Bee Colony losses

library(tidyverse)

colony <- readr::read_csv('https://raw.githubusercontent.com/rfordatascience/tidytuesday/master/data/2022/2022-01-11/colony.csv')
stressor <- readr::read_csv('https://raw.githubusercontent.com/rfordatascience/tidytuesday/master/data/2022/2022-01-11/stressor.csv')

df <- colony %>%
  full_join(stressor,by=c("year","months","state"))

df<-df%>%filter(!is.na(colony_n))

map <- ggplot2::map_data("state")
map

library(maps)
data(state.fips)
abb<-state.fips%>%select(polyname,abb)

map <-map%>%left_join(abb,by=c("region"="polyname"))%>%
  mutate(abb=case_when(region=="massachusetts"~"MA",
                       region=="michigan"~"MI",
                       region=="new york"~"NY",
                       region=="north carolina"~"NC",
                       region=="virginia"~"VA",
                       region=="washington"~"WA",
                       TRUE ~ abb))

library(extrafont)
library(showtext)
showtext::showtext_auto()
showtext::showtext_opts(dpi=320)
library(sysfonts)
font_families_google()
font_add_google(name="Baskervville",family="bees1")


#font_add_google(name ="Black Han Sans" ,family = "my_font")
#font_add_google(name ="Odibee Sans" ,family = "my_font1")

family = "bees1"

tidy_df <- df%>% 
  count(state,year,colony_lost_pct,stressor,stress_pct)%>%
  filter(year==c(2015,2020))%>%
  mutate(state=tolower(state))%>%
  filter(!state%in%c("hawaii","other states","united states"))%>%
  filter(!is.na(stress_pct))%>%
  select(-n) %>% # 
  pivot_wider(names_from = year,values_from=stress_pct,
              values_fill = 0.00001, values_fn={mean}) %>%
  mutate(stress_pct_diff=round(((`2020`/`2015`) *100)-100))
  
tidy_df_geo <- tidy_df%>% left_join(map,by=c("state"="region"))

bees_map_df <- tidy_df_geo%>%
  group_by(state)%>%
  mutate(lat2=median(range(lat)),
         long2=median(range(long)))%>% # this is to positioning the numbers 
  ungroup()%>%
  count(state,abb,long2,lat2,group,stress_pct_diff)%>%
  group_by(state) %>%
  mutate(m_stress_pct_diff=round(mean(stress_pct_diff)/10000000,2))%>%
  ungroup()
 
bees_map <-ggplot()+
  geom_polygon(data=tidy_df_geo,
               mapping=aes(x=long, y=lat, group = group),
               alpha=0.2,fill="gold",show.legend = F)+
    
  stat_summary_hex(data=tidy_df_geo,aes(x=long,y=lat,z=group),
                   fill="orange",color="gold") +
  geom_point(data=bees_map_df,mapping = aes(x=long2, y=lat2, group = group,
                           size=m_stress_pct_diff),
             shape=21,stroke=0.1,color="#299E50") +
  geom_text(data=bees_map_df,
            mapping = aes(x=long2, y=lat2, group = group,
                           label=abb),size=3,color="grey25") +
  scale_size_identity(guide="legend")+
  guides(size = guide_legend(override.aes = list(color = "grey25",stroke=1)))+
  labs(title="US Bees colony lost and stressor",
       subtitle="(%) difference 2015 - 2020",
       size="AVG Stressor (%)") +
  ggthemes::theme_map()+
  theme(text = element_text(family=family,face="bold"),
        legend.background = element_blank(),
        legend.box.background = element_blank(),
        legend.position = c(0.1,-0.15),
        legend.key = element_rect(fill="orange",color="gold",size=2),
        legend.text = element_blank(),
        plot.background = element_blank(),
        plot.title = element_text(size=25,face="bold"),
        plot.subtitle =  element_text(size=15),
        panel.background = element_blank())

# bees_map

library(ggimage)

bees_fly <-df%>%
  filter(year%in%c(2015,2020))%>%
  select(state,stressor,stress_pct,colony_lost,year) %>% 
  mutate(stress_pct=ifelse(is.na(stress_pct),0,stress_pct)) %>% 
  #group_by(state)%>%summarize(mean=mean(stress_pct))
  pivot_wider(names_from = year,values_from=colony_lost,
              values_fn={mean},values_fill=0) %>%
  mutate(diff_colony_lost=round(`2020`-`2015`)) %>%
  #select(-`2015`,-`2020`)%>%
  mutate(stressor=case_when(stressor=="Other pests/parasites"~"Other",
                            stressor=="Unknown"~"Other",
                            TRUE~stressor)) %>%
  group_by(stressor) %>%
  mutate(m_colony_lost=mean(diff_colony_lost))%>%
  ungroup()%>%
  #mutate(img = "<img src='w2_bees/bees.png' width='12'/>") %>%
  mutate(img = "bees.png",
         img=as.factor(img)) %>%as.data.frame()


pct_decr_lost<- bees_fly %>%
  count(stressor,m_colony_lost=round(m_colony_lost))%>%
  mutate(tot_loss=round(m_colony_lost*n),
         pct=paste0(round(tot_loss/sum(tot_loss)*100),"%"))


range(bees_fly$m_colony_lost)


bees_fly_plot<-bees_fly%>%
  left_join(select(pct_decr_lost,stressor,pct),by="stressor")%>%
  ggplot(aes(x=fct_reorder(stressor,m_colony_lost),y=m_colony_lost))+
  geom_line(orientation = "x",aes(group=1))+
  ggimage::geom_image(aes(image=img), size=.1) +
  geom_vline(aes(xintercept=fct_reorder(stressor,-m_colony_lost)),alpha=0.2,color="gold")+
  geom_text(aes(label=stressor),vjust=-2.5,hjust=0.65)+
  geom_text(aes(label=pct),vjust=2.5)+
  expand_limits(x=0,y=c(-1300 , -900))+
  scale_y_reverse()+ #limits=rev)+
  scale_x_discrete(limits=rev)+ #limits=rev)+
  labs(caption="Datasource: USDA | DataViz: Federica Gazzelloni")+
  theme_void()+
  theme(text = element_text(family=family,face="bold"),
        plot.caption=element_text(size=11,face="bold"))


# bees_fly_plot

library(cowplot)

final <- ggdraw()+
  draw_plot(bees_fly_plot,scale = 0.6,x=0.19,y=-0.13)+
  draw_plot(bees_map,scale = 0.8,x=-0.1,y=0.1)+
  draw_image("https://d3l4q0oih2c6yv.cloudfront.net/assets/esmis/cornell_seal_simple_b31b1b-54caf4668562db6b35fe259a44a4f9dc5db28a966230652ae2b175edcb9d56f0.svg",
             scale=0.1,x=0.45,y=0.43)+
  draw_image("usda_logo.png",
             scale = 0.1, x=0.35,y=0.43)+
  draw_image("bee_informed.png",scale = 0.09,x=-0.37,y=-0.315)+
  draw_image("bee_informed.png",scale = 0.055,x=-0.37,y=-0.12)+
  draw_label("The Stressors are the causes for bees colony loss\n the (%) difference 2015-2020 shows some states are more affected then othes by\n stressors.",
             x=0.38,y=0.07,fontfamily = family,size=11)+
  draw_label("Low",x=0.2,y=0.3,fontfamily = family)+
  draw_label("High",x=0.2,y=0.2,fontfamily = family)+
  draw_label("Includes unknwon and parasites",x=0.77,y=0.5,
             fontfamily = family,size=11)+
  draw_line(x=c(0.78,0.8),y=c(0.44,0.49),color="orange")+
  draw_label("Percentange of the stressor affecting the colonies",x=0.8,y=0.2,fontfamily = family,size=10)+
  draw_line(x=c(0.8,0.78),y=c(0.21,0.31),color="orange")+
  draw_label("The least contributing to bees loss",x=0.85,y=0.66,
             size=11,fontfamily = family)+
  draw_line(x=c(0.89,0.9),y=c(0.56,0.65),color="orange")+
  draw_label("Leading parasite affecting \nbees colony\n named Varroa destructor",x=0.38,y=0.2,size=11,fontfamily = family)+
  draw_line(x=c(0.42,0.5),y=c(0.18,0.2),color="orange")+
  draw_image("bee_flying.png",scale = 0.55,x=0.2,y=0.3)
    
    
#final

ggsave(
  paste0("bees_", format(Sys.time(), "%d%m%Y"), ".png"),
   plot =final,
  bg="white",
  dpi = 320,
  width = 11,
  height = 6
)