen.Description)
cbsas_shape_full <- readRDS('./data/cbsa_shapes_with_data.RDS')
load('./data/cbsa_pred_tmean.Rdata')
pooled <- readRDS('./data/full_list_pooled_ests.RDS')
pooled.99 <- readRDS('./data/full_list_pooled_ests_99.RDS')
sub_rr_af_an <- readRDS('./data/subgroup_all_results.RDS')
# Define HTML style for dashboard
box.style <- ".box.box-solid.box-primary>.box-header {
color:#fff;
background:#F8F8F8}
.box.box-solid.box-primary{
border-bottom-color:#F8F8F8;
border-left-color:#F8F8F8;
border-right-color:#F8F8F8;
border-top-color:#F8F8F8;}"
tabbox.style <- ".nav-tabs {background: #f4f4f4;}
.nav-tabs-custom .nav-tabs li.active:hover a, .nav-tabs-custom .nav-tabs li.active a {background-color: #fff;
border-color: #fff;}
.nav-tabs-custom .nav-tabs li.active {border-top-color:
#314a6d;}"
# User interface (UI) function
ui <- navbarPage("Dashboard",id="tabs",selected="Overall & Subpopulation Results",
header = tagList(
useShinydashboard(),
shinyjs::useShinyjs()
),
theme = bslib::bs_theme(bootswatch = "minty"),
tabPanel(title="About",
fluidRow(
box(width=11,solidHeader = TRUE,title="About this Dashboard",status="primary",
htmlOutput("about_text")
)
)
),
# Tab for the Overall & Subpopulation Results
tabPanel(title="Overall & Subpopulation Results",
fluidRow(
column(width=2,
box(width=15, title="Options", solidHeader = TRUE,status="primary",
htmlOutput("overall_info_text"),
radioButtons("subpop", tags$span(style = "font-weight: bold;", "Subpopulation:"),
c("All" = "All",
"Age" = "Age",
"Sex" = "Sex",
"Race" = "Race",
"Diabetes" = "Diabetes",
"Chronic Kidney Disease (CKD)" = "CKD"
)
),
radioButtons("sub", tags$span(style = "font-weight: bold;", "Stratification:"),
c("Overall" = "Primary",
"Urban Heat Island Intensity (UHII)" = "UHII"
)
),
radioButtons("type", tags$span(style = "font-weight: bold;", "Plot Type:"),
c("Cumulative (Lags 0-21)" = "pooled",
"Lags at Extreme Heat" = "lags")
)
)
),
box(width=5, title="Exposure-Lag-Response Curves",solidHeader = TRUE,status="primary",
plotOutput("pooled_curve") %>% withSpinner(color="#a9a9a9"),
div(htmlOutput("pooled_curve_text"),style="font-size:90%")
),
box(width=5,title="Primary Results",solidHeader=TRUE,status="primary",align='right',
radioButtons("bar.var",NULL,c("AN","AR"),inline=T),
plotlyOutput("pooled_plots") %>% withSpinner(color="#a9a9a9"),
div(htmlOutput("pooled_plot_text"),style="font-size:90%",align='left')
)
),
fluidRow(
box(width=2, title="Key Takeaways", solidHeader = TRUE,status="primary",
tags$style(HTML("ul { list-style-position: outside; padding-left: 1em;} ")),
htmlOutput("main_takeaway") %>% withSpinner(color="#a9a9a9")
),
box(width=10,title="Table of Results",solidHeader=TRUE,status="primary",
div(DT::dataTableOutput("pooled_table") %>% withSpinner(color="#a9a9a9"),style = "font-size:80%"),
tags$style(type="text/css", "#downloadAllData {background-color:#F8F8F8;border-color:#dbd9d9;color: black}"),
downloadButton("downloadAllData", "Download all results")
)
)
),
# Tab for the MSA-Specific Results
tabPanel(title="MSA-Specific Results",
fluidRow(
column(width=2,
box(width=15, title="Options", solidHeader = TRUE,status="primary",
htmlOutput("cbsa_info_text"),
radioButtons("forest_variable", tags$span(style = "font-weight: bold;", "Variable:"),
c("RR (99th vs. MHP)" = "rr.99",
"Heat AN (Temp. >= MHP)" = "an.heat",
"Heat AR (per 100k)" = "ar.heat",
"MHT (\u00b0C)" = "mht"
)),
radioButtons("forest_type", tags$span(style = "font-weight: bold;", "Stratification:"),
c("Overall" = "Primary",
"Urban Heat Island Intensity (UHII)" = "UHII"
)),
radioButtons("forest_color",tags$span(style = "font-weight: bold;", "Color by MSA Characteristic:"),
c("None" = "none",
"Avg. Ambient Temperature" = "avg.temp",
"Avg. Temperature Range" = "avg.range",
"Region" = "region",
"Climate Type" = "climate")),
checkboxInput("sort", "Sort by MSA Characteristic",
value=FALSE)
),
box(width=15, title="Key Takeaways", solidHeader = TRUE,status="primary",
tags$style(HTML("ul { list-style-position: outside; padding-left: 1em;} ")),
htmlOutput("msa_takeaway")%>% withSpinner(color="#a9a9a9")
)
),
tabBox(width=6,title="",id="cbsa_tabs",
tabPanel("Forest/Bar Plot",
tags$style(tabbox.style),
tags$style(type = "text/css", "#forest_plot {height: calc(100vh + 1000px) !important;}"),
plotlyOutput('forest_plot') %>% withSpinner(color="#a9a9a9")
),
tabPanel("Interactive Map",
tags$style(type = "text/css", "#cbsa_map {height: calc(100vh - 180px) !important;}",
".shiny-output-error { visibility: hidden; }",
".shiny-output-error:before { visibility: hidden; }"),
leafletOutput("cbsa_map") %>% withSpinner(color="#a9a9a9")
)
),
box(width=4,title="MSA-Specific Results",solidHeader = TRUE,status="primary",
selectInput(inputId="cbsa_choice",
label="Select an MSA (below or in the forest/bar plot or map to the left):",
choices = unique(cbsa_all$CBSA.Title)),
htmlOutput("cbsa_title"),
plotOutput("cbsa_curve",height=300) %>% withSpinner(color="#a9a9a9"),
DT::dataTableOutput("cbsa_table") %>% withSpinner(color="#a9a9a9"),
tags$style(type="text/css", "#downloadMSAData {background-color:#F8F8F8;border-color:#dbd9d9;color: black}"),
downloadButton("downloadMSAData", "Download results for all MSAs")
)
)
),
# Tab for the Exposure & Outcome Maps
tabPanel(title="Exposure & Outcome Maps",
fluidRow(tags$style(HTML(box.style)),
box(width=2, title="Options", solidHeader = TRUE,status="primary",
htmlOutput("map_info_text"),
radioButtons("variable", tags$span(style = "font-weight: bold;", "Variable:"),
c("Avg. Ambient Temperature" = "temp",
"Avg. Temperature Range" = "range",
"99th Temperature Percentile"="temp.99",
"# Hospitalizations" = "hosp",
"Urban Heat Island Intensity (UHII)" = "uhi",
"UHII Quartile" = "uhiq"
)),
tags$head(tags$script(HTML("
$(document).ready(function(e) {
$('input[value=\"temp\"]').parent().parent().before('<i><u>Exposure</u><i>');
})
"))),
tags$head(tags$script(HTML("
$(document).ready(function(e) {
$('input[value=\"temp.99\"]').parent().parent().after('<br><i><u>Outcome</u><i>');
})
"))),
tags$head(tags$script(HTML("
$(document).ready(function(e) {
$('input[value=\"hosp\"]').parent().parent().after('<br><i><u>UHI</u><i>');
})
")))
),
box(width=10,title="Interactive Map", solidHeader = TRUE,status="primary",
tags$style(type = "text/css", "#leaflet_map {height: calc(100vh - 180px) !important;}"),
leafletOutput("leaflet_map") %>% withSpinner(color="#a9a9a9"),
htmlOutput("leaflet_text")
)
)
),
inverse=F
)
# Server function
server <- function(input, output,session) {
# Observe event used to generate leaflet maps
observe({
# Maps for the Exposure & Outcome Maps tab
if (input$tabs == "Exposure & Outcome Maps") {
if (input$variable=="uhi") {
var = "UHI_summer_day.Wght"; title = "UHII (\u00b0C)"
rev=F
} else if (input$variable=="hosp") {
var="n.HAs"; title = "# Hospitalizations"
bins = c(0,1500,3000,4500,6000,7500,9000,10500,12000,70000)
labs = c("0-1,500","1,500-3,000","3,000-4,500","4,500-6,000","6,000-7,500","7,500-9,000","9,000-10,500","10,500-12,000",">12,000")
rev=T
} else if (input$variable=="temp") {
var = "m.temp"; title = "Mean Temp. (\u00b0C)"
rev=T
} else if (input$variable=="range") {
var = "r.temp"; title = "Temp. Range (\u00b0C)"
rev=T
} else if (input$variable=="temp.99") {
var = "temp.99";title = "99th Temp. %ile (\u00b0C)"
rev=T
} else if (input$variable == "uhiq") {
var = "UHI_group"; title = "UHII Quartile"
}
if (input$variable=="uhiq") {
pal <- colorFactor(
palette = c("#66B7D6","#DCF2FA","#FAD0C8","#E34D34"),
domain = eval(parse(text=paste0("zips_shape$",var))),
reverse=F
)
popup_text <- paste("<b>ZIP Code:</b>", zips_shape$ZIP, "<br>",
"<b>MSA:</b>",zips_shape$CBSA.Title,"<br>",
"<b>",title,":</b>", eval(parse(text=paste0("zips_shape$",var))))
labeller_function <- labelFormat(prefix="")
} else if (input$variable=="uhi") {
pal <- colorNumeric(
palette = c( "#5385BC", "#6C9ECE", "#85B7E0", "#9FD1F2", "#B5DBF2", "#C4C6CE", "#D4B1AA", "#E39C86", "#E7886D", "#E6745A", "#E46047", "#E34D34"),
domain = eval(parse(text=paste0("zips_shape$",var))),
reverse = rev
)
popup_text <- paste("<b>ZIP Code:</b>", zips_shape$ZIP, "<br>",
"<b>MSA:</b>",zips_shape$CBSA.Title,"<br>",
"<b>",title,":</b>", round(eval(parse(text=paste0("zips_shape$",var))),1))
labeller_function <- labelFormat(prefix = "")
} else if (input$variable%in%c("temp","range","temp.99")) {
pal <- colorNumeric(
palette = hcl.colors(10,palettes[palettes$Variable==input$variable,2]),
domain = eval(parse(text=paste0("zips_shape$",var))),
reverse = rev
)
popup_text <- paste("<b>ZIP Code:</b>", zips_shape$ZIP, "<br>",
"<b>MSA:</b>",zips_shape$CBSA.Title,"<br>",
"<b>",title,":</b>", round(eval(parse(text=paste0("zips_shape$",var))),1))
labeller_function <- labelFormat(prefix = "")
} else {
pal <- colorBin(
palette = hcl.colors(10,palettes[palettes$Variable==input$variable,2]),
domain = eval(parse(text=paste0("zips_shape$",var))),
bins = bins,
reverse = rev
)
popup_text <- paste("<b>ZIP Code:</b>", zips_shape$ZIP, "<br>",
"<b>MSA:</b>",zips_shape$CBSA.Title,"<br>",
"<b>",title,":</b>", round(eval(parse(text=paste0("zips_shape$",var))),1))
labeller_function <- function(type, breaks) {
return(labs)
}
}
leafletProxy("leaflet_map") %>%
clearShapes() %>% clearControls() %>%
addPolygons(data=cbsas_shape_full,color="#d7d7d7",weight=1,opacity=0.7,smoothFactor = 0.5,
fillColor = "#e9e9e9",fillOpacity = 0.25) %>%
addPolygons(data=zips_shape,color = ~pal(get(var)), weight=1,
fillColor=~pal(get(var)),
smoothFactor = 0.5,fillOpacity=0.7,
label=lapply(popup_text, htmltools::HTML),
highlight = highlightOptions(color = "lightyellow",weight = 2, bringToFront = T, opacity = 0.7)) %>%
addLegend(data=zips_shape,"bottomright", pal = pal, values = ~get(var),
title = title,
opacity = 1,
labFormat = labeller_function)
}
# Maps for the MSA-Specific Results tabs
if (input$tabs=="MSA-Specific Results" & input$cbsa_tabs == "Interactive Map") {
rev = F
if (input$forest_variable == "rr.99") {
x="RR.99";xmin="RR.99.low";xmax="RR.99.high";leg_lab="RR (99th vs. MHP)";hover.lab = "RR (95% CI)"
bins <- c(0.5,0.97,1,1.03,1.06,1.09,1.3)
labs <- c("< 0.97","0.97-1.00","1.00-1.03","1.03-1.06","1.06-1.09","> 1.09")
rounding=3
} else if (input$forest_variable == "an.heat") {
x="heat_an";xmin="heat_an_lower";xmax="heat_an_upper";leg_lab="AN (Temp. \u2265 MHP)";hover.lab = "AN (95% CI)"
if (input$forest_type == "Primary") {
bins <- c(-10000,-500,0,500,1000,1500,12000)
labs <- c("< -500","-500-0","0-500","500-1,000","1,000-1,500","> 1,500")
} else {
bins <- c(-10000,-250,0,250,500,750,12000)
labs <- c("< -250","-250-0","0-250","250-500","500-750","> 750")
}
rounding=0
} else if (input$forest_variable == "ar.heat") {
x="ann_an_rate100k";xmin="ann_an_rate100k_lower";xmax="ann_an_rate100k_upper";leg_lab="AR (per 100k)";hover.lab = "AR (95% CI)"
bins <- c(-100,-5,0,5,15,25,150)
labs <- c("< -5","-5-0","0-5","0-15","15-25","> 25")
rounding=2; rev=T
} else if (input$forest_variable == "mht") {
x="cen";xmin="cen.low";xmax="cen.high";leg_lab="MHT (\u00b0C)";hover.lab = "MHT (95% CI)"
bins <- c(17,21,24,27,30,33,45)
labs <- c("< 21","21-24","24-27","27-30","30-33","> 33")
rounding=1
}
cbsas_shape <- cbsas_shape_full[cbsas_shape_full$group == input$forest_type,]
pal <- colorBin(
palette = hcl.colors(8,palettes_cbsa[palettes_cbsa$CBSAVariable==input$forest_variable,2]),
bins = bins,
reverse=rev
)
labeller_function <- function(type, breaks) {
return(labs)
}
if (input$forest_type == "Primary") {
popup_text <- paste0("<b>MSA:</b> ",cbsas_shape$CBSA.Title,
'<br><b>',hover.lab,":</b> ", trimws(format(round(eval(parse(text=paste0("cbsas_shape$",x))),rounding),rounding, big.mark = ',')),
" (",trimws(format(round(eval(parse(text=paste0("cbsas_shape$",xmin))),rounding),rounding,big.mark=',')),", ",
trimws(format(round(eval(parse(text=paste0("cbsas_shape$",xmax))),rounding),rounding,big.mark=',')),")")
leafletProxy("cbsa_map") %>%
clearShapes() %>% clearControls() %>%
addPolygons(data=cbsas_shape,
layerId=cbsas_shape$CBSA.Title,
color = ~pal(get(x)), weight=1,
fillColor=~pal(get(x)),
smoothFactor = 0.5,fillOpacity=0.8,
label=lapply(popup_text, htmltools::HTML),
highlight = highlightOptions(color = "lightyellow",weight = 2, bringToFront = T, opacity = 0.7)) %>%
addLegend(data=cbsas_shape,"bottomright",
pal = pal, values = ~get(x),
labFormat = labeller_function,
title = leg_lab,
opacity = 1)
} else {
cbsas_shape.1 <- cbsas_shape[cbsas_shape$var=="UHII-Q1",]
popup_text.1 <- paste0("<b>MSA:</b> ",cbsas_shape.1$CBSA.Title,
"<br><b>UHII Level:</b> Low UHII",
'<br><b>',hover.lab,":</b> ", trimws(format(round(eval(parse(text=paste0("cbsas_shape.1$",x))),rounding),rounding,big.mark=',')),
" (",trimws(format(round(eval(parse(text=paste0("cbsas_shape.1$",xmin))),rounding),rounding,big.mark=',')),", ",
trimws(format(round(eval(parse(text=paste0("cbsas_shape.1$",xmax))),rounding),rounding,big.mark=',')),")")
cbsas_shape.4 <- cbsas_shape[cbsas_shape$var=="UHII-Q4",]
cbsas_shape.4$CBSA.Title <- paste0(cbsas_shape.4$CBSA.Title," ")
popup_text.4 <- paste0("<b>MSA:</b> ",cbsas_shape.4$CBSA.Title,
"<br><b>UHII Level:</b> High UHII",
'<br><b>',hover.lab,":</b> ", trimws(format(round(eval(parse(text=paste0("cbsas_shape.4$",x))),rounding),rounding,big.mark = ',')),
" (",trimws(format(round(eval(parse(text=paste0("cbsas_shape.4$",xmin))),rounding),rounding,big.mark=',')),", ",
trimws(format(round(eval(parse(text=paste0("cbsas_shape.4$",xmax))),rounding),rounding,big.mark=',')),")")
leafletProxy("cbsa_map") %>%
clearShapes() %>% clearControls() %>%
addPolygons(data=cbsas_shape.1,group="Low UHII",
layerId=cbsas_shape.1$CBSA.Title,
color = ~pal(get(x)), weight=1,
fillColor=~pal(get(x)),
smoothFactor = 0.5,fillOpacity=0.8,
label=lapply(popup_text.1, htmltools::HTML),
highlight = highlightOptions(color = "lightyellow",weight = 2, bringToFront = T, opacity = 0.7)) %>%
addPolygons(data=cbsas_shape.4,group="High UHII",
layerId=cbsas_shape.4$CBSA.Title,
color = ~pal(get(x)), weight=1,
fillColor=~pal(get(x)),
smoothFactor = 0.5,fillOpacity=0.8,
label=lapply(popup_text.4, htmltools::HTML),
highlight = highlightOptions(color = "lightyellow",weight = 2, bringToFront = T, opacity = 0.7)) %>%
addLegend(data=cbsas_shape.4,
"bottomright",
pal = pal, values = ~get(x),
title = leg_lab,
labFormat = labeller_function,
opacity = 1)%>%
addLayersControl(
position = 'topleft',
baseGroups = c("Low UHII","High UHII"),
options = layersControlOptions(collapsed = F)
) %>%
htmlwidgets::onRender("
function() {
var map = this;
var legends = map.controls._controlsById;
function addActualLegend() {
var sel = $('.leaflet-control-layers-base').find('input[type=\"radio\"]:checked').siblings('span').text().trim();
$.each(map.controls._controlsById, (nm) => map.removeControl(map.controls.get(nm)));
map.addControl(legends[sel]);
}
$('.leaflet-control-layers-base').on('click', addActualLegend);
addActualLegend();
}"
)
}
}
})
#############################################################################
######## Outputs for Overall & Subpopulation Results Tab ####################
#############################################################################
# Code to render the plots of the exposure-lag-response curves
output$pooled_curve <- renderPlot({
if (input$type == "pooled") {
curves <- pooled[lapply(pooled, '[[',"type")==input$sub]
curves <- curves[lapply(curves, '[[',"group")==input$subpop]
colors <- eval(parse(text=paste0('sub_palettes$',paste0(input$sub,input$subpop))))
ltypes <- eval(parse(text=paste0('sub_linetypes$',paste0(input$sub,input$subpop))))
inds <- c(50,60,70,80,90,99,100)
limits <- c(round(min(pooled[["Primary"]]$tmeancbsa[names(pooled[["Primary"]]$tmeancbsa) %in% paste0(inds,".0%")]),1)-.1,round(max(pooled[["Primary"]]$tmeancbsa[names(pooled[["Primary"]]$tmeancbsa) %in% paste0(inds,".0%")]),1))
if (!(input$sub == "Primary" && input$subpop == "All")) {
if (input$sub != "Primary" && input$subpop != "All") {
groups <- unique(unlist(lapply(curves, '[[',"subgroup")))
if (input$subpop=="Age") {n.col = 3} else { n.col = 2}
par(mfrow = c(1, n.col), xaxs = "i",mar=c(5.1+1, 4.1, 4.1, 2.1-1))
} else {
groups <- c("All")
par(mfrow = c(1, 1),mar=c(5.1+1, 4.1, 2.1, 2.1-1))
}
} else {
if (input$sub != "Primary" && input$subpop != "All") {
groups <- unique(unlist(lapply(curves, '[[',"subgroup")))
if (input$subpop=="Age") {n.col = 3} else { n.col = 2}
par(mfrow = c(1, n.col), xaxs = "i",mar=c(5.1, 4.1, 4.1, 2.1-1))
} else {
groups <- c("All")
par(mfrow = c(1, 1),mar=c(5.1, 4.1, 2.1, 2.1-1))
}
}
curr_min=100;curr_max=0
curves.orig <- curves
plist <- list()
for (j in 1:length(groups)) {
if (length(groups) > 1) {
curves <- curves.orig[lapply(curves.orig, '[[',"subgroup")==groups[j]]
} else {
curves <- curves.orig
}
names(curves)[names(curves) == "sexWomen"] <- "sexFemale"
curves <- curves[order(names(curves))]
for (i in 1:length(curves)) {
pred <- curves[[i]]$pred.metareg
cen <- curves[[i]]$cen.metareg
if (input$sub == "Primary" & input$subpop == "All") {
predvar <- curves[[i]]$tmeancbsa
indlab <- names(predvar) %in% paste0(inds,".0%")
plot(pred,"overall",type="l",lwd=2.5,col=colors[i],lty=ltypes[i],ylim=c(0.9,1.3),xlim=limits,axes=F,xlab="",
ylab="RR", ci.arg=list(density=20+((i-1)*5),lty=ltypes[i],col=adjustcolor(colors[i],alpha.f=0.2)))
abline(v=cen,lty=2)
axis(1,at=predvar[indlab],labels=inds)
loc = 14.25
mtext("%ile",1,line=1,at=loc,col="black",adj=1,cex=1)
axis(1,at=seq(15,33,2),line=2.5,col="black",col.ticks="black",col.axis="black")
axis(1,at=seq(15,33,1),labels=NA,line=2.5,col="black",col.ticks="black",col.axis="black",tck=-0.009)
mtext(expression(paste(degree, "C")),1,line=3.5,at=loc,col="black",adj=1,cex=1)
axis(2)
} else {
plot(pred,"overall",type="l",lwd=2.5,col=colors[i],lty=ltypes[i],ylim=c(0.9,1.3),xlim=limits,axes=F,xlab="",
ylab="RR", ci.arg=list(density=20+((i-1)*5),lty=ltypes[i],col=adjustcolor(colors[i],alpha.f=0.25)))
abline(v=cen,lty=2,col=colors[i])
predvar <- curves[[i]]$tmeancbsa
indlab <- names(predvar) %in% paste0(inds,".0%")
if (i != 1) {axis(1,at=predvar[indlab],labels=NA,col=NA,col.ticks=colors[i],tck=-0.03); tckcol = NA} else { tckcol = colors[i]}
axis(1,at=predvar[indlab],labels=inds,col=NA,col.ticks=tckcol,
col.axis=colors[i],cex.axis=0.95,line=((i-1)/1.5))
if (min(predvar[indlab]) < curr_min) {curr_min<-min(predvar[indlab])}
if (max(predvar[indlab]) > curr_max) {curr_max<-max(predvar[indlab])}
if (i == length(curves)) {
loc = 14.25
axis(1,at=c(curr_min,curr_max),labels=NA,col="black",col.ticks=NA,col.axis=NA)
mtext("%ile",1,line=1,at=loc,col="black",adj=1)
extra <- (1-length(curves))*(2/3)
axis(1,at=seq(15,33,2),line=2.5-extra,col="black",col.ticks="black",col.axis="black")
axis(1,at=seq(15,33,1),labels=NA,line=2.5-extra,col="black",col.ticks="black",col.axis="black",tck=-0.009)
mtext(expression(paste(degree, "C")),1,line=3.5-extra,at=loc,col="black",adj=1)
axis(2)
par(new = F)
} else {
par(new=T)
}
}
}
if (!(input$sub == "Primary" && input$subpop == "All")) {
if (input$sub != "Primary" && input$subpop != "All") {
title(main = paste0(input$subpop, ", ", groups[j]))
legend(x=par("usr")[1]+0.25,y=par("usr")[4], legend=c("Low UHII","High UHII"),
col=colors, lty=ltypes, lwd=1.5,cex=1,box.lty=0)
} else if (input$sub=="Primary") {
legend(x=par("usr")[1]+0.25,y=par("usr")[4], legend=paste0(unlist(lapply(curves, `[`, c('group'))),', ',unlist(lapply(curves, `[`, c('subgroup')))),
col=colors, lty=ltypes, lwd=1.5,cex=1,box.lty=0)
} else if (input$subpop == "All") {
legend(x=par("usr")[1]+0.25,y=par("usr")[4], legend=c("Low UHII","High UHII"),
col=colors, lty=ltypes, lwd=1.5,cex=1,box.lty=0)
}
}
}
} else if (input$type == "lags") {
curves <- pooled.99[lapply(pooled.99, '[[',"type")==input$sub]
curves <- curves[lapply(curves, '[[',"group")==input$subpop]
colors <- eval(parse(text=paste0('sub_palettes$',paste0(input$sub,input$subpop))))
ltypes <- eval(parse(text=paste0('sub_linetypes$',paste0(input$sub,input$subpop))))
if (input$sub != "Primary" && input$subpop != "All") {
groups <- unique(unlist(lapply(curves, '[[',"subgroup")))
if (input$subpop=="Age") {n.col = 3} else { n.col = 2}
par(mfrow = c(1, n.col),mar=c(5.1, 4.1, 4.1, 2.1-1))
} else {
groups <- c("All")
par(mfrow = c(1, 1),mar=c(5.1, 4.1, 2.1, 2.1-1))
}
curves.orig <- curves
plist <- list()
for (j in 1:length(groups)) {
if (length(groups) > 1) {
curves <- curves.orig[lapply(curves.orig, '[[',"subgroup")==groups[j]]
} else {
curves <- curves.orig
}
names(curves)[names(curves) == "sexWomen"] <- "sexFemale"
curves <- curves[order(names(curves))]
for (i in 1:length(curves)) {
pred <- curves[[i]]$pred.99
if (input$sub == "Primary" & input$subpop=="All") {
plot(pred,"overall",ylim=c(0.98,1.03),xlim=c(0,21),axes=T,xlab="Lag",
ylab="RR",lwd=2.5,xlab=c(0:21))
} else {
plot(pred,"overall",col=colors[i],lty=ltypes[i],ylim=c(0.98,1.03),xlim=c(0,21),axes=T,xlab="Lag",
ylab="RR",lwd=2.5,xlab=c(0:21),
ci.arg=list(density=20+((i-1)*5),lty=ltypes[i],col=adjustcolor(colors[i],alpha.f=0.25)))
if (input$sub != "Primary" && input$subpop != "All") {
title(main=paste0(input$subpop, ", ", groups[j]))
legend(x=par("usr")[1]+0.25,y=par("usr")[4], legend=c("Low UHII","High UHII"),
col=colors, lty=ltypes, lwd=1.5,cex=1,box.lty=0)
} else if (input$sub=="Primary") {
legend(x=par("usr")[1]+0.25,y=par("usr")[4], legend=paste0(unlist(lapply(curves, `[`, c('group'))),', ',unlist(lapply(curves, `[`, c('subgroup')))),
col=colors, lty=ltypes, lwd=1.5,cex=1,box.lty=0)
} else if (input$subpop == "All") {
legend(x=par("usr")[1]+0.25,y=par("usr")[4], legend=c("Low UHII","High UHII"),
col=colors, lty=ltypes, lwd=1.5,cex=1,box.lty=0)
}
if (i == length(curves)) {
par(new=F)
} else {
par(new=T)
}
}
}
}
}
})
# Informational text for user selection
output$overall_info_text <- renderText({
paste("Select the subpopulation, stratification, and plot type to display:<br><br>")
})
# Figure caption for the exposure-lag-response curve
output$pooled_curve_text <- renderText({
if (input$type == "lags") {
type = "Lag-response at extreme heat (99th temperature percentile) for the association(s) between daily mean ambient temperature and daily cardiovascular disease hospitalizations in the urban cores of 120 contiguous US metropolitan statistical areas, 2000-2017."
} else {
type = "The 21-day cumulative exposure-response association(s) between daily mean ambient temperature and daily cardiovascular disease hospitalizations in the urban cores of 120 contiguous US metropolitan statistical areas, 2000-2017. The vertical dashed line indicates the location of the minimum hospitalization percentile (MHP)."
}
if (input$subpop == "All") {
if (input$sub=="UHII") {
caption = paste0(type," Results shown for the entire study population in low and high urban heat island intensity (UHII) areas.")
} else if (input$sub == "Primary") {
caption = paste0(type, " Results shown for the entire study population.")
}
} else {
if (input$sub == "Primary") {
if (input$subpop %in% c("Diabetes","CKD")) {
label <- ifelse(input$subpop=="Diabetes",tolower(input$subpop),input$subpop)
caption = paste0(type, " Results shown by ", label, " status.")
} else {
caption = paste0(type, " Results shown by ", tolower(input$subpop), ".")
}
} else if (input$sub == "UHII") {
if (input$subpop %in% c("Diabetes","CKD")) {
label <- ifelse(input$subpop=="Diabetes",tolower(input$subpop),input$subpop)
caption = paste0(type, " Results shown by ", label, " status in low and high urban heat island intensity (UHII) areas.")
} else {
caption = paste0(type, " Results shown by ", tolower(input$subpop), " in low and high urban heat island intensity (UHII) areas.")
}
}
}
})
# Code to render the primary results plots (forest plot + bar plot)
output$pooled_plots <- renderPlotly({
### FOREST PLOT
data.forest <- sub_rr_af_an[,c(1:11,15:17)]; names(data.forest) <- c(names(data.forest)[1:11],"RR","RR.low","RR.high")
data.forest$variable_name <- rep("Relative Risk (99th vs. MHP)",nrow(data.forest))
data.forest[,c("RR","RR.low","RR.high","cen.metareg")] <- sapply( data.forest[,c("RR","RR.low","RR.high","cen.metareg")],as.numeric)
data.forest <- data.forest[data.forest$type == input$sub & data.forest$group == input$subpop,]
data.forest$uhigroup <- ifelse(data.forest$subtype == "Primary","Overall",ifelse(data.forest$subtype=="Q1","Low UHII","High UHII"))
data.forest$label <- ifelse(data.forest$type=="Primary"&data.forest$group=="All","",
ifelse(data.forest$group=="All",data.forest$uhigroup,paste0(data.forest$group,", ",data.forest$subgroup)))
data.forest$label2 <- ifelse(data.forest$type=="Primary"&data.forest$group=="All","",
ifelse(data.forest$group=="All",data.forest$uhigroup,
ifelse(data.forest$type=="Primary",
paste0(data.forest$group,", ",data.forest$subgroup),
paste0(data.forest$group,", ",data.forest$subgroup," - ",data.forest$uhigroup)
)))
hover.lab = "RR (95% CI)"; rounding=3; xline=1; ylab = "RR"
if (input$sub != "Primary" & input$subpop != "All") {
pd <- position_dodge(width = 0.4)
col.val <- "uhigroup"
} else {
pd <- position_dodge(width = 0)
col.val <- "label"
}
if (input$sub != "Primary") {
pal <- rev(eval(parse(text=paste0('sub_palettes$',paste0(input$sub,input$subpop)))))
} else {
pal <- eval(parse(text=paste0('sub_palettes$',paste0(input$sub,input$subpop))))
}
facet.name <- c( "Relative Risk (99th vs. MHP)" = "Relative Risk\n(99th vs. MHP)")
forest.pooled <- ggplot(data=data.forest[data.forest$variable_name == "Relative Risk (99th vs. MHP)", ],
aes(x=label,y=RR, ymin=RR.low, ymax=RR.high,color=.data[[col.val]],shape=.data[[col.val]],
text = paste0("<b>",label2,"</b>",
'<br><b>',hover.lab,":</b> ", format(round(RR,rounding),rounding)," (",
format(round(RR.low,rounding),rounding),", ",
format(round(RR.high,rounding),rounding),")",'<br>',
'<b>MHP (MHT):</b> ',cen.per.metareg,' (',round(cen.metareg,1),' \u00b0C)'))) +
geom_point(position=pd,size=2) +
scale_color_manual(values=pal) +
geom_errorbar(width=0.1,position=pd) + theme_bw(base_size=10) +
geom_hline(yintercept=xline, color='black', linetype='dashed', alpha=.5) +
ylab(ylab) + facet_wrap(~variable_name,labeller = as_labeller(facet.name)) +
theme(axis.title.x = element_blank(),
strip.background = element_rect(fill = "white",color="white"),
strip.text = element_text(angle=0,face="bold"),
axis.text.x = element_text(angle = 30, hjust=1)
) +
ylim(0.96,1.06)
p1 <- ggplotly(forest.pooled,tooltip="text",source="pooled_plots") %>%
layout(hoverlabel=list(bgcolor="white",align='left'),
yaxis = list(titlefont = list(size = 12),title = ylab), dragmode = F,
legend = list(title = list(text = ""),orientation = "h", x = -0.5, y =-1)) %>% config(displayModeBar = F)
### BAR PLOT
data <- sub_rr_af_an[sub_rr_af_an$type == input$sub&sub_rr_af_an$group == input$subpop,]
if (input$bar.var == "AN") {
lab = "Attributable Number (MHP+)"
hover.lab = "AN (95% CI)";ylab="AN"
facet.name <- c("Attributable Number (MHP+)"="Attributable Number\n(Temp. \u2265 MHP)")
lims <- c(-362,38000); rounding=0
y="ha_heat";ymin="ha_heat_lower";ymax="ha_heat_upper"
} else {
lab = "Attributable Rate (Annual, per 100k)"
hover.lab = "AR (95% CI)";ylab="AR"
facet.name <- c("Attributable Rate (Annual, per 100k)"="Attributable Rate\n(Annual, per 100k)")
lims <- c(-2,50); rounding=2
y="ann_an_rate100k";ymin="ann_an_rate100k_lower";ymax="ann_an_rate100k_upper"
}
data$exposure <- rep(lab,nrow(data)); data$exposure.f = factor(data$exposure, levels=c(lab))
data$uhigroup <- ifelse(data$subtype == "Primary","Overall",ifelse(data$subtype=="Q1","Low UHII","High UHII"))
data$label <- ifelse(data$type=="Primary"&data$group=="All","",
ifelse(data$group=="All",data$uhigroup,paste0(data$group,", ",data$subgroup)))
data$label2 <- ifelse(data$type=="Primary"&data$group=="All","",
ifelse(data$group=="All",data$uhigroup,
ifelse(data$type=="Primary",
paste0(data$group,", ",data$subgroup),
paste0(data$group,", ",data$subgroup," - ",data$uhigroup)
)))
xline=0
sub_palettes.temp <- sub_palettes; sub_palettes.temp[1] <- "grey40"
if (input$sub != "Primary") {
pal <- rev(eval(parse(text=paste0('sub_palettes.temp$',paste0(input$sub,input$subpop)))))
} else {
pal <- eval(parse(text=paste0('sub_palettes.temp$',paste0(input$sub,input$subpop))))
}
if (input$sub != "Primary" & input$sub != "All") { pd <- position_dodge(width = 0.9) } else { pd <- position_dodge(width = 0.0)}
bar.pooled <- ggplot(data=data[data$exposure == lab,],
aes(x=label,y=.data[[y]], ymin=.data[[ymin]], ymax=.data[[ymax]],fill=.data[[col.val]],
text = paste0("<b>",label2,"</b>",
'<br><b>',hover.lab,":</b> ", format(round(.data[[y]],rounding),big.mark =',',trim=T),
" (",format(round(.data[[ymin]],rounding),big.mark=',',trim=T),", ",
format(round(.data[[ymax]],rounding),big.mark=',',trim=T),")",
'<br><b>','MHP (MHT):</b> ',cen.per.metareg,' (',round(cen.metareg,1),' \u00b0C)'))) +
geom_col(alpha=0.85,position=pd) + geom_errorbar(width=.1,color='black',position=pd) + theme_bw(base_size=10) +
scale_fill_manual(values=pal) +
geom_hline(yintercept=xline, color='black', linetype='dashed', alpha=.5) +
ylab(ylab) + facet_wrap(~exposure.f,labeller = as_labeller(facet.name)) +
theme(axis.title.x = element_blank(),
strip.background = element_rect(fill = "white",color="white"),
strip.text = element_text(angle=0,face="bold"),
axis.text.x = element_text(angle = 30, hjust=1)
) + ylim(lims)
p2 <- ggplotly(bar.pooled,tooltip="text",source="pooled_plots") %>%
layout(hoverlabel=list(bgcolor="white",align='left'), yaxis = list(titlefont = list(size = 12),title = ylab), dragmode = F,
legend = list(title = list(text = ""),orientation = "h", x = 0, y =0.125)) %>%
config(displayModeBar = F)
if (input$sub=="UHII") {
subplot(p1, style(p2,showlegend=F),margin = 0.075,titleY=T)
} else {
subplot(style(p1,showlegend=F), style(p2,showlegend=F),margin = 0.075,titleY=T)
}
})
# Figure caption for the primary results forest + bar plot
output$pooled_plot_text <- renderText({
type = "Heat-related risk and burden"
if (input$subpop == "All") {
if (input$sub=="UHII") {
caption = paste0(type," for the entire study population in low and high urban heat island intensity (UHII) areas, 2000-2017.")
} else if (input$sub == "Primary") {
caption = paste0(type, " for the entire study population, 2000-2017.")
}
} else {
if (input$sub == "Primary") {
if (input$subpop %in% c("Diabetes","CKD")) {
label <- ifelse(input$subpop=="Diabetes",tolower(input$subpop),input$subpop)
caption = paste0(type, " by ", label, " status.")
} else {
caption = paste0(type, " by ", tolower(input$subpop), ".")
}
} else if (input$sub == "UHII") {
if (input$subpop %in% c("Diabetes","CKD")) {
label <- ifelse(input$subpop=="Diabetes",tolower(input$subpop),input$subpop)
caption = paste0(type, " by ", label, " status in low and high urban heat island intensity (UHII) areas.")
} else {
caption = paste0(type, " by ", tolower(input$subpop), " in low and high urban heat island intensity (UHII) areas.")
}
}
}
caption = paste0(caption," Metrics include the relative risk (RR) at extreme heat (99th temperature percentile compared to the minimum hospitalization percentile [MHP]) and the heat-attributable (temperatures above the MHP) number (AN) / annual rate (AR) of cardiovascular hospitalizations.")
})
# Code to render the table of results
output$pooled_table <- DT::renderDataTable({
sub_rr_af_an$Total_HAs <- as.numeric(sub_rr_af_an$Total_HAs)
sub_rr_af_an$Total_Heat_HAs <- as.numeric(sub_rr_af_an$Total_Heat_HAs)
sub_rr_af_an$subpop <- ifelse(sub_rr_af_an$group=="All","All",paste0(sub_rr_af_an$group,", ",sub_rr_af_an$subgroup))
sub_rr_af_an$uhigroup <- ifelse(sub_rr_af_an$type=="Primary","Primary",
ifelse(sub_rr_af_an$subtype == "Q1",
"Low UHII","High UHII"))
sub_rr_af_an$group_lab <- ifelse(sub_rr_af_an$type == "Primary", ifelse(sub_rr_af_an$group == "All","All",sub_rr_af_an$subpop),
ifelse(sub_rr_af_an$group == "All",
sub_rr_af_an$uhigroup,paste0(sub_rr_af_an$subpop,"<br>",sub_rr_af_an$uhigroup)))
table <- sub_rr_af_an[sub_rr_af_an$type == input$sub&sub_rr_af_an$group == input$subpop,
c("group_lab","n.cbsas","Num_Zips","Total_HAs","temp.99",
"mhp","mht","RR.99.full","Attr_HAs_Heat","Ann_AN_Rate100k")]
table[is.na(table)] <- "-"
table$per_HAs <- (table$Total_HAs / sub_rr_af_an[sub_rr_af_an$type=="Primary" & sub_rr_af_an$group == "All",]$Total_HAs)*100
table[,c("Total_HAs","Num_Zips")] <- sapply(table[,c("Total_HAs","Num_Zips")],
function(x)paste0(format(round(x),scientific=F,big.mark=','),''))
table[,c("per_HAs")] <- sapply(table[,c("per_HAs")],
function(x)paste0(round(x,1),"%"))
table$Total_HAs <- paste0(table$Total_HAs," (",table$per_HAs,")")
table[,c("temp.99")] <- sapply(table[,c("temp.99")],function(x)paste0(round(x,1)))
table <- table[,setdiff(colnames(table),c("per_HAs"))]
names(table) <- c("Group","# MSAs","# ZIP Codes","# Hospitalizations (% Total)", "99th Temp. Percentile (\u00b0C)",
"MHP (95% CI)","MHT (\u00b0C) (95% CI)","RR (99th vs. MHP) (95% CI)",
"AN (Temp. \u2265 MHP) (95% CI)", "AR (Annual, per 100k) (95% CI)")
type = "Exposure and outcome information and heat-related cardiovascular risk and burden results"
if (input$subpop == "All") {
if (input$sub=="UHII") {
caption = paste0(type," for the entire study population in low and high urban heat island intensity (UHII) areas, 2000-2017.")
} else if (input$sub == "Primary") {
caption = paste0(type, " for the entire study population, 2000-2017.")
}
} else {
if (input$sub == "Primary") {
if (input$subpop %in% c("Diabetes","CKD")) {
label <- ifelse(input$subpop=="Diabetes",tolower(input$subpop),input$subpop)
caption = paste0(type, " by ", label, " status, 2000-2017.")
} else {
caption = paste0(type, " by ", tolower(input$subpop), ", 2000-2017.")
}
} else if (input$sub == "UHII") {
if (input$subpop %in% c("Diabetes","CKD")) {
label <- ifelse(input$subpop=="Diabetes",tolower(input$subpop),input$subpop)
caption = paste0(type, " by ", label, " status in low and high urban heat island intensity (UHII) areas, 2000-2017.")
} else {
caption = paste0(type, " by ", tolower(input$subpop), " in low and high urban heat island intensity (UHII) areas, 2000-2017.")
}
}
}
caption = paste0(caption," MSA = Metropolitan Statistical Area; MHP = Minimum Hospitalization Percentile; MHT = Minimum Hospitalization Temperature; RR = Relative Risk; AN = Heat-Attributable Number; AR = Heat-Attributable Rate")
DT::datatable(table,
options = list(paging = T,searching = T,dom='t',ordering=T,scrollX = TRUE,
autoWidth = F,
columnDefs = list(
list(className = "nowrap", targets = "_all")
)
),
rownames=FALSE,escape=F,class = 'cell-border stripe',
selection = 'none',
caption = htmltools::tags$caption(
style = 'caption-side: bottom; text-align: left;',
caption
))
})
# Bulleted list of the main takeaways
output$main_takeaway <- renderText({
"<ul>
<li>Notably larger heat-related burden in high UHII areas, attributed to a moderately higher risk</li>
<li>Females, individuals aged 75-114, those with CKD, and those with diabetes had an elevated heat-related risk and burden</li>
<li>High UHII exacerbated heat-related impacts among already heat-vulnerable subpopulations</li>
<li>Heat posed a delayed, rather than immediate, threat</li>
</ul>"
})
# Button to download all results for subpopulatuon analyses
output$downloadAllData <- downloadHandler(
filename <- function() {
paste("data/Overall-Subpop-Results.csv")
},
content <- function(file) {
file.copy("data/Overall-Subpop-Results.csv", file)
},
contentType = "text/csv"
)
#############################################################################
#### Outputs for Exposure & Outcome Maps Tab ################################
#############################################################################
# Code to render the leaflet map
output$leaflet_map <- renderLeaflet({
leaflet() %>%
addProviderTiles(providers$CartoDB.Positron,group="States") %>%
fitBounds(-123.36119,25.13313,-70.02285,48.30850)
})
# Figure caption for the leaflet map
output$leaflet_text <- renderText({
if (input$variable=="uhi") {
part1 = "population-weighted urban heat island intensity (UHII)"
} else if (input$variable == "uhiq") {
part1 = "population-weighted urban heat island intensity (UHII) quartile (Q1 = 'low' UHII areas, Q4 = 'high' UHII areas)"
} else if (input$variable=="hosp") {
part1 = "counts of daily cardiovascular-related hospitalizations among Medicare enrollees (age 65-114)"
} else if (input$variable == "temp") {
part1 = "population-weighted daily mean ambient temperature"
} else if (input$variable == "range") {
part1 = "range of population-weighted daily mean ambient temperature"
} else if (input$variable == "temp.99") {
part1 = "99th percentile of population-weighted daily mean ambient temperature"
}