if (!file.exists("zikaDat.rds")) {
  rmarkdown::render("01-clean-combine.Rmd")
}
zika <- readRDS("zikaDat.rds")
if (!file.exists("latLonDat.rds")) {
  source("geolocate.R")
}
latLonDat <- readRDS("latLonDat.rds")

Map

library(leaflet)
leaflet(latLonDat) %>% addTiles() %>% addCircleMarkers(
    lng = ~lng, lat = ~lat, label = ~location,
    clusterOptions = markerClusterOptions()
)
library(dplyr)
library(plotly)
library(crosstalk)

# ggplot2 version
ggplot_values <- function(cntry = "United_States", type = "state") {
  d <- zika %>%
    filter(country %in% cntry) %>%
    filter(location_type %in% type) %>%
    SharedData$new(~location)
  p <- ggplot(d, aes(report_date, value, color = data_field, text = location)) +
    geom_line(alpha = 0.5) +
    scale_x_date(date_breaks = "1 month", date_labels = "%B") +
    facet_wrap(~location_type, ncol = 1, scales = "free_y") +
    labs(x = NULL, y = "Number of Cases Reported")
  highlight(ggplotly(p, crosstalkOpts = o), "plotly_hover", "plotly_doubleclick")
}
ggplot_values(type = c("state", "territory"))

plot_values <- function(cntry = "United_States", type = "state") {
  d <- zika %>%
    filter(country %in% cntry) %>%
    filter(location_type %in% type)
  dats <- split(d, d$location_type)
  plots <- lapply(dats, function(x) {
    SharedData$new(x, ~location) %>%
      plot_ly(x = ~report_date, y = ~value, text = ~location) %>%
      add_lines(color = ~data_field, alpha = 0.3) %>%
      layout(
        title = paste0("Location type: ", unique(x$location_type)),
        xaxis = list(title = ""),
        yaxis = list(title = "")
      )
  })
  subplot(plots, nrows = length(plots), shareX = TRUE) %>%
    highlight("plotly_hover", "plotly_doubleclick")
}
plot_values(type = c("state", "territory"))
plot_values("Brazil", "state")

latLonDat %>%
  filter(location %in% unique(zika$country))

d <- fuzzyjoin::stringdist_left_join(zika, latLonDat, by = "location")

us <- zika %>%
  filter(country == "United_States") %>%
  filter(location_type != "county")

plot_ly(us, x = ~report_date, y = ~value) %>%
  group_by(location) %>%
  add_lines(color = ~data_field, alpha = 0.3)


# TODO:
# (1) automatically add crosstalk key to hoverinfo






#p <- ggplot(zika, aes(value, color = country)) +
#  facet_wrap()
#  geom_boxplot() + coord_flip()


cpsievert/zikar documentation built on Aug. 13, 2017, 7:38 a.m.