New release RQGIS

From an announcement from the QGIS mailing list: RQGIS has released a new version of RQGIS! RQGIS establishes an interface between R and QGIS, i.e. it allows the user to access the QGIS geoalgorithms from within R. With the new release, it is possible to run the most recent QGIS releases (>=2.18.2) with RQGIS.

RQGIS establishes an interface between R and QGIS, i.e. it allows the user to access QGIS functionalities from within R. It thus serves a similar goal as rgrass7 which provides an interface between R and GRASS GIS and rsaga, which provides access to geocomputing and terrain analysis functions of SAGA GIS from within R.

RQGIS provides access to all functions available through QGIS’s processing framework, which includes among others GRASS GIS and SAGA GIS (others are GDAL, the Orfeo Toolbox, TauDEM and tools for LiDAR data). Thus, RQGIS RQGIS offers an (partial) replacement of rgrass7 and rsaga packages. However, note that the latter two packages offer various other advantages.

I personally find rgrass7 and rsaga great tools that allow easy access to respectively GRASS and SAGA. I have less experience with RQGIS, but I can already tell that what I particularly like about RQGIS is that it makes it easier to combined different tools in an unified interface (which is of course the same reason I like the processing toolbox in QGIS). Take for example the find_algorithms function. This allows you to search for algorithms across all available toolboxes using keywords, similar to the search box in the processing toolbox in QGIS itself. I will certainly explore this package more!

You can find more information on the github page, including installation instructions and some use examples. See also the blog post of one of the RQGIS authors.







Use R to get gbif data into a GRASS database



The Global Biodiversity Information Facility (GBIF) is an international open data infrastructure that allows anyone, anywhere to access data about all types of life on Earth, shared across national boundaries via the Internet. GBIF provides a single point of access through to species records shared freely by hundreds of institutions worldwide. The data accessible through GBIF relate to evidence about more than 1.6 million species, collected over three centuries of natural history exploration and including current observations from citizen scientists, researchers and automated monitoring programs.

There are various ways to import GBIF data, including directly from the website as comma delimited file (csv) and using the addon for GRASS (I’ll post an example using this addon at a later stage). Here, however, I’ll use the rgbif package for R to obtain the data. In the link section some tutorials are listed that illustrate the use of other R packages. Continue reading “Use R to get gbif data into a GRASS database”

Importing GLCF MODIS woody plant cover

The data set

The Global Land Cover Facility offers, amongst many other data sets, the MODIS Vegetation Continuous Fields data set for download. These are layers that contain proportional estimates for vegetative cover types (woody vegetation, herbaceous vegetation, and bare ground). As such they are very suitable depict areas of heterogeneous land cover.

Their MODIS products differ from DAAC editions by coming in GeoTIFF format, geographic coordinates, WGS84 datum, and a tiling system designed to fit well with Landsat imagery. Currently the collection 5 is available, which contains proportional estimates for woody cover vegetation for the years 2000 to 2010. It can be downloaded as tiles (195 in total) via a ftp server.

Below I’ll provide an example Continue reading “Importing GLCF MODIS woody plant cover”

Access R from GRASS GIS on Windows

Since I have switch from Windows to Linux, many years ago, things have started to look a lot brighter for those wanting to use GRASS on Windows. I won’t switch back to Windows any time soon, but I recently had to install WinGRASS for somebody else. And it was a whole lot easier than I had feared (or even hoped).

But there is one thing I couldn’t immediately figure out; how to run R from within GRASS. I should add that I installed GRASS using the OSGEO4W installer. When installing GRASS using the stand alone installer, access to R from the GRASS command line should work out-of-the-box (see comment from Helmut in the comment section below).

After a bit of trial and error, I came up with the steps below. It involves editing a file to tell GRASS where to look for executables. In the example below I am adding the path to the R and rstudio executables to this file. Having done that, I can now type R.exe or rstudio.exe on the GRASS command line to open these programs. Continue reading “Access R from GRASS GIS on Windows”

A new search engine to search the R documentation

Just to quickly share this great new website where you can search the documentation of all R packages and functions available on CRAN (6688 R packages and 136342 R functions at the moment of writing!). It offers instant or advanced search options in an easy interface, and there is even a package that allows you to use the search functionality from within R. Check it out on

A new method and tool (ExDet) to evaluate novelty environmental conditions

A common objective of correlative species distribution model is to be able to project the potential distribution of the target species into a new environmental space. This can be a new geographic space (e.g., invasive species) or projected future conditions.

One should be very careful in interpreting results if extrapolating to areas with conditions that fall outside the range of reference environmental variation. There are several methods to visualize this uncertainty. On this blog I have for example mentioned the multi-environmental similarity tool in Maxent (also implemented in R in amongst others the dismo package and as an addon for GRASS GIS), which allows you to create maps that provides the similarity of each point to a set of reference points (Elith et al. 2010) and thus provide a quick overview of areas with ‘novel’ conditions.

A disadvantage of this and other methods is that they only consider the ranges of the individual predictors, and ignore the correlation structure of the covariates used to build the model. In reality, it is not unlikely that at a given locations values of each univariate factor fall within the original range of values, but the combination of environmental conditions is new. Continue reading “A new method and tool (ExDet) to evaluate novelty environmental conditions”

Import GRASS function console output as data.frame in R

In R you can use system calls or the spgrass6 package to run GRASS GIS functions. To do this, you need to run R from within GRASS GIS. This is as simple as starting GRASS GIS and subsequently starting R from the command line. See the GRASS-wiki for a more detailed background.

The issue at hand
One of the user-cases is when you want to (1) run a GRASS function on e.g., a raster layer and (2) capture the console output in a R data frame. For example, you can run the following in R:

MyVariables <- execGRASS("r.stats", flags="c", input="MyMap", separator=",", intern=TRUE)

However, the output is not in a very convenient format. Continue reading “Import GRASS function console output as data.frame in R”