animation.R

library(tidyverse)
library(gganimate)
library(ggmap)
library(viridis)
library(lubridate)

# We need three things: The data to plot, the map and the location of the samples

# For me,  the data looked like a long table with five columns: Site, Date, Species, prevalence and abundance

data.to.plot <- tibble (Site = rep(c("LK", "FH", "CP", "SA", "TR"), each = 10),
                        Date = ymd(rep(c("20171001", "20171101","20171201","20180101","20180201", "20180301","20180401","20180501","20180601","20180701"), 5)),
                        Species = rep("Species A", 50),
                        prevalence = abs(rnorm(50, mean = 0.5, sd = 0.25)),
                        abundance = abs(rnorm(50, mean = 2000, sd = 5000)))
                        
# The location of the samples

loc <- tibble (Site = c("LK", "FH", "CP", "SA", "TR"),
               lat = c(48.51450, 48.54509, 48.44983, 47.85677, 47.60896),
               lon = c(-123.1510, -123.0120, -122.9632, -122.6077, -122.9847))

# Getting the map - you need to get a Google maps API key, and paste it on the get_map call

map.for.samples <- get_map(location = c(-125,47,-122,49),
                        maptype = "terrain",
                        source = "google",
                        api_key = "YOUR_KEY_HERE")
                        
# Prepare data for plotting

data.to.plot %>% 
   left_join(loc) %>%
   rownames_to_column(var = "grouping") -> to.plot    # Mock variable to make each observation its own point, and the bubles won't move around the map
   
# the base plot

ggmap(map.for.samples) +
  geom_point(data = to.plot, aes(x = lon, y = lat, size = prevalence , color = abundance, group = grouping)) +
  scale_size(range = c(2,10)) +
  scale_color_viridis()-> p
  
  
# The animation #####

p +
    facet_wrap(~Species) + # In theory won't need this as there is only one species
    labs(title = 'Date: {closest_state}') +
  transition_states(fct_reorder(paste(month(Date,label = T), year(Date), sep = "'"),Date), # I wanted the label to look prettier
                    transition_length = 2,
                    state_length = 1) +
    enter_fade()+
    exit_shrink() -> anim
    
 # Saving the animation
 
  anim_save(filename = "animated.map.gif",
            animation = anim)