pegi3s/gis

Sponsored OSS

By i3S

Updated 4 months ago

GIS docker image.

Image
Data Science
Databases & Storage

65

This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles)

(Please note that the original software licenses still apply)

This image facilitates the usage of GIS (Geographic Information System), a system designed to capture, store, manipulate, analyze, manage, and present spatial or geographic data.

Using the GIS image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/gis bash -c "Rscript /opt/gis && pdfcrop --margins '0 0 0 0' /data/Rplots.pdf && rm /data/Rplots.pdf"

In this command, you should replace:

  • /your/data/dir to point to the directory that contains the input files you want to analyze.

Test data

Please make sure you first create a file named data.csv containing the latitude and longitude coordinates where your species was observed. The file header must be "latitude,longitude".

Your data.csv should present the following format:

latitude,longitude
-37.4,145
-35,-65
-34.4,-58.3
-33.3,-70.4
...
Note 1

The previous command generates two files:

  • statistics: a results file containing some statistics on the species presence points.
  • Rplots-crop.pdf: a PDF file showing the presence and predicted distribution of the species (probabilities are given as color codes). The prediction model used is the Bioclim model.
Note 2

A folder named wc2-5 containing data on 19 abiotic variables from WorldClim will be created, if not present.

Docker Pull Command

docker pull pegi3s/gis