inst/shiny-app/server.R
In gopalpenny/covid19vis:
#
# This is the server logic of a Shiny web application. You can run the
# application by clicking 'Run App' above.
#
# Find out more about building applications with Shiny here:
#
# http://shiny.rstudio.com/
#
if (FALSE) {
library(profvis)
profvis({shiny::runApp("inst/shiny-app")})
}
library(shiny)
# library(leaflet)
library(covid19vis)
library(dplyr)
# library(magrittr)
# library(ggplot2)
# library(plotly)
# library(readr)
library(sf)
# library(rgeos)
# library(rnaturalearth)
# library(DT)
# if (!interactive()) {
# dir <- "./"
# } else {
# dir <- "inst/shiny-app"
# }
dir <- "./"
formnumber <- function(x, ...) {
gsub(" ","",format(x, ...))
}
# Define server logic required to draw a histogram
shinyServer(function(input, output) {
# Get and prepare data
### US DATA
# # NY Times data (no longer used)
# covid_data_us_prep1 <- readr::read_csv(url("https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-states.csv")) %>%
# rename(name=state,id=fips) %>%
# left_join(us_states %>% dplyr::select(abbrev,lat=latitude,lon=longitude,name),by="name")
# # CSSE data from Johns Hopkins
us_cases_url <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_US.csv"
us_deaths_url <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_US.csv"
covid_data_us_prep <- prep_covid_raw_us(us_cases_url,us_deaths_url)
covid_data_us <- prep_covid_data(covid_data_us_prep)
covid_totals_us <- prep_covid_totals(covid_data_us)
map_data_us <- usaboundaries_usstates %>% dplyr::rename(abbrev=stusps) %>%
dplyr::left_join(covid_totals_us,by=c("abbrev"))
### WORLD DATA
world_cases_url <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv"
world_deaths_url <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv"
covid_data_world_prep <- prep_covid_raw_world(world_cases_url, world_deaths_url)
covid_data_world <- prep_covid_data(covid_data_world_prep)
# covid_data <- covid_data_us
covid_totals_world <- prep_covid_totals(covid_data_world) %>% dplyr::arrange(name)
map_data_world <- rnatural_worldmap %>%
left_join(covid_totals_world,by="id") %>%
filter(!is.na(name))
## additional data
umin <- floor(log10(min(covid_totals_us$cases,na.rm=TRUE)))
umax <- ceiling(log10(max(covid_totals_us$cases,na.rm=TRUE)))
usbins <- 10^c(umin:umax)
uspal <- leaflet::colorBin("YlOrRd", domain = c(10^umin,10^umax), bins = usbins)
wmin <- floor(log10(min(covid_totals_world$cases,na.rm=TRUE)))
wmax <- ceiling(log10(max(covid_totals_world$cases,na.rm=TRUE)))
worldbins <- 10^c(wmin:wmax)
worldpal <- leaflet::colorBin("YlOrRd", domain = c(10^wmin,10^wmax), bins = worldbins)
# Reactive data objects -- change depending on maintab
covid_data <- reactive({
if (input$maintab=="us") {
covid_data <- covid_data_us
} else if (input$maintab=="world") {
covid_data <- covid_data_world
}
covid_data
})
covid_totals <- reactive({
if (input$maintab=="us") {
covid_totals <- covid_totals_us
} else if (input$maintab=="world") {
covid_totals <- covid_totals_world
}
covid_totals
})
covid_summary <- reactive({
covid_summary <- covid_totals() %>%
select(cases,deaths,cases_daily,deaths_daily) %>%
group_by() %>%
summarize_all(sum) %>%
mutate(cases_pct_change=cases_daily/(cases-cases_daily)*100,
deaths_pct_change=deaths_daily/(deaths-deaths_daily)*100)
})
map_data <- reactive({
if (input$maintab=="us") {
map_data <- map_data_us
} else if (input$maintab=="world") {
map_data <- map_data_world
}
map_data
})
map_labels <- reactive({
map_data_df <- map_data()
map_labels_vector <- paste0("<strong>",map_data_df$name,"</strong><br/>",
formnumber(map_data_df$cases,big.mark=",",width=0)," (+",formnumber(map_data_df$cases_daily,big.mark=",",width=0),") cases<br/>",
formnumber(map_data_df$deaths,big.mark=",",width=0)," (+",formnumber(map_data_df$deaths_daily,big.mark=",",width=0),") deaths")
map_labels <- lapply(map_labels_vector,function(x) htmltools::HTML(x))
# map_labels <- sprintf(
# "<strong>%s (%s)</strong><br/>%g (+%g) cases<br/>%g (+%g) deaths",
# map_data_df$name, map_data_df$abbrev, map_data_df$cases, map_data_df$cases_daily, map_data_df$deaths, map_data_df$deaths_daily
# ) %>% lapply(htmltools::HTML)
# print("map_data")
# print(map_data_df)
map_labels
# print("map_labels")
# print(map_labels)
})
mappal <- reactive({
if (input$maintab=="us") {
mappal <- uspal
} else if (input$maintab=="world") {
mappal <- worldpal
}
mappal
})
output$us_cases_summary <- renderText({
text <- with(covid_summary(),
paste0("<strong>Total cases</strong><br/>",format(cases,big.mark = ",")," (+",
format(cases_daily,big.mark = ","),", ",format(cases_pct_change,big.mark = ",",digits = 3),"%)"))
HTML(text)
})
output$us_deaths_summary <- renderText({
text <- with(covid_summary(),
paste0("<strong>Total deaths</strong><br/>",format(deaths,big.mark = ",")," (+",
format(deaths_daily,big.mark = ","),", ",format(deaths_pct_change,big.mark = ",",digits = 3),"%)"))
HTML(text)
})
map_info <- reactiveValues(
usbounds = list(north = 61.8, east = -60.3, south = 0.879, west = -135),
worldbounds = NULL
# bounds = NULL
)
# when bounds change, update bounds for US or World
observeEvent(input$usmap_bounds,{
if (input$maintab=="us") {
map_info$usbounds <- input$usmap_bounds
# map_info$bounds <- input$usmap_bounds
} else if (input$maintab=="world") {
map_info$worldbounds <- input$usmap_bounds
map_info$bounds <- input$usmap_bounds
}
})
# current bound are always stored in a reactive contect
mapbounds <- reactive({
if (input$maintab=="us") {
mapbounds <- map_info$usbounds
} else if (input$maintab=="world") {
mapbounds <- map_info$worldbounds
}
mapbounds
})
observeEvent(input$maintab,{
pal <- mappal()
map_bounds <- mapbounds()
leaflet::leafletProxy("usmap") %>%
leaflet::clearGroup("poly") %>% leaflet::clearControls() %>%
leaflet::addPolygons(data=map_data(),stroke=TRUE,weight=2,opacity=0.3,fillOpacity = 0.3,
fillColor = ~pal(cases),color=~pal(cases),group="poly",
# highlightOptions = highlightOptions(
# weight = 5,
# color = "#666",
# dashArray = "",
# fillOpacity = 0.7,
# bringToFront = TRUE),
label=map_labels()) %>%
# addLayersControl(baseGroups = c("Map"),#overlayGroups = c("Red","Blue") ,
# options = layersControlOptions(collapsed = FALSE)) %>%
# leaflet::addCircles(~lon,~lat,~log(cases)*1e4,data=covid_totals,stroke=FALSE) %>%
leaflet::addLegend(position = "bottomleft",pal=pal,data=map_data(),values = ~cases) %>%
leaflet::fitBounds(lng1 = map_bounds$west , lng2 = map_bounds$east, lat1 = map_bounds$south , lat2=map_bounds$north)
})
output$usmap <- leaflet::renderLeaflet({
leaflet::leaflet() %>%
leaflet::addProviderTiles(leaflet::providers$CartoDB.Positron) %>%
# leafem::addMouseCoordinates() %>%
# addProviderTiles("Esri.WorldImagery", group="Satellite") %>%
leaflet::addScaleBar(position = c("bottomright"), options = leaflet::scaleBarOptions())%>%
leaflet::setView(lng = 5, lat = 0, zoom=1)
})
output$table <- DT::renderDT({
covid_DT <- prep_covid_DT(covid_totals())
covid_DT
})
output$plot <- plotly::renderPlotly({
# debug:
if(FALSE) {
y_axis_name <- "cases_daily"
x_axis_name <- "days30"
rank_name <- "rank_cases_name"
map_bounds <- list(north=44.5,south=0,east=-77.7,west=-117.7)
input <- list(ngroup=8)
cov_total <- covid_totals_world
cov_data <- covid_data_world
}
foo <- "bar"
print(str(input$usmap_bounds))
map_bounds <- mapbounds()
print(str(map_bounds))
# cov_data <- covid_data()
# print('covid_data')
# print(covid_data())
if (!is.null(map_bounds)) {
cov_total <- covid_totals()
cov_data <- covid_data()
y_axis_name <- case_when(
input$yaxis_val == "Cases" & input$yaxis_type == "New" ~ "cases_daily",
input$yaxis_val == "Cases" & input$yaxis_type == "Total" ~ "cases",
input$yaxis_val == "Cases" & input$yaxis_type == "% change" ~ "cases_pct_change",
input$yaxis_val == "Deaths" & input$yaxis_type == "New" ~ "deaths_daily",
input$yaxis_val == "Deaths" & input$yaxis_type == "Total" ~ "deaths",
input$yaxis_val == "Deaths" & input$yaxis_type == "% change" ~ "deaths_pct_change"
)
rank_name <- case_when(
input$rankname == "Cases (Total)" ~ "rank_cases_name",
input$rankname == "Deaths (Total)" ~ "rank_deaths_name",
input$rankname == "Cases (New)" ~ "rank_cases_daily_name",
input$rankname == "Deaths (New)" ~ "rank_deaths_daily_name"
)
x_axis_name <- case_when(
input$xaxis == "Last 30 days" ~ "date",
input$xaxis == "Days since Nth" & input$yaxis_val == "Cases" ~ "cases100days",
input$xaxis == "Days since Nth" & input$yaxis_val == "Deaths" ~ "deaths25days"
)
x_axis_label <- case_when(
input$xaxis == "Last 30 days" ~ paste("Last",input$ndays,"days"),
input$xaxis == "Days since Nth" & input$yaxis_val == "Cases" ~ "Days since 100th case",
input$xaxis == "Days since Nth" & input$yaxis_val == "Deaths" ~ "Days since 25th death"
)
if (x_axis_name == "date") {
cov_data$date[Sys.Date() - cov_data$date > input$ndays] <- NA
} else if (x_axis_name == "cases100days") {
cov_data$cases100days[cov_data$cases100days > input$ndays] <- NA
} else if (x_axis_name == "deaths25days") {
cov_data$cases100days[cov_data$deaths25days > input$ndays] <- NA
}
# var_name <- "state"
covid_top <- cov_total %>%
rename(rank = !!rank_name) %>%
dplyr::filter(lat>map_bounds$south,lat<map_bounds$north,
lon>map_bounds$west,lon<map_bounds$east) %>%
dplyr::arrange(rank) %>%
dplyr::slice(1:input$ngroup)
covid_plot_data_prep <- cov_data
covid_plot_data_prep$xvar <- cov_data[,x_axis_name][[1]]
covid_plot_data_prep$yvar <- cov_data[,y_axis_name][[1]]
covid_plot_data_prep <- covid_plot_data_prep %>%
dplyr::filter(name %in% covid_top$name) %>%
# dplyr::select(xvar,yvar,name) %>%
group_by()
# cov_data %>% mutate(xvar = !! x_axis_name,
# yvar = vars(y_axis_name)) %>%
# covid_plot_data_prep2 <- covid_data() %>%
# dplyr::filter(name %in% covid_top$name) %>%
# dplyr::select(!!y_axis_name,!!x_axis_name,name) %>%
# group_by()
if("7-day avg" %in% input$plotoptions) {
print("smoothing...")
covid_plot_data_prep <- covid_plot_data_prep %>%
group_by(name) %>% arrange(name,date) %>%
mutate(yvar=as.numeric(stats::filter(yvar,rep(1/7,7),sides=1))) %>%
group_by()
}
covid_plot_data <- covid_plot_data_prep %>%
filter(!is.na(yvar), !is.na(xvar)) %>%
left_join(covid_top %>% select(name,rank),by="name")
### plotly
if ("log(y)" %in% input$plotoptions) {
covid_plot_data <- covid_plot_data %>% mutate(yvar = ifelse(yvar==0,NA,yvar))
}
plot1 <- plotly::plot_ly(type='scatter',mode='lines+markers')
for (i in 1:nrow(covid_top)) {
plot_data_df <- covid_plot_data %>% filter(name==covid_top$name[i])
plot1 <- plot1 %>%
plotly::add_trace(data=plot_data_df,
x=~xvar,y=~yvar,name=~rank,
text=~paste0('<b>',date,'</b>',
'<br>',name,' (',abbrev,')',
'<br>',formnumber(cases,big.mark = ","),' (+',formnumber(cases_daily,big.mark = ","),') cases',
'<br>',formnumber(deaths,big.mark = ","),' (+',formnumber(deaths_daily,big.mark = ","),') deaths'),
hoverinfo='text')
}
avg_7_note <- ifelse("7-day avg" %in% input$plotoptions,", 7-day avg","")
x_list <- list(title = x_axis_label)
y_list <- list(title = paste0(input$yaxis_val," (",input$yaxis_type,avg_7_note,")"))
if ("log(y)" %in% input$plotoptions) {
y_list <- list(title = paste0(input$yaxis_val," (log ",input$yaxis_type,avg_7_note,")"),type="log")
}
plot1 <- plot1 %>% plotly::layout(yaxis = y_list, xaxis = x_list) %>%
plotly::layout(legend = list(orientation = 'h',y = 1,yanchor="bottom"))
###
# plot <- ggplot2::ggplot(covid_plot_data,ggplot2::aes(xvar,yvar,color=rank)) +
# ggplot2::geom_line() + ggplot2::geom_point() +
# ggplot2::labs(y=input$yaxis,x=input$xaxis) +
# ggplot2::`%+replace%`(ggplot2::theme_bw(),ggplot2::theme(legend.title = ggplot2::element_blank()))
#
# if (input$logy) {
# plot <- plot + ggplot2::scale_y_log10()
# }
# plotly::ggplotly(plot) %>%
# plotly::layout(legend = list(orientation = 'h',
# y = 1,
# yanchor="bottom"))
plot1
} else {
# p_empty <- ggplot2::ggplot(data.frame(x=1,y=1,label="Loading...")) +
# ggplot2::geom_text(ggplot2::aes(x,y,label=label))
# plotly::ggplotly(p_empty)
plot_null <- NULL
plot_null
}
})
output$maintab_title <- renderText({
scale_text <- dplyr::case_when(
input$maintab == "us"~"United States",
input$maintab == "world"~"World"
)
paste("COVID19:",scale_text)
})
output$tableheader <- renderText({
covid_tot <- covid_totals()
last_update <- covid_tot$last_date %>% max() %>% strftime("%b %d, %Y")
if (input$maintab=="us") {
# data_source <- "the NY Times"
data_source <- "JHU CSSE"
} else if (input$maintab=="world") {
data_source <- "JHU CSSE"
}
tableheader <- paste0("Latest data from ",data_source," (",last_update,")")
tableheader
})
})
gopalpenny/covid19vis documentation built on July 24, 2020, 8:23 a.m.
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#
# This is the server logic of a Shiny web application. You can run the
# application by clicking 'Run App' above.
#
# Find out more about building applications with Shiny here:
#
# http://shiny.rstudio.com/
#
if (FALSE) {
library(profvis)
profvis({shiny::runApp("inst/shiny-app")})
}
library(shiny)
# library(leaflet)
library(covid19vis)
library(dplyr)
# library(magrittr)
# library(ggplot2)
# library(plotly)
# library(readr)
library(sf)
# library(rgeos)
# library(rnaturalearth)
# library(DT)
# if (!interactive()) {
# dir <- "./"
# } else {
# dir <- "inst/shiny-app"
# }
dir <- "./"
formnumber <- function(x, ...) {
gsub(" ","",format(x, ...))
}
# Define server logic required to draw a histogram
shinyServer(function(input, output) {
# Get and prepare data
### US DATA
# # NY Times data (no longer used)
# covid_data_us_prep1 <- readr::read_csv(url("https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-states.csv")) %>%
# rename(name=state,id=fips) %>%
# left_join(us_states %>% dplyr::select(abbrev,lat=latitude,lon=longitude,name),by="name")
# # CSSE data from Johns Hopkins
us_cases_url <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_US.csv"
us_deaths_url <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_US.csv"
covid_data_us_prep <- prep_covid_raw_us(us_cases_url,us_deaths_url)
covid_data_us <- prep_covid_data(covid_data_us_prep)
covid_totals_us <- prep_covid_totals(covid_data_us)
map_data_us <- usaboundaries_usstates %>% dplyr::rename(abbrev=stusps) %>%
dplyr::left_join(covid_totals_us,by=c("abbrev"))
### WORLD DATA
world_cases_url <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv"
world_deaths_url <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv"
covid_data_world_prep <- prep_covid_raw_world(world_cases_url, world_deaths_url)
covid_data_world <- prep_covid_data(covid_data_world_prep)
# covid_data <- covid_data_us
covid_totals_world <- prep_covid_totals(covid_data_world) %>% dplyr::arrange(name)
map_data_world <- rnatural_worldmap %>%
left_join(covid_totals_world,by="id") %>%
filter(!is.na(name))
## additional data
umin <- floor(log10(min(covid_totals_us$cases,na.rm=TRUE)))
umax <- ceiling(log10(max(covid_totals_us$cases,na.rm=TRUE)))
usbins <- 10^c(umin:umax)
uspal <- leaflet::colorBin("YlOrRd", domain = c(10^umin,10^umax), bins = usbins)
wmin <- floor(log10(min(covid_totals_world$cases,na.rm=TRUE)))
wmax <- ceiling(log10(max(covid_totals_world$cases,na.rm=TRUE)))
worldbins <- 10^c(wmin:wmax)
worldpal <- leaflet::colorBin("YlOrRd", domain = c(10^wmin,10^wmax), bins = worldbins)
# Reactive data objects -- change depending on maintab
covid_data <- reactive({
if (input$maintab=="us") {
covid_data <- covid_data_us
} else if (input$maintab=="world") {
covid_data <- covid_data_world
}
covid_data
})
covid_totals <- reactive({
if (input$maintab=="us") {
covid_totals <- covid_totals_us
} else if (input$maintab=="world") {
covid_totals <- covid_totals_world
}
covid_totals
})
covid_summary <- reactive({
covid_summary <- covid_totals() %>%
select(cases,deaths,cases_daily,deaths_daily) %>%
group_by() %>%
summarize_all(sum) %>%
mutate(cases_pct_change=cases_daily/(cases-cases_daily)*100,
deaths_pct_change=deaths_daily/(deaths-deaths_daily)*100)
})
map_data <- reactive({
if (input$maintab=="us") {
map_data <- map_data_us
} else if (input$maintab=="world") {
map_data <- map_data_world
}
map_data
})
map_labels <- reactive({
map_data_df <- map_data()
map_labels_vector <- paste0("<strong>",map_data_df$name,"</strong><br/>",
formnumber(map_data_df$cases,big.mark=",",width=0)," (+",formnumber(map_data_df$cases_daily,big.mark=",",width=0),") cases<br/>",
formnumber(map_data_df$deaths,big.mark=",",width=0)," (+",formnumber(map_data_df$deaths_daily,big.mark=",",width=0),") deaths")
map_labels <- lapply(map_labels_vector,function(x) htmltools::HTML(x))
# map_labels <- sprintf(
# "<strong>%s (%s)</strong><br/>%g (+%g) cases<br/>%g (+%g) deaths",
# map_data_df$name, map_data_df$abbrev, map_data_df$cases, map_data_df$cases_daily, map_data_df$deaths, map_data_df$deaths_daily
# ) %>% lapply(htmltools::HTML)
# print("map_data")
# print(map_data_df)
map_labels
# print("map_labels")
# print(map_labels)
})
mappal <- reactive({
if (input$maintab=="us") {
mappal <- uspal
} else if (input$maintab=="world") {
mappal <- worldpal
}
mappal
})
output$us_cases_summary <- renderText({
text <- with(covid_summary(),
paste0("<strong>Total cases</strong><br/>",format(cases,big.mark = ",")," (+",
format(cases_daily,big.mark = ","),", ",format(cases_pct_change,big.mark = ",",digits = 3),"%)"))
HTML(text)
})
output$us_deaths_summary <- renderText({
text <- with(covid_summary(),
paste0("<strong>Total deaths</strong><br/>",format(deaths,big.mark = ",")," (+",
format(deaths_daily,big.mark = ","),", ",format(deaths_pct_change,big.mark = ",",digits = 3),"%)"))
HTML(text)
})
map_info <- reactiveValues(
usbounds = list(north = 61.8, east = -60.3, south = 0.879, west = -135),
worldbounds = NULL
# bounds = NULL
)
# when bounds change, update bounds for US or World
observeEvent(input$usmap_bounds,{
if (input$maintab=="us") {
map_info$usbounds <- input$usmap_bounds
# map_info$bounds <- input$usmap_bounds
} else if (input$maintab=="world") {
map_info$worldbounds <- input$usmap_bounds
map_info$bounds <- input$usmap_bounds
}
})
# current bound are always stored in a reactive contect
mapbounds <- reactive({
if (input$maintab=="us") {
mapbounds <- map_info$usbounds
} else if (input$maintab=="world") {
mapbounds <- map_info$worldbounds
}
mapbounds
})
observeEvent(input$maintab,{
pal <- mappal()
map_bounds <- mapbounds()
leaflet::leafletProxy("usmap") %>%
leaflet::clearGroup("poly") %>% leaflet::clearControls() %>%
leaflet::addPolygons(data=map_data(),stroke=TRUE,weight=2,opacity=0.3,fillOpacity = 0.3,
fillColor = ~pal(cases),color=~pal(cases),group="poly",
# highlightOptions = highlightOptions(
# weight = 5,
# color = "#666",
# dashArray = "",
# fillOpacity = 0.7,
# bringToFront = TRUE),
label=map_labels()) %>%
# addLayersControl(baseGroups = c("Map"),#overlayGroups = c("Red","Blue") ,
# options = layersControlOptions(collapsed = FALSE)) %>%
# leaflet::addCircles(~lon,~lat,~log(cases)*1e4,data=covid_totals,stroke=FALSE) %>%
leaflet::addLegend(position = "bottomleft",pal=pal,data=map_data(),values = ~cases) %>%
leaflet::fitBounds(lng1 = map_bounds$west , lng2 = map_bounds$east, lat1 = map_bounds$south , lat2=map_bounds$north)
})
output$usmap <- leaflet::renderLeaflet({
leaflet::leaflet() %>%
leaflet::addProviderTiles(leaflet::providers$CartoDB.Positron) %>%
# leafem::addMouseCoordinates() %>%
# addProviderTiles("Esri.WorldImagery", group="Satellite") %>%
leaflet::addScaleBar(position = c("bottomright"), options = leaflet::scaleBarOptions())%>%
leaflet::setView(lng = 5, lat = 0, zoom=1)
})
output$table <- DT::renderDT({
covid_DT <- prep_covid_DT(covid_totals())
covid_DT
})
output$plot <- plotly::renderPlotly({
# debug:
if(FALSE) {
y_axis_name <- "cases_daily"
x_axis_name <- "days30"
rank_name <- "rank_cases_name"
map_bounds <- list(north=44.5,south=0,east=-77.7,west=-117.7)
input <- list(ngroup=8)
cov_total <- covid_totals_world
cov_data <- covid_data_world
}
foo <- "bar"
print(str(input$usmap_bounds))
map_bounds <- mapbounds()
print(str(map_bounds))
# cov_data <- covid_data()
# print('covid_data')
# print(covid_data())
if (!is.null(map_bounds)) {
cov_total <- covid_totals()
cov_data <- covid_data()
y_axis_name <- case_when(
input$yaxis_val == "Cases" & input$yaxis_type == "New" ~ "cases_daily",
input$yaxis_val == "Cases" & input$yaxis_type == "Total" ~ "cases",
input$yaxis_val == "Cases" & input$yaxis_type == "% change" ~ "cases_pct_change",
input$yaxis_val == "Deaths" & input$yaxis_type == "New" ~ "deaths_daily",
input$yaxis_val == "Deaths" & input$yaxis_type == "Total" ~ "deaths",
input$yaxis_val == "Deaths" & input$yaxis_type == "% change" ~ "deaths_pct_change"
)
rank_name <- case_when(
input$rankname == "Cases (Total)" ~ "rank_cases_name",
input$rankname == "Deaths (Total)" ~ "rank_deaths_name",
input$rankname == "Cases (New)" ~ "rank_cases_daily_name",
input$rankname == "Deaths (New)" ~ "rank_deaths_daily_name"
)
x_axis_name <- case_when(
input$xaxis == "Last 30 days" ~ "date",
input$xaxis == "Days since Nth" & input$yaxis_val == "Cases" ~ "cases100days",
input$xaxis == "Days since Nth" & input$yaxis_val == "Deaths" ~ "deaths25days"
)
x_axis_label <- case_when(
input$xaxis == "Last 30 days" ~ paste("Last",input$ndays,"days"),
input$xaxis == "Days since Nth" & input$yaxis_val == "Cases" ~ "Days since 100th case",
input$xaxis == "Days since Nth" & input$yaxis_val == "Deaths" ~ "Days since 25th death"
)
if (x_axis_name == "date") {
cov_data$date[Sys.Date() - cov_data$date > input$ndays] <- NA
} else if (x_axis_name == "cases100days") {
cov_data$cases100days[cov_data$cases100days > input$ndays] <- NA
} else if (x_axis_name == "deaths25days") {
cov_data$cases100days[cov_data$deaths25days > input$ndays] <- NA
}
# var_name <- "state"
covid_top <- cov_total %>%
rename(rank = !!rank_name) %>%
dplyr::filter(lat>map_bounds$south,lat<map_bounds$north,
lon>map_bounds$west,lon<map_bounds$east) %>%
dplyr::arrange(rank) %>%
dplyr::slice(1:input$ngroup)
covid_plot_data_prep <- cov_data
covid_plot_data_prep$xvar <- cov_data[,x_axis_name][[1]]
covid_plot_data_prep$yvar <- cov_data[,y_axis_name][[1]]
covid_plot_data_prep <- covid_plot_data_prep %>%
dplyr::filter(name %in% covid_top$name) %>%
# dplyr::select(xvar,yvar,name) %>%
group_by()
# cov_data %>% mutate(xvar = !! x_axis_name,
# yvar = vars(y_axis_name)) %>%
# covid_plot_data_prep2 <- covid_data() %>%
# dplyr::filter(name %in% covid_top$name) %>%
# dplyr::select(!!y_axis_name,!!x_axis_name,name) %>%
# group_by()
if("7-day avg" %in% input$plotoptions) {
print("smoothing...")
covid_plot_data_prep <- covid_plot_data_prep %>%
group_by(name) %>% arrange(name,date) %>%
mutate(yvar=as.numeric(stats::filter(yvar,rep(1/7,7),sides=1))) %>%
group_by()
}
covid_plot_data <- covid_plot_data_prep %>%
filter(!is.na(yvar), !is.na(xvar)) %>%
left_join(covid_top %>% select(name,rank),by="name")
### plotly
if ("log(y)" %in% input$plotoptions) {
covid_plot_data <- covid_plot_data %>% mutate(yvar = ifelse(yvar==0,NA,yvar))
}
plot1 <- plotly::plot_ly(type='scatter',mode='lines+markers')
for (i in 1:nrow(covid_top)) {
plot_data_df <- covid_plot_data %>% filter(name==covid_top$name[i])
plot1 <- plot1 %>%
plotly::add_trace(data=plot_data_df,
x=~xvar,y=~yvar,name=~rank,
text=~paste0('<b>',date,'</b>',
'<br>',name,' (',abbrev,')',
'<br>',formnumber(cases,big.mark = ","),' (+',formnumber(cases_daily,big.mark = ","),') cases',
'<br>',formnumber(deaths,big.mark = ","),' (+',formnumber(deaths_daily,big.mark = ","),') deaths'),
hoverinfo='text')
}
avg_7_note <- ifelse("7-day avg" %in% input$plotoptions,", 7-day avg","")
x_list <- list(title = x_axis_label)
y_list <- list(title = paste0(input$yaxis_val," (",input$yaxis_type,avg_7_note,")"))
if ("log(y)" %in% input$plotoptions) {
y_list <- list(title = paste0(input$yaxis_val," (log ",input$yaxis_type,avg_7_note,")"),type="log")
}
plot1 <- plot1 %>% plotly::layout(yaxis = y_list, xaxis = x_list) %>%
plotly::layout(legend = list(orientation = 'h',y = 1,yanchor="bottom"))
###
# plot <- ggplot2::ggplot(covid_plot_data,ggplot2::aes(xvar,yvar,color=rank)) +
# ggplot2::geom_line() + ggplot2::geom_point() +
# ggplot2::labs(y=input$yaxis,x=input$xaxis) +
# ggplot2::`%+replace%`(ggplot2::theme_bw(),ggplot2::theme(legend.title = ggplot2::element_blank()))
#
# if (input$logy) {
# plot <- plot + ggplot2::scale_y_log10()
# }
# plotly::ggplotly(plot) %>%
# plotly::layout(legend = list(orientation = 'h',
# y = 1,
# yanchor="bottom"))
plot1
} else {
# p_empty <- ggplot2::ggplot(data.frame(x=1,y=1,label="Loading...")) +
# ggplot2::geom_text(ggplot2::aes(x,y,label=label))
# plotly::ggplotly(p_empty)
plot_null <- NULL
plot_null
}
})
output$maintab_title <- renderText({
scale_text <- dplyr::case_when(
input$maintab == "us"~"United States",
input$maintab == "world"~"World"
)
paste("COVID19:",scale_text)
})
output$tableheader <- renderText({
covid_tot <- covid_totals()
last_update <- covid_tot$last_date %>% max() %>% strftime("%b %d, %Y")
if (input$maintab=="us") {
# data_source <- "the NY Times"
data_source <- "JHU CSSE"
} else if (input$maintab=="world") {
data_source <- "JHU CSSE"
}
tableheader <- paste0("Latest data from ",data_source," (",last_update,")")
tableheader
})
})
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