29

library(geojsonio)

## 
## Attaching package: 'geojsonio'

## The following object is masked from 'package:base':
## 
##     pretty

library(leaflet)
library(leaflet.extras)

# you gave me a spreadsheet
library(readxl)
coronavirus_19 <- read_excel("~/Downloads/coronavirus 19th May.xlsx", 
                             col_types = c("text", "numeric"))

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B5 / R5C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B9 / R9C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B19 / R19C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B30 / R30C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B32 / R32C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B48 / R48C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B49 / R49C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B70 / R70C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B71 / R71C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B72 / R72C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B78 / R78C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B81 / R81C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B86 / R86C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B91 / R91C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B93 / R93C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B98 / R98C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B100 / R100C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B112 / R112C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B114 / R114C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B115 / R115C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B116 / R116C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B118 / R118C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B121 / R121C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B133 / R133C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B141 / R141C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B142 / R142C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B148 / R148C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B158 / R158C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B161 / R161C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B167 / R167C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B168 / R168C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B169 / R169C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B170 / R170C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B173 / R173C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : Expecting numeric in B175 / R175C2: got '9867
## '

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B177 / R177C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B181 / R181C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B184 / R184C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B186 / R186C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B200 / R200C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B203 / R203C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B206 / R206C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B208 / R208C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B215 / R215C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B216 / R216C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, : Expecting numeric in B218 / R218C2: got '30618
## '

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B225 / R225C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B226 / R226C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B230 / R230C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B231 / R231C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B232 / R232C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B240 / R240C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B244 / R244C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B245 / R245C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B248 / R248C2: got 'NA'

## Warning in read_fun(path = enc2native(normalizePath(path)), sheet_i = sheet, :
## Expecting numeric in B250 / R250C2: got 'NA'

# import the geojson as sp (spacial format - allows us to work with leaflet)
world_map <- geojson_read("https://opendata.arcgis.com/datasets/a21fdb46d23e4ef896f31475217cbb08_1.geojson", what = "sp")

# tigris has the handy geo_join
library(tigris)

## To enable 
## caching of data, set `options(tigris_use_cache = TRUE)` in your R script or .Rprofile.

## 
## Attaching package: 'tigris'

## The following object is masked from 'package:graphics':
## 
##     plot

library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

# join our datasets - tell it the two files and then the two columns to join by
world_data <- geo_join(world_map, coronavirus_19, "CNTRY_NAME", "map_names")

#test a simple map to see if our shapes work
leaflet(world_data) %>%
  addTiles() %>%
  addPolygons()

# use old-school R (base R) to get rid of the NAs (subset to give us anything not an NA)
world_data <- subset(world_data, !is.na(total.cases))

# testing a text popup
hovertext <- paste0("Total cases: ", as.character(world_data$total.cases), " in ",as.character(world_data$CNTRY_NAME))
# set the colour palette - google this you can do so much better
pal <- colorNumeric("Reds", domain = world_data$total.cases)
# test our map to see if it works
wolrdcase <-leaflet(options = leafletOptions(minZoom = 2,maxZoom = 4,dragging = TRUE)) %>%
            addTiles() %>%  clearBounds() %>%
            addPolygons(data = world_data, fillColor = ~pal(world_data$total.cases), 
               fillOpacity = 0.8, 
               weight = 0.3, 
               smoothFactor = 0.2, 
               label = ~hovertext) %>% addSearchOSM()
       
   
wolrdcase %>% addLegend(pal = pal,
          opacity = 0.75,values = c(10000:300000),
          title = "Total Cases",
          position = "topleft") 

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