OBJECTIVE
To animate occurrences of threatened antarctic/subantarctic species in year 2003 by month.
LOAD LIBRARIES
ImageMagick is required in order to use gganimate convert().
library(jsonlite)
library(maps)
library(mapproj)
library(robis)
library(dplyr)
library(ggplot2)
library(RColorBrewer)
library(gganimate) # require ImageMagick
REQUEST USING IUCN REDLIST API
Note: You will need a token from IUCN redlist to do this.
Request for all IUCN redlist species with country code = AQ (antarctica)
request <- paste("http://apiv3.iucnredlist.org/api/v3/country/getspecies/AQ?token=", token, sep = "")
rl <- fromJSON(request)
rl <- rl$result
Subset data frame to entries with vulnerable, critical and endangered species only.
# filter for results with categories == vulnerable, critical and endangered (threatened)
not.lc.dd <- rl %>% filter(category %in% c("CR", "EN", "VU"))
unique(not.lc.dd$category)
## [1] "VU" "CR" "EN"
REQUEST FOR OCCURRENCES USING ROBIS
Request for all occurrence records of these threatened species within antarctic and subantarctic zone from OBIS.
# get the occurrence of these threatened species from OBIS using API
# polygon include antarctic and subantarctic area
occ <- occurrence(scientificname = not.lc.dd$scientific_name, geometry = "POLYGON((180 -90, -180 -90, -180 -45, 180 -45, 180 -90))")
# convert eventDate from string to date time format
occ$eventDate <- as.POSIXct(strptime(occ$eventDate, format = "%Y-%m-%d %H:%M:%S", tz = "GMT"))
occ$month <- as.numeric(format(occ$eventDate, "%m"))
occ$year <- as.numeric(format(occ$eventDate, "%Y"))
obs <- occ %>% filter(year == 2003)
# remove preservedSpecimen occurrences
obs <- occ %>% filter(basisOfRecord != "PreservedSpecimen")
PLOT ORTHOGRAPHIC PROJECTED MAP AND ANIMATE WITH GGANIMATE
Plot map with orthographic projection from South Pole and add a layer of occurrences, color by genus.
Animate the plots and create a gif file called occ_by_month.gif
# plot map with orthographic projection from South Pole
world <- map_data("world")
head(world)
## long lat group order region subregion
## 1 -69.89912 12.45200 1 1 Aruba
## 2 -69.89571 12.42300 1 2 Aruba
## 3 -69.94219 12.43853 1 3 Aruba
## 4 -70.00415 12.50049 1 4 Aruba
## 5 -70.06612 12.54697 1 5 Aruba
## 6 -70.05088 12.59707 1 6 Aruba
p <- ggplot() +
geom_path(data = world, aes(x = long, y = lat, group = group), colour = "#707070") +
scale_y_continuous(name = "latitude", breaks = (-2:2) * 30) +
scale_x_continuous(name = "longitude", breaks = (-4:4) * 45) +
coord_map("ortho", orientation = c(-90, 0, 0)) +
geom_point(data = obs, aes(x = decimalLongitude, y = decimalLatitude, color = genus, frame = month), size = 1, alpha = 0.5) +
scale_color_brewer(palette = "Dark2")
# animate it
animation <- gganimate(p, interval=.5, "occ_by_month.gif")
animation
Animate occurrence data for year 2003 using gif. Top left corner shows month.
REMARKS
Please note that this exercise is not based on science. For instance, there are a lot more occurrence records from November to March, maybe because there are more people at field in Antarctica during that period. I am assuming that all occurrences here means presence. Not observing an occurrence do not means its absence either.
That’s it for now!
Written by Yi Ming Gan