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Mittwoch, 19. November 2014

Joint effort needed for biodiversity

Open data and open source software may be a guide for such an joint effort. Let's have a look on the data side at ressources of EEA, GBIF and Natural Earth, on the software side at QGIS and R.

GBIF facilitates free and open access to biodiversity data, e.g. species distribution data. This kind of data can be accessed and processed by R and its packages dismo, sp, rgdal and maptools.

# load libraries
# download species distribution data as spatial points data frame, e.g. Myricaria germanica
myrger <- gbif("Myricaria", "germanica", geo = TRUE, sp = TRUE, removeZeros = TRUE)

# visualize data for a quick check
plot(wrld_simpl, col = "light yellow", axes = T)
points(myrger$lon, myrger$lat, col = "red", cex = 0.5)
text(-140, -50, "Myricaria\ngermanica")
GBIF species distribution data of Myricaria germanica (accessed: 2014-11-18)
# define projection of the spatial data
proj4string(myrger) <- "+proj=longlat +datum=WGS84"

# export to shape file to use it in QGIS
writeOGR(myrger3, dsn = ".", driver= "ESRI Shapefile", layer = "gbif_mg_ll")
Natural Earth has a nice compilation of cultural, physical and raster GIS data; in this example the boundaries of countries are used. The European Environment Agency (EEA) delivers data of the biogeographical regions and the article 17 report GIS data on the conservation status of habitat types and species for the reporting period 2001-2006 required by the Habitat directive. The European Topic Centre on Biological Diversity supplies data of the article 17 report for the period 2007-2012.

Let's collect all the GIS data for e.g. habitat type "3230 Alpine rivers and their ligneous vegetation with Myricaria germanica" and load the data into QGIS. Data for France and Slovenia of the reporting period 2007-2012 isn't available yet.

Data: countries - Natural Earth; biogeographical regions and article 17 period 2001-2006 - EEA;
article 17 period 2007-2012 - European Topic Centre on Biodiversity
And zoom into several European mountain regions:


Scandinavian mountains

Scandinavian mountains quite in the North
A closer look to Austria


and a recent article about the actual and historic distribution of Myricaria germanica in Austria (Stapfia 99; see also here)

taken from Kudrnovsky & Stöhr, 2013. Myricaria germanica (L.) Desv. historisch und aktuell in Österreich: ein dramatischer Rückgang einer Indikatorart von europäischem Interesse. STAPFIA 99 (2013): 13–34.
As differences in the state of knowledge and differences in important datasets like GBIF and article 17 report are getting obvious, a joint effort of knowlegde transfer and boosted data exchange may be needed to achieve the targets of the EU Biodiversity Strategy to 2020.

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