Happy Polar Week!

It’s polar week right now! Check out some of the amazing activities put together by APECS:

And much more all around the world…



Twelve positions in polar climate research available in Belgium

Not one, but twelve (!) positions including PhD student, post doc, and computer scientist become available at universities throughout Belgium (UCL, ULB, KU Leuven, VUB, ULiege).

Find all details here.

[Free entrance] Belgium and Antarctica… Researchers’ views

Archives Antarctiques Belges – Belgische Antarctische Archieven (AABBAA – asbl) and APECS Belgium are proud to present a conference evening where researchers share their findings and experiences in Antarctica!

Belgium and Antarctica… Researchers’ views
21 March 2018 (Wednesday)
Campus Solbosch, ULB Building D Local DC2.223
Open to public and FREE of charge!

AABBAA is a non-profit organization which gathers archives on Belgian Antarctic expeditions. Please join us for this great initiative!

Screen Shot 2018-03-10 at 10.58.21 AM

[R]Animate time-series occurrence data


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(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"))
## [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")
##        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")
Animate occurrence data for year 2003 using gif. Top left corner shows month.


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!




[D-3] Belgica120!

3 more days for the crew to begin their journey to Antarctica Peninsula through Argentina!! Excited about this low-emission expedition? Remember to bookmark and checkout their blog!!

We wish the crew all the best for the expedition! May the weather be kind to you and have a fruitful journey! \o/