ArcGIS tool and tutorial to convert the shapefiles into network format. The latest version of the tool is available at http://csun.uic.edu/codes/GISF2E.htmlUpdate: we now have added QGIS and python tools. To download them and learn more, visit http://csun.uic.edu/codes/GISF2E.htmlPlease cite: Karduni,A., Kermanshah, A., and Derrible, S., 2016, "A protocol to convert spatial polyline data to network formats and applications to world urban road networks", Scientific Data, 3:160046, Available at http://www.nature.com/articles/sdata201646

QGIS Intro and Instructions for Mapping Species Occurrences

This dataset shows the results of mapping the connectivity of key values (natural heritage, indigenous heritage, social and historic and economic) of the Great Barrier Reef with its neighbouring regions (Torres Strait, Coral Sea and Great Sandy Strait). The purpose of this mapping process was to identify values that need joint management across multiple regions. It contains a spreadsheet containing the connection information obtained from expert elicitation, all maps derived from this information and all GIS files needed to recreate these maps. This dataset contains the connection strength for 59 attributes of the values between 7 regions (GBR Far Northern, GBR Cairns-Cooktown, GBR Whitsunday-Townsville, GBR Mackay-Capricorn, Torres Strait, Coral Sea and Great Sandy Strait) based on expert opinion. Each connection is assessed based on its strength, mechanism and confidence. Where a connection was known to not exist between two regions then this was also explicitly recorded. A video tutorial on this dataset and its maps is available from https://vimeo.com/335053846.

Methods:

The information for the connectivity maps was gathered from experts (~30) during a 3-day workshop in August 2017. Experts were provided with a template containing a map of Queensland and the neighbouring seas, with an overlay of the regions of interest to assess the connectivity. These were Torres Strait, GBR:Far North Queensland, GBR:Cairns to Cooktown, GBC: Townsville to Whitsundays, GBR: Mackay to Capricorn Bunkers and Great Sandy Strait (which includes Hervey bay). A range of reference maps showing locations of the values were provided, where this information could be obtained. As well as the map the template provided 7x7 table for filling in the connectivity strength and connection type between all combinations of these regions. The experts self-organised into groups to discuss and complete the template for each attribute to be mapped. Each expert was asked to estimate the strength of connection between each region as well as the connection mechanism and their confidence in the information. Due to the limited workshop time the experts were asked to focus on initially recording the connections between the GBR and its neighbouring regions and not to worry about the internal connections in the GBR, or long-distance connections along the Queensland coast. In the second half of the workshop the experts were asked to review the maps created and expand on the connections to include those internal to the GBR. After the workshop an initial set of maps were produced and reviewed by the project team and a range of issues were identified and resolved. Additional connectivity maps for some attributes were prepared after the workshop by the subject experts within the project team. The data gathered from these templates was translated into a spreadsheet, then processing into the graphic maps using QGIS to present the connectivity information. The following are the value attributes where their connectivity was mapped: Seagrass meadows: pan-regional species (e.g. Halophila spp. and Halodule spp.) Seagrass meadows: tropical/sub-tropical (Cymodocea serrulata, Syringodium isoetifolium) Seagrass meadows: tropical (Thalassia, Cymodocea, Thalassodendron, Enhalus, Rotundata) Seagrass meadows: Zostera muelleri Mangroves & saltmarsh Hard corals Crustose coralline algae Macroalgae Crown of thorns starfish larval flow Acropora larval flow Casuarina equisetifolia & Pandanus tectorius Argusia argentia Pisonia grandis: cay vegetation Inter-reef gardens (sponges + gorgonians) (Incomplete) Halimeda Upwellings Pelagic foraging seabirds Inshore and offshore foraging seabirds Migratory shorebirds Ornate rock lobster Yellowfin tuna Black marlin Spanish mackerel Tiger shark Grey nurse shark Humpback whales Dugongs Green turtles Hawksbill turtles Loggerhead turtles Flatback turtles Longfin & Shortfin Eels Red-spot king prawn Brown tiger prawn Eastern king prawns Great White Shark Sandfish (H. scabra) Black teatfish (H. whitmaei) Location of sea country Tangible cultural resources Location of place attachment Location of historic shipwrecks Location of places of social significance Location of commercial fishing activity Location of recreational use Location of tourism destinations Australian blacktip shark (C. tilstoni) Barramundi Common black tip shark (C. limbatus) Dogtooth tuna Grey mackerel Mud crab Coral trout (Plectropomus laevis) Coral trout (Plectropomus leopardus) Red throat emperor Reef manta Saucer scallop (Ylistrum balloti) Bull shark Grey reef shark

Limitations of the data:

The connectivity information in this dataset is only rough in nature, capturing the interconnections between 7 regions. The connectivity data is based on expert elicitation and so is limited by the knowledge of the experts that were available for the workshop. In most cases the experts had sufficient knowledge to create robust maps. There were however some cases where the knowledge of the participants was limited, or the available scientific knowledge on the topic was limited (particularly for the ‘inter-reefal gardens’ attribute) or the exact meaning of the value attribute was poorly understood or could not be agreed up on (particularly for the social and indigenous heritage maps). This information was noted with the maps. These connectivity maps should be considered as an initial assessment of the connections between each of the regions and should not be used as authoritative maps without consulting with additional sources of information. Each of the connectivity links between regions was recorded with a level of confidence, however these were self-reported, and each assessment was performed relatively quickly, with little time for reflection or review of all the available evidence. It is likely that in many cases the experts tended to have a bias to mark links with strong confidence. During subsequent revisions of some maps there were substantial corrections and adjustments even for connections with a strong confidence, indicating that there could be significant errors in the maps where the experts were not available for subsequent revisions. Each of the maps were reviewed by several project team members with broad general knowledge. Not all connection combinations were captured in this process due to the limited expert time available. A focus was made on capturing the connections between the GBR and its neighbouring regions. Where additional time was available the connections within 4 regions in the GBR was also captured. The connectivity maps only show connections between immediately neighbouring regions, not far connections such as between Torres Strait and Great Sandy Strait. In some cases the connection information for longer distances was recorded from the experts but not used in the mapping process. The coastline polygon and the region boundaries in the maps are not spatially accurate. They were simplified to make the maps more diagrammatic. This was done to reduce the chance of misinterpreting the connection arrows on the map as being spatially explicit.

Format:

This dataset is made up of a spreadsheet that contains all the connectivity information recorded from the expert elicitation and all the GIS files needed to recreate the generated maps.

original/GBR_NESP-TWQ-3-3-3_Seascape-connectivity_Master_v2018-09-05.xlsx: ‘Values connectivity’: This sheet contains the raw connectivity codes transcribed from the templates produced prepared by the subject experts. This is the master copy of the connection information. Subsequent sheets in the spreadsheet are derived using formulas from this table. 1-Vertical-data: This is a transformation of the ‘Values connectivity’ sheet so that each source and destination connection is represented as a single row. This also has the connection mechanism codes split into individual columns to allow easier processing in the map generation. This sheet pulls in the spatial information for the arrows on the maps (‘LinkGeom’ attribute) or crosses that represent no connections (‘NoLinkGeom’) using lookup tables from the ‘Arrow-Geom-LUT’ and ‘NoConnection-Geom-LUT’ sheets. 2.Point-extract: This contains all the ‘no connection’ points from the ‘Values connectivity’ dataset. This was saved as working/ GBR_NESP-TWQ-3-3-3_Seascape-connectivity_no-con-pt.csv and used by the QGIS maps to draw all the crosses on the maps. This table is created by copy and pasting (values only) the ‘1-Vertical-data’ sheet when the ‘NoLinkGeom’ attribute is used to filter out all line features, by unchecking blank rows in the ‘NoLinkGeom’ filter. 2.Line-extract: This contains all the ‘connections’ between regions from the ‘Values connectivity’ dataset. This was saved as working/GBR_NESP-TWQ-3-3-3_Seascape-connectivity_arrows.csv and used by the QGIS maps to draw all the arrows on the maps. This table is created by copy and pasting (values only) the ‘1-Vertical-data’ sheet when the ‘LinkGeom’ attribute is used to filter out all point features, by unchecking blank rows in the ‘LinkGeom’ filter. Map-Atlas-Settings: This contains the metadata for each of the maps generated by QGIS. This sheet was exported as working/GBR_NESP-TWQ-3-3-3_Seascape-connectivity_map-atlas-settings.csv and used by QGIS to drive its Atlas feature to generate one map per row of this table. The AttribID is used to enable and disable the appropriate connections on the map being generated. The WKT attribute (Well Known Text) determines the bounding box of the map to be generated and the other attributes are used to display text on the map. map-image-metadata: This table contains metadata descriptions for each of the value attribute maps. This metadata was exported as a CSV and saved into the final generated JPEG maps using the eAtlas Image Metadata Editor Application

Study area

The Kalmthoutse Heide is a nature reserve situated north of Kalmthout, in the province of Antwerp, Flanders, Belgium. It is part of the Cross-Border Nature Park De Zoom - Kalmthoutse Heide in the Netherlands and Belgium. The Kalmthoutse Heide is managed by the Flemish Agency for Nature and Forest and consists of wet and dry heathlands, inland dunes, forests and moorland pools. In this area, there is particular interest in monitoring the encroachment of the heathlands by Molinia caerulea and Campylopus introflexus.

Data collection

Data were collected by the Research Institute for Nature and Forest (INBO) with a fixed wing drone Gatewing X100 in 2015 and 2016 (8 flights). RGB data were acquired using an off-the-shelf Ricoh GR Digital IV camera, with the following image bands: 1: red, 2: green, 3: blue, 4: alpha channel.

Data processing

The raw data were processed to Digital Surface Models and orthophotos by the Flemish Institute for Technological Research (VITO) in 2017. Images with coarse GPS coordinates were imported and processed in Agisoft PhotoScan Pro 1.4.x, a structure-from-motion (SfM) based photogrammetry software program. After extraction and matching of tie points, a bundle adjustment leads to a sparse point cloud and a refined set of camera position and orientation values. Ground control points (either artificially installed markers on the terrain, or other photo-identifiable points, measured on the ground with RTK GNSS) were used to further refine the camera calibration and obtain a pixel-level georeferencing accuracy. From there, a point cloud densification and classification into ground and non-ground points was performed, leading to a rasterized digital surface model (DSM) and digital terrain model (DTM). Finally, a true orthomosaic was projected onto the DTM.

Coordinate reference system

All geospatial data have the coordinate reference system EPSG:31370 - Belgian Lambert 72.

Files

• Raw flight data: images and logs collected by the drone during flight. These files are zipped per flight, with the date (yyyymmdd) and flight number (x) indicated in the file name (flight_yyyymmdd_KH_x.zip).
• Processed data: Digital Surface Models (filename_DSM.tif) and orthophotos (filename_Ortho.tif) stitched together from the raw data. The included flights are indicated in the file name (e.g. 3 flights for 20150717_KH_1-3_DSM.tif).
• Ground control points: temporary ground control points were placed for the first flights on 2015-07-17 (visible in 20150717_KH_1-3_Ortho.tif). Coordinates for these are available in GCP_20150717_KH.tsv.

Cloud Optimized GeoTIFF

The most efficient way to explore the processed data is by loading the Cloud Optimized GeoTIFFs we created for each processed file. Copy one of the file URLs below and follow e.g. the QGIS tutorial to load this type of file.

• http://s3-eu-west-1.amazonaws.com/lw-remote-sensing/cogeo/20150717_KH_1-3_DSM.tif
• http://s3-eu-west-1.amazonaws.com/lw-remote-sensing/cogeo/20150717_KH_1-3_Ortho.tif RGB
• http://s3-eu-west-1.amazonaws.com/lw-remote-sensing/cogeo/20151020_KH_1-2_DSM.tif
• http://s3-eu-west-1.amazonaws.com/lw-remote-sensing/cogeo/20151020_KH_1-2_Ortho.tif RGB
• http://s3-eu-west-1.amazonaws.com/lw-remote-sensing/cogeo/20151020_KH_3_DSM.tif
• http://s3-eu-west-1.amazonaws.com/lw-remote-sensing/cogeo/20151020_KH_3_Ortho.tif RGB
• http://s3-eu-west-1.amazonaws.com/lw-remote-sensing/cogeo/20160205_KH_1-2_DSM.tif
• http://s3-eu-west-1.amazonaws.com/lw-remote-sensing/cogeo/20160205_KH_1-2_Ortho.tif RGB

See this page for an overview of public INBO RPAS data.