R code for Polychlorinated Biphenyl (PCB) Reactive Transport Model

Christian M. Bako; Andres Martinez

doi:10.25820/code.006163

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R code for Polychlorinated Biphenyl (PCB) Reactive Transport Model

Christian M. Bako and Andres Martinez

University of Iowa

06/06/2022

DOI: 10.25820/code.006163

Files and links (9)

txt

00_PCB_Reactive_Transport_Model_ReadMe9.63 kBDownload View

READMEContains a brief description of the project, a description of files also associated with the IRO deposit, prerequisite software, installation instructions for software, and user contribution information.Open Software License V3.0, Open Access

01_PCB_Reactive_Transport_Model_R11.57 kBDownload View

Code/ScriptContains the raw code for the PCB Reactive Transport model in "R" which uses PCB 52 data from 08_Dataset_FinalPCBMass_2021-12-06.csv to compare simulated results to experimental observations.Open Software License V3.0, Open Access

Rmd

02_PCB_Reactive_Transport_Model_RMD47.69 kBDownload View

Code/ScriptContains the raw code for the model and detailed documentation in "R Markdown"; accessible using R studio.Open Software License V3.0, Open Access

html

03_PCB_Reactive_Transport_Model_RMD_out_HTML891.43 kBDownload View

TextHTML file output of "R Markdown" document containing detailed description of model code; accessible using any web browser.Open Software License V3.0, Open Access

pdf

04_PCB_Reactive_Transport_Model_RMD_out_PDF421.84 kBDownload View

PDFPDF file output of "R Markdown" document containing detailed description of model code; accessible using Adobe Acrobat Reader or similar software.Open Software License V3.0, Open Access

Abstract

This Iowa Research Online (IRO) Data Repository deposit describes documentation of code developed in "R" software for a "Polychlorinated Biphenyl (PCB) reactive transport model". The PCB Reactive Transport Model produces simulations of congener-specific PCB concentration in the aqueous and gas phase of laboratory-scale bioreactors containing PCB-contaminated sediment slurry. The script uses experimental passive sampler measurements and minimization of least squares procedures to fit congener-specific adsorption and desorption coefficients to the model. Finally, the model can simulate the reduction in volatile release of PCBs from sediment slurry to air resulting from the presence of an aerobic PCB-degrading microorganism with a known PCB biotransformation rate. As written, the model script calls data resulting from bioreactor experiments described in the peer-reviewed journal article ("Aerobic Bioaugmentation to Decrease Polychlorinated Biphenyl (PCB) Emissions from Contaminated Sediments to Air") linked to this IRO deposit. In this deposit, the full "R" script is available for PCB 52 to provide documentation for the underlying code and to provide a framework for future re-use. The code is documented and described in detail within an "R Markdown" (.RMD) file which can be viewed as .html, .pdf, or .docx. The purpose of this IRO deposit is to promote reuse of the underlying experimental dataset from the linked publication and the PCB reactive transport model. We hope other researches will use this model to conduct inform other analyses, investigations, and / or interpretive insights. It is recommended that a user first reads the linked publication and one of the R Markdown output files to interpret and contexualize the model script.

Bioavailability

Biodegradation

Bioremediation

Polychlorinated Biphenyls

Contaminant fate and transport

Paraburkholderia zenovorans LB400

Kinetic Phase Passive Sampling

Biosurfactants

GC-MS/MS

Details

Title: Subtitle: R code for Polychlorinated Biphenyl (PCB) Reactive Transport Model
Creators: Christian M. Bako - University of Iowa
Andres Martinez - University of Iowa, IIHR--Hydroscience and Engineering
Resource Type: Code
Publisher: University of Iowa
DOI: 10.25820/code.006163
Locations: Latitude: 37.114 Longitude: -79.272
Format: R Markdown
Grants: Airborne PCBs: Sources, Exposures, Toxicities, Remediation, P42ES013661, National Institutes of Health (United States, Bethesda) - NIH
Language: English
Date published: 06/06/2022
Academic Unit: IIHR--Hydroscience and Engineering; Iowa Superfund Research Program
Record Identifier: 9984214657602771

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R code for Polychlorinated Biphenyl (PCB) Reactive Transport Model

Files and links (9)

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