travisyeah / loonhg

Loon mercury models

Code to analyze loon blood mercury

Kenow, K.P., Erickson, R.A., Hrrison, T.J. 2018. Code to analyze loon blood mercury; U.S. Geological Survey code release, https://doi.org/10.5066/P9QHT2DG

This code supports the manuscript Kenow KP, Houdek SC, Fara LJ, Erickson RA, Gray BR, Harrison TJ, Monson BA, Henderson CL. In Press. Patterns of mercury and selenium exposure in Minnesota common loons. Environ Toxicol Chem XXXX:XX-XX; DOI: 10.1002/etc.4331. Specifically, we used this code to examine Loon blood Hg concentrations were related with predictions of Hg concentrations in standardized 12-cm whole organism yellow perch (Perca flavescens), based on fish Hg records from lakes throughout Minnesota, using the U.S. Geological Survey National Descriptive Model for Mercury in Fish.

Data: https://doi.org/10.5066/P9TDCH3F

Code files

The follow files of code were used for this project:

• fixingLakeID2018_03_09.R: The file cleans up Lake Data and then runs a censored regression to estimate standard fish Hg concentraitons. The censored regression takes several hours to run due to the large dataset.
• LoonDataClean2018_03_09.R: Thie file organizes lakes and makes sure codes are correct. It also fixes erronious lake codes. In general, this file does data cleanup and reformatting prior to analysis.
• LoonAnalysis2018_03_09.R: This file runs analysis of the loon data, with fish and lake details as predictor variables.
• perch_map_2018_03_09.R: This file creates coordinats for joining and mapping water data.
• coords/utmToDec.py: This file is a tool for converting utm to decimal coordinates.

Contact for code

Primary code developer: Richard A. Erickson ([email protected]).
Secondary code developer: Travis J. Harrison ([email protected]).

Disclaimer

This software is in the public domain because it contains materials that originally came from the U.S. Geological Survey, an agency of the United States Department of Interior. For more information, see the official USGS copyright policy.

This software has been approved for release by the U.S. Geological Survey (USGSW). Although the software has been subjected to rigorous review, the USGS reserves the right to update the software as needed pursuant to further analysis and review. No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. Furthermore, the software is released on condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from its authorized or unauthorized use."

This software is provided "AS IS".

loonhg's Issues

Complete README

Complete and review the README file.