ALOC (short for Allocation) is a highly efficient yet simple classification method from the PATN package (http://www.patn.com.au) designed to classify large volumes of data. Think of ALOC as combining multiple layers of environmental data (e.g. mean annual temperature, slope, and precipitation) into one new layer that captures the essence of all chosen layers.

You select environmental layers and the number of groups required and ALOC produces a map of the resulting groups for the defined area. These groups are called “environmental domains” after work done by Henry Nix (reference below).

Such classifications are done for many reasons. Examples include:

  • Understanding the distribution of factors that you have some indication of controlling the distribution of a particular class of organisms. Viewing environmental domains of important factors should provide useful insights.
  • Generating a regionalisation for areas where suitable biological data is not available for biodiversity analysis or for reserve design.
  • Exploring the relationships between environmental layers.

From the menu option, select ‘Tools’, and then ‘Classify’.

Run the Classification Wizard

Classify Step 1

Step 1 of 4 - Select an area for Analysis

Note the ‘Define new area’ will involve an extra step (please refer to Add Area for additional information).

Classify Step 2_640

Step 2 of 4 - Select two or more Environmental Layers

Select two or more environmental layers to be used for the classification. The layers must be environmental (not contextual) and therefore they contain continuous values such as temperature, precipitation or slope. Any number of layers can be selected to be classified. It is however wiser to use fewer layers that you know provide a significant, yet independent signals, but this will depend on the intent of the classification.

The Spatial Portal has over 200 environmental layers covering an extremely wide range of environmental scenarios, that experts believe could have some control on the distribution of organisms. Many of these layers are highly correlated. If highly correlated layers are used, the classification will be weighted accordingly, regardless of how ‘intelligent’ ALOC is.

To assist, the Spatial Portal has built a form of correlation between all environmental layers (see http://spatial.ala.org.au/files/inter_layer_association.csv). It is important to note that the relationship between pairs of layers are calculated on their spatial extent. In most cases, this extent will be the Australian ‘region’ but some layers such as the worldclim (terrestrial) and CARS (marine) layers have near global extent. The comparison between grid cells are made ONLY when both layers have data. This implies that

  • Terrestrial layers are not compared with marine layers
  • World extent layers will be compared over their full extent
  • Australian region extent layers will compared over their Australian extent
  • World extent layers will be compared with smaller extent layers over only the smallest spatial extent.

When a layer is added to the classification, the Portal examines the relationship between it and all other environmental layers. It then colour codes the remaining layers in ‘traffic light’ colours. Green against a layer suggests that there appears to be little correlation between that layer and the closest-related selected layer. Orange is intermediate while red suggests that there is a fairly high correlation between the layer and at least one of those already-selected layers. Remember that while there may be a high correlation, a layer may still provide a subtley  different factor that may be important. When a new layer is added, the colours are re-calculated on the basis of the closest relationship to any existing layer added to the classification.

NOTES:

  • The layer dissimilarity matrix is updated weekly to reflect new environmental layers.
  • The more layers that are selected for Classification, the greater is the likelihood of high correlation between layers producing a biased classification.
  • The relationships between the layers has been calculated at the national extents. Layers may therefore be more or less related at different scale
  • When the extent of the layers used differs, the extent of the classification layer will be the same as the layer with minimal extent. What this means is that for comparing grid cells, comparisons will only be made when grid cells have a full complement of the selected layers. If you get a surprisingly small extent classification layer – this will be the reason. This effect will most often be seen with marine layers where some have near global coverage while others are limited to the Australian or even just the coastal Australian region.
Classify Step 3

Step 3 of 4 - Enter number of groups to generate

Select the number of groups to be generated in the classification. The greater the number of groups, the finer will be the differences between the environmental domains.

Note: The algorithm may not produce exactly the number of groups requests because that number of groups is unstable. The classification algorithm seeks the closest number of stable groups. If you ask for 20 groups for example, it may produce 21.

Note: The more layers that are used and the larger the Active Area, the longer the analysis will take.

Classify Step 4

Step 4 of 4 - Name Classification Layer

Enter a name for the classification layer.

Classify Step 4 Data preparation Dialogue Box

Classification progress dialogue box.

The data preparation progress dialogue box tells you roughly how long it will take before the results are produced.

Classify Zipped Results File

Classification results and readme.txt are available in the downloadable zip file

Once completed the Opening My Classification dialogue box will appear. This allows you to open/save your classification.

Classify map_640

A map will be produced with the requested number of groups. The colours of the groups are not arbitrary: similar group/domain colours indicate similar characteristics; and the reverse is true for very different group colours.

Faceting on Classification groups

When a classification layer is active (its legend is displayed), you can facet on classification groups via its legend. When you want to highlight/identify a single classification group on the map, select that group in the legend and the group will be highlighted in red on the map. The only conrol over the highlight is its transparency. To turn of group fecting, simply select ‘none’ in the facet drop down in the legend.

Highlighting a classification group

Faceting on a classification group

 

Metadata

Classify Metadata

The metadata and the results from the classification.

When the layer metadata icon icon is clicked in the layers list the metadata popup is displayed for the Classification layer. The metadata can be displayed in a separate window.

  • Each model is assigned a unique identifier that allows it to be displayed in subsequent sessions e.g. Reference number: 1312786878649. This value is given in the metadata of the layer. The Restore Prior Analysis tool uses this identifier to restore a model created earlier. It can be from a totally different session, browser or even PC.
  • The number of final groups. This can be slightly different from the number of groups requested. This occurs if the classification does not naturally fit the selected number of groups.
  • The layers used in the Classification.
  • The ‘inter-layer dissimilarity matrix’. This matrix shows the ‘environmental distance’ between all pairs of layers. Values close to zero mean that they layers are closely related (a small distance apart in environmental space) while values near one mean that the layers have no relationship – they are independent.
  • Active Area polygon – the bounding box’s longitudes and latitudes. The definition at the time of the classification is listed.
  • Group means and colours. This is a CSV (comma-separated values) formatted file with one record for each group and with the following columns:
    • Group number
    • Red, green and blue saturation. The colours relate to the characteristics of the groups.
    • Layer values. Each Layer used in the classification will be represented by a mean for each group. This is the ‘stereotype’ of the group.

Steps used by ALOC to produce a Classification

  1. Build a set of seed groups that are greater than a threshold distance apart (using Gower Metric).
  2. Allocate all points on the map to the seed groups.
  3. Calculate the group centroids.
  4. Iterate by removing each point from its allocated group, calculate the association (Gower metric) to all groups and then allocate it to the closest group.
  5. Repeat 4 until no points change groups.
  6. The colours are produced by a Principal Component Analysis using the inter-group distances (dissimilarity based on all the layers).

NOTE: When environmental layers selected for the classification do not have the same spatial extent, the classification will only be performed on grid cells that contain values for all layers. If this occurs, the resulting classification layer will only cover the area of the layer with the smallest spatial extent (area). While comparisons between grid cells could be made taking available data into account, it was deemed expedient to remove such cells as in many GIS circumstances, the classification could be  extremely biased if such cells were included.

A case study

A case study on using the Classification Tools to investigate the classification of landscapes in Australia, is given by Prof Brendan Mackey of the Australian National University, Canberra.

Read the Case Study »

Referenced Links

Belbin, Lee, Marshall, C. and Faith, D.P. (1983). Representing relationships by the automatic assignment of colour. Australian Computer Journal, vol. 15, no. 4, pp. 160-163.

Belbin, L. (1987). The Use of Non-hierarchical Allocation Methods for Clustering Large Sets of Data. Australian Computing Journal, vol. 19, no. 1, pp. 32-41.

Gower J.C. (1967). Multivariate analysis and multidimensional geometry. The Statistician, vol. 17, no. 1, pp. 13-28.

Nix, H.A. (1986). A biogeographic analysis of Australian elapid snakes, In: Atlas of Elapid Snakes of Australia. (Ed.) R Longmore, pp. 4-15. Australian Flora and Fauna Series Number 7. Australian Government Publishing Service: Canberra.

The Predict option under the Tools Menu helps you to identify where a species could occur – not just where it has been observed!

The method used is called “MaxEnt” for Maximum Entropy and was developed by Stephen Phillips.
See (Maxent software for species habitat modeling).


To start a Prediction, select from the Menu Option, “Tools”, then “Predict”.

MaxEnt looks at where species occur in terms of location and environment, and also where the species does not seem to occur. A model is built using the available species and environmental data and the result is essentially, a probability surface showing where the model suggests the species could occur.

You need considerable expertise in modelling, to understand the environmental variables and areas to factor into the prediction tool. Only then can you extrapolate any meaning into the results of the predictions.

Important: The area used for the prediction will be the defined active area. If you have not specifically defined an active area, then the current map extent in the mapping window forms the active area. This is extremely important in prediction as you will not want to extrapolate too far beyond the environmental conditions where the species occurs. It is strongly recommended that you circumscribe the active area to fit the occurrence locations as well as cover the area of interest (which may extend beyond the mapped occurrences). This is always the trade-off!

Run the Prediction Wizard

Prediction Step 1

Step 1 of 5 - Select an area for analysis

(Please refer to Add Area for additional information).

Prediction Step 2

Step 2 of 5 - Select Species (or genus, family or order).

The auto-complete section mechanism is the same as on the Add to Map ->Species. Type the first three letters using either a scientific or common name and a list of suggestions is produced. Select a species (or higher taxonomic class) by clicking on it. The number of occurrences is given alongside the species (or higher taxonomic class).

Selected species will be mapped, if not mapped previously. See Add to Map ->Species.

The last mapped species (or genus, family or order) is included as a species selection choice in Step 2 of 5 of the wizard. (See image below).

Species can also be uploaded using two other methods:

Prediction Species preselected

The last mapped species (Macropus rufus) is included as a species selection choice

Predict Step 3_640

Step 3 of 5 - Select your environmental layers


Prediction is mainly based upon environmental layers, but after some research a new version of MaxEnt is able to accept a subset of the contextual layers as predictors. The contextual layers available for prediction are:

  • Land cover
  • Land use
  • Vegetation - condition
  • Vegetation types - native
  • Vegetation types - present

The selection of appropriate layers is extremely important if an effective model is to be built. The Spatial Portal has around 300 layers covering an extremely wide range of environmental and contextual variables that experts believe could have some control on the distribution of organisms. Many of these variables / layers are highly correlated. If highly correlated layers are used, the model will be weighted accordingly by those variables, regardless of how 'intelligent' the method. It always pays to know your organisms well! Know what environmental and contextual factors can influence or control their distribution.

NOTE: The relationships between the layers for the colour coding has been calculated at the national extents. Layers may therefore be more or less related at different scales.

Every layer added to the model may improve it, or over-fit it. To assist, the Spatial Portal has built a form of correlation between all its environmental layers. When a layer is added to the model, the Portal examines the relationship between it and all other environmental layers. It then colour codes the remaining layers in 'traffic light' colours. Green against a layer suggests that there appears to be (not necessarily 'is') little correlation between that layer and the selected layer. Orange is intermediate while red suggests that there is a fairly high correlation. Remember that while there may be a high correlation, a layer may still have a subtle different factor that may be important. When a new layer is added, the colours are re-calculated on the basis of the closest relationship to any existing layer added to the model.

Other traps for the unwary include using occurrences that have a wide range of observation dates. In this case, the model may be poor because of migration, changed environments or even evolution. A key issue is that the species should be in equilibrium with the environmental variables. The worst case may occur with an invasive species where it's spread may be rapid and where it is far from reaching 'environmental equilibrium'.

Step 4 of 5 - Select Optional MaxEnt parameters

  • Jacknife in MaxEnt - selecting this option examines the significance of the environmental variables - one at a time. Jacknife tests identify environmental variables with highest gain when used in isolation. High-gain variables have the most useful information when used by themselves. The environmental variable that decreases the gain the most when it is omitted has the most information, that is not obviously present in the other variables.
  • Each model is assigned a unique identifier that allows it to be displayed in subsequent sessions e.g. Model reference number: 1310016793060. This value is given in the metadata of the layer. The Restore Prior Analysis tool uses this identifier to restore a model created earlier. It can be from a totally different session, browser or even PC.
  • Create response curves. This option creates a graph for each layer value (x-axis) against probability (y-axis). These curves are useful for evaluating how well the selected layers have captured the species environment.
  • Random test percentage. This option allows the user to define the percentage of the occurrences for testing against the output model.
  • See in the Referenced Links a tutorial on running MaxEnt.

Step 5 of 5 - Enter a name for the Prediction Model

Click on the 'Next' button to run MaxEnt.

The map window becomes grayed-out and a Prediction data preparation and running time dialogue popup appears on the screen, to indicate how long it should take before the MaxEnt output is displayed.

Note: Building a MaxEnt model can take some time. The time is dependent on a combination of factors: the number of occurrences, the size of the geographic extent of the model, and the number of environmental layers selected.

Prediction estimated generation time dialogue box

Opening My Prediction Results

Opening My Prediction Results Results, including environmental response graphs, are available in the downloadable zip file

The map is not included in MaxEnt results zip file, as might be expected. The reason for this omission is to hide the location of potentially sensitive species. The Spatial Portal does however display the prediction map - and as with all mapped objects, this layer is added to the list of active layers.

Prediction_640

Map window displays the prediction probability layer

Metadata

When the layer metadata icon icon is clicked in the layers list the metadata popup is displayed for the Prediction layer. The metadata can be displayed in a separate window.

Metadata Prediction

The metadata and the results from the prediction. Click to see the Model Reference Number.

The Model Reference number used to restore prior analysis is shown at the top of the metadata.

The metadata contains the methods and modelling used to create the prediction. Response graphs show the impact each of the chosen environmental layers had on the prediction. An image of the prediction probability map layer is also included.

A Case Study

A case study on using the MaxEnt Prediction tool to predict the distribution of the Greater Glider, was prepared by Dr Jane Elith, of The University of Melbourne.

Read the Case Study »

References

  • Elith, J., Phillips, S.J., Hastie, T., Dudik, M., Chee, Y.E. and Yates, C.J. (2011). A statistical explanation of MaxEnt for Ecologists. Diversity and Distributions, 17, 43-57.
  • Phillips, S.J., Dudík, M., A and Schapire, R.E., Maximum entropy approach to species distribution modeling PDF (185 KB)
  • Phillips, S.J., Anderson, R.P. and Schapire, R.E., 2006. Maximum entropy modeling of species geographic distributions. Ecological Modelling, vol. 190, pp. 231-259. PDF (902 KB).
  • Phillips, S.J., A Brief Tutorial on Maxent. Word (4.3 MB).

Demonstration Youtube Video

By Lee Belbin, Geospatial Team Leader

The Spatial Portal will remember a previous set of (environmental) layers where there is an option to select multiple layers, as in most of the analysis tools and for adding layers to the map.

Any set of environmental layers can be uploaded, pasted, or downloaded for later use. The ‘Short name’ of the layer is used for brevity. See About Short Names »

Layer Set Options

  • Choose to use the pre-set 5 most independent terrestrial layers for analysis. More info »
  • Upload a set of names of layers using the layer ‘Short name’. More info »
  • Paste in a list a set of names of layers using the layer ‘Short name’. More info »
  • Use a search field to find and select layers. More info »
  • Download a set of selected ‘Short name’ layers as a text file. More info »
  • Allow the system (via a cookie) to remember up to 20 of the user’s latest layer sets. More info »

About Short Names for Layers

Layer Short names are used to select environmental layers in the upload, download, and paste in a set of layers. (They are also used behind the scenes in the layer cookie and the best 5 terrestrial layers).

To see a list of all the ‘Short name’ (column four) layers, click on the layers link in the various dialogue boxes (See Example 1, Example 2).

A CSV or JSON layers file can be downloaded for later reference.

Layers list - see the Short names

Layers list - see the Short names

Pre-set Five Best Terrestrial Layers

Best 5 independent terrestrial environmental layers

Best 5 independent terrestrial environmental layers

Select the ‘Best 5 layers’ from the pull down list and the layers will be checked. The user can continue to select / deselect layers.

Import/Upload Short Name Layer Set

Upload a text file of comma-delimited 'Short name' environmental layers

Upload a text file of comma-delimited short name environmental layers

Press the ‘Upload set’ button, browse to find the text file, and matching layers will be selected. The user can continue to select / deselect layers.

Example Upload 'Short name' Layers Set text file

Example Upload short name layers set text file

Example selected layers »

Paste in Short Name Layers

Paste in your own comma-delimited short name layer text

Paste in your own comma-delimited short name layer text

Select the ‘paste a layer set’ from the pull down list. The ‘Paste in a layer list’ dialogue box comes up.

Paste into the text box a comma-delimited set of layer short names

Paste into the text box a comma-delimited set of layer short names

Press the ‘Next’ button and the layers will be imported. The user can continue to select / deselect layers.

Layers selected after pasting in a set of layer short names

Layers selected after pasting in a set of layer short names

Select layers by searching in the 'Add from search' field

Select layers by searching in the Add from search field

The ‘Add from search’ field is an auto-complete select box. Partially typing in the Layer’s name or Short name will reduce the available selection. Click on the desired layer in the pull down list and the layer will be checked.

The user can continue to select / deselect layers.

Example selected layers »

Download a Layer Set

Download a text file set of comma-delimited 'Short name' environmental layers

Download a text file set of comma-delimited short name environmental layers

Press the ‘Download set’ button to save a text file with a set of comma-delimited ‘Short name’ environmental layers.

Download sample layers set

Download sample layers set

This ‘Short name’ set can be later Uploaded to reselect the same set.

My Sampling shows up to 20 of the user’s last layer sets available for reuse

My Sampling shows up to 20 of the user’s last layer sets available for reuse

Select the ‘My Sampling’ set from the pull down list and the layers will be checked. The user can continue to select / deselect layers.

Example selected layers »

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