Species Sensitivity Distribution models, calculated using ssdtools R package, used to derive site-specific environmental quality guideline values for fuel contaminated soils at sub-Antarctic Macquarie Island.

Full description

This data record provides the raw data and analysis code used to generate a series of Species Sensitivity Distributions (SSDs) for Macquarie Island fuel contaminated soils. These data and results are presented in a publication by King, Wasley and Richardson, submitted to Integrated Environmental Assessment and Management (IEAM) in 2024. The data and code are provided here to allow the manuscript results to be fully reproducible.

Raw data is provided in the /data directory, where there are 2 files:

File: data/MaccaSSD_Data-Compilation.xlsx
This file is also provided as Supplementary Information B with the publication. The data presented is a full compilation of published Critical Effect Concentration data known for Macquarie Island fuel contaminated soils. A subset of 13 values were selected for subsequent analysis and are indicated with pale blue highlight. The rationale for selection is described. Data sources are fully referenced within the file.

File: data/MaccaSSD.csv
This file is the subset of 13 selected values (from the compilation file: MaccaSSD_Data-Compilation.xlsx) for use in Species Sensitivity Distribution models used to derive site-specific environmental quality guideline values for fuel contaminated soils at sub-antarctic Macquarie Island. The 13 values are analysed using the ssdtools R package (version 1.0.6.9009). The data files includes:

Group = invertebrate, plant or microbe    
Taxa.Label = species name or description; F=Fresh Fuel, A=Aged Fuel, %= soil carbon content.     
EC20 = Concentration causing 20% effect, provided in or converted from published source for soil carbon content used in study    
EC20.C1 = Concentration causing 20% effect, normalised to 1% soil carbon
EC20.C3 = Concentration causing 20% effect, adjusted to 3% soil carbon    
EC20.C15 = Concentration causing 20% effect, adjusted to 15% soil carbon.
EC20.C48 = Concentration causing 20% effect, adjusted to 48% soil carbon.
EC10 = Concentration causing 10% effect; calculated as EC20/2

R files:
- 0-ssdtools_Install.Rmd
- 1-ssdtools_EC20.Rmd
- 2-ssdtools_EC20_Normalised.Rmd
- Supplementary Information C_EC10.Rmd (saves as: Supplementary Information C_EC10.nb.html)
- Supplementary Information D_EC20.Rmd (saves as: Supplementary Information D_EC20.nb.html)

These are presented in a workflow that provide derived SSD models for EC20 data (using published soil carbon content) and subsequent alternative SSD models for normalised and adjusted soil carbon levels (3, 15, 48%) and for EC10. The code are annotated throughout to allow interpretation.

The code will direct output files (plots and tables) to the /output directory.
Supplementary Information C & D save as html files via R notebook.

The folder named /predicted contains a series of .Rdata files that are saved predicted values (model average) which were generated within the code provided. The code lines where these were generated are hashed out as they take a long time to run. They are subsequently loaded for plotting predicted values, named:
- pred_EC10.Rdata
- pred_EC20.Rdata
- pred_EC20_C3.Rdata
- pred_EC20_C15.Rdata
- pred_EC20_C48.Rdata
Where pred = predicted values, EC = Effect Concentration (10 or 20) and C3, 15, 48 = EC values have been normalised and adjusted to 3, 15, 48% carbon.

Lineage

Progress Code: completed

Statement: No problems with data collection were encountered. All data quality issues are addressed within the submitted file named "MaccaSSD_Data-Compilation.xlsx" An updated dataset (for formatting) was provided on 2024-07-17.

Notes

Purpose
To provide raw data and analysis code, to allow published work to be fully reproducible.