This tool samples environmental and contextual data layers at locations defined by species, genus, family etc. occurrences in a defined area.
Think of this tool as driving a needle through through the occurrence locations and reading off all the values of a user-selected environmental and contextual layers. In other words, the occurrences define the geographic locations where the layers are sampled.
The data produced from Sampling contains records of all the species occurrence details (mainly in Darwin Core fields), data quality checks and with chosen environmental and contextual values appended to the record.
From the Menu Option, select ‘Export’ and then ‘Point Sample’.
Note the ‘Define new area’ will involve an extra step (please refer to Add Area for additional information).
If you have a one or more predefined areas already mapped, then these will be available as an option to restrict the sample to any one of these active area layers, e.g., ‘My Area’, or in this case the named area ‘Queanbeyan’.
Sampling, select one of the following methods:
Environmental data will return a numeric value, for example a value of the mean annual temperature at each of the point locations. Sampling contextual layers will return a category/class, for example, a land-use category such as ‘Forestry’ or a State / Territory such as ‘Victoria’.
The download data file also contains TRUE/FALSE values for a range of data quality checks processed by the Atlas, or issues raised by users (e.g., ‘Suspected outlier’). Each column will only appear, if at least one record has a value of TRUE. See the Google Spreadsheet below for more details.
There are several ways to easily select multiple layers, or to reuse a layer set from a previous session. A pre-set best 5 terrestrial layer set is also available. See Selection of multiple layers »
Clicking on the icon (to the RHS of the name column) when selecting environmental or contextual layers to sample, shows the metadata describing the layer.
Press the ‘Next’ button on Step 3 Sampling to access the Download dialogue window.
Fill in the fields and then press the ‘Download All Records’ button.
Following the selection of the layers, a zip file is produced containing the occurrence records as a data.csv file, and the citation details of each of the data providers as citation.csv.
NOTE: Data files can be potentially very large so they are zipped for efficient downloading. The citation file is included to ensure data providers are acknowledged accurately. You will need an application that can unpack zip files.
NOTE: When dealing with ‘sensitive species’, the records may flagged and/or altered. The following can occur
It is therefore important to carefully view the downloaded records and the associated README.HTML file to ensure that you are aware of information that may affect any subsequent analysis of the data. For example, while Prediction will not run on sensitive species, downloading the records and uploading them for use in Prediction would be extremely unwise.
The data.csv file can be used in a wide range of analysis packages. For example, the ‘R’ language and environment for statistical computing and graphics.
‘R’ compiles and runs on a wide variety of UNIX platforms, Windows and MacOS. For more information see (http://www.r-project.org/).
The data.csv file downloaded from the spatial portal can be used directly in the command line in ‘R’. It takes only two lines of ‘R’ script, or four, if comments are included (as shown below). Paste them into the ‘R’ console. Remember to change the path to reflect where your data.csv file is kept.
Sample ascii text file for loading data.csv into ‘R’ – r_samples_load.txt (1 KB)
##### Reads the results of a download from the ALA spatial portal into
##### R dataframe 'data.csv' from default path, currently C:/Data/R
samples<-read.table("C:/Data/R/data.csv", sep=",", header = T)
|Information withheld during processing|