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app.R
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app.R
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#### Library and Data Imports ####
library(shinythemes)
library(tidyverse)
library(ggplot2)
library(RCurl)
source("modules/Source.R")
source("modules/data_load.R")
source("modules/preprocessing.R")
source("modules/ggplot_gen.R")
source("modules/leaflet_gen.R")
source("modules/gt_gen.R")
sourceDir("modules/shiny/R")
update_date <- read_rds("data_downloaders/today.Rds")$date
moving.avg.window <-
7 # WARNING: Behavior for moving.avg.window > number of report dates for a region is undefined.
# (i.e. a 20 day window if Catskill /Region has 19 report dates.)
height <- "600px"# plot heights
# Leaving this in case we need it
# TODO: Implement other text as strings like this...
rpi_accessibility_link <-
"<div class='center'><p><a href='https://info.rpi.edu/statement-of-accessibility'>Rensselaer Statement of Accessibility</a></p></div>"
footer_text <-
"<p>COVID<b>MINDER</b> analysis and visualizations</b> are by students and staff
of <a href='http://idea.rpi.edu/'>The Rensselaer Institute for Data Exploration
and Applications</a> at <a href='http://rpi.edu/'>Rensselaer Polytechnic Institute</a>
with generous support from the United Health Foundation. COVID<b>MINDER</b> is an open
source project implemented on the <a href='https://shiny.rstudio.com/'>R Shiny platform</a>;
see the <a href='https://github.com/TheRensselaerIDEA/COVIDMINDER'>COVIDMINDER github</a>
for more information. COVID<b>MINDER</b> was directed by Kristin P. Bennett and John S. Erickson.<br><br>
<img src='comment.png' alt = 'Small text bubble icon' style='float:left;width:40px;margin-right:5px;' >
Thanks for using <b>COVIDMINDER!</b> Please take a few moments
to fill out our short <a href='https://forms.gle/8LwiYAVXXN7mu9wR6'>comments form.</a></p><br><br>
"
#<i><a href='https://info.rpi.edu/statement-of-accessibility'>Rensselaer Statement
#of Accessibility</a></i></div>"
whatisit_text_abt <-
"<p>COVID<b>MINDER</b> reveals the regional disparities
in outcomes, determinants, and mediations of the COVID-19 pandemic. Outcomes are the direct
effects of COVID-19. Social and Economic Determinants are pre-existing risk factors that impact
COVID-19 outcomes. Mediations are resources and programs used to combat the pandemic.</p>"
whatisit_text <-
"COVIDMINDER reveals the regional disparities in outcomes, determinants, and mediations of the COVID-19 pandemic. Outcomes are the direct effects of COVID-19. Social and Economic Determinants are pre-existing risk factors that impact COVID-19 outcomes. Mediations are resources and programs used to combat the pandemic."
comments_link <-
"<img src='comment.png' style='float:left;width:40px;padding-right:2px;' >
Thanks for using <b>COVIDMINDER!</b> Please take a few moments
to fill out our short <a href='https://forms.gle/8LwiYAVXXN7mu9wR6'>comments form.</a><br><br>
<i><a href='https://info.rpi.edu/statement-of-accessibility'>Rensselaer Statement
of Accessibility</a></i>"
# For URL parameterization
url1 <- url2 <- ""
#### UI Code ####
### Footer ####
footer <- fluidRow(
column(
width = 12,
fluidRow(
column(
width = 8,
offset = 2,
tags$hr()
)
),
fluidRow(
column(
width = 1,
offset = 2,
HTML("<a href='?tab=about'>About</a> "),
),
column(
width = 3,
HTML(
"<a href='https://idea.rpi.edu/'>Institute for Data Exploration and Applications (IDEA)</a> "
)
),
column(
width = 1,
HTML(
"<a href='https://github.com/TheRensselaerIDEA/COVIDMINDER'>COVIDMINDER GitHub</a> "
)
),
column(
width = 1,
HTML(
"<a href='https://info.rpi.edu/statement-of-accessibility'>Accessibility</a> "
)
),
column(
width = 1,
HTML(
"<a href='https://forms.gle/8LwiYAVXXN7mu9wR6'>
<span title='Thanks for using COVIDMINDER! Please take a few moments to fill out our short comments form.'>Comments</span></a> "
)
),
column(
width = 1,
tags$a(href = "#top", "Back to Navbar")
)
)
)
)
# get rid of footer class code in css doc
header <- tags$div(
class = "header",
tags$div(
class = "headerchild",
HTML("<b>COVIDMINDER</b>"),
)
)
ui <- function(request) {
tagList(
tags$html(lang = "en-us"),
tags$head(includeHTML("www/analytics.html")),
navbarPage(
id = "tab",
theme = "style.css",
title = tags$a(
class = "title-text",
title = whatisit_text,
name = "top",
href = "/",
img(class = "logo", src = "Rensselaer.png",
alt = "Rensselaer Polytechnic Institute Logo")
# HTML("<span style='text-align: right;'> COVID<b>MINDER</b></span>")
),
collapsible = TRUE,
windowTitle = "COVIDMINDER: Where you live matters",
tabPanel(
title = HTML("<b>NATIONAL REPORT CARD</b>"),
value = "national_report_card",
fluidRow(column(
width = 2,
offset = 10,
tags$span(style = "float:right; padding: 5px 40px",
tags$b("Data last pulled:"),
HTML(update_date)),
)),
fluidRow(column(
8,
style = "text-align:center;font-weight:bold;background-color: #EBEBEB;",
tags$h1("COVIDMINDER: Where you live matters"),
offset = 2
)),
fluidRow(column(
8,
style = "text-align:center;",
tags$h1("United States Overview"),
offset = 2
)),
fluidRow(
column(
8,
style = "text-align:center;",
tags$h2("United States COVID-19 Case Curve"),
tags$h3(
"How have United States overall COVID-19 Cases changed over time?"
),
offset = 2
)
),
fluidRow(column(
8,
plotOutput(
outputId = "US.CoT",
height = height,
hover = hoverOpts(
id = "US.CoT.hover",
delay = 100,
delayType = "throttle"
)
),
uiOutput("US.CoT.tooltip"),
downloadButton("US.CoT.dl", label = "Download Case Barplot"),
downloadButton("US.CoT.data.dl", label = "Download Data For This Plot"),
offset = 2
)),
fluidRow(
column(
8,
style = "text-align:center;",
tags$h2("United States COVID-19 Mortality Curve"),
tags$h3(
"How have United States overall COVID-19 deaths changed over time?"
),
offset = 2
)
),
fluidRow(
column(
8,
plotOutput(
outputId = "US.DoT",
height = height,
hover = hoverOpts(
id = "US.DoT.hover",
delay = 100,
delayType = "throttle"
)
),
uiOutput("US.DoT.tooltip"),
downloadButton("US.DoT.dl", label = "Download Mortality Barplot"),
downloadButton("US.DoT.data.dl", label = "Download Data For This Plot"),
offset = 2
),
),
fluidRow(
column(
8,
style = "text-align:center;",
tags$h2("Flattening the Curve"),
tags$p(
"Nationwide, states have taken various approaches to mitigate the spread of coronavirus, such as social distancing interventions and encouraging mask use where social distancing is not possible. Studies by the CDC have shown these methods reduce new COVID-19 cases, hospitalizations, and deaths."
),
tags$b("Data Source: "),
tags$a("CDC", href = "https://wwwnc.cdc.gov/eid/article/26/8/20-1093_article"),
offset = 2
)
),
fluidRow(column(8, gt_output("US.report"),
offset = 2)),
fluidRow(column(
8,
style = "text-align:center;",
tags$h1("State Level Breakdown"),
offset = 2
)),
fluidRow(
column(
width = 8,
offset = 2,
style = "text-align:center;position:relative;",
uiOutput("US.trends.title"),
)
),
fluidRow(
column(
width=4,
offset=2,
tags$div(
style = "height:130px;",
uiOutput("US.report.state.selector"),
radioButtons(
inputId = "NRC.rate",
label = "Rate",
choices = c("Overall", "Per/100k"),
selected = "Per/100k"
)
),
)
),
fluidRow(
column(
width=8,
offset=2,
tags$div(style="padding: 20px 0px;", "Use the above form to select 1 or more States."),
)
),
fluidRow(
column(
width=8,
offset = 2,
plotOutput(
outputId = "US.trends",
height = height,
hover = hoverOpts(
id = "US.trends.hover",
delay = 100,
delayType = "throttle"
),
dblclick = "trends.dbl_click",
brush = brushOpts(id = "trends.brush",
resetOnNew = TRUE)
),
uiOutput("US.trends.tooltip"),
downloadButton("US.trends.dl", label = "Download Case Trend Plot"),
downloadButton("US.trends.data.dl", label = "Download Data For This Plot")
),
),
tags$br(),
fluidRow(column(
8,
offset = 2,
style = "text-align:center;",
tags$div(
class = "info",
HTML(
"<h2>Disparity Color Legend</h2>
Colors on maps below represent:<br><br>
<div>
<div><span style='background: #BD0026; font-size: 11px; opacity: 0.7;'>    </span>
<span style='background: #D73027; font-size: 11px; opacity: 0.7;'>    </span>
<span style='background: #F46D43; font-size: 11px; opacity: 0.7;'>    </span> State rate is<strong> Higher</strong> than national average rate</div>
<div><span style='background: #f7f7f7; border:solid 1px; font-size: 11px; opacity: 0.7;'>    </span> State rate is<strong> About Equal</strong> to national average rate</div>
<div><span style='background: #253494; font-size: 11px; opacity: 0.7;'>    </span>
<span style='background: #4575B4; font-size: 11px; opacity: 0.7;'>    </span>
<span style='background: #74ADD1; font-size: 11px; opacity: 0.7;'>    </span> State rate is<strong> Lower</strong> than national average rate</div>
<i style='display:inline;'>Darker shades indicate greater disparity.</i><br><br>
</div>"
)
)
)),
fluidRow(
column(
8,
tags$h2(style = "text-align:center;", "US COVID-19 Case Hotspots"),
tags$h3(
style = "text-align:center;",
paste0(
"What are the Nationwide disparities in Daily Case Rates? (",
time.period,
" day average)"
)
),
radioButtons(
inputId = "NRC.case.time",
label = "Time Frame",
choices = c("Daily", "Overall"),
selected = "Daily",
inline = T
),
leafletOutput("US.map.cases", height = height),
downloadButton("US.map.cases.dl", label = "Download Case Map"),
downloadButton("US.map.cases.data.dl", label = "Download Data For This Plot"),
offset = 2
),
column(
8,
tags$h2(style = "text-align:center;", "US COVID-19 Mortality Hotspots"),
tags$h3(
style = "text-align:center;",
paste0(
"What are the Nationwide disparities in Daily Mortality Rates? (",
time.period,
" day average)"
)
),
radioButtons(
inputId = "NRC.deaths.time",
label = "Time Frame",
choices = c("Daily", "Overall"),
selected = "Daily",
inline = T
),
leafletOutput("US.map.deaths", height = height),
downloadButton("US.map.deaths.dl", label = "Download Mortality Map"),
downloadButton("US.map.deaths.data.dl", label = "Download Data For This Plot"),
offset = 2
),
# column(
# 8,
# tags$h2(style = "text-align:center;", "US COVID-19 Testing Disparities"),
# tags$h3(
# style = "text-align:center;",
# "What are the Nationwide disparities in COVID-19 Testing?"
# ),
# leafletOutput("US.map.testing", height = height),
#
# downloadButton("US.maps.testing.dl", label = "Download Testing Map"),
# downloadButton("US.maps.testing.data.dl", label = "Download Data For This Plot"),
# offset = 2
# ),
column(
8,
tags$h2(style = "text-align:center;", "US COVID-19 Vaccination Disparities"),
tags$h3(
style = "text-align:center;",
"What are the Nationwide disparities in COVID-19 Vaccination Rates?"
),
tags$h4(
style = "text-align:center;font-style:italic;",
"Based on US mean vaccination rate (completed series per 100K population) across all states."
),
leafletOutput("US.map.vaccination", height = height),
downloadButton("US.maps.vaccination.dl", label = "Download Vaccination Map"),
downloadButton("US.maps.vaccination.data.dl", label = "Download Data For This Plot"),
offset = 2
),
column(
8,
tags$h2(style = "text-align:center;", "US COVID-19 Vaccination Disparities (children 12-18 years old)"),
tags$h3(
style = "text-align:center;",
"What are the Nationwide disparities in COVID-19 vaccination rates for children aged 12-18 years?"
),
tags$h4(
style = "text-align:center;font-style:italic;",
"Based on US mean vaccination rate (completed series per 100K population) for children aged 12-18 years across all states."
),
leafletOutput("US.map.vaccination1218", height = height),
downloadButton("US.maps.vaccination1218.dl", label = "Download Vaccination Map"),
downloadButton("US.maps.vaccination1218.data.dl", label = "Download Data For This Plot"),
offset = 2
),
column(
8,
tags$h2(style = "text-align:center;", "EXPERIMENTAL: US COVID-19 Vaccination Disparities (children 5-12 years old)"),
tags$h3(
style = "text-align:center;",
"What are the Nationwide disparities in COVID-19 vaccination rates for children aged 5-12 years?"
),
tags$h4(
style = "text-align:center;font-style:italic;",
"Based on US mean vaccination rate (completed series per 100K population) for children aged 5-12 years across all states."
),
leafletOutput("US.map.vaccination512", height = height),
downloadButton("US.maps.vaccination512.dl", label = "Download Vaccination Map"),
downloadButton("US.maps.vaccination512.data.dl", label = "Download Data For This Plot"),
offset = 2
)
),
tags$br(),
tags$br(),
tags$br(),
fluidRow(
column(width=8,
offset=2,
style = "text-align:center;",
tags$h1("Rankings")
)
),
fluidRow(
column(width=8,
offset=2,
selectInput(
inputId = "US.entries",
label = "Entries",
choices = c(
`Show 10` = 10,
`Show 25` = 25,
`Show 50` = 50
),
selected = 10,
width = "100px"
),
radioButtons(
inputId = "US.rank.order",
label = "Order",
choices = c("Ascending", "Descending"),
selected = "Descending",
width = "200px"
)
)
),
fluidRow(
column(width=8, offset=2,
gt_output("US.ranking.table")
)
),
footer
),
tabPanel(
title = HTML("<div><b>STATE REPORT CARDS</b></div>"),
value = "state_report_cards",
fluidRow(column(
width = 2,
offset = 10,
tags$span(style = "padding: 5px 40px;float:right;",
tags$b("Data last pulled:"),
HTML(update_date)),
)),
fluidRow(column(
8,
style = "text-align:center;font-weight:bold;background-color: #EBEBEB;",
tags$h1("COVIDMINDER: Where you live matters"),
offset = 2
)),
fluidRow(column(
width=8,
offset=2,
selectInput(
inputId = "state_name",
label = "State Selector",
choices = state.abr$name,
selected = as.character(unlist(ranking[ranking$rank ==
50, "name"]))
),
)),
fluidRow(column(
8,
style = "text-align:center;",
uiOutput("main_title"),
offset = 2
)),
fluidRow(column(
8,
style = "text-align:center;",
tags$b(
tags$sup("*"),
"States are ranked best to worst by their percentage change in COVID-19 cases over the past ",
time.period,
" days."
),
offset = 2
)),
fluidRow(column(
8,
offset=2,
style = "text-align:center;",
uiOutput("state.CoT.title"),
)),
fluidRow(
column(
width = 8,
offset = 2,
plotOutput(
outputId = "state.CoT",
height = height,
hover = hoverOpts(
id = "state.CoT.hover",
delay = 15,
delayType = "debounce"
)
),
uiOutput("state.CoT.tooltip"),
downloadButton("state.CoT.dl", label = "Download Case Barplot"),
downloadButton("state.CoT.data.dl", label = "Download Data For This Plot")
)
),
fluidRow(column(
8,
offset = 2,
style = "text-align:center;",
uiOutput("state.DoT.title")
)),
fluidRow(column(
8,
plotOutput(
outputId = "state.DoT",
height = height,
hover = hoverOpts(
id = "state.DoT.hover",
delay = 15,
delayType = "debounce"
)
),
uiOutput("state.DoT.tooltip"),
downloadButton("state.DoT.dl", label = "Download Mortality Barplot"),
downloadButton("state.DoT.data.dl", label = "Download Data For This Plot"),
offset = 2
)),
fluidRow(
column(
8,
style = "text-align:center;",
tags$h2("Flattening the Curve"),
tags$p(
"Nationwide, states have taken various approaches to mitigate the spread of coronavirus, such as social distancing interventions and encouraging mask use where social distancing is not possible. Studies by the CDC have shown these methods reduce new COVID-19 cases, hospitalizations, and deaths."
),
tags$b("Data Source: "),
tags$a("CDC", href = "https://wwwnc.cdc.gov/eid/article/26/8/20-1093_article"),
offset = 2
)
),
fluidRow(column(8, gt_output("state.report"),
offset = 2)),
fluidRow(column(
8,
style = "text-align:center;",
tags$h1("County Level Breakdown"),
offset = 2
)),
fluidRow(column(
8,
offset = 2,
style = "text-align:center;",
uiOutput("state.trends.title"),
)),
fluidRow(
column(
width=8,offset=2,
tags$div(
style = "height:130px;width:100%;text-align:left;",
uiOutput("state.report.county.selector"),
radioButtons(
inputId = "SRC.rate",
label = "Rate",
choices = c("Overall", "Per/100k"),
selected = "Per/100k"
)
)
)
),
fluidRow(
column(width=8,offset=2,
tags$div(style="padding: 20px 0px;", "Use the above form to select 1 or more Counties."),
)
),
fluidRow(
column(width=8,offset=2,
plotOutput(
outputId = "state.trends",
height = height,
hover = hoverOpts(
id = "state.trends.hover",
delay = 15,
delayType = "debounce"
),
dblclick = "trends.dbl_click",
brush = brushOpts(id = "trends.brush",
resetOnNew = TRUE)
),
uiOutput("state.trends.tooltip"),
downloadButton("state.trends.dl", label = "Download Case Trends Plot"),
downloadButton("state.trends.data.dl", label = "Download Data For This Plot"),
)
),
fluidRow(column(
8,
style = "text-align:center;",
tags$div(
class = "info",
HTML(
"<h2>Disparity Color Legend</h2>
Colors on maps below represent:<br><br>
<div>
<div><span style='background: #BD0026; font-size: 11px; opacity: 0.7;'>    </span>
<span style='background: #D73027; font-size: 11px; opacity: 0.7;'>    </span>
<span style='background: #F46D43; font-size: 11px; opacity: 0.7;'>    </span> County rate is <strong>Higher</strong> than national average rate</div>
<div><span style='background: #f7f7f7; border:solid 1px; font-size: 11px; opacity: 0.7;'>    </span> County rate is <strong>About Equal</strong> to national average rate</div>
<div><span style='background: #253494; font-size: 11px; opacity: 0.7;'>    </span>
<span style='background: #4575B4; font-size: 11px; opacity: 0.7;'>    </span>
<span style='background: #74ADD1; font-size: 11px; opacity: 0.7;'>    </span> County rate is <strong>Lower</strong> than national average rate</div>
<i style='display:inline;'>Darker shades indicate greater disparity.</i><br><br>
</div>"
)
),
offset = 2
)),
fluidRow(
column(
8,
tags$div(style = "text-align:center;", uiOutput("state.county.cases")),
radioButtons(
inputId = "SRC.case.time",
label = "Time Frame",
choices = c("Daily", "Overall"),
selected = "Daily",
inline = T
),
leafletOutput("map.cases", height = height),
downloadButton("map.cases.dl", label = "Download Case Map"),
downloadButton("map.cases.data.dl", label = "Download Data For This Plot"),
offset = 2
),
column(
8,
tags$div(style = "text-align:center;", uiOutput("state.county.deaths")),
radioButtons(
inputId = "SRC.death.time",
label = "Time Frame",
choices = c("Daily", "Overall"),
selected = "Daily",
inline = T
),
leafletOutput("map.deaths", height = height),
downloadButton("map.deaths.dl", label = "Download Mortality Map"),
downloadButton("map.deaths.data.dl", label = "Download Data For This Plot"),
offset = 2
)
),
tags$br(),
fluidRow(column(
8,
style = "text-align:center;",
tags$h1("Comorbidities and Other Determinants"),
offset = 2
)),
fluidRow(
column(
8,
style = "text-align:center;",
uiOutput("determinant.title"),
offset = 2
),
column(
8,
selectInput(
inputId = "state.determinant",
label = "Determinant",
choices = c("Diabetes", "Obesity", "CRD Mortality"),
selected = "Diabetes"
# selected = "GOP Vote"
),
leafletOutput("maps.determinant", height = height),
downloadButton("map.determinant.dl", label = "Download Determinant Map"),
downloadButton("map.determinant.data.dl", label = "Download Data For This Plot"),
offset = 2
),
column(
8,
style = "text-align:center;",
tags$p(
textOutput("determinant.text"),
tags$br(),
tags$b("Data Source: "),
tags$a("CDC", href = "www.cdc.gov/diabetes/data"),
", ",
tags$a("CHR", href =
"https://www.countyhealthrankings.org/explore-health-rankings/measures-data-sources/county-health-rankings-model/health-factors/health-behaviors/diet-exercise/adult-obesity")
),
offset = 2
)
),
tags$br(),
tags$br()
,
fluidRow(
column(8, offset = 2,style = "text-align:center;",
tags$h1("Rankings"),
tags$a(name = "ranking"),
)),
fluidRow(
column(
width=8,
offset=2,
selectInput(
inputId = "entries",
label = "Entries",
choices = c(
`Show 10` = 10,
`Show 25` = 25,
`Show 50` = 50
),
selected = 10,
width = "100px"
),
radioButtons(
inputId = "rank.order",
label = "Order",
choices = c("Ascending", "Descending"),
selected = "Descending",
width = "200px"
),
)
),
fluidRow(
column(
width=8,offset=2,
gt_output("ranking.table")
)
),
footer
),
#### State Determinants UI ####
navbarMenu(
menuName = "determinant_menu",
HTML("<div><b>DETERMINANT ANALYSIS</b></div>"),
tabPanel(
tags$div(
class = "tab-title",
style = "text-align:center;",
HTML("<div><b>State Analysis</b></div>")
),
value = "state_social_det",
fluidRow(column(
8,
style = "text-align:center;font-weight:bold;background-color: #EBEBEB;",
tags$h1("COVIDMINDER: Where you live matters"),
offset = 2
)),
fluidRow(column(
8,
selectInput("social_det_picker", "Select a state to display", state.name, selected = NULL, multiple = FALSE,
selectize = TRUE, width = NULL, size = NULL),
plotOutput("social_det_graph", width = "100%", height = "1600px"),
offset = 2
))
),
tabPanel(
tags$div(
class = "tab-title",
style = "text-align:center;",
HTML("<div><b>Determinant Descriptions</b></div>")
),
value = "state_social_det_descriptions",
fluidRow(column(
8,
style = "text-align:center;font-weight:bold;background-color: #EBEBEB;",
tags$h1("COVIDMINDER: Where you live matters"),
offset = 2
)),
fluidRow(column(
8,
gt_output("determinant_descriptions"),
offset = 2
))
),
tabPanel(
tags$div(
class = "tab-title",
style = "text-align:center;",
HTML("<div><b>DISCLAIMER</b></div>")
),
value = "determinant_disclaimer",
fluidRow(column(
8,
style = "text-align:center;font-weight:bold;background-color: #EBEBEB;",
tags$h1("COVIDMINDER: Where you live matters"),
offset = 2
)),
fluidRow(column(
8,
class = "about",
tags$h1("Disclaimer"),
tags$p(
"Determinant tabs are experimental and expected to change substantially, current displayed data may not be accurate."
),
offset = 2
)),
footer
)
),
tabPanel(
HTML("<div><b>ABOUT</b></div>"),
value = "about",
fluidRow(column(
8,
style = "text-align:center;font-weight:bold;background-color: #EBEBEB;",
tags$h1("COVIDMINDER: Where you live matters"),
offset = 2
)),
fluidRow(column(
8,
offset = 2,
class = "about",
tags$h1("About the Project"),
HTML(whatisit_text_abt),
HTML(footer_text)
),),
footer
)
),
)
}
#### Server Code ####
server <- function(input, output, session) {
# Leaflet plot colors
colors <-
c(
"#253494",
"#4575B4",
"#74ADD1",
"#ABD9E9",
"#f7f7f7",
"#FDAE61",
"#F46D43",
"#D73027",
"#BD0026"
)
bins <- c(5, 3, 2, 1, .2,-.2,-1,-2,-3,-5)
#### State Report Cards Code ####
output$state.report.county.selector <- renderUI ({
state_name <- input$state_name
state_initial <- state.abr[state.abr$name == state_name, "abr"]
# Grab state subset for dataframe
state.df <- covid_TS_counties_long.cases %>%
select(-c(countyFIPS, StateFIPS)) %>%
filter(State == state_initial)
if (state_initial == "NY") {
nyc.population <- state.df %>%
filter(County %in% c("New York", "Kings", "Queens", "Bronx", "Richmond")) %>%
group_by(County) %>%
top_n(n = 1, wt = date) %>%
select(population)
nyc.population <- sum(nyc.population$population)
NYC <- state.df %>%
filter(County %in% c("New York", "Kings", "Queens", "Bronx", "Richmond")) %>%
group_by(State, date) %>%
summarise(
County = "New York City",
cases = sum(cases),
deaths = sum(deaths),
population = nyc.population,
p_cases = sum(cases) * 100000 / nyc.population,
p_deaths = sum(deaths) * 100000 / nyc.population,
diff = sum(diff),
p_diff = sum(diff) * 100000 / nyc.population,
d_diff = sum(d_diff),
p.d_diff = sum(p.d_diff) * 100000 / nyc.population
)
state.df <- state.df %>%
filter(!County %in% c("New York", "Kings", "Queens", "Bronx", "Richmond")) %>%
rbind.data.frame(NYC)
}
counties <- state.df %>%
select(County) %>%
unlist() %>%
unique()
selected <- state.df %>%
group_by(County) %>%
top_n(1, cases) %>%
arrange(desc(cases)) %>%
select(County) %>%
unlist() %>%
unique()
if (length(selected) > 5) {
selected <- selected[1:5]
}
selectInput(
inputId = "SRC.county",
label = "County Selector",
choices = sort(counties),
selected = selected,
multiple = TRUE,
selectize = FALSE,
size = min(5, length(counties))
)
})
output$US.report.state.selector <- renderUI({
state.names <- states %>%
filter(NAME != "District of Columbia") %>%
select(NAME) %>%
unlist() %>%
unique() %>%
sort()