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This repository is part of the working draft for an upcoming an academic paper describing the methods and results of the City of Chicago Clear Water project.
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predicting-e-coli-concentrations.Rmd
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README.md

Predicting E. coli concentrations using limited qPCR deployments at Chicago

This repository is part of the working draft for an upcoming paper tentatively titled Predicting E. coli concentrations using limited qPCR deployments at Chicago. It is an academic paper describing the methods and results of the City of Chicago Clear Water project.

Document

This document uses RMarkdown to format the paper, uses knitr to compile it, and the rticles package to format the document. The simpliest way to compile the document is downloading the repo and opening the predicting-e-coli-concentrations.Rproj file in RStudio. Use the built-in knit button to compile the documentation. Before knitting the document, install the rticles package.

Bibliography

This project uses knitcitations to compile the project bibliography. Articles should be stored in a Zotero library.

References from the Zotero library should be exported as BibTeX to bibliography/zotero-references.bib. The document should reference the BibTeX document, e.g., r citep(biblio["whitman_summer_2008"]).

Examples:

  • Parenthetical citation (e.g, (Whiteman, 2008)) by entry in zotero-references.bib.: r citep(biblio["whitman_summer_2008"])
  • Inline citation (e.g., Whiteman (2008)): r citet(biblio["whitman_summer_2008"])
  • Cite by entry position: r citep(biblio[[2]])
  • Cite multiple authors: r citep(biblio[c("whitman_summer_2008","boehm_decadal_2002"])

Dependencies

This project has been tested using both R 3.4 and 3.5. Source code and version number for all R package dependencies is located in the packrat directory and managed using Packrat.

Packrat

Some users have reported difficulty compiling R packages data.table and rgdal from source code on some systems, especially Mac OS X. Packrat will fail to complete loading all packages if any single package fails to compile. If you are having difficulty with a specific package, try removing the entry for the package in the file packrat/packrat.lock. Then once Packrat completes installing all the other packages, install the missing package as you normally would outside Packrat.

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