Area reports

Area reports

The Area Report options generate a report for a selected region/area. There is a simpler interactive version and a detailed PDF area report that contains more detail.

  • Note: The Detailed area report can take more than 10 minutes to generate. Please therefore be cautious about the size of the area you are reporting on. We will endevour to develop a faster method, but there is a lot of data to find, collate and report.

From the menu option, select “Tools” and then “Area Report” or “Detailed Area Report”.

Select an area to analyse.

Click the “Next” button. Note the “Define new area” involves an extra step to define the area of interest (please refer to Add Area for additional information).

Any predefined area listed as a map layer in the top left layer list can be used to for an Area Report.

Area Report Step1 Use My Active Area

The following details then appear in the pop-up Area Report:

  1. Area (sq km): The area in square kilometers of the selected area. With an Info hyperlink to explain about the World Area bounding box we are using
  2. Number of species: A list of all unique species derived from the occurrence records for the area. Clicking on the List button will produce a species list. Note that only the ‘most-preferred’ common name (if any) will be listed for each species. The list can be downloaded in CSV format.
  3. Number of species – spatially valid only: This is a potential subset of (2) above without any species that have any type of flag questioning their location. For example, a record of a marine species on land (or vice versa) will be flagged.
  4. Number of endemic species: This list will contain those species that only occur within the area. The list can be downloaded in CSV format.
  5. Number of endemic species – spatially valid only: The same as (3) above except for endemic species.
  6. Occurrences: The number of point occurrence records for all species in the area (observations, specimens etc.). The Map all button will map all occurrences in the area (only available if the active area contains <= 2,000,000 occurrences). Sample button: Will start the process of sampling any of the user-selected  environmental or contextual layers at the points. View Records: Will open a new window displaying all the details of the records in the area.
  7. Occurrences – spatially valid only: As for (3) and (5) above. Only those records that do not have have any spatially validity flags set.
  8. Expert distributions: The number of species for which we have expert-defined areas of their distributions that intersect the area of interest. List: Will list the species and some associated detail and allow for the polygon/s for individual species to be mapped. The list can be downloaded in CSV format.
  9. Checklist areas : “Checklists” are lists of species that are known to occur within a defined area that we call a “Checklist area”.   The specific location of the species in the area is unknown, only that they are known to occur within that checklist area. List: Enables the checklist areas to be listed an optionally mapped.
  10. Checklist species: The number of species that have been assigned to Checklist areas that intersect the area. List: Will list the species that occur within the checklist areas. Any of the listed species can be mapped from this list.
  11.  Journalmap documents: The number of documents in JournalMap that have a reference to an area that intersects the area of interest.
  12. Gazetteer points: The number of gazetteer locations from the 2010 Australian gazetteer. This option was added (among other reasons) to help identify ‘islands’ without formal names.
  13. Various Lists such as Migratory species, Threatened’ species (species that have any conservation status via IUCN, State/Territory or Federal agencies) – based on the Threatened lists in http://lists.ala.org.au, ‘Invasive’ species (species that have been deemed in any way invasive in any part of the Australian region) – based on the ‘Invasive’ lists in http://lists.ala.org.au

The Detailed Area Report (PDF) also contains for the area-

  1. Spatial context map
  2. Map of national Dynamic Land Cover
  3. Map of Global Terrestrial Ecoregions
  4. Map of Global Marine Ecoregions
  5. Map of Global Freshwater Ecoregions
  6. Further links
  7. References

—–Preliminary fields that may be included

  1. Points of interest:  In MERIT (https://fieldcapture.ala.org.au/) a point of interest (POI) is a spatially referenced attribute of a site. It has a name, description, type, coordinate and bearing (optional). We currently only support one type of POI (ie. photo points), but the intent is also support other types such as: natural feature, cultural feature, works area, observation point/hide, trap site, etc. Photo points are a special kind of POI as, when they are associated with a site and that site is associated with an activity with a “photo point” output, images for the photo points can be recorded as part of the data collected for a record event.
Interactive Area Report

Interactive Area Report

Table of Contents of the Detailed Area Report (PDF)

Table of Contents of the Detailed Area Report (PDF)

The map can be downloaded in a variety of formats for print quality use in documents or to preview on the screen. The ‘Download map’ is available as one of the Map Options in the LHS Legend Pane, and from the menu option Export Map.

Export Map

To export a map directly for previewing or download, on the menu select ‘Export’ and then ‘Map’.

Export Map menu option

Export Map menu option

Map Options

To preview or download a map from the Map Options pane, press the ‘Download map’ button.

Export Area download map

Export Area download map

Export Map dialogue window

Both methods evoke the Download map dialogue window

Enter a caption for the map; the date is included as part of the caption.

Choose whether to overlay a longitude / latitude grid over the map.

The image formats are: jpg, pdf and png.

The image resolutions are: screen (low resolution) and print (high resolution).

Then press the ‘Preview’ or ‘Download’ buttons.

Export Map preview

Press the Preview button to preview the map

Export Area download save

Press the Download button to save the map zip file to your file system

Export Area downloaded

Viewing the saved image file

 Maps for Publications

If you are seeking a way to produce a small map of say a species or assemblage distribution, keep it simple. Here are some ideas that should be useful for producing simple maps-

  1. Select the Outline basemap option in the legend. This provides for black country boundaries on a white base; ideal for publication
  2. If desired, use Add to Map | Layers to add States and Territories, IBRA, IMCRA or similar simple polygon layer. Choice obviously depends on what you want to show.
  3. Use Add to Map | Species to map a species or assemblage to map the occurrence records
  4. Use the legend parameters to ensure the points are rendered as you want them
  5. Zoom and pan to display the area of interest
  6. Use Export | Map
    1. Add optional caption. Usually leave blank for publication
    2. Optional grid overlay. Usually better not to use this.
    3. Select PNG format as this is lossless.
    4. Select Print resolution. At the moment, we are limited to 200 dpi but it is hoped that we will add up to 600 dpi in the future. This will come at the cost of losing the WYSIWYG function as there are aspects of the rendered layers that will not be supported by resolutions above 200 dpi.
    5. Press ‘Download’
Publication map

Example of a distribution map for publication

Layers are used to overlay both environmental and contextual layers on the map.

To add a new layer, select from the Menu Option, “Add To Map”, then “Layers”.

This Layers option maps any of the layers available in our Layer Library. On this page, there are a few links to view/download information in the form of a table about each of the layers in the Atlas. These layers can be viewed, sampled and generally used in analysis but cannot currently be downloaded in raw data form due to licensing constraints. The Atlas has been given most of these layers with an agreement not to pass them on to a third party. The agencies responsible for each layer are listed in the CSV download file along with the license type. When agencies move to Creative Commons licences, we will provide various options to download the layers.

There are two distinct types of layers available:

  • Environmental: These are layers that are based on a regular grid. In most cases, the Atlas has aligned a wide range of layers to have the same grid origin, size and orientation. The values of the grid cells are continuous numeric, for example, temperature in degrees centigrade or precipitation in mm. Generally, the environmental layers in the Spatial Portal are included because they are thought by experts to have some control or relationship with the distribution of organisms.
  • Contextual: These layers are essentially polygonal even though some are generated on a grid basis. The values within each of the polygons is a class such as “forestry” as a land-use class. Generally, contextual layers are used to interpret the distribution of organisms rather than controlling them in some way, hence the name.  Contextual data may also be helpful in interpreting the output of an analysis. For example, what is the distribution of land-use classes where this species is found or could be predicted to be found.

LGA Boundries_640

There are three distinct ways to map layers:

  • If you know the name of the layer you want, you can start typing the name into the Layer text box. As with species names, the system will know some synonyms (e.g.: rainfall=precipitation). Typing the first three letters will start to bring up a list of matching names. Once a layer name has been clicked, it will be mapped.
  • If you do not know the name of the layer you want, you can type in a keyword and the auto-complete feature will suggest possible matches.  A list of keywords can be viewed in the layer list. Once a layer name has been clicked, it will be mapped.
  • All ~500 (environmental and contextual) layers have been assigned to a 2-level classification. If you want to browse the available layers, use the classification tree.

Layer selection box

The box for selecting layers to map or to use in analysis contains a range of functions. This list and selection box enables you to

  • Select one or multiple layers individually from the table using the check boxes. You can map one or any number of available layers at one time. NOTE: Use the Map option box to select or deselect all mapped layers.
  • Add set of layers entry box
    • Select previously used layers (a list of your most recent layers is kept)
    • Select a predefined suite of layers, for example the ‘Best 5’ (see below for details on how these suites are generated).
    • Import a list of layer names saved or generated previously. The format uses short-names separated by commas (CSV-format). To see an example of the format, use the fexport option once layers have been selected.
  • Add from Search entry box
    • Search for a layer using auto-complete (the same type of function as used for species selection, but in the case of layers, the search covers any words in the long name, short name, classification and keywords: See http://spatial.ala.org.au/layers). Just start typing and he auto-complete will start displaying layers that match what you have typed.
  • Clear selection deselects any selected layers
  • Export layer set creates a text file comtaning the (short-name) list of selected layers. This can be used for subsequent import.
Layers list box

Layers list box

When you first see the layers selection table, you will see

  • A link to the list of all available layers. At the time of writing, there are close to 500 layers available.
  • The checkboxes for the selection of layers
  • The classification of the layers. The classification has two levels as for example ‘Area management’ | ‘Biodiversity’ or ‘Substrate | moisture’.
  • The long name of the layer
  • A colour. As the text to the left of the layer list suggests, “The colours against the layers are like traffic lights. Green implies the layer is uncorrelated to all selected layers, orange implies some correlation while red implies high correlation. As you select layers, the colours change to reflect correlation with already selected layers. For example a red layer implies high correlation with at least one selected layer while a green layer implies little or no correlation to any selected layer

    Note: The correlations are currently based on full layer spatial extents and not any selected sub-area.”

    Note: Even though there may be some spatial overlap between terrestrial and marine layers, they are designated as mutually independent suites.

  • A clear layers button. This resets any selected layers
  • An Export set button that will save the list of selected layers to a CSV file.

The “Next” button will be enabled when at least one layer has been selected.

Layer suites

There are a number of predefined suites of layers that you may find useful for a range of biodiversity applications. In all current suites, the same algorithm has been applied. The philosophy behind the suites is relatively simple – can we identify a subset of all available environmental layers that appear to cover the range of terrestrial environments? The strategy developed (by Lee Belbin in 2011) is related to the traffic light colours noted above:

  1. Use the inter-layer association matrix (http://spatial.ala.org.au/files/) to generate an (SSH 3d) ordination using http://www.patn.com.au
  2. Select the layer that is at the extreme end of the spatial distribution as the first of the subset
  3. Select the layer that is furthest away in the ordination (environmental space) from the first selected layer that also shows the most complementary spatial distribution of values. In some cases, the layer selected may indeed be complementary but also be degenrate in that it may have little or no spatial variation of values over most of the continent. If this is the case, a spatially adjacent layer in the ordination that has a more complementary distribution of values to the first layer is selected.
  4. Select a third layer that is most somplementary to the both already selected layers (that is also not ‘spatially degerate’).
  5. Continue the selection of layers until no remaining layer is greater than a respectable (ordination) distance from all selected layers.

Generally, it has been found that 5 layers appear to cover most of the variation in terrestrial environments across the Australian continent.

Layers suite selection box

Layers suite, previous, import selection box

There are currently three predefined suites of layers in the Spatial Portal-

  1. A suite of the best 5 layers based on bioclim-only layers. These layers are based on the work of Nix, Hutchinson, Stein and others (see http://fennerschool.anu.edu.au/files/panel/448/creswww_pdf_54059.pdf). These layers have names with “Bioxx” where xx are the values 1-35.
  2. A suite of the best 5 layers of a set of environmental layers provided by Dr Kristen Williams (CSIRO Ecosystems Sciences). These layers are 1960 centred.
  3. The best 5 2030 equivalents to layers in (2) as provided by Dr Kristen Williams (CSIRO Ecosystems Sciences).

NOTE: If a smaller area was to be used, the inter-layer dissimilarity matrix for all layers would have to be generated. Currently, due to the processing required, the Spatial Portal of the Atlas only generates the association matrix when new environmental layers are added.

NOTE: Terrestrial layers are treated independently to marine layers and even though there are few stream/lake layers so far, they should also be considered separate environments. The association matrix shows the relationship between all terrestrial layers and between all marine layers but not between terrestrial and marine layers (no overlap).

NOTE: Only ENVIRONMENTAL layers are used in generating the associations. For the formula used for the association matrix, see

Williams, K.J., Belbin, Lee, Austin, Michael P, Stein, J., Ferrier, S. (2012). Which environmental variables should I use in my biodiversity model? Special Issue of International Journal of Geographical Information Science, iFirst, 1–39. DOI:10.1080/13658816.2012.698015

Viewing environmental and contextual values

The legend for each mapped layer displays the range of values for that layer and provides the links to hide, delete, zoom to extent and metadata. To view a value of the layer at  a specific location (as it may not be easy to get an exact value from matching colours in the legend), look at the bottom right of the map window. All the mapped layers will be listed here with the value of each layer at the cursor. To get an exact value at a point, simply zoom and pan to the area of interest and place the pointer over the point and a few seconds later, the values of all displayed layers at that point will be displayed.

As you move the mouse moves across the map, the values will be updated in near real time.

Hover tool

Hover tool

Layer Metadata

Metadata for an environmental layer

When the layer metadata icon  icon is selected in the layers list the metadata is displayed. In this case it displays information about Precipitation – annual (Bio12). In the classification tree, metadata can also be displayed by clicking on the Gridded metadata icon for environmental layers or Contextual metadata icon for contextual layers.

Legends

The map legends in the Spatial Portal are context dependent. Environmental or gridded layers have continuous values and the associated legend looks like this-

Environmental layer legend

The colours on the map indicate the value of the mapped layer value. The figure above shows the legend for the layer mean annual temperature varies from 3.4c to 29.7c. There is no interaction with the legend for environmental layers other than adjusting the opacity/transparency between 0% and 100%.

Contextual or class/polygon layers have class values rather than continuous values so the legends look like this-

Contextual layer legend

Contextual layer legend

The figure above shows the legend and part of the map for the land cover for Australia. There are 11 distinct classes, each with a corresponding colour on the legend and map. Unlike environmental layers, the contextual layers allow you to highlight one class on the map by clicking on the class name in the bottom part of the legend (call it the sub-legend). The highlight can be cleared by clicking on the Clear highlight button at the bottom of the sub-legend. This method using the legend is a quick way of scanning through the areas associated with legend classes.  You can page through the various classes or search for a class by name.

If you want to create a new layer from one class of the contextual layer click on the plus symbol to the right of the class name.  This method is a quick alternative to using ‘Add to Map | Areas |Gazetteer polygon’ and selecting the class name. This latter process works because all contextual layers classes have been entered into the ALA’s gazetteer database.

Layers that are automatically updated weekly

There are four layers that are recalculated weekly due to the additions of occurrence records

  1. Endemism (see Crisp et al. 2001)
  2. Edemism non-marine (see Crisp et al. 2001)
  3. Occurrence density and
  4. Species richness
Each of these values are calculated at global extent using a 0.1 degree (~10km) grid. It is likely that additional similarly derived layers will be added when we become aware of their potential utility. Suggestions always welcomed to support@ala.org.au.

Viewing all available layers in the Spatial Portal

A complete list of available layers with thumbnail images and metadata can be found at http://spatial.ala.org.au/layers. This list can also be downloaded as a Comma-separated variable (CSV) or JSON (JavaScript Object Notation) formats. See the links on the top of the page.

The Display Name contains a link to available metadata for each layer. The Short Name provides a shorcut for entering layer names in the Spatial Portal. For example, Bio01 can be used in place of “Bioclim Temperature – annual mean”.

NOTE: The list contains 400+ layers and can take many minutes to generate.

Layers list

Layers list

 

References

Belbin, L., Williams, K.J. (2015). Towards a national bio-environmental data facility: experiences from the Atlas of Living Australia. International Journal of Geographical Information Science. http://dx.doi.org/10.1080/13658816.2015.1077962.

Crisp, M.D., Laffan, S., Linder, H.P. and Monro, A (2001). Endemism in the Australian Flora. Journal of Biogeography 28, 183-198.

Williams, K.J., Belbin, Lee, Austin, Michael P, Stein, J., Ferrier, S. (2012). Which environmental variables should I use in my biodiversity model? Special Issue of International Journal of Geographical Information Science, iFirst, 1–39. DOI:10.1080/13658816.2012.698015

There are three types of data that can be mapped:

  • Species (or assemblages of taxa)
  • Areas (14 options available)
  • Layers (environmental/gridded or contextual/polygonal)
  • Facets (occurrence record attributes)

Add to Map options

Each of these layer types play an important role in the analysis tools. As you add new layers to the map, be sure to keep an eye on the hints section (located at the bottom left) to see possible actions that can be performed on your map layers.

Hints area

 

 

Export menu option

Export menu option

The list of layers in the top left of the Spatial Portal window are layers in the Geographic Information System (GIS) sense. Each layer can be related to either species/assemblage, an area or an environmental/contextual layer. You can export information related to most of these mapped layers

  • Species can be downloaded as points in CSV format (but will soon also be available as Shapefiles, KML and WKT).
  • Areas can be optionally combined and downloaded as polygons in on of Shapefile, KML or WKT formats.
  • Environmental and contextual layers provided by external data providers cannot be downloaded, only sampled by points. The main reason for this is licensing arrangements for the supplied layers.
  • Environmental layers produced by analysis as in MaxEnt and Points to grid (and soon GDM), and contextual layers that are produced by Classification (are all downloaded as a part of the output).

Links to:

The Map pane has a number of functions that assist with the navigation and interpretation of data on the map.

Note that the pan and zoom operations can be accomplished by using the mouse: left click and drag to perform a pan operation, and use the mouse wheel to zoom in and out. You can also hold down the shift key and drag over an area to zoom to that area (when the mouse button is released).

The layer value hover tool is discussed in the Layers (Add to Map) section.

Current map scale and current mouse pointer latitude and longitude is shown on the lower right of the map. Both are dynamic and reflecting the current mouse position, zoom and map location.

Note that the icon beneath the slider bar marked marked previously as the Layer Hover Tool has been replaced by a Panoramio (image) icon and function. Clicking on this will display a subset of all available images within the map extent. The link above provides details of use.

The Spatial Portal focuses on where a chosen species was located, what species were found in a defined area and what are the environmental conditions in that area.

NOTE: This help documentation is complemented by a comprehensive manual for the Spatial Portal.

The Spatial Portal combines three basic data types – species, areaslayers and facets – to provide a suite of powerful visualisation and analysis tools. Species can also include assemblages of species or high taxa (genus, family etc) as a single mapped layer. Areas can be defined by 14 different options including digitizing on screen to importing. ‘Layers’ refer to either environmental (gridded structure with continuous values such as temperature) or contextual (polygonal areas with class values such as a land use layer with a forestry land-use class) geographic data that can be thought of as a layer draped over the map; commonly used in Geographic Information Systems (GIS).

You will soon be also be able to map occurrences of species based on an associated facet such as the institutional provider or the record type (specimen or human observation for example).

Tabs and their functions

Summary of the Functionality

  • Define areas of interest on the map in many different ways including address lookup, defining environmental envelopes and drawing polygons on a map More info »
  • Map and list all occurrences of one, many or all species within an area (limits apply) More info »
  • Map environmental (gridded) and contextual (polygonal) data layers More info »
  • Map named geographic features using the ALA gazetteer services More info »
  • Find geographic features using the ALA gazetteer services nearest to a point More info »
  • Create an area report summarising the information held by the Atlas for an area More info »
  • Produce species lists for a chosen area More info »
  • Sample environmental and contextual data together with species occurrences More info »
  • Predict where a species could occur More info »
  • Produce a scatterplot to visualise the relationship between species occurrence points on the map and the underlying environmental variables More info »
  • Classify an area into environmental domains (areas of similar environmentl profiles) based to groups multiple environmental layers More info »
  • Generate gridded data from point occurrences. For example, generate species richness and occurrence density from a species assemblage. More info »
  • Add layers to a map and interact with the layers More info »
  • Use the map interaction tools to manipulate the map More info »
  • Change the style of the base map and save and print maps for offline analysis (png or pdf) More info »

Spatial Portal Example Screenshots

These screenshots should give you a indication of what the portal can do:

Example Layers Added to the Map_640

Example Layers Added to Map

Area Report, this gives the option to download data for an area of interest, by clicking on any hyperlinked information.

Predict_640

Prediction of where the Tasmanian Devil could occur based on chosen environmental layers and contextual layers

Scatterplot_640

A scatterplot of the Eucalyptus globidea plotted against two different environment variables.

In this example we have also shown that you can also manipulate the display settings and faceting options using the ‘Species display settings’ button.  You can also download the image and the data using the buttons located on the left hand side.

Saving your session

When you are logged into the Atlas, you can save your session. If you have completed an extensive analysis or just a display of a suite of species and layers, you can save your session and share the Session ID with anyone. Anyone with the ID can enter it and restore the status of the layers mapped.

Save Session function

Clicking Save Session will bring up a window with the Session information and the ID-

Save Session information

You can import or upload an area into the Spatial Portal using one of three standard geospatial polygon area definitions.

The choices are to import:

  • A zip file containing an ESRI shape file set
  • A Google Earth KML polygon definition file or
  • Paste in a well known text (WKT) polygon definition.

Note that imported data should use the datum WGS84. This is the datum used by most GPS units and also by Google Maps and Google Earth. Also, if the polygon contains more than 5,000 vertices, it will be geometrically generalised to <= 5,000 vertices and you will get a pop-up warning about it. The reason for this is that our system currently struggles to handle areas more complex than that. If this limitation causes you problems, please contact support@ala.org.au.

When an area is imported/uploaded, it is added to the map and creates a new active layer available in the layers list.

Import Areas menu option

Import Areas menu option

To import a geospatial polygon area directly, on the menu select ‘Import’ and then ‘Areas’.

Import Areas choose one of three import options

Import Areas choose one of three import options

Note: The same import options are also to be found wherever an area can be defined, for example, under Add to Map Areas, or in the steps of Tools options that require a definition of an area.

Upload Areas via Add to Map Areas

Upload Areas via Add to Map Areas

Import/Upload a Shapefile

ESRI Shapefiles are a common open file format used to encode polygonal data. A shapefile is a zip file containing a number of files relating to different aspects of the definition of the area.

For more information please refer to http://en.wikipedia.org/wiki/Shapefile.

Shapefiles of defined areas can be exported from the Spatial Portal. (RL: Add link to export)

Upload a shapefile zip to create an area layer

Upload a shapefile zip to create an area layer

Name the area layer

Name the area layer

The uploaded shapefile layer is added to the map. The satellite base map is shown above.

The uploaded shapefile layer is added to the map. The satellite base map is shown above.

The uploaded shapefile becomes an active layer available for use in the analysis and export.

Import KML

KML is an international (OGC: Open Geospatial Consortium) standard used by Google Earth and Google Maps for encoding polygon data.

For more information on KML, see http://en.wikipedia.org/wiki/Kml.

A KML file can be exported from the Spatial Portal or Google earth. (RL: Add link to export)

Import KML file (*.kml) to create an area layer

Import KML file (*.kml) to create an area layer

Name the area layer for the imported KML file

Name the area layer for the imported KML file

The uploaded KML layer is added to the map. The satellite base map is shown above.

The uploaded KML layer is added to the map. The satellite base map is shown above.

The imported KML becomes an active layer available for use in analysis and export.

Paste Well Known Text (WKT)

Well-known text is an extremely simple standard for encoding geographic features. For details about the WKT markup syntax, please refer to http://en.wikipedia.org/wiki/Well-known_text.

Unlike the other formats used in the Spatial Portal, WKT is pasted into the box rather than imported as a file, but we will probably also support the import file version shortly.

WKT of defined areas can be exported from the Spatial Portal. (RL: Add link to export).

Choose to submit WKT to create an area layer

Choose to submit WKT to create an area layer

Paste in the WKT polygon details into the text field

Paste in the WKT polygon details into the text field

The uploaded WKT layer is added to the map. The normal base map is shown above.

The uploaded WKT layer is added to the map. The normal base map is shown above.

The pasted WKT becomes an active layer available for use in analysis and export.

Layer Metadata

It is there, but then again, for these temporary layers, it is minimal.

A new entry is added to the layer list for each layer added to the map; species, area or layer. All layers have a set of associated functions.

Layer list

 

Layer interaction panel

 

Layer hints panel

Layer List Panel

The layer list panel reveals the features that are associated with each layer.

Layer Types

The five different types of layers can be identified by the icons to the left of the layer name. Species are usually (occurrence) points but can be polygons in the case of checklists (list of species within an area) or ‘expert distributions’. Areas are polygons. ‘Layers’ can either be contextual (polygonal) or environmental (gridded). Contextual layers contain polygons that are described by a class. For example the contextual layer called Land Use has a class called ‘Forestry’. Environmental layers have grid cells (square polygons:) that contain numeric values. For example, the layer called Mean Annual Temperatures has grid cells containing temperature values such as ‘18.8c’,

There are links between the data of type ‘Areas’ and the data type ‘Layers’ when the layer is a contextual layer. An example may help clarify this link. One of our (contextual/polygonal) layers is called ‘Australian States and Territories’ and one of the classes in this layer is called ‘Tasmania”. You can map the layer and see all of the States and Territories or you can add an area to the map called ‘Tasmania’ – one of the layer’s polygons (in this case, multiple polygons as the Tasmanian islands are included). Mind you, if you map ‘Tasmania’ from the Add to Map | Areas function, Tasmania becomes a layer. Confusing isn’t it?!

Legend Panel

The contents of this panel is based on the type of layer that is selected in the Layers Panel or the result of analysis tool operation. These specific functions are discussed in their respective help sections.

Hints Panel

As layers are added to the map, a list of potential actions will be listed in the Hints Panel. Selecting a ‘hint’ will initiate the action and take you to the appropriate step of the wizard to add in the extra information.

The hints operate on the highest layer of the particular type (species, area, environmental or contextual layer) shown in the list. So the topmost species, topmost area and topmost environmental or contextual layer of the layer list have hints applied to them. Layers can be reordered by clicking a layer to select it, then dragging it up or down thereby causing the hints to change.

The hints are indicative rather than all inclusive. The hints try to predict the likely actions the user will want to carry out, based on the layers added to the map.

Each of the layer types have their own set of actions added to the hints. However if both species and areas are added to the map, then their hints combine.

Summary of hints for layer type:

Layer (environmental and contextual layers)

  • View Metadata for the layer

Area

  • Area reports
  • View Metadata for My Area
  • Download Species List for My Area
  • Download All records for My Area
  • Generate Classification for My Area

Species

  • View Metadata for the Species
  • Download All Records for the Species
  • Generate Scatterplot for the Species
  • Generate Prediction for the Species

Area and Species and Layers

Note: the Area and Species hints that combine are shown in bold

  • Area report
  • View Metadata for My Area
  • View Metadata for Species
  • View Metadata for the environmental or contextual layer
  • Download Species List for My Area
  • Download All records of the Species for the Area
  • Generate Classification for My Area
  • Generate Scatterplot for the Species in My Area
  • Generate Prediction for the Species in My Area

 

Tools available

Tools available

Tools operate on one or more of the three basic data types.  Data does not have to be pre-mapped, but will be used as a prompt by default if it is. Area can be the base of a function as in reporting species,  occurrences and associated data. Area can also be used in conjunction with other tools such as scatterplots (species plotted against layer values), classification (integrating gridded layers) or prediction (interpolating species based on gridded layers).

The Spatial Portal now permits re-use of analysis layers. There are three types of layers produced from the tools

  • Points (from Generate points)
  • Environmental – gridded layers with continuous values in each grid cell and
  • Contextual – polygonal layers with class values for each polygon

Not all combinations of re-use are possible, for example contextual layers cannot be used in classification. The following table summarizes the possibilities. The table is read left to right, the rows represent tools that have been run while the columns represent tools that could be run on those outputs.

2. Tool
1. Tool Tool Layer Type # Layers Hover tool Sampling Scatterplot Classify Predict Tabulate Area Reports GDM
Area reports
AOO and EOO
Nearest locality
Scatterplots
 Points to Grid Environmental 2 Yes Yes Yes Yes Yes  Yes
Generate points Point  1  Yes Yes
Phylogenetic diversity
Classify Contextual 1 Yes Yes Yes Not yet
Predict Environmental 1 Yes Yes Yes Yes Yes  Yes
GDM Environmental Many Yes Yes Yes Yes Yes