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wiki:yalefall2015

Geo-spatial and environmental analysis using open-source software

Dr. Giuseppe Amatulli , Dr. Sami Domisch, Mao-ning Tuanmu, Ryan Powers, Dr. Marta Jarzyna

These workshops integrate the computational skills to process geo-data for environmental analysis, Geographic Information Systems and Remote Sensing application and species distribution using Open Source software in a Linux OS.

The workshops are drop-in, but we strongly encourage people to pre-register by sending an email to giuseppe.amatulli@yale.edu to have full access to the material needed for the workshops and the Linux-like Virtual Machine (LVM) pre-installed in participants’ personal computers. This LVM is an ad-hoc customization of the Ubuntu distribution with Remote Sensing, GIS and Statistics open source software; with sample geo-data, scripts, and example exercises linked with the material stored at http://www.spatial-ecology.net. The installation of the LVM effectively installs Linux inside Windows or MacOS. In other words, your main OS will remain Windows or MacOS, and you will boot the PC as before. There is no risk to your data or for your main OS.

Workshop times & dates:

  • Workshop 1: Wednesday, September 16th - 4.30pm:7.00pm - Location: OML 201
  • Workshop 2: Wednesday, September 30th - 4.30pm:7.00pm - Location: OML 201
  • Workshop 3: Wednesday, October 14th - 4.30pm:7.00pm - Location: OML 201
  • Workshop 4: Wednesday, October 28th - 4.30pm:7.00pm - Location: OML 201
  • Workshop 5: Wednesday, November 4th - 4.30pm:7.00pm - Location: OML 201
  • Workshop 6: Wednesday, November 18th - 4.30pm:7.00pm - Location: OML 201
  • Workshop 7: Wednesday, December 2nd - 4.30pm:7.00pm - Location: OML 201

Workshop 1: Introduction to Linux as platform for open source spatial analysis (Giuseppe)

Wednesday, September 16th

This introductory session will focus upon the fundamental concepts and skills needed to begin using Linux OS for the exploration and analysis of spatial data. During the first half of the workshop, we will install a Linux Virtual Machine (LVM) on your lap-top and explore the materials available at http://www.spatial-ecology.net . During the second half of the workshop we, will learn essential Linux commands to navigate directories, copy and move files, compress/uncompress files, etc.

This workshop assumes NO PRIOR KNOWLEDGE of any programming language or Linux OS functionality, but does require working knowledge of the fundamentals of an Operating Systems (Files, Folders, etc…). The LVM installed during this workshop will be used during the full workshop series.

Workshop 2: Introduction to GRASS GIS (Giuseppe)


Wednesday, September 30th

This workshop introduces students to the powerful Geographic Resources Analysis Support System (GRASS) GIS software to manipulate raster and vector data. We will see the graphical user interface and use simple BASH scripts to automate many common geo-data processing tasks such as cropping and re-projecting images. You will learn how to script processes for complex geo-functions.

This workshop assumes BASIC KNOWLEDGE of BASH command lines and basic knowledge of Geographic Information Systems concepts (projection, buffer, overlay, etc…). Participants will need a pre-installed Linux Virtual Machine in their own laptops to follow the workshop.

Workshop 3: Hydrological application with GRASS GIS (Sami)

Wednesday, October 14th

This workshop will give an introduction into the hydrological tools in GRASS GIS. The aim is to generate environmental predictors within the freshwater environment for biodiversity analyses and species distribution models. GRASS offers a suite of hydrological functions, and we will demonstrate a custom-made add-on in GRASS that automatically calculates watersheds and relates the upstream-contributing environment of a given variable to each stream reach.

This workshop assumes BASIC KNOWLEDGE of BASH command lines and basic knowledge of Geographic Information Systems as well as skills acquired during Workshop 1,2 and 3. Participants will need a pre-installed Linux Virtual Machine in their own laptops to follow the workshop.

Workshop 4: Raster/Vector processing using GDAL/OGR libraries and pktools

Wednesday, October 28th

This workshop introduces students to the powerful Geospatial Data Abstraction Library (GDAL), the OGR libraries, and pktools software to perform Geographic Information Systems and Remote Sensing analysis. You will use simple BASH scripts to automate many common geo-data processing tasks such as cropping and re-projecting, mosaicking, and filtering images. You will learn how to script processes for complex geo-functions.

This workshop assumes PRIOR KNOWLEDGE of BASH command lines (acquired during Workshop 1) and basic knowledge of Geographic Information Systems and Remote Sensing concepts (projection, spectral signature, etc…). Participants will need a pre-installed Linux Virtual Machine on their own laptops to follow the workshop.

Workshop 5: Basics of Remote Sensing for Ecologists (Ryan?/Mao-Ning?)

Wednesday, November 4th

This workshop builds upon the lessons given in the previous Raster/Vector processing workshop by using basic scripts to process LANDSAT imagery and develop vegetation indices. A presentation will also provide (i) some examples of current remote sensing technologies and applications, and (ii) a cursory overview of vegetation spectral analysis.

This workshop assumes PRIOR KNOWLEDGE of BASH command lines (acquired during Workshop 1) and basic knowledge of Geographic Information Systems and Remote Sensing concepts (projection, spectral signature, etc…). Participants will need a pre-installed Linux Virtual Machine on their own laptops to follow the workshop.

Workshop 6: Species Distribution Modeling I (Marta)

Wednesday, November 18th

This workshop will introduce students to basics of species distribution modeling. We will teach students how to retrieve species occurrence data from the Map of Life and pre-process environmental data. We will then fit a generalized linear model to estimate the species distribution and predict across the landscape.

To follow the workshop, PRIOR BASIC KNOWLEDGE of R language and statistics is required. Participants will need a pre-installed Linux Virtual Machine in their own laptops to follow the workshop.

Workshop 7: Species Distribution Modeling II (Marta)

Wednesday, December 2nd

This workshop will introduce students to the issue of species’ imperfect detection and why it matters in species distribution modeling. We will also demonstrate techniques developed to account for species imperfect detection. We will use opportunistic species occurrence data for occupancy modelling and hSDM R package to fit hierarchical distribution model and compare output from models built with interpolated and satellite-derived environmental data.

This workshop assumes PRIOR BASIC KNOWLEDGE of R language, statistics, and skills acquired during Workshop 6. Participants will need a pre-installed Linux Virtual Machine in their own laptops to follow the workshop.

wiki/yalefall2015.txt · Last modified: 2017/12/05 22:53 (external edit)