Animation (gganimate) and interactive leaflet map of Japanese stiltgrass invasion history in R

Craig F. Barrett
April 07, 2021
Department of Biology
West Virginia University
Morgantown, WV USA 26506
cfb0001@mail.wvu.edu

# install packages if needed
# install.packages(c("rgbif", "knitr", "ggplot2", "tidyverse", "gganimate", "ggthemes", "sf", "tools", "maps", "rnaturalearth", "rnaturalearthdata"))

# load libraries
library(shiny)
library(ggplot2)
library(tidyverse)
library(gganimate)
library(ggthemes)
library(sf)
library("tools")
library(maps)
library("rnaturalearth")
library("rnaturalearthdata")
library(knitr)

#read in data, convert to data.frame, set "awn" as a factor
setwd(choose.dir())
awn <- read.csv("awndatanew.csv")
awn <- data.frame(awn)

# remove duplicate records based on latitude
awn <- awn %>% distinct(decimalLatitude, .keep_all = TRUE)
awns <- as.factor(awn$awn)
awn <- data.frame(awn)

world <- ne_countries(scale = "medium", returnclass = "sf")
## class(world)
states <- st_as_sf(map("state", plot = FALSE, fill = TRUE))
## head(states)
states <- cbind(states, st_coordinates(st_centroid(states)))

#Generate the map and coordinate boundaries
usa <- ggplot(data = world) +
    #mutate(year = as.numeric(awn$year)) + 
    geom_sf(data = states, fill = NA) + 
    coord_sf(xlim = c(-96, -70), ylim = c(28, 45), expand = FALSE)

# map the occurrence data
JSmap <- usa +
  geom_point(data = awn, shape = 21, colour="black", aes(x=decimalLongitude, y=decimalLatitude, fill=awns), size=6, stroke=1) +
  #transition_states(year, transition_length = 1, state_length = 1) + 
  scale_fill_manual(values=c("red", "blue")) +
  transition_time(year) +
  labs(title = 'Digitized herbarium records of Microstegium vimineum', subtitle = 'Year: {round(frame_time,0)}') +
  shadow_mark()

#animate!
JSmap

#save animation as a .gif
  anim_save("Js_awn_map_red_blue.gif", JSmap)
include_graphics("Js_awn_map_red_blue.gif")

Animation