Understanding GIS

1. Understanding GIS P.Quek p.quek@cgiar.org Training Workshop on Forest Biodiversity Conservation and Management of Forest Genetic Resources Kuala Lumpur, Malaysia 5 - 16 June 2006 Parts of this presentation were derived from A.Jarvis and P.Mathur ppt

2. What is GIS? A Geographic Information System is a set of computer programs that can organize, display, and analyze spatially distributed data • spatial data in graphics form • and related, logically-attached, non-spatial, attribute data

3. GIS Image Handling GIS handles images commonly in one of two forms: Raster: A grid of rows and columns of cells.These might represent photographic or scanned images. Vector: A geometric shape, including points, lines, and polygons.These might represent buildings, roads, and counties. Both of these may have tables of attribute data associated with them, e.g. species, population, numbers, etc.Such associated data can be used to colour a map to convey information in a visual manner.

4. Information required to use GIS • Spatial or Locality information • Coordinates of the locality • Other information on the environment of the area in maps, description of location • Attribute or Taxonomic information • Accepted scientific name • Other information relating to taxonomic, ecological, ethnobotanical, etc.

5. What can we use it for? • Ecogeographic survey for locating diversity • Planning field exploration and germplasm collecting • Design, management and monitoring of in situ reserves • Site identification for germplasm introduction • Site identification for germplasm evaluation

6. Methodologies: published by others IPGRI collaborative studies, linked to training Software: Commercial software ArcView ArcInfo IDRISI MapInfo Specialized for PGR FloraMap DIVA SID Data: Genebank and herbarium passport characterization evaluation Thematic production environmental socio-economic Sources national programmes CGIAR Centres Methodologies, software and data sources

7. Likely to contain target material predicting species/ecotypes distributions Trait specific highly diverse – characterization/ evaluation traits point-centred methods grid methods Areas complementary to each other Under-conserved gap analysis Threatened areas mapping the risk of genetic erosion Ecogeographic surveys locate areas which are:

8. So why isn’t everybody using it? • PGR programmes, particularly in developing countries, have significant resource constraints, and • GIS hardware, software and data are perceived as being • expensive • difficult to obtain (very much easier now) • complex to use • and therefore not a priority compared to other things

9. Application of GIS for PGR management • What is required? • Geo-references and data • Associated data • What we can get? • Generating maps • Generating climatic database • Interpretation of results for: • Gap analysis • Diversity analysis

10. Application of GIS for crop diversity mapping and diversity assessment Possible outputs of GIS use in PGR management: • Update passport information for collecting sites with respect to geo-reference information. • Map the crop diversity collected for individual countries and also on global basis. • Analyze crop diversity collected for different passport and characterization information. • Complementary diversity analysis for combination of traits. • Based on past collecting information, identify potential matching sites for cultivation of crop under biotic and abiotic stress conditions.

11. Application of GIS for crop diversity mapping and diversity assessment Classify collections based on climatic adaptation. • Provide climatic information (Monthly rainfall, minimum and maximum temperature) for individual collecting sites. • Providing climate maps for various climatic parameters and their combinations as well as for altitude of collecting sites. • Providing guidelines to further develop collecting strategies for new collections as well as for re-collecting of germplasm.

12. Global Positioning Systems (GPS) Acquiring locality data Training Workshop on Forest Biodiversity Conservation and Management of Forest Genetic Resources Kuala Lumpur, Malaysia 5 - 16 June 2006

13. Figure from http://franson.com/coordtrans/index.asp Global Positioning System, usually called GPS, is the only fully-functional satellite navigation system

14. Principles

17. Taking a Position 2D position (i.e. lat/long) - a minimum of 3 satellites must be in view, with good signals. 3D position (i.e. lat/long/altitude) - minimum of 4 satellites must be in view, with good signals Good geometry Bad geometry

18. Accuracy • Depends on : • Geometry of satellites • Local environmental conditions (clouds/vegetation/buildings) • Quality of GPS receiver (a question of cost) Accuracy varies from a matter of millimetres to around 50m in latitude/longitude, and 1m to 100m in altitude

19. Which GPS Receiver to Use? Trimble • Both off the shelf “supermarket” brands • Approximate cost $100-200 • Maximum accuracy - 5 -10m • Both offer navigation facilities • Direct connection to computer to download data Garmin 12 XL

20. Recommendation Garmin 12 XL Ease of use Better antenna for use in forest canopies

21. Taking a Position in Forest Canopies • Canopy interferes heavily with signal. Steps to take: • Patience…..wait 5-10 minutes for good satellite coverage before taking an average position • Try to take the position under a dry canopy • Use the almanac function in cases of very poor coverage to time the collection of the geo-position with good satellite coverage

22. Measurement of Altitude • GPS vs Altimeter • GPS better under clear skied, low vegetated flat areas • Altimeter preferable in forested areas/mountain regions

23. What data to take and in what format Descriptive data: ADM1 – first level administrative subdivisionADM2 – second level administrative subdivisionADM3 – third level administrative subdivisionADM4 – fourth level administrative subdivision “At km 21 marker along Route 120 S of Morelia, on W side of Route 120.” GPS Data : Decimal degrees - i.e. 45.34256N, 76.54864W (North and East are +ve numbers, South and West are -ve numbers) Five decimal points (indicates 10m accuracy at Equator) The circumference of the earth at the equator 40,075 kilometers

24. Conversion of 30o 31’ 32’’ E = 30 + 31/60 + 32/3600 =30 + .51667 +0.00889 =30.52556

25. North + Longitude : -180o till +180o Latitude : -90o till +90o - East West Equator 0o + Greenwich - South 0o

26. Bottom Line • No GIS analysis is possible without geo-referenced accessions. The adoption of this technology relies upon careful data collection using GPS in the field • Garmin XL12 is the recommended GPS • Data taken in decimal degrees with 5 decimal points of precision • As much descriptive information about locality noted as a backup source • Post-collection checking of GPS data before sending off to PGR databases

27. References GPS Brands: http://www.garmin.com http://www.trimble.com More info on GPS technology and systems : http://www.colorado.Edu/geography/gcraft/notes/gps/gps_f.html http://en.wikipedia.org/wiki/Global_Positioning_System

28. http://www.gpstm.com

29. GIS tools for PGR research • FloraMap (CIAT) • A computer tool for predicting the distribution of plants and other organisms in the wild • DIVA (CIP, IPGRI, SGRP) • A GIS for the management and spatial analysis of genetic resources data

30. FloraMap http://isa.ciat.cgiar.org

31. Introduction to FloraMap • Introduction • Minimum hardware and software requirements • Installation • Setting up the Map properties • Checking the data quality

32. New GIS tools for PGR research • FloraMap • developed by CIAT • software + climate data • on CD-ROM, $100 • you provide latitude, longitude, (altitude) • can be used to • check data quality • predict species distributions • identify gaps in collections • identify climatic adaptation groups within collections • compare climatic adaptation of species • predict adaptation in other areas • what it does not do • take soils etc. into account • give you a once and for all answer

33. Introduction to FloraMap • FloraMap is a system for producing the predicted distribution OR • Areas of possible adaptation for a given species However, • It is assumed that the climate at the point of collection of a set of germplasm collections or herbarium specimens, is representative of the environmental range of the species • The climate at these collection points is used as calibration set to compute a climate probability model

34. Introduction to FloraMap FloraMap file types: • Accession point files • ACP.files – space delimited ASCII files with column headings • DBF files – They may contain accession points data, climate data, or information about polygons in the shape files • SHP files: are shape files that delineate point, line or polygon data. They are also compatible with ArcView • SHX files: are specialised index files that give meaning to the shape file • TXT files: Are produced when a report file is saved. These are ASCII space-delimited data files

35. Introduction to FloraMap ESRI shapefile: • Consists of – Main file, and Index file, and a dBase table. • Main file is a direct access, variable-record-length file in which each record describe a shape with a list of its vertices. • In the Index file, each record contains the offset of the corresponding main file record from the beginning of the main record. • The dBase table contains features attributes with one record per feature. The one-to-one relationship between geometry and attributes is based on record number. Attributes records in the dBase file must be in the same order as records in the main file

36. Introduction to FloraMap Example: Main file: Counties.shp Index file: counties.shx dBase table: counties.dbf These three files above describe a map layer MAP files:are FloraMap files that contains the information to associated DBF files, accession point files, and shapefiles in a map coverage. A MAP file contains references to the several map layers combined together to represent a map. FloraMap will construct a set of all the files necessary for the map and name them following the name you give to the MAP file.

37. Mapping Taro Collection Mapping PNG taro collections using FloraMap

38. Taro Diversity Prediction Similar sites for taro diversity or introduction (based on PNG taro collections) Prediction based on FloraMap

39. Cowpea collections Climatic matching probability distribution map of Sri Lanka

40. Prediction of similar climatic grids across region

41. Prediction of similar climatic grids across continents

42. New GIS tools for PGR research • DIVA • developed by CIP with IPGRI, SGRP and FAO support • software + data • on CD-ROM, downloadable from WWW • Cost - $ FREE • you provide latitude, longitude and characterization data • can be used to • check data quality • map diversity using grids of different sizes • identify areas of complementary diversity • map occurrence of single traits or combinations of traits • what it does not do • make predictions outside the data area

43. Introduction to DIVA-GIS Free GIS software

44. Introduction to DIVA-GIS With DIVA you can: • Map the location of sites where population of plant and animal species were observed • Make grid maps of the distribution of biological diversity • Identify hotspots and areas of complementary levels of diversity • Extract climate data for localities points • Predict presence of species based on climate – using BIOCLIM or DOMIN models for either: • Current climate (1960-90) • Predicted future climate (2040-60)

45. Introduction to DIVA-GIS Aimed at users who: • Cannot afford commercial GIS • Do not have time to learn how to use • Want a GIS tailor-made to analyse biological distribution

46. Installing DIVA-GIS • Provided on CD • Can download from web (http:/www.diva-gis.org) • If download, unzip downloaded files • Click setup.exe to install DIVA • After installation following folders: • Bin • Environ • Gazet • Tutor

50. File types and Formats • DIVA uses various types and formats • Most important are: • Shape files • Grid files • Image files (For spatial database) • dBase IV (DBF) format for reading and writing external (non spatial) database