Blue bird map

library(tidyverse)
library(extrafont)
library(sf)

ebird<-read_csv("ebird_GA_Sep2019.csv") #Individual observation data

species<-ebird %>%
  distinct(`COMMON NAME`)
species_blue<-species %>%
  filter(str_detect(tolower(`COMMON NAME`),"blue"))

common_blue<-ebird %>%
  filter(`COMMON NAME` %in% species_blue$`COMMON NAME`) %>%
  count(`COMMON NAME`) %>%
  filter(n>15000)

ebird_map<-ebird %>%
  filter(`COMMON NAME` %in% common_blue$`COMMON NAME`) %>%
  st_as_sf(coords=c("LONGITUDE","LATITUDE"),crs=4326,remove=FALSE)

#Binned map
ga<-st_read("data/US_county_2012_Georgia.shp") %>% #County shapefile
  distinct() %>%
  st_transform(2240) %>%
  summarise() 

library(tmap)
tm_shape(ga) + tm_polygons()

hex<-st_make_grid(ga,cellsize=30000,square=FALSE) %>%
  st_intersection(ga) %>%
  st_sf() %>%
  mutate(hexrow=row_number())

tm_shape(hex) + tm_polygons()

bluehex<-ebird_map %>%
  st_transform(2240) %>%
  st_join(hex,join=st_within) %>%
  rename(Bird=`COMMON NAME`) %>%
  count(Bird,hexrow,name="count")

hex_count<-hex %>%
  left_join(bluehex %>% 
              st_set_geometry(NULL) %>%
              filter(is.na(Bird)==FALSE)) %>%
  group_by(Bird) %>%
  mutate(total=sum(count)) %>%
  ungroup() %>%
  mutate(title=paste(Bird," (",
                     formatC(total, format="d", big.mark=","),
                     ")",sep="")) %>%
  filter(is.na(Bird)==FALSE) %>%
  arrange(-total)
          
bluemap<-tm_shape(ga) +
  tm_polygons(fill="grey") +
tm_shape(hex_count) +
  tm_polygons("count",style="quantile",palette="Blues",
              border.alpha=0.1) +
  tm_facets(by="title",free.scales.fill=TRUE,free.coords=FALSE,
            nrow=2)+
  tm_legend(show=FALSE)+
  tm_layout(main.title = "Where to see blue birds in Georgia, based on eBird", main.title.position = "left",
            attr.outside=TRUE,panel.label.size = 1.1)+
  tm_credits("Data: eBird | Tool: R (sf, tmap) | Map by @jerry_shannon", 
             position = c("left", "BOTTOM"),size=1)

bluemap

tmap_save(bluemap,"bluebirds.pdf",width=11,height=6)