This model and associated code was developed for the article:
Sun, J.M., Kelly, B.C., Gobas, F.A.P.C., Sunderland, E.M. A food web bioaccumulation model for the accumulation of per- and polyfluoroalkyl substances (PFAS) in fish: how important is renal elimination? Environmental Science Processes & Impacts (2022) DOI: 10.1039/D2EM00047D
Please cite this article if you use this model in your work.
The three datasets used for PFAA model evaluation in the paper are provided as example input files in the folder /data. These input files correspond to tables presented in the source paper's ESI. Each model run requires several inputs:
- numSpecies: integer, number of species modeled (i.e. not including phytoplankton)
- oceanData: environmental parameters
- chemicalParams: chemical parameters
- chemicalData: chemical concentrations in exposure matrices, including the fraction of chemical in the dissolved phase (Phi)
- organismData: species-specific parameters
- foodWebData: table of dietary relationships
Model versions run with renal elimination require a dataframe of renal elimination:branchial elimination ratios for each PFAS. This object (df_krkbratio) is currently generated by running model Section 3, which includes the method for calculation renal elimination as described in the source paper. This dataframe object can be added to the input files of subsequent model runs.
Alternate versions of empirically derived parameters used in different model applications are specified in the "settings" dictionary. To add additional parameter options, update the following:
- Section 1, #1: Add elements to the "Settlings" class initialization
- Section 1, #3: Add alternate parameter versions. This may be most easily accomplished using an if statement(see example for Ed)
- Section 2: Add additional arguments or values to the settings dictionaries
Questions or comments? Contact: Jennifer Sun, Harvard University
Email: jennifersun@g.harvard.edu
Last updated: May 31, 2022