LYME DISEASE INCIDENCE IN MICHIGAN

LYMEDMI

library(ggplot2) 
library(dplyr) 
library(viridis) 
library(reshape2)
library(gganimate)
library(animation)
library(maps)
devtools::install_github("dgrtwo/gganimate")

###LYME DISEASE CASES- DATA 
#stringsasFactors = False, I'm telling R to treat the county names as strings not
#a categorical variable
main.dat <- read.csv("lyme_county_0015.csv",stringsAsFactors = FALSE)
head(main.dat)
#I only want Michigan so I only subset and I get rid of the last row because
#that is not related
MI.main.dat <- subset(main.dat, STNAME=="Michigan")
MI.main.dat <- MI.main.dat[-nrow(MI.main.dat),]

#I want to rename the CTYNAME to county 
colnames(MI.main.dat)[2] <- 'county'

unique(MI.main.dat$county)

###SPATIAL MAP DATA
map <- map_data("county", "michigan") 
#I want to rename the subregion to county
colnames(map)[6] <- 'county'
unique(map$county) 


###Eyeballing- I just check to make sure that the counties are the same 
#between the columns so I can use the county column from the spatial map dataframe
#to replace the tick data's county column
cbind(MI.main.dat$county, unique(map$county))


###Replacement

MI.main.dat$county <- unique(map$county)

###Merged dataframe
tick.dat.map <- left_join(map,MI.main.dat, by= c('county'))

###RESHAPING OUR DATA
tick.dat.map_sub<- tick.dat.map[,c(1,2,3,6,10:25)]
colnames(tick.dat.map_sub)[5:20]<- (seq(2000,2015,1))
tick_melt<-melt(tick.dat.map_sub, id = c('long','lat','group','county'))



###PLOTTING
ggplot(tick_melt, aes(x = long, y= lat, group=group))+ 
  geom_polygon(aes(fill = value),color='black')+
  facet_wrap(~variable)+coord_map()+ 
  scale_fill_viridis(option='plasma')+
  theme_void()


###RUN THIS IF PROBLEMS OCCUR
#magickPath <- shortPathName("C:\\Program Files\\ImageMagick-7.0.5-Q16\\magick.exe")
#ani.options(convert=magickPath)


p<- ggplot(tick_melt, aes(x = long, y= lat, group=group,frame = variable))+ geom_polygon(aes(fill = value),color='black')+
  coord_map()+ scale_fill_viridis()+theme_void()

gganimate(p, "output.gif")