- Learn more about:
- What analytical tools are available on the Spatial Portal?
- What is sampling?
- What is filtering
- What is prediction?
- What is classification?
- What is a scatterplot?
- What can I map?
- Can I save a map or analysis and come back to it later?
- Can I use the mapping tool on my own website?
- How accurate are the locations displayed on a map?
- Why are there no species records for my area?
- Where do the map layers come from?
- Can I map my own list of species?
- Can I map my own list of occurrences?
- Where does this environment occur?
What analytical tools are available on the Spatial Portal?
The Spatial Portal provides a range of analytical tools that demonstrate the value of integrating spatial information:
- area report
- nearest locality
- scatterplot list
- points to grid
- generalized dissimilarity modelling
What is sampling?
The term ‘sampling’ comes from the concept that records in the Atlas of species locations can be used to take a sample of the values of any of the environmental and contextual layers available in the Spatial Portal. For example, if you have two records of a species at two separate locations and want to find out what the annual rainfall and mean annual temperature associated with the sightings, then Sampling is how to do it. In this case, sampling will produce a spreadsheet file containing the two locations (=rows) and associated data such as the species names, data flags etc and two additional columns; one for precipitation and one for mean annual temperature.
What is filtering?
Filtering is subsetting your data using the facets available via ‘Add to map | Facets‘ and on the legends in the Spatial Portal. If you wanted to map all species occurrences that were recorded between 1900 and 1920, you are effectively filtering on the total Atlas holdings for those particular records. To do this, you would use ‘Add to Map | Facet’, select the Facet called “Decade” and check boxes for 1900 and 1910. The result will be a map of all occurrences between 1900 and 1920. You could for example also filter occurrence records that came from certain institutions or by a group of Collectors.
If you have mapped a species (or genus or even list of species), you can use the same mechanism in the legend area of the map to select the facet of interest and then the values of that facet and then create a new mapped layer that has only the selected characteristics.
Filtering can also be applied to a set of occurrence records that has been uploaded, as long as it has a set of fields that are facetable.
What is a scatterplot?
A scatterplot is an X-Y graph of the sampled values of a pair of environmental variables from a set of species (or genus etc.) locations. Each point on the scatterplot represents the values of the pair of environmental values for a single occurrence record. You could for example plot mean annual temperature (called Bio01 in the Spatial Portal) against annual precipitation (Bio12) for say Eucalyptus gunnii (Cider Gum). In this case, temperature will form the X-axis and rainfall the Y axis and the points on the graph will show you what combinations each observation has. The distribution of points is usually informative.
See Scatterplot case study for an example of how this tool can be used.
What is prediction?
If you want to find out where a species could occur, you need to use the environment at known species locations. Once you know what environment a species prefers, you can determine where those environmental conditions occur and would therefore expect the species to occur. This approach is called ‘niche modelling’. The spatial portal uses a modelling technique called MaxEnt developed by Steven Phillips. This method is robust for handling presence-only—data the situation where we know where a species occurs but are unsure about where it does not occur.
Input to MaxEnt is a list of species occurrences and a set of hopefully relevant environmental layers. The outputs are a probability surface map and a suite of diagnostic graphs and values.
See Prediction case study for an example of how this tool can be used.
What is classification?
Classification combines a set of environmental layers into one new layer that retains most of the information in all the input layers. The classification groups on the output layer are referred to as ‘environmental domains’. Each environmental domain (group) on the map is colour coded to reflect the relationships with all other domains; similar coloured groups represent similar environments.
Why is this used? The distribution of species is controlled by environmental conditions and species interactions. When there is inadequate biological data, which is most of the time, environmental domains may be a useful surrogate for biodiversity in environmental planning and management. The classification method used in the spatial portal is called ALOC from the ecological analysis package called PATN.
See Classification case study for an example of how this tool can be used.
What can I map?
In the Atlas Spatial Portal, you can map:
- taxa (species, genus etc.) occurrences as points
- species polygons as best spatial estimates of their distributions
- areas as defined interactively on the map, defined by named features or uploaded
- environmental layers as grids of continuous values, eg annual rainfall, and contextual layers of polygons with class values, eg land use.
Can I save a map or analysis and come back to it later?
Maps can be downloaded in various formats and an analysis can be restored by entering the analysis id displayed at the time of the run.
Can I use the mapping tool on my own website?
Most of the functions of the Atlas are written as web services. This means that most of the functions that are used on the Spatial Portal can be embedded in your own web site. For example to display a map of the Tasmanian Devil, you would use the URL http://biocache.ala.org.au/ws/density/map?q=Sarcophilus%20harrisii.
See Web Services for a list of available spatial web services.
How accurate are the locations displayed on a map?
The data supplied by our data providers determines the accuracy of features on a map, and the accuracy of occurrence locations varies greatly. Some records will only state that the species was observed in Australia while others will be accurate to within less than 5m on the ground. Named locations are generally accurate to within 100m but this will depend on the context, eg the centre of a town in 1950 will probably not be the same as it is today.
Why are there no species records for my area?
No species may be reported for your area because:
- the Atlas doesn’t know about them yet; the information has not be supplied to us by our data providers. If you are aware of records from your area, please contact us [mail to data]
- the location of occurrences in your area may have been rounded by a data provider and consequently, may incorrectly fall outside your area.
Where do the map layers come from?
The Spatial Portal uses a variety of map layers. The basemaps come from Google, OpenStreetmap and a simple world political boundary outline map useful for publishing thumbnails of species distributions. The environmental and contextual layers come from a wide range of providers.
See http://spatial.ala.org.au/layers for a list of the layers with links to the data providers and other layer details.
Why do some maps show dots outside the real range for the species?
Sometimes the data used to generate maps is incorrect. This may be because:
- location data transcribed from a specimen label is too general to be converted into a latitude and longitude, eg what is the latitude and longitude of the location ‘Atherton Tableland’?
- the coordinates provided are too coarse, eg whole degrees rather than to three decimal places.
At other times the location is correct and the specimen was found in, eg a botanic garden, a reptile park or supermarket (especially with insects, frogs and other small creatures).
Can I create and map my own list of species?
Yes, you can use http://lists.ala.org.au to create a list of any combination of species and use that list in a variety of places in the Atlas. To create a List, you will need to have a login as the List is stored against your name. The List can simply be a set of species names, one per line in a CSV file. Names should be the standard genus species pair.
The Atlas matches the uploaded names against the National Species List. Any unmatched names are flagged. You can then use the Google search option to find out more about any of the unmatched names.
Once the List has been created, you can share administration of it with any other registered users. The choice is yours.
When the list has been created, it can be used in the Spatial portal anywhere a species can be entered; use “Use existing species list”
Can I map my own list of occurrences?
Yes, you can map your own list of species (taxa) or map a set of taxa locations and associated data. All that is required is a CSV-formatted file with the records starting with three values
- An identifier (some alpha or numeric code)
- Longitude in decimal degrees
- Latitude in decimal degrees (-ve south latitude)
and then any number of optional values that you may want to filter/display on. Those additional fields can be either alpha or numeric.
Use the Spatial Portal menu item ‘Import | Points
Where does this environment occur?
This question can be viewed as the reverse of sampling. A user selects environmental layers of interest and lower/upper bound values for each layer. Filtering then identifies how many species are to be found within the defined environmental envelope. You can access this tool from the Spatial Portal menu item ‘Add to Map > Areas > Environmental envelope‘.
Why would you want to use this tool? If, for example, you know the environment that best suits Pinot Noir grapes, you can find out where in Australia (or the world) suitable conditions occur (see the Pinot case study), if we have the required environmental layers.