In the Species Trait Experiment (STM) you can analyse the effect of environmental variables on 1 or more species traits, and also test how traits differ among multiple species.
Run an STM on EcoCommons
On the top of the page click on “Analysis Hub” and then on “Modelling Wizards”. Under “Primary experiments” choose “Species Trait Modelling Experiment”.
Step 1: Description tab
Enter the title for your experiment in the first box (e.g. Summer vs winter distribution of Monarch butterfly).
(optional) You can also add a description of your experiment in the box below if you want to convey more information. Some researchers use this box to record their research questions or hypotheses for later referral.
Click “Next” on the bottom of the page.
Step 2: Algorithms tab
You can run two different trait analyses on EcoCommons:
1. Test the effect of environmental variables on traits: This will run an additive model that will test how the selected species traits are affected by all selected environmental variables (e.g. trait 1 ~ env1 + env2
2. Test the differences in traits among species: This will run a model that will test how the selected traits differ among species (e.g. trait 1 ~ species).
Note: Your input dataset that you select in the next tab will need to include multiple species to be able to run this test.
- Select the algorithm you would like to use to calibrate your model. You can choose one or all algorithms to run your experiment.
- (optional) Configuration can be changed by changing the value or making a different selection from the drop down menu. The configuration options are currently set to the standard default values of the R packages. More information about each configuration option can be found on the support page for that particular algorithm.
- Click “Next” on the bottom of the page.
Step 3: Input Datasets tab
- Select your pre-loaded species trait dataset by clicking on "+Select an occurrence dataset".
Note: If you click this and you have no loaded species occurrence datasets you will need to visit the dataset page and upload the required data.
- In the pop-up box select the dataset you wish to use in your STM.
- Click "Next" on the bottom of the page.
Step 4: Configuration tab
- The first 5 rows of data will be shown in this tab. You can select which traits and/or environmental variables should be used in the analyses by using the drop down menus under each column. You need to indicate whether your trait data are continuous, nominal (categorical data with no order, such as color) or ordinal (categorical data with an order, such as cover: low-medium-high), and whether your environmental variables are continuous or categorical. Note: you have to nominate at least a column for latitude, longitude and one trait variable. Environmental variables are optional here, as EcoCommons provided environmental data can be selected in the next tab.Note: Whether or not you select a 'species' column will define whether you run the experiment for individual trait measurements or for species-level trait measurements. Species-level analysis will use the entire dataset as a whole in the analysis. If you want to account for repeated measurements per species, select the species column as random factor and make sure you select a Generalized Linear Mixed Model on the Algorithm tab.
- Click "Next" on the bottom of the page.
Step 5: Climate & Environmental Data tab
Note: This tab is optional if your input dataset includes environmental data and you have selected these columns on the Configuration tab. You can choose to add environmental layers from datasets provided by EcoCommons. If you have not selected any environmental variables in the Configuration tab, this tab is required.
- Click on " Select datasets".
- In the pop-up box you can enter search terms to filter for required datasets or filter by collection, resolution and/or domain.
- Once you have found the dataset/s you are looking for select them and click “Close”.
- When back on the Climate & Environmental Data tab you can select/deselect data layers on the left site of the white box
- (optional) You can visualise each of the data layers by clicking the green eye icon, and on the right hand side of the map you can toggle which data layer you want to visualise.
- Once you have selected all your environmental and climate layers for each subset click “Next” on the bottom of the page
- Note: If you choose data layers that do not have the same resolution you can choose whether they should be scaled to the finest or coarsest resolution.
Step 6: Constraints tab
In this section you can select the area in which to train your model. This means that only the occurrence records from the constrained area are used, and pseudo-absence or background points are only generated in this area. It is good practice to remove parts of the geographic or environmental space where you are certain your species will not be found.
The default constraint is the convex hull (= minimum polygon) around all occurrence records indicated by a blue outline on the map. The different constraint options are:
Use Convex Hull for each individual species
- You can add a buffer around the convex hull by nominating a distance in km. The buffer will be added on the map once you click outside the white box.
Select constraints by pre-defined region
- Select one of the region types that are currently available in the BCCVL: Local Government Areas, National Resource Management Regions, Australian States and Territories, IBRA 7 regions, River Regions, Drainage Divisions Level 1 or 2, Marine Ecoregions of the World, Integrated Marine and Coastal Regionalisation of Australia (IMCRA4) Provincial or Meso-scale Bioregions.
- Find the region of your interest in the drop-down menu. You can select multiple regions.
- You can also add a buffer around the pre-defined region constraints.
Use Environmental Envelope
- This is the geographic extent of where all selected climate/environmental datasets overlap.
Draw constraints on Map
- Click on “Start drawing”, then click on the map to draw a shape on the map to which the model will be constrained.
- Select a shapefile from your computer to use as the constraint.
Note: The model will be trained on the selected area, and the results will include a predicted distribution map for the constrained area, as well as a projection to the geographic extent of your environmental/climate layers.
Once you selected the constrained area click “Next” on the bottom of the page
Step 7: Run tab
Ensure you are happy with your experiment design.
If none of the tabs have a triangle with an exclamation mark, your experiment is ready to go.
Click “Start Experiment”.
If any of your tabs have a triangle with an exclamation mark, revisit them and ensure you have filled in each component correctly.
A log file will now be sent to our virtual machines where your experiment will be run.
You can view the progress of your job under “My job”. Once your job is finished you can view the results by either clicking “View all results” inside your job or click on the “My results” tab under Workspace.
For now, sit back and relax, grab a coffee, or do some other work without being hampered by a slower computer that is running heavy models in the background.